From 0c9f327961dde9dac6e32cf7337f1417d870a32b Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Wed, 3 Jan 2024 15:02:59 -0500 Subject: [PATCH] Deployed 91b0962e with MkDocs version: 1.5.3 --- functions/index.html | 2 + search/search_index.json | 2 +- sitemap.xml | 3868 +++++++++++++++++++------------------- sitemap.xml.gz | Bin 9808 -> 9809 bytes 4 files changed, 1937 insertions(+), 1935 deletions(-) diff --git a/functions/index.html b/functions/index.html index 26767c92a..34f040e13 100644 --- a/functions/index.html +++ b/functions/index.html @@ -1820,6 +1820,8 @@

Common Parameters

The following options are available for most functions unless stated otherwise.

inputfile

Use the option --inputfile to specify a path to a file containing input text.

+

For the extract command, this may be a single file or a directory of files.

+

In the latter case, all .txt files will be assumed to be input, and the path will not be parsed recursively.

template

Use the option --template to specify a template to use. This is a required parameter.

Only the name is required, without any filename suffix.

diff --git a/search/search_index.json b/search/search_index.json index 38b143b3f..8d9ad8392 100644 --- a/search/search_index.json +++ b/search/search_index.json @@ -1 +1 @@ -{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Introduction","text":"

OntoGPT is a Python package for extracting structured information from text with large language models (LLMs), instruction prompts, and ontology-based grounding. It works well with OpenAI's GPT-3.5 and GPT-4 models as well as a selection of other LLMs. OntoGPT's output can be used for general-purpose natural language tasks (e.g., named entity recognition and relation extraction), summarization, knowledge base and knowledge graph construction, and more.

"},{"location":"#methods","title":"Methods","text":"

Two different strategies for knowledge extraction are currently implemented in OntoGPT:

"},{"location":"#quick-start","title":"Quick Start","text":"

Please see the Setup page on the left for more detailed instructions.

OntoGPT runs on the command line, though there's also a minimal web app interface (see Web Application section below).

  1. Ensure you have Python 3.9 or greater installed.

  2. Install with pip:

    bash pip install ontogpt

  3. Set your OpenAI API key:

    bash runoak set-apikey -e openai <your openai api key>

  4. See the list of all OntoGPT commands:

    bash ontogpt --help

  5. Try a simple example of information extraction:

    bash echo \"One treatment for high blood pressure is carvedilol.\" > example.txt ontogpt extract -i example.txt -t drug

    OntoGPT will retrieve the necessary ontologies and output results to the command line. Your output will provide all extracted objects under the heading extracted_object.

"},{"location":"#web-applications","title":"Web Applications","text":"

There is a bare bones web application for running OntoGPT and viewing results.

First, install the required dependencies with pip by running the following command:

pip install ontogpt[web]\n

Then run this command to start the web application:

web-ontogpt\n

NOTE: We do not recommend hosting this webapp publicly without authentication.

Gene enrichment has its own webapp powered by Streamlit:

streamlit run src/ontogpt/streamlit/spindoctor.py\n
"},{"location":"#citation","title":"Citation","text":"

SPIRES is described further in: Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, Matentzoglu N, et al. Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning. arXiv publication: http://arxiv.org/abs/2304.02711

SPINDOCTOR is described further in: Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv publication: http://arxiv.org/abs/2305.13338

"},{"location":"#contributing","title":"Contributing","text":"

Contributions are welcome! One way to get started with contributing to OntoGPT is to submit an

Contributions on recipes to test welcome from anyone! Just make a PR here. See this list for accepted URLs

"},{"location":"#acknowledgements","title":"Acknowledgements","text":"

We gratefully acknowledge Bosch Research for their support of this research project.

"},{"location":"custom/","title":"Custom Schemas","text":""},{"location":"custom/#build-a-custom-schema","title":"Build a custom schema","text":"

Define a schema (using a subset of LinkML) that describes the structure in which you want to extract knowledge from your text.

There are a number of pre-defined LinkML data models already developed here - src/ontogpt/templates/ which you can use as reference when creating your own data models.

"},{"location":"custom/#the-header","title":"The header","text":"

The header of the schema defines metadata, parameters instructing LinkML to interpret prefixes in specific ways, and names of imports.

You will find these fields in the schema header:

An example:

id: http://w3id.org/ontogpt/gocam\nname: gocam-template\ntitle: GO-CAM Template\ndescription: >-\n  A template for GO-CAMs\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\nprefixes:\n  linkml: https://w3id.org/linkml/\n  gocam: http://w3id.org/ontogpt/gocam/\n  GO: http://purl.obolibrary.org/obo/GO_\n  CL: http://purl.obolibrary.org/obo/CL_\n\ndefault_prefix: gocam\ndefault_range: string\n\nimports:\n  - linkml:types\n  - core\n
"},{"location":"custom/#the-classes","title":"The classes","text":"

The classes in the schema define the \"things\" you are interested in extracting. LinkML doesn't make many assumptions about the difference between a class and a relationship, a node and an edge, or a relation and a property. It's designed to be flexibile enough to handle a variety of data models.

The start of this section is indicated by classes:.

A minimal class may look like this:

  ClassName:\n    is_a: NamedEntity\n    attributes:\n      entity:\n        range: string\n        description: >- \n          A named entity.\n

In practice, this class won't do much, as it doesn't contain much for OntoGPT to work with or many instructions to form an LLM prompt out of. And that's fine, because we can do more.

These fields may be used in classes:

An example, continuing from where the header left off:

classes:\n  GoCamAnnotations:\n    tree_root: true\n    attributes:\n      genes:\n        description: semicolon-separated list of genes\n        multivalued: true\n        range: Gene\n      organisms:\n        description: semicolon-separated list of organism taxons\n        multivalued: true\n        range: Organism\n      gene_organisms:\n        annotations:\n          prompt: semicolon-separated list of asterisk separated gene to organism relationships\n        multivalued: true\n        range: GeneOrganismRelationship\n      activities:\n        description: semicolon-separated list of molecular activities\n        multivalued: true\n        range: MolecularActivity\n      gene_functions:\n        description: semicolon-separated list of gene to molecular activity relationships\n        multivalued: true\n        range: GeneMolecularActivityRelationship\n      cellular_processes:\n        description: semicolon-separated list of cellular processes\n        multivalued: true\n        range: CellularProcess\n      pathways:\n        description: semicolon-separated list of pathways\n        multivalued: true\n        range: Pathway\n      gene_gene_interactions:\n        description: semicolon-separated list of gene to gene interactions\n        multivalued: true\n        range: GeneGeneInteraction\n      gene_localizations:\n        description: >-\n          semicolon-separated list of genes plus their location in the cell;\n          for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\n        multivalued: true\n        range: GeneSubcellularLocalizationRelationship\n\n  Gene:\n    is_a: NamedEntity\n    id_prefixes:\n      - HGNC\n      - PR\n      - UniProtKB\n    annotations:\n      annotators: gilda:, bioportal:hgnc-nr\n  Pathway:\n    is_a: NamedEntity\n    id_prefixes:\n      - GO\n      - PW\n    annotations:\n      annotators: sqlite:obo:go, sqlite:obo:pw\n  CellularProcess:\n    is_a: NamedEntity\n    id_prefixes:\n      - GO\n    annotations:\n      annotators: sqlite:obo:go\n  MolecularActivity:\n    is_a: NamedEntity\n    id_prefixes:\n      - GO\n    annotations:\n      annotators: sqlite:obo:go\n  GeneLocation:\n    is_a: NamedEntity\n    id_prefixes:\n      - GO\n      - CL\n      - UBERON\n    annotations:\n      annotators: \"sqlite:obo:go, sqlite:obo:cl\"\n    slot_usage:\n      id:\n        values_from:\n          - GOCellComponentType\n          - CellType\n  Organism:\n    is_a: NamedEntity\n    id_prefixes:\n      - NCBITaxon\n      - EFO\n    annotations:\n      annotators: gilda:, sqlite:obo:ncbitaxon\n  Molecule:\n    is_a: NamedEntity\n    id_prefixes:\n      - CHEBI\n      - PR\n    annotations:\n      annotators: gilda:, sqlite:obo:chebi\n\n  GeneOrganismRelationship:\n    is_a: CompoundExpression\n    attributes:\n      gene:\n        range: Gene\n      organism:\n        range: Organism\n\n  GeneMolecularActivityRelationship:\n    is_a:   CompoundExpression\n    attributes:\n      gene:\n        range: Gene\n        annotations:\n          prompt: the name of the gene in the pair. This comes first.\n      molecular_activity:\n        range: MolecularActivity\n        annotations:\n          prompt: the name of the molecular function in the pair. This comes second. May be a GO term.\n\n  GeneMolecularActivityRelationship2:\n    is_a:   CompoundExpression\n    attributes:\n      gene:\n        range: Gene\n        annotations:\n          prompt: the name of the gene.\n      molecular_activity:\n        range: MolecularActivity\n        annotations:\n          prompt: the name of the molecular activity, for example, ubiquitination. May be a GO term.\n      target:\n        range: Molecule\n        annotations:\n          prompt: the name of the molecular entity that is the target of the molecular activity.\n\n  GeneSubcellularLocalizationRelationship:\n    is_a:   CompoundExpression\n    attributes:\n      gene:\n        range: Gene\n      location:\n        range: GeneLocation\n\n  GeneGeneInteraction:\n    is_a:   CompoundExpression\n    attributes:\n      gene1:\n        range: Gene\n      gene2:\n        range: Gene\n
"},{"location":"custom/#enums","title":"Enums","text":"

LinkML supports defining enums, or sets of values. In OntoGPT this allows schemas to work with subsets of identifiers. Enums have their own hierarchy. In the example below, the reachable_from slot is used to define sets of values: in GOCellComponentType these are all children of the GO term with the ID GO:0005575 (cellular component), so restricting a set of identifiers based on this enum will ensure they all correspond to cellular components.

Example, starting where the classes left off above:

enums:\n\n  GeneLocationEnum:\n    inherits:\n      - GOCellComponent\n      - CellType\n\n  GOCellComponentType:\n    reachable_from:\n      source_ontology: obo:go\n      source_nodes:\n        - GO:0005575 ## cellular_component\n  CellType:\n    reachable_from:\n      source_ontology: obo:cl\n      source_nodes:\n        - CL:0000000 ## cell\n
"},{"location":"custom/#schema-design-tips","title":"Schema design tips","text":"

It helps to have an understanding of the LinkML schema language, but it should be possible to define your own schemas using the examples in src/ontogpt/templates as a guide.

We recommend following an established schema like BioLink Model, but you can define your own.

Once you have defined your own schema / data model and placed in the correct directory, you can run the extract command.

Ex.:

ontogpt extract -t mendelian_disease.MendelianDisease -i marfan-wikipedia.txt\n

OntoGPT-specific extensions are specified as annotations.

You can specify a set of annotators for a field using the annotators annotation.

Ex.:

  Gene:\n    is_a: NamedThing\n    id_prefixes:\n      - HGNC\n    annotations:\n      annotators: gilda:, bioportal:hgnc-nr, obo:pr\n

The annotators are applied in order.

Additionally, when performing grounding, the following measures can be taken to improve accuracy:

Ex.:

classes:\n  ...\n  GeneLocation:\n    is_a: NamedEntity\n    id_prefixes:\n      - GO\n      - CL\n    annotations:\n      annotators: \"sqlite:obo:go, sqlite:obo:cl\"\n    slot_usage:\n      id:\n        values_from:\n          - GOCellComponentType\n          - CellType\n\nenums:\n  GOCellComponentType:\n    reachable_from:\n      source_ontology: obo:go\n      source_nodes:\n        - GO:0005575 ## cellular_component\n  CellType:\n    reachable_from:\n      source_ontology: obo:cl\n      source_nodes:\n        - CL:0000000 ## cell\n
"},{"location":"custom/#multiple-levels-of-nesting","title":"Multiple levels of nesting","text":"

Currently no more than two levels of nesting are recommended.

If a field has a range which is itself a class and not a primitive, it will attempt to nest.

Ex. the gocam schema has an attribute:

  attributes:\n      ...\n      gene_functions:\n        description: semicolon-separated list of gene to molecular activity relationships\n        multivalued: true\n        range: GeneMolecularActivityRelationship\n

The range GeneMolecularActivityRelationship has been specified inline, so it will nest.

The generated prompt is:

gene_functions : <semicolon-separated list of gene to molecular activities relationships>\n

The output of this is then passed through further SPIRES iterations.

"},{"location":"custom/#text-length-limit","title":"Text length limit","text":"

LLMs have context sizes limiting the combined length of their inputs and outputs. The gpt-3.5-turbo model, for example, has a 4,096 token limit (prompt + completion), while the gpt-3.5-turbo-16k model has a larger context of 16,384 tokens.

"},{"location":"custom/#advanced-functionality-with-linkml-owl","title":"Advanced functionality with linkml-owl","text":"

A LinkML schema used in OntoGPT may include annotations describing how each component relates to OWL syntax.

This level of detail may be necessary if your data model includes complex logic beyond simple hierarchical relationships.

For example, if you are extracting details of chemical reactions, it may be necessary to keep track of details like stoichiometry or charge. See a relevant example here.

Incorporating OWL annotations into the custom schema (remember to export using the -O owl option) also supports importing the results into an ontology editor like Protege, at which point it may be reasoned over.

The recipe template in OntoGPT incorporates several OWL annotations:

classes:\n  Recipe:\n    tree_root: true\n    close_mappings:\n      - FOODON:00004081\n    attributes:\n      url:\n        identifier: true\n        range: uriorcurie\n        slot_uri: rdf:Resource\n        annotations:\n          prompt.skip: true\n      label:\n        description: the name of the recipe\n        slot_uri: rdfs:label\n        annotations:\n          owl: AnnotationProperty, AnnotationAssertion\n      description:\n        description: a brief textual description of the recipe\n        slot_uri: dcterms:description\n        annotations:\n          owl: AnnotationProperty, AnnotationAssertion\n      categories:\n        description: a semicolon separated list of the categories to which this recipe belongs\n        range: RecipeCategory\n        multivalued: true\n        slot_uri: dcterms:subject\n        annotations:\n          owl: AnnotationAssertion\n      ingredients:\n        description: a semicolon separated list of the ingredients plus quantities of the recipe\n        multivalued: true\n        range: Ingredient\n        slot_uri: FOODON:00002420\n        annotations:\n          owl: ObjectProperty, ObjectSomeValuesFrom\n      steps:\n        description: a semicolon separated list of the individual steps involved in this recipe\n        multivalued: true\n        range: Step\n        annotations:\n          owl: ObjectProperty, ObjectSomeValuesFrom\n    annotations:\n      owl: Class\n      owl.template: |\n        EquivalentClasses(\n          {{url}}\n          ObjectIntersectionOf(\n            recipe:Recipe\n\n            {% for step in steps %}\n            ObjectSomeValuesFrom(\n              recipe:steps\n              {{tr(step)}}\n            )\n            {% endfor %}\n            {% for ingredient in ingredients %}\n            ObjectSomeValuesFrom(\n              FOODON:00002420\n              {{tr(ingredient)}}\n            )\n            {% endfor %}\n          )\n        )\n...\n

Several of the slots above, like close_mappings and slot_uri, aren't exclusive to OWL but define the parts of this data model in terms of existing vocabularies, so the schema and any extracted results will be more compatible with other models and methods. Here, close_mappings is used to show that the Recipe class is close but not necessarily identical to FOODON:00004081, or \"food recipe\".

The owl slot under annotations for these attributes defines one or more corresponding OWL axiom types. Because the label attribute may be AnnotationProperty, AnnotationAssertion in OWL (see the OWL2 syntax on Annotations) we know it can be applied as a property for something else, like an axiom or a specific entity with an IRI. This is how the rdfs:label annotation property usually works so this isn't surprising.

The owl.template slot defines template logic relating a Recipe to its component objects: steps and ingredients. It begins with an EquivalentClasses axiom to define the identifier of the recipe, which we assume to be a URL, as identical to the class expression in subsequent lines. Specifically, that Recipe must include both a series of steps (e.g., \"fry\", \"chop\", etc.) and a series of ingredients. The ingredients relate to the recipe through the property FOODON:00002420, or \"has ingredient\".

Note that everything in {curly brackets} is a template of some kind. The Jinja template system is used in the example in lines like {% for step in steps %} where a loop is used. Template slots like {{url}} may be accessed directly with their names. So what makes {{tr(step)}} different from {{step}}? The tr() function used here translates its input into an OWL entity so it may be used to generate valid OWL axioms.

See also: the documentation page on OWL exports and the linkml-owl documentation.

"},{"location":"custom/#install-a-custom-schema","title":"Install a custom schema","text":"

If you have installed OntoGPT directly from its GitHub repository, then you may install a custom schema like this:

  1. Move the schema file to the src/ontogpt/templates directory.
  2. Run make from the root of the repository to generate Pydantic versions of the schema.

If you have installed OntoGPT from pip, or if you can't use the make command, the process is similar, though it will depend on where the package is installed.

  1. Use the LinkML gen-pydantic tool to generate Pydantic classes. If your schema is named alfred.yaml, then run the following:

    bash gen-pydantic --pydantic_version 2 alfred.yaml > alfred.py

  2. Move both the .yaml and the .py versions of your schema to the templates directory of wherever OntoGPT is installed. In a virtual environment named temp that may be something like /temp/lib/python3.9/site-packages/ontogpt/templates.

You may then use the schema like any other. For example, if your schema is named albatross.yaml, then an extract command is:

ontogpt extract -t albatross -i input.txt\n
"},{"location":"evaluations/","title":"Evaluations","text":"

OpenAI's functions have been evaluated on test data sets.

All evaluation results include OpenAI cache databases (openai_cache.db.gz) as a reference of the prompts and responses obtained during the evaluation. This may be used by extracting the cache database to the root directory of the project.

Tests may be run with the eval command followed by the test name, e.g., for the BC5CDR test below:

ontogpt eval EvalCTD \n

By default, the evaluation will only be executed over a subset of the test corpus.

The exact number of inputs to run the test over can be controlled with the --num-tests option, like this:

ontogpt eval --num-tests 1 EvalCTD\n

To run the full set of tests, set num-tests to the input count for a given evaluation, as defined below.

For each document, the evaluation process will attempt to process the full text without preprocessing.

If the --chunking option is used, then the input text will instead be chunked into segments of a few tokens each, essentially creating new queries for each segment. This alternate strategy may impact test results and will result in longer run time.

"},{"location":"evaluations/#bc5cdr","title":"BC5CDR","text":"

Test Name: EvalCTD Input Count: 500

Results for OntoGPT on the BioCreative V Chemical Disease Relation Task (BC5CDR) are available on Zenodo here: https://zenodo.org/record/7657763

Evaluation functions for BC5CDR are available in src/ontogpt/evaluation/ctd/eval_ctd.py.

Note that the project also includes test and train data (CDR_TestSet.BioC.xml.gz and CDR_TrainSet.BioC.xml.gz, respectively) as well as a set of synonyms for MeSH terms (see synonyms.yaml).

"},{"location":"evaluations/#template","title":"Template","text":"

This evaluation uses the following schema template:

id: http://w3id.org/ontogpt/ctd\nname: ctd\ntitle: Chemical to Disease Template\ndescription: >-\n  A template for Chemical to Disease associations.\n\n  This template is intended to represent associations between chemicals and diseases,\n  and for evaluating Semantic Llama against BioCreative V Chemical Disease\n  Relation (CDR) Task (BC5CDR).\nsee_also:\n  - https://biocreative.bioinformatics.udel.edu/media/store/files/2015/BC5CDR_overview.final.pdf\n  - https://academic.oup.com/database/article/doi/10.1093/database/baw068/2630414\nsource: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/track-3-cdr/\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\nprefixes:\n  linkml: https://w3id.org/linkml/\n  drug: http://w3id.org/ontogpt/drug/\n\ndefault_prefix: drug\ndefault_range: string\n\nimports:\n  - linkml:types\n  - core\n\nclasses:\n\n  ChemicalToDiseaseDocument:\n    description: A document that contains chemical to disease relations.\n    is_a: TextWithTriples\n    slot_usage:\n      triples:\n        range: ChemicalToDiseaseRelationship\n        annotations:\n          prompt: >-\n            A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES\n            or TREATS.\n            for example: Lidocaine INDUCES cardiac asystole; \n            Hydroxychloroquine NOT TREATS COVID-19;\n            Methyldopa INDUCES Hypotension;\n            Monosodium Glutamate NOT INDUCES Headache;\n            Imatinib TREATS cancer\n          exclude: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer\n\n\n  ChemicalToDiseaseRelationship:\n    is_a: Triple\n    description: A triple where the subject is a chemical and the object is a disease.\n    slot_usage:\n      subject:\n        range: Chemical\n        description: >-\n          The chemical substance, drug, or small molecule. \n          For example: Lidocaine, Monosodium Glutamate, Imatinib.\n      object:\n        range: Disease\n        description: >-\n          The disease or condition that is being treated or induced by the chemical.\n          For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache.\n      predicate:\n        range: ChemicalToDiseasePredicate\n        description: The relationship type, e.g. INDUCES, TREATS.\n      subject_qualifier:\n        range: NamedEntity\n        description: >-\n          An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"\n      object_qualifier:\n        range: NamedEntity\n        description: >-\n          An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"\n\n  Disease:\n    is_a: NamedEntity\n    annotations:\n      annotators: \"sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra\"\n      prompt.examples: cardiac asystole, COVID-19, Headache, cancer\n    id_prefixes:\n      - MESH\n    slot_usage:\n      id:\n        pattern: \"^MESH:[CD][0-9]{6}$\"\n        values_from:\n          - MeshDiseaseIdentifier\n\n  Chemical:\n    is_a: NamedEntity\n    annotations:\n      annotators: \"sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:\"\n      prompt.examples: Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib\n    id_prefixes:\n      - MESH\n    slot_usage:\n      id:\n        pattern: \"^MESH:[CD][0-9]{6}$\"\n        values_from:\n          - MeshChemicalIdentifier\n\n  ChemicalToDiseasePredicate:\n    is_a: RelationshipType\n    description: >-\n      A predicate for chemical to disease relationships\n    comments:\n      - for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored.\n\nenums:\n\n  MeshChemicalIdentifier:\n    reachable_from:\n      source_ontology: obo:mesh\n      source_nodes:\n        - MESH:D000602 ## Amino Acids, Peptides, and Proteins\n        - MESH:D001685 ## Biological Factors\n        - MESH:D002241 ## Carbohydrates\n        - MESH:D004364 ## Pharmaceutical Preparations\n        - MESH:D006571 ## Heterocyclic Compounds\n        - MESH:D007287 ## Inorganic Chemicals\n        - MESH:D008055 ## Lipids\n        - MESH:D009706 ## Nucleic Acids, Nucleotides, and Nucleosides\n        - MESH:D009930 ## Organic Chemicals\n        - MESH:D011083 ## Polycyclic Compounds\n        - MESH:D013812 ## Therapeutics\n        - MESH:D019602 ## Food and Beverages\n        - MESH:D045424 ## Complex Mixtures\n        - MESH:D045762 ## Enzymes and Coenzymes\n        - MESH:D046911 ## Macromolecular Substances\n  MeshDiseaseIdentifier:\n    reachable_from:\n      source_ontology: obo:mesh\n      source_nodes:\n        - MESH:D001423 ## Bacterial Infections and Mycoses\n        - MESH:D001523 ## Mental Disorders\n        - MESH:D002318 ## Cardiovascular Diseases\n        - MESH:D002943 ## Circulatory and Respiratory Physiological Phenomena\n        - MESH:D004066 ## Digestive System Diseases\n        - MESH:D004700 ## Endocrine System Diseases\n        - MESH:D005128 ## Eye Diseases\n        - MESH:D005261 ## Female Urogenital Diseases and Pregnancy Complications\n        - MESH:D006425 ## Hemic and Lymphatic Diseases\n        - MESH:D007154 ## Immune System Diseases\n        - MESH:D007280 ## Disorders of Environmental Origin\n        - MESH:D009057 ## Stomatognathic Diseases\n        - MESH:D009140 ## Musculoskeletal Diseases\n        - MESH:D009358 ## Congenital, Hereditary, and Neonatal Diseases and Abnormalities\n        - MESH:D009369 ## Neoplasms\n        - MESH:D009422 ## Nervous System Diseases\n        - MESH:D009750 ## Nutritional and Metabolic Diseases\n        - MESH:D009784 ## Occupational Diseases\n        - MESH:D010038 ## Otorhinolaryngologic Diseases\n        - MESH:D010272 ## Parasitic Diseases\n        - MESH:D012140 ## Respiratory Tract Diseases\n        - MESH:D013568 ## Pathological Conditions, Signs and Symptoms\n        - MESH:D014777 ## Virus Diseases\n        - MESH:D014947 ## Wounds and Injuries\n        - MESH:D017437 ## Skin and Connective Tissue Diseases\n        - MESH:D052801 ## Male Urogenital Diseases\n        - MESH:D064419 ## Chemically-Induced Disorders\n
"},{"location":"functions/","title":"OntoGPT Functions","text":"

All OntoGPT functions are run from the command line.

Precede all commands with ontogpt.

To see the full list of available commands, run this:

ontogpt --help\n
"},{"location":"functions/#basic-parameters","title":"Basic Parameters","text":"

To see verbose output, run:

ontogpt -v\n

The options -vv and -vvv will enable progressively more verbose output.

"},{"location":"functions/#cache-db","title":"cache-db","text":"

Use the option --cache-db to specify a path to a sqlite database to cache the prompt-completion results.

"},{"location":"functions/#skip-annotator","title":"skip-annotator","text":"

Use the option --skip-annotator to skip one or more annotators (e.g. --skip-annotator gilda).

"},{"location":"functions/#common-parameters","title":"Common Parameters","text":"

The following options are available for most functions unless stated otherwise.

"},{"location":"functions/#inputfile","title":"inputfile","text":"

Use the option --inputfile to specify a path to a file containing input text.

"},{"location":"functions/#template","title":"template","text":"

Use the option --template to specify a template to use. This is a required parameter.

Only the name is required, without any filename suffix.

To use the gocam template, for example, the parameter will be --template gocam

This may be one of the templates included with OntoGPT or a custom template, but in the latter case, the schema, generated Pydantic classes, and any imported schemas should be present in the same location.

"},{"location":"functions/#target-class","title":"target-class","text":"

Use the option --target-class to specify a class in a schema to treat as the root.

If a schema does not already specify a root class, this is required.

Alternatively, the target class can be specified as part of the --template option, like so: --template mendelian_disease.MendelianDisease

"},{"location":"functions/#model","title":"model","text":"

Use the option model to specify the name of a large language model to be used.

For example, this may be --model gpt-4.

Consult the full list of available models with:

ontogpt list-models\n
"},{"location":"functions/#recurse","title":"recurse","text":"

Use the option recurse to specify whether recursion should be used when parsing the schema.

Recursion is on by default.

Disable it with --no-recurse.

"},{"location":"functions/#use-textract","title":"use-textract","text":"

Use the option use-textract to specify whether to use the textract package to extract text from the input document. Textract supports retrieving raw text from PDFs, images, audio, and a variety of other formats.

Textract extraction is off by default.

Enable it with --use-textract.

"},{"location":"functions/#output","title":"output","text":"

Use the option output to provide a path to write an output file to.

If this path is not provided, OntoGPT will write to stdout.

"},{"location":"functions/#output-format","title":"output-format","text":"

Use the option output-format to specify the desired output file format.

This may be one of:

"},{"location":"functions/#auto-prefix","title":"auto-prefix","text":"

Use the option auto-prefix to define a prefix to use for entities without a matching namespace.

When OntoGPT's extract functions find an entity matching the input schema but cannot ground it, the entity will still be included in the output.

By default, these entities will be assigned identifiers like AUTO:tangerine. If you ground this term to the Food Ontology, however, the entity may be FOODON:00003488 instead.

"},{"location":"functions/#show-prompt","title":"show-prompt","text":"

Use the option show-prompt to show all prompts constructed and sent to the model. Otherwise, only the final prompt will be shown.

Showing the full prompt is off by default.

Enable it by using --show-prompt and setting the verbosity level to high (-vvv).

"},{"location":"functions/#functions","title":"Functions","text":""},{"location":"functions/#categorize-mappings","title":"categorize-mappings","text":"

Categorize a collection of mappings in the Simple Standard for Sharing Ontological Mappings (SSSOM) format.

Mappings in this format may not include their specific mapping types (e.g., broad or close mappings).

This function will attempt to apply more specific mappings wherever possible.

Example:

Using an example SSSOM mapping collection

ontogpt categorize-mappings -i mp-hp-exact-0.0.1.sssom.tsv\n

Note that OntoGPT will attempt to retrieve the resources specified in the mapping (in the above example, that will include HP and MP). If it cannot find a corresponding resource it will raise a HTTP 404 error.

"},{"location":"functions/#clinical-notes","title":"clinical-notes","text":"

Create mock clinical notes.

Options:

Example:

ontogpt clinical-notes -d \"middle-aged female patient with syncope and recent travel to the Amazon rainforest\"\n
"},{"location":"functions/#complete","title":"complete","text":"

Prompt completion.

Given the path to a file containing text to continue, this command will simply pass it to the model as a completion task.

Example:

The file example2.txt contains the text \"Here's a good joke about high blood pressure:\"

ontogpt complete example2.txt\n

We take no responsibility for joke quality or lack thereof.

"},{"location":"functions/#convert","title":"convert","text":"

Convert output format.

Rather than a direct format translation, this function performs a full SPIRES extraction on the input file and writes the output in the specified format.

Example:

ontogpt convert -o outputfile.md -O md inputfile.yaml\n
"},{"location":"functions/#convert-examples","title":"convert-examples","text":"

Convert training examples from YAML.

This can be necessary for performing evaluations.

Given the path to a YAML-format input file containing training examples in a format like this:

---\nexamples:\n    - prompt: <text prompt>\n      completion: <text of completion of the prompt>\n    - prompt: <another text prompt>\n      completion: <text of completion of another prompt>\n

the function will convert it to equivalent JSON.

Example:

ontogpt convert-examples inputfile.yaml\n
"},{"location":"functions/#convert-geneset","title":"convert-geneset","text":"

Convert gene set to YAML.

The gene set may be in JSON (msigdb format) or text (one gene symbol per line) format.

See also the create-gene-set command (see below).

Options:

Example:

ontogpt convert-geneset -U inputfile.json\n
"},{"location":"functions/#create-gene-set","title":"create-gene-set","text":"

Create a gene set.

This is primarily relevant to the TALISMAN method for creating gene set summaries.

It creates a gene set given a set of gene annotations in two-column TSV or GAF format.

The function also requires a single argument for the term to create the gene set with.

The output is provided in YAML format.

Options:

Example:

ontogpt create-gene-set -A inputfile.tsv \"positive regulation of mitotic cytokinesis\"\n
"},{"location":"functions/#diagnose","title":"diagnose","text":"

Diagnose a clinical case represented as one or more Phenopackets.

This function takes one or more file paths as arguments, where each must contain a phenopacket in JSON format.

Example inputs may be found at the Phenomics Exchange repository.

Example:

ontogpt diagnose case1.json case2.json \n
"},{"location":"functions/#dump-completions","title":"dump-completions","text":"

Dump cached completions.

OntoGPT saves queries and successful text completions to an sqlite database.

Caching is not currently supported for local models.

Use this function to retrieve the contents of this database.

See also: the cache-db parameter described above.

Options:

Example:

ontogpt dump-completions -m \"soup\"\n
"},{"location":"functions/#embed","title":"embed","text":"

Embed text.

This function will return an embedding vector for the input text or texts.

Embedding retrieval is not currently supported for local models.

Options:

Example:

ontogpt embed \"obstreperous muskrat\"\n

For OpenAI's \"text-embedding-ada-002\" model, the output will be a vector of length 1536, like so:

[-0.015013165771961212, -0.013102399185299873, -0.005333086010068655, ...]\n
"},{"location":"functions/#enrichment","title":"enrichment","text":"

Gene class summary enriching. This is OntoGPT's implementation of TALISMAN.

The goal of gene summary enrichment is to assemble a textual summary of the functions of a set of genes and their products.

TALISMAN can run in three different ways:

  1. Map gene symbols to IDs using the resolver (unless IDs are specified)
  2. Fetch gene descriptions using Alliance API
  3. Create a prompt using descriptions

Options:

Example:

ontogpt enrichment -r sqlite:obo:hgnc -U tests/input/genesets/EDS.yaml\n

In this case, the prompt will include gene summaries retrieved from the database.

The response text will include, among other fields, a summary like this:

Summary: The common function among these genes is their involvement in the regulation and organization of the extracellular matrix, particularly collagen fibril organization and biosynthesis.\n
"},{"location":"functions/#entity-similarity","title":"entity-similarity","text":"

Determine similarity between ontology entities by comparing their embeddings.

Options:

Example:

ontogpt entity-similarity -r sqlite:obo:hp HP:0012228 HP:0000629\n

In this case, the output will look like this:

subject_id      subject_label   object_id       object_label    embedding_cosine_similarity     object_rank_for_subject\nHP:0012228      Tension-type headache   HP:0012228      Tension-type headache   0.9999999999999999      0\nHP:0012228      Tension-type headache   HP:0000629      Periorbital fullness    0.7755551231762359      1\nHP:0000629      Periorbital fullness    HP:0000629      Periorbital fullness    1.0000000000000002      0\nHP:0000629      Periorbital fullness    HP:0012228      Tension-type headache   0.7755551231762359      1\n
"},{"location":"functions/#eval","title":"eval","text":"

Evaluate an extractor.

See the Evaluations section for more details.

Options:

Example:

ontogpt eval --num-tests 1 EvalCTD\n
"},{"location":"functions/#eval-enrichment","title":"eval-enrichment","text":"

Run enrichment (TALISMAN) using multiple methods.

This function runs a set of evaluations specific to the TALISMAN gene set summary process.

It will iterate through all relevant models to compare results.

The function assumes genes will have HGNC identifiers.

Options:

Example:

ontogpt enrichment -U tests/input/genesets/EDS.yaml\n
"},{"location":"functions/#extract","title":"extract","text":"

Extract knowledge from text guided by a schema.

This is OntoGPT's implementation of SPIRES.

Output includes the input text (or a truncated part), the raw completion output, the prompt (specifically, the last iteration of the prompts used), and an extracted object containing all parts identified in the input text, as well as a list of named entities and their labels.

Options:

Examples:

ontogpt extract -t gocam.GoCamAnnotations -i tests/input/cases/gocam-33246504.txt\n

In this case, you will an extracted object in the output like:

extracted_object:\n  genes:\n    - HGNC:5992\n    - AUTO:F4/80\n    - HGNC:16400\n    - HGNC:1499\n    - HGNC:5992\n    - HGNC:5993\n  organisms:\n    - NCBITaxon:10088\n    - AUTO:bone%20marrow-derived%20macrophages\n    - AUTO:astrocytes\n    - AUTO:bipolar%20cells\n    - AUTO:vascular%20cells\n    - AUTO:perivascular%20MPs\n  gene_organisms:\n    - gene: HGNC:5992\n      organism: AUTO:mononuclear%20phagocytes\n    - gene: HGNC:16400\n      organism: AUTO:F4/80%2B%20mononuclear%20phagocytes\n    - gene: HGNC:1499\n      organism: AUTO:F4/80%2B%20mononuclear%20phagocytes\n    - gene: HGNC:5992\n      organism: AUTO:perivascular%20macrophages\n    - gene: HGNC:5993\n      organism: AUTO:None\n  activities:\n    - GO:0006954\n    - AUTO:photoreceptor%20death\n    - AUTO:retinal%20function\n  gene_functions:\n    - gene: HGNC:5992\n      molecular_activity: GO:0006954\n    - gene: AUTO:F4/80\n      molecular_activity: AUTO:mononuclear%20phagocyte%20recruitment\n    - gene: HGNC:1499\n      molecular_activity: GO:0006954\n    - gene: HGNC:5992\n      molecular_activity: AUTO:immune-specific%20expression\n    - gene: HGNC:5993\n      molecular_activity: AUTO:IL-1%CE%B2%20receptor\n    - gene: AUTO:rytvela\n      molecular_activity: AUTO:IL-1R%20modulation\n    - gene: AUTO:Kineret\n      molecular_activity: AUTO:IL-1R%20antagonism\n  cellular_processes:\n    - AUTO:macrophage-induced%20photoreceptor%20death\n  gene_localizations:\n    - gene: HGNC:5992\n      location: AUTO:subretinal%20space\n

Or, we can extract information about a drug and specify which model to use:

ontogpt extract -t drug -i tests/input/cases/drug-DB00316-moa.txt --auto-prefix UNKNOWN -m gpt-4\n

The ontology_class schema may be used to perform more domain-agnostic entity recognition, though this is generally incompatible with grounding.

ontogpt extract -t ontology_class -i tests/input/cases/human_urban_green_space.txt\n
"},{"location":"functions/#fill","title":"fill","text":"

Fill in missing values.

Requires the path to a file containing a data object to be passed (as an argument) and a set of examples as an input file.

Options:

"},{"location":"functions/#generate-extract","title":"generate-extract","text":"

Generate text and then extract knowledge from it.

This command runs two operations:

  1. Generate a natural language description of something
  2. Parse the generated description using SPIRES

For example, given a cell type such as Acinar Cell Of Salivary Gland, generate a description using GPT describing many aspects of the cell type, from its marker genes through to its function and diseases it is implicated in.

After that, use the cell-type schema to extract this into structured form.

As an optional next step use linkml-owl to generate OWL TBox axioms.

See also: iteratively-generate-extract below.

Example:

ontogpt generate-extract -t cell_type CL:0002623\n
"},{"location":"functions/#iteratively-generate-extract","title":"iteratively-generate-extract","text":"

Iterate through generate-extract.

This runs the generate-extract command in iterative mode. It will traverse the extracted subtypes with each iteration, gradually building up an ontology that is entirely generated from the \"latent knowledge\" in the LLM.

Currently each iteration is independent so the method remains unaware as to whether it has already made a concept. Ungrounded concepts may indicate gaps in available knowledgebases.

Unlike the generate-extract command, this command requires some additional parameters to be specified.

Please specify the input ontology and the output path.

Options:

Example:

ontogpt iteratively-generate-extract -t cell_type -r sqlite:obo:cl -D cells.yaml CL:0002623 \n
"},{"location":"functions/#list-models","title":"list-models","text":"

List all available models.

Example:

ontogpt list-models\n
"},{"location":"functions/#list-templates","title":"list-templates","text":"

List the templates.

Alternatively, run make list_templates.

Example:

ontogpt list-templates\n
"},{"location":"functions/#pubmed-annotate","title":"pubmed-annotate","text":"

Retrieve a collection of PubMed IDs for a given search, then perform extraction on them with SPIRES.

The search argument will accept all parameters known to PubMed search, such as filtering by publication year.

Works for single publications, too - set the --limit parameter to 1 and specify a PubMed ID as the search argument.

Options:

Examples:

ontogpt pubmed-annotate -t phenotype \"Takotsubo Cardiomyopathy: A Brief Review\" --get-pmc --model gpt-3.5-turbo-16k --limit 3\n
ontogpt pubmed-annotate -t environmental_sample \"33126925\" --limit 1\n
ontogpt pubmed-annotate -t composite_disease \"(earplugs) AND ((\"1950\"[Date - Publication] : \"1990\"[Date - Publication]))\" --limit 4\n
"},{"location":"functions/#pubmed-extract","title":"pubmed-extract","text":"

Extract knowledge from a single PubMed ID.

DEPRECATED - use pubmed-annotate instead.

"},{"location":"functions/#recipe-extract","title":"recipe-extract","text":"

Extract from a recipe on the web.

This uses the recipe template and the recipe_scrapers package. The latter supports many different recipe web sites, so give your favorite a try.

Pass a URL as the argument, or use the -R option to specify the path to a file containing one URL per line.

Options:

Example:

ontogpt recipe-extract https://www.allrecipes.com/recipe/17445/grilled-asparagus/\n

In this case, expect an extracted object like the following:

extracted_object:\n  url: https://www.allrecipes.com/recipe/17445/grilled-asparagus/\n  label: Grilled Asparagus\n  description: Grilled asparagus with olive oil, salt, and pepper.\n  categories:\n    - AUTO:None\n  ingredients:\n    - food_item:\n        food: FOODON:03311349\n        state: fresh, spears\n      amount:\n        value: '1'\n        unit: UO:0010034\n    - food_item:\n        food: FOODON:03301826\n      amount:\n        value: '1'\n        unit: UO:0010042\n    - food_item:\n        food: AUTO:salt\n        state: and pepper\n      amount:\n        value: N/A\n        unit: AUTO:N/A\n  steps:\n    - action: AUTO:Preheat\n      inputs:\n        - food: AUTO:outdoor%20grill\n          state: None\n      outputs:\n        - food: AUTO:None\n          state: None\n      utensils:\n        - AUTO:None\n    - action: dbpediaont:season\n      inputs:\n        - food: FOODON:00003458\n          state: coated\n        - food: AUTO:salt\n          state: None\n        - food: FOODON:00003520\n      outputs:\n        - food: FOODON:00003458\n          state: seasoned\n      utensils:\n        - AUTO:None\n    - action: AUTO:cook\n      inputs:\n        - food: FOODON:03311349\n          state: None\n      outputs:\n        - food: FOODON:03311349\n          state: cooked\n      utensils:\n        - AUTO:grill\n
"},{"location":"functions/#synonyms","title":"synonyms","text":"

Extract synonyms, based on embeddings.

The context parameter is required.

Options:

Example:

ontogpt synonyms --context astronomy star\n
"},{"location":"functions/#text-distance","title":"text-distance","text":"

Embed text and calculate euclidian distance between the embeddings.

The terms must be separated by an @ character.

Options:

Example:

ontogpt text-distance pancakes @ syrup\n
"},{"location":"functions/#text-similarity","title":"text-similarity","text":"

Like text-distance, this command compares the embeddings of input terms.

This command returns the cosine similarity of the embedding vectors.

Options:

Example:

ontogpt text-similarity basketball @ basket-weaving\n
"},{"location":"functions/#web-extract","title":"web-extract","text":"

Extract knowledge from web page.

Pass a URL as an argument and OntoGPT will use the SPIRES method to extract information based on the specified template.

Because this depends upon scraping a page, results may vary depending on a site's complexity and structure.

Even relatively short pages may exceed a model's context size, so larger context models may be necessary.

Example:

ontogpt web-extract -t reaction.Reaction -m gpt-3.5-turbo-16k https://www.scienceofcooking.com/maillard_reaction.htm \n
"},{"location":"functions/#wikipedia-extract","title":"wikipedia-extract","text":"

Extract knowledge from a Wikipedia page.

Pass an article title as an argument and OntoGPT will use the SPIRES method to extract information based on the specified template.

Even relatively short pages may exceed a model's context size, so larger context models may be necessary.

Example:

ontogpt wikipedia-extract -t mendelian_disease.MendelianDisease -m gpt-3.5-turbo-16k \"Cartilage\u2013hair hypoplasia\"\n
"},{"location":"functions/#wikipedia-search","title":"wikipedia-search","text":"

Extract knowledge from Wikipedia pages based on a search.

Pass a search phrase as an argument and OntoGPT will use the SPIRES method to extract information based on the specified template.

Even relatively short pages may exceed a model's context size, so larger context models may be necessary.

Example:

ontogpt wikipedia-search -t biological_process -m gpt-3.5-turbo-16k \"digestion\"\n
"},{"location":"operation/","title":"Operation","text":""},{"location":"operation/#getting-started","title":"Getting Started","text":"

OntoGPT is run from the command line. See the full list of commands with:

ontogpt --help\n

For a simple example of text completion and testing to ensure OntoGPT is set up correctly, create a text file containing the following, saving the file as example.txt:

Why did the squid cross the coral reef?\n

Then try the following command:

ontogpt complete example.txt\n

You should get text output like the following:

Perhaps the squid crossed the coral reef for a variety of reasons:\n\n1. Food: Squids are known to feed on small fish and other marine organisms, and there could have been a rich food source on the other side of the reef.\n\n...\n

OntoGPT is intended to be used for information extraction. The following examples show how to accomplish this.

"},{"location":"operation/#strategy-1-knowledge-extraction-using-spires","title":"Strategy 1: Knowledge extraction using SPIRES","text":""},{"location":"operation/#working-mechanism","title":"Working Mechanism","text":"
  1. You provide an arbitrary data model, describing the structure you want to extract text into. This can be nested (but see limitations below). The predefined templates may be used.
  2. Provide your preferred annotations for grounding NamedEntity fields
  3. OntoGPT will:
    • Generate a prompt
    • Feed the prompt to a language model
    • Parse the results into a dictionary structure
    • Ground the results using a preferred annotator (e.g., an ontology)
"},{"location":"operation/#input","title":"Input","text":"

Consider some text from one of the input files being used in the OntoGPT test suite. You can find the text file here. You can download the raw file from the GitHub link to that input text file, or copy its contents over into another file, say, abstract.txt. An excerpt:

The cGAS/STING-mediated DNA-sensing signaling pathway is crucial for interferon (IFN) production and host antiviral responses

... [snip] ...

The underlying mechanism was the interaction of US3 with \u03b2-catenin and its hyperphosphorylation of \u03b2-catenin at Thr556 to block its nuclear translocation ... ...

We can extract knowledge from the above text this into the GO pathway datamodel by running the following command:

"},{"location":"operation/#command","title":"Command","text":"
ontogpt extract -t gocam.GoCamAnnotations -i ~/path/to/abstract.txt\n

Note: The value accepted by the -t / --template argument is the base name of one of the LinkML schema / data model which can be found in the templates folder.

"},{"location":"operation/#output","title":"Output","text":"

The output returned from the above command can be optionally redirected into an output file using the -o / --output.

The following is a small part of what the larger schema-compliant output looks like:

genes:\n- HGNC:2514\n- HGNC:21367\n- HGNC:27962\n- US3\n- FPLX:Interferon\n- ISG\ngene_gene_interactions:\n- gene1: US3\n  gene2: HGNC:2514\ngene_localizations:\n- gene: HGNC:2514\n  location: Nuclear\ngene_functions:\n- gene: HGNC:2514\n  molecular_activity: Transcription\n- gene: HGNC:21367\n  molecular_activity: Production\n...\n
"},{"location":"operation/#local-models","title":"Local Models","text":"

To use a local model, specify it with the -m or --model option.

Example:

ontogpt extract -t drug -i ~/path/to/abstract.txt -m nous-hermes-13b\n

See the list of all available models with this command:

ontogpt list-models\n

When specifying a local model for the first time, it will be downloaded to your local system.

"},{"location":"operation/#strategy-2-gene-enrichment-using-spindoctor","title":"Strategy 2: Gene Enrichment using SPINDOCTOR","text":"

Given a set of genes, OntoGPT can find similarities among them.

Ex.:

ontogpt enrichment -U tests/input/genesets/sensory-ataxia.yaml\n

The default is to use ontological gene function synopses (via the Alliance API).

This strategy does not currently support using local models.

"},{"location":"owl_exports/","title":"OWL Exports","text":"

The extract command will let you export the results as OWL axioms, utilizing linkml-owl mappings in the schema.

Ex.:

ontogpt extract -t recipe -i recipe-spaghetti.txt -o recipe-spaghetti.owl -O owl\n

src/ontogpt/templates/recipe.yaml is an example schema that uses linkml-owl mappings.

See the Makefile for a full pipeline that involves using robot to extract a subset of FOODON and merge in the extracted results. This uses recipe-scrapers.

OWL output: recipe-all-merged.owl

Classification:

"},{"location":"setup/","title":"Setup","text":""},{"location":"setup/#prerequisites","title":"Prerequisites","text":"

OntoGPT may be installed through pip or used directly from the GitHub repository. In the latter case, you will need to install the poetry dependency manager and precede commands with poetry run. See the poetry installation documentation for more details.

"},{"location":"setup/#additional-requirements-and-options","title":"Additional requirements and options","text":"

You may also set additional API keys for optional resources:

"},{"location":"setup/#installation","title":"Installation","text":"

To simply start using the package in your workspace:

pip install ontogpt\n

Note that some features require installing additional, optional dependencies. These may be installed as:

pip install ontogpt[extra_name]\n

where extra_name is one of the following:

For installation from the GitHub repository, particularly if you plan to contribute to feature development or other package code:

git clone https://github.com/monarch-initiative/ontogpt.git\ncd ontogpt/\npoetry install\n

Extras listed above may be installed as:

poetry install --extras extra_name\n

All commands should then be preceded by poetry run, or simply run poetry shell to create and enter a virtual environment for the project.

"},{"location":"setup/#setting-api-keys","title":"Setting API keys","text":"

One OntoGPT and all of its dependencies are installed, you will need to set your API keys using the Ontology Access Kit:

runoak set-apikey -e openai <your openai api key>\n

The optional keys may be set as follows:

runoak set-apikey -e bioportal <your bioportal api key>\nrunoak set-apikey -e ncbi-email <your email address>\nrunoak set-apikey -e ncbi-key <your NCBI api key>\nrunoak set-apikey -e hfhub-key <your HuggingFace Hub api key>\n
"},{"location":"setup/#running-local-models","title":"Running local models","text":"

Using local models currently depends upon using the gpt4all package and may require additional setup steps specific to your computing environment.

See the gpt4all documentation for more details.

"},{"location":"start_with_owl/","title":"Starting with OWL","text":"

OWL, or Web Ontology Language, is a popular format for ontologies, so what is the best way to start working with OntoGPT if you have an OWL ontology already?

OWL is a data model for expressing ontologies, oriented around set-theoretic logical Axioms. OWL is not strictly an ontology format, but it may be represented in the RDF language, among others. Much, much more detail here.

OWL may encode a data schema, or it may encode something else. In the latter case, think very carefully about what data you wish to extract and how it relates to what is present in your OWL.

The crucial question is this: does your OWL literally contain a set of terms you wish to ground extractions to, or does it define a set of concepts and their relationships you would like to extract?

For example, let's use this very simple example ontology:

<rdf:RDF\n    xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n    xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"\n    xmlns:owl=\"http://www.w3.org/2002/07/owl#\"\n    xmlns:fruits=\"http://example.org/fruits#\">\n\n  <!-- Classes -->\n  <owl:Class rdf:about=\"#Fruit\"/>\n  <owl:Class rdf:about=\"#CitrusFruit\">\n    <rdf:type rdf:resource=\"http://www.w3.org/2002/07/owl#Class\"/>\n    <rdfs:subClassOf rdf:resource=\"#Fruit\"/>\n  </owl:Class>\n\n  <!-- Individuals -->\n  <owl:NamedIndividual rdf:about=\"#Apple\">\n    <rdf:type rdf:resource=\"#Fruit\"/>\n    <rdfs:label>Apple</rdfs:label>\n  </owl:NamedIndividual>\n  <owl:NamedIndividual rdf:about=\"#Orange\">\n    <rdf:type rdf:resource=\"#CitrusFruit\"/>\n    <rdfs:label>Orange</rdfs:label>\n  </owl:NamedIndividual>\n\n</rdf:RDF>\n

If you want to extract entities from text (and they may be anything - foods, flavors, etc.) and then ground them to individuals in the ontology, then continue to Option 1.

If you want to extract all Fruit entities from input text while also recognizing that some of them may be CitrusFruit, then continue to Option 2.

"},{"location":"start_with_owl/#option-1-grounding-to-a-set-of-terms","title":"Option 1 - grounding to a set of terms","text":"

You may use an OWL file the same way as any other annotator.

Note that the example ontology above doesn't use prefixes, so let us imagine that each named individual has an identifier like FRUIT:12345.

If your input text contains the word \"orange\", then it will be grounded based on the provided OWL, but any terms not in the OWL, like \"snakeskin fruit\" will not be grounded unless you provide additional annotators capable of grounding the term.

If your ontology is in fruit.owl, then your schema may define a class like this:

  Fruit:\n    is_a: NamedEntity\n    id_prefixes:\n      - FRUIT   \n    annotations:\n      annotators: fruit.owl\n

The OWL file should be in the same path as where you will run ontogpt from.

If your ontology is already in the OBO Foundry, then you may also specify the annotator as something like sqlite:obo:fruit (that's just an example, but try something like the Food Ontology with sqlite:obo:foodon for an equivalent).

"},{"location":"start_with_owl/#option-2-transforming-an-owl-into-ontogpt-schema","title":"Option 2 - transforming an OWL into OntoGPT schema","text":"

This path is a bit more complicated.

If you'd rather use the OWL more like a schema to develop a corresponding extraction schema for OntoGPT, you may be able to do so with the schema-automator tool.

After installing the tool, try something like this:

$ schemauto import-owl fruit.owl\n... schema-automator attempts to transform the OWL ...\n

This process may encounter some errors along the way. One frequent issue is that the input ontology may not be in functional syntax, but may be converted using the robot tool like this:

$ robot convert -i fruit.owl -o fruit.ofn\n... a magical transformation happens ...\n$ schemauto import-owl fruit.ofn\n

The process may still go poorly if the input ontology is heavily dependent on imports.

If everything goes well, however, you should get a LinkML YAML version of the ontology. It will still require addition of description and annotation slots to each class before it will be useful for extraction operations.

Overall, you may find that it is easier to modify an existing OntoGPT schema to fit your schema.

"},{"location":"troubleshooting/","title":"Troubleshooting","text":"

Encountering an error, mystery, or other unexplained oddity? Open a ticket on the GitHub repository: https://github.com/monarch-initiative/ontogpt/issues

"},{"location":"troubleshooting/#i-get-an-error-like-typeerror-configuredbasemodel__init_subclass__-takes-no-keyword-arguments","title":"I get an error like TypeError: ConfiguredBaseModel.__init_subclass__() takes no keyword arguments","text":"

This can happen if you have installed a version of the Pydantic package older than version 2 and/or if you're using a schema generated for Pydantic v1. Versions of OntoGPT of v0.3.3 and above should prevent this from happening, but if you're still seeing the error, then running make again may fix it.

"},{"location":"troubleshooting/#i-get-an-error-like-urlliberrorhttperror-http-error-404-not-found","title":"I get an error like urllib.error.HTTPError: HTTP Error 404: Not Found","text":"

There are a variety of reasons why this may happen, but one cause is if your schema specifies an annotator which does not exist. If the stack trace of the error includes the get_adapter method from oaklib, then this is a likely cause, and you may want to verify that all annotators are accessible to OAK.

"},{"location":"troubleshooting/#i-get-a-lot-of-warnings-like-warningrootcould-not-find-any-mappings-for-and-i-dont-get-the-expected-identifiers-in-my-extracted-object","title":"I get a lot of warnings like WARNING:root:Could not find any mappings for ... and I don't get the expected identifiers in my extracted object","text":"

Verify that the id_prefixes you specify in your schema correspond to those provided by the annotator. If your annotator is sqlite:obo:hp, for example, the prefix will be HP rather than HPO.

"},{"location":"troubleshooting/#i-need-to-store-the-annotator-files-ontogpt-downloads-somewhere-other-than-dataoaklib","title":"I need to store the annotator files OntoGPT downloads somewhere other than ~/.data/oaklib","text":"

OntoGPT uses oaklib to handle the ontologies it uses as annotators, and oaklib uses the pystow package to determine where downloads should go.

To change the download location, set the PYSTOW_HOME variable in your environment to your preferred path.

For example, to save downloads to /tmp/oaklib, set the varible like this:

export PYSTOW_HOME='/tmp/'\n

You may then reset that variable with this command:

unset PYSTOW_HOME\n

Or make the change more permanent by adding it to your .bashrc file and then run

source ~/.bashrc\n
"},{"location":"biological_process/","title":"Biological Process Template","text":"

A template for GO-CAMs

URI: https://w3id.org/ontogpt/biological_process

Name: biological-process-template

"},{"location":"biological_process/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nBiologicalProcess {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\n\nBiologicalProcess ||--|o BiologicalProcess : \"subclass_of\"\nBiologicalProcess ||--}o ChemicalEntity : \"inputs\"\nBiologicalProcess ||--}o ChemicalEntity : \"outputs\"\nBiologicalProcess ||--}o MolecularActivity : \"steps\"\nBiologicalProcess ||--}o Gene : \"genes\"\nBiologicalProcess ||--}o GeneMolecularActivityRelationship : \"gene_activities\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\n\n
"},{"location":"biological_process/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text GeneMolecularActivityRelationship None NamedEntity None BiologicalProcess None ChemicalEntity None Gene None MolecularActivity None RelationshipType None Publication None TextWithTriples None"},{"location":"biological_process/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text description a textual description of the biological process extracted_object The complex objects extracted from the text full_text The full text of the publication gene gene_activities semicolon-separated list of gene to molecular activity relationships genes id A unique identifier for the named entity input_id input_text input_title inputs the inputs of the biological process label the name of the biological process molecular_activity named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text outputs the outputs of the biological process predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output steps the steps involved in this biological process subclass_of the category to which this biological process belongs subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text synonyms alternative names of the biological process title The title of the publication triples"},{"location":"biological_process/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"biological_process/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"biological_process/#subsets","title":"Subsets","text":"Subset Description"},{"location":"biological_process/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: bp:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"biological_process/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"biological_process/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:AnnotatorResult native bp:AnnotatorResult"},{"location":"biological_process/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n\n
"},{"location":"biological_process/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"biological_process/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"biological_process/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"biological_process/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"biological_process/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Any/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native bp:Any"},{"location":"biological_process/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/biological_process\nclass_uri: linkml:Any\n\n
"},{"location":"biological_process/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/biological_process\nclass_uri: linkml:Any\n\n
"},{"location":"biological_process/BiologicalProcess/","title":"Class: BiologicalProcess","text":"

URI: bp:BiologicalProcess

erDiagram\nBiologicalProcess {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\n\nBiologicalProcess ||--|o BiologicalProcess : \"subclass_of\"\nBiologicalProcess ||--}o ChemicalEntity : \"inputs\"\nBiologicalProcess ||--}o ChemicalEntity : \"outputs\"\nBiologicalProcess ||--}o MolecularActivity : \"steps\"\nBiologicalProcess ||--}o Gene : \"genes\"\nBiologicalProcess ||--}o GeneMolecularActivityRelationship : \"gene_activities\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\n\n
"},{"location":"biological_process/BiologicalProcess/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/BiologicalProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 0..1 String the name of the biological process direct description 0..1 String a textual description of the biological process direct synonyms 0..* String alternative names of the biological process direct subclass_of 0..1 BiologicalProcess the category to which this biological process belongs direct inputs 0..* ChemicalEntity the inputs of the biological process direct outputs 0..* ChemicalEntity the outputs of the biological process direct steps 0..* MolecularActivity the steps involved in this biological process direct genes 0..* Gene direct gene_activities 0..* GeneMolecularActivityRelationship semicolon-separated list of gene to molecular activity relationships direct id 1..1 String A unique identifier for the named entity NamedEntity"},{"location":"biological_process/BiologicalProcess/#usages","title":"Usages","text":"used by used in type used BiologicalProcess subclass_of range BiologicalProcess"},{"location":"biological_process/BiologicalProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/BiologicalProcess/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/BiologicalProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:BiologicalProcess native bp:BiologicalProcess"},{"location":"biological_process/BiologicalProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/BiologicalProcess/#direct","title":"Direct","text":"
name: BiologicalProcess\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  description:\n    name: description\n    description: a textual description of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  synonyms:\n    name: synonyms\n    description: alternative names of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n  subclass_of:\n    name: subclass_of\n    description: the category to which this biological process belongs\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: BiologicalProcess\n  inputs:\n    name: inputs\n    description: the inputs of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n  outputs:\n    name: outputs\n    description: the outputs of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n  steps:\n    name: steps\n    description: the steps involved in this biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: MolecularActivity\n  genes:\n    name: genes\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: Gene\n  gene_activities:\n    name: gene_activities\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: GeneMolecularActivityRelationship\ntree_root: true\n\n
"},{"location":"biological_process/BiologicalProcess/#induced","title":"Induced","text":"
name: BiologicalProcess\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: label\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n  description:\n    name: description\n    description: a textual description of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: description\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: string\n  synonyms:\n    name: synonyms\n    description: alternative names of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: string\n  subclass_of:\n    name: subclass_of\n    description: the category to which this biological process belongs\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: subclass_of\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: BiologicalProcess\n  inputs:\n    name: inputs\n    description: the inputs of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: inputs\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: ChemicalEntity\n  outputs:\n    name: outputs\n    description: the outputs of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: outputs\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: ChemicalEntity\n  steps:\n    name: steps\n    description: the steps involved in this biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: steps\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: MolecularActivity\n  genes:\n    name: genes\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: Gene\n  gene_activities:\n    name: gene_activities\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: gene_activities\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: GeneMolecularActivityRelationship\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: BiologicalProcess\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\ntree_root: true\n\n
"},{"location":"biological_process/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"biological_process/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/ChemicalEntity/","title":"Class: ChemicalEntity","text":"

URI: bp:ChemicalEntity

erDiagram\nChemicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biological_process/ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biological_process/ChemicalEntity/#usages","title":"Usages","text":"used by used in type used BiologicalProcess inputs range ChemicalEntity BiologicalProcess outputs range ChemicalEntity"},{"location":"biological_process/ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biological_process/ChemicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"biological_process/ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ChemicalEntity native bp:ChemicalEntity"},{"location":"biological_process/ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\n\n
"},{"location":"biological_process/ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalEntity\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"biological_process/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: bp:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"biological_process/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"biological_process/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:CompoundExpression native bp:CompoundExpression"},{"location":"biological_process/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/biological_process\nabstract: true\n\n
"},{"location":"biological_process/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/biological_process\nabstract: true\n\n
"},{"location":"biological_process/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"biological_process/Curie/#comments","title":"Comments","text":""},{"location":"biological_process/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Curie/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"biological_process/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Date/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"biological_process/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"biological_process/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"biological_process/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"biological_process/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Double/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: bp:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"biological_process/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"biological_process/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ExtractionResult native bp:ExtractionResult"},{"location":"biological_process/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biological_process/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biological_process/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"biological_process/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Float/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Gene/","title":"Class: Gene","text":"

URI: bp:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biological_process/Gene/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biological_process/Gene/#usages","title":"Usages","text":"used by used in type used BiologicalProcess genes range Gene GeneMolecularActivityRelationship gene range Gene"},{"location":"biological_process/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biological_process/Gene/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hgnc"},{"location":"biological_process/Gene/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Gene native bp:Gene"},{"location":"biological_process/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\n\n
"},{"location":"biological_process/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"biological_process/GeneMolecularActivityRelationship/","title":"Class: GeneMolecularActivityRelationship","text":"

URI: bp:GeneMolecularActivityRelationship

erDiagram\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\n\n
"},{"location":"biological_process/GeneMolecularActivityRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct molecular_activity 0..1 MolecularActivity direct"},{"location":"biological_process/GeneMolecularActivityRelationship/#usages","title":"Usages","text":"used by used in type used BiologicalProcess gene_activities range GeneMolecularActivityRelationship"},{"location":"biological_process/GeneMolecularActivityRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/GeneMolecularActivityRelationship/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/GeneMolecularActivityRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:GeneMolecularActivityRelationship native bp:GeneMolecularActivityRelationship"},{"location":"biological_process/GeneMolecularActivityRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/GeneMolecularActivityRelationship/#direct","title":"Direct","text":"
name: GeneMolecularActivityRelationship\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  gene:\n    name: gene\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: MolecularActivity\n\n
"},{"location":"biological_process/GeneMolecularActivityRelationship/#induced","title":"Induced","text":"
name: GeneMolecularActivityRelationship\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  gene:\n    name: gene\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: gene\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneMolecularActivityRelationship\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: molecular_activity\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneMolecularActivityRelationship\n    range: MolecularActivity\n\n
"},{"location":"biological_process/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"biological_process/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Integer/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/MolecularActivity/","title":"Class: MolecularActivity","text":"

URI: bp:MolecularActivity

erDiagram\nMolecularActivity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biological_process/MolecularActivity/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/MolecularActivity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biological_process/MolecularActivity/#usages","title":"Usages","text":"used by used in type used BiologicalProcess steps range MolecularActivity GeneMolecularActivityRelationship molecular_activity range MolecularActivity"},{"location":"biological_process/MolecularActivity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/MolecularActivity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biological_process/MolecularActivity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"biological_process/MolecularActivity/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/MolecularActivity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:MolecularActivity native bp:MolecularActivity"},{"location":"biological_process/MolecularActivity/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/MolecularActivity/#direct","title":"Direct","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\n\n
"},{"location":"biological_process/MolecularActivity/#induced","title":"Induced","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MolecularActivity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: MolecularActivity\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"biological_process/NamedEntity/","title":"Class: NamedEntity","text":"

URI: bp:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biological_process/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"biological_process/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"biological_process/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:NamedEntity native bp:NamedEntity"},{"location":"biological_process/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/biological_process\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"biological_process/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/biological_process\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"biological_process/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"biological_process/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"biological_process/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"biological_process/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"biological_process/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"biological_process/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"biological_process/Objectidentifier/#comments","title":"Comments","text":""},{"location":"biological_process/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Publication/","title":"Class: Publication","text":"

URI: bp:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"biological_process/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"biological_process/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"biological_process/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Publication/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Publication native bp:Publication"},{"location":"biological_process/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/biological_process\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n\n
"},{"location":"biological_process/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/biological_process\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"biological_process/RelationshipType/","title":"Class: RelationshipType","text":"

URI: bp:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biological_process/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biological_process/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"biological_process/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biological_process/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:RelationshipType native bp:RelationshipType"},{"location":"biological_process/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\n\n
"},{"location":"biological_process/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"biological_process/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"biological_process/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/String/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: bp:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"biological_process/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"biological_process/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:TextWithTriples native bp:TextWithTriples"},{"location":"biological_process/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biological_process/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biological_process/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"biological_process/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Time/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: bp:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"biological_process/Triple/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"biological_process/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"biological_process/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Triple/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Triple native bp:Triple"},{"location":"biological_process/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"biological_process/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"biological_process/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"biological_process/Uri/#comments","title":"Comments","text":""},{"location":"biological_process/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Uri/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"biological_process/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: bp:abstract

"},{"location":"biological_process/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biological_process/abstract/#properties","title":"Properties","text":""},{"location":"biological_process/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/abstract/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biological_process/biological-process-template/","title":"biological-process-template","text":"

A template for GO-CAMs

URI: https://w3id.org/ontogpt/biological_process

"},{"location":"biological_process/combined_text/","title":"Slot: combined_text","text":"

URI: bp:combined_text

"},{"location":"biological_process/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biological_process/combined_text/#properties","title":"Properties","text":""},{"location":"biological_process/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biological_process/description/","title":"Slot: description","text":"

a textual description of the biological process

URI: bp:description

"},{"location":"biological_process/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/description/#properties","title":"Properties","text":""},{"location":"biological_process/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/description/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a textual description of the biological process\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: description\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: string\n\n
"},{"location":"biological_process/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: bp:extracted_object

"},{"location":"biological_process/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/extracted_object/#properties","title":"Properties","text":""},{"location":"biological_process/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"biological_process/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: bp:full_text

"},{"location":"biological_process/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biological_process/full_text/#properties","title":"Properties","text":""},{"location":"biological_process/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/full_text/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biological_process/gene/","title":"Slot: gene","text":"

URI: bp:gene

"},{"location":"biological_process/gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship no"},{"location":"biological_process/gene/#properties","title":"Properties","text":""},{"location":"biological_process/gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/gene/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/gene/#linkml-source","title":"LinkML Source","text":"
name: gene\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: gene\nowner: GeneMolecularActivityRelationship\ndomain_of:\n- GeneMolecularActivityRelationship\nrange: Gene\n\n
"},{"location":"biological_process/gene_activities/","title":"Slot: gene_activities","text":"

semicolon-separated list of gene to molecular activity relationships

URI: bp:gene_activities

"},{"location":"biological_process/gene_activities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/gene_activities/#properties","title":"Properties","text":""},{"location":"biological_process/gene_activities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/gene_activities/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/gene_activities/#linkml-source","title":"LinkML Source","text":"
name: gene_activities\ndescription: semicolon-separated list of gene to molecular activity relationships\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: gene_activities\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: GeneMolecularActivityRelationship\n\n
"},{"location":"biological_process/genes/","title":"Slot: genes","text":"

URI: bp:genes

"},{"location":"biological_process/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/genes/#properties","title":"Properties","text":""},{"location":"biological_process/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/genes/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: genes\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: Gene\n\n
"},{"location":"biological_process/id/","title":"Slot: id","text":"

URI: bp:id

"},{"location":"biological_process/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no Gene no MolecularActivity no ChemicalEntity no NamedEntity no RelationshipType no Publication no"},{"location":"biological_process/id/#properties","title":"Properties","text":""},{"location":"biological_process/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"biological_process/input_id/","title":"Slot: input_id","text":"

URI: bp:input_id

"},{"location":"biological_process/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/input_id/#properties","title":"Properties","text":""},{"location":"biological_process/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/input_id/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biological_process/input_text/","title":"Slot: input_text","text":"

URI: bp:input_text

"},{"location":"biological_process/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/input_text/#properties","title":"Properties","text":""},{"location":"biological_process/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/input_text/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biological_process/input_title/","title":"Slot: input_title","text":"

URI: bp:input_title

"},{"location":"biological_process/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/input_title/#properties","title":"Properties","text":""},{"location":"biological_process/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/input_title/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biological_process/inputs/","title":"Slot: inputs","text":"

the inputs of the biological process

URI: bp:inputs

"},{"location":"biological_process/inputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/inputs/#properties","title":"Properties","text":""},{"location":"biological_process/inputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/inputs/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/inputs/#linkml-source","title":"LinkML Source","text":"
name: inputs\ndescription: the inputs of the biological process\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: inputs\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: ChemicalEntity\n\n
"},{"location":"biological_process/label/","title":"Slot: label","text":"

URI: bp:label

"},{"location":"biological_process/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no Gene no MolecularActivity no ChemicalEntity no NamedEntity no RelationshipType no"},{"location":"biological_process/label/#properties","title":"Properties","text":""},{"location":"biological_process/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- BiologicalProcess\n- NamedEntity\nrange: string\n\n
"},{"location":"biological_process/molecular_activity/","title":"Slot: molecular_activity","text":"

URI: bp:molecular_activity

"},{"location":"biological_process/molecular_activity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship no"},{"location":"biological_process/molecular_activity/#properties","title":"Properties","text":""},{"location":"biological_process/molecular_activity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/molecular_activity/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/molecular_activity/#linkml-source","title":"LinkML Source","text":"
name: molecular_activity\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: molecular_activity\nowner: GeneMolecularActivityRelationship\ndomain_of:\n- GeneMolecularActivityRelationship\nrange: MolecularActivity\n\n
"},{"location":"biological_process/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: bp:named_entities

"},{"location":"biological_process/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/named_entities/#properties","title":"Properties","text":""},{"location":"biological_process/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biological_process/object/","title":"Slot: object","text":"

URI: bp:object

"},{"location":"biological_process/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/object/#properties","title":"Properties","text":""},{"location":"biological_process/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/object/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biological_process/object_id/","title":"Slot: object_id","text":"

URI: bp:object_id

"},{"location":"biological_process/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biological_process/object_id/#properties","title":"Properties","text":""},{"location":"biological_process/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/object_id/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biological_process/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: bp:object_qualifier

"},{"location":"biological_process/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/object_qualifier/#properties","title":"Properties","text":""},{"location":"biological_process/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biological_process/object_text/","title":"Slot: object_text","text":"

URI: bp:object_text

"},{"location":"biological_process/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biological_process/object_text/#properties","title":"Properties","text":""},{"location":"biological_process/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/object_text/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biological_process/outputs/","title":"Slot: outputs","text":"

the outputs of the biological process

URI: bp:outputs

"},{"location":"biological_process/outputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/outputs/#properties","title":"Properties","text":""},{"location":"biological_process/outputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/outputs/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/outputs/#linkml-source","title":"LinkML Source","text":"
name: outputs\ndescription: the outputs of the biological process\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: outputs\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: ChemicalEntity\n\n
"},{"location":"biological_process/predicate/","title":"Slot: predicate","text":"

URI: bp:predicate

"},{"location":"biological_process/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/predicate/#properties","title":"Properties","text":""},{"location":"biological_process/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/predicate/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"biological_process/prompt/","title":"Slot: prompt","text":"

URI: bp:prompt

"},{"location":"biological_process/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/prompt/#properties","title":"Properties","text":""},{"location":"biological_process/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/prompt/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biological_process/publication/","title":"Slot: publication","text":"

URI: bp:publication

"},{"location":"biological_process/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"biological_process/publication/#properties","title":"Properties","text":""},{"location":"biological_process/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"biological_process/publication/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"biological_process/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: bp:qualifier

"},{"location":"biological_process/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/qualifier/#properties","title":"Properties","text":""},{"location":"biological_process/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"biological_process/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: bp:raw_completion_output

"},{"location":"biological_process/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/raw_completion_output/#properties","title":"Properties","text":""},{"location":"biological_process/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biological_process/steps/","title":"Slot: steps","text":"

the steps involved in this biological process

URI: bp:steps

"},{"location":"biological_process/steps/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/steps/#properties","title":"Properties","text":""},{"location":"biological_process/steps/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/steps/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/steps/#linkml-source","title":"LinkML Source","text":"
name: steps\ndescription: the steps involved in this biological process\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: steps\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: MolecularActivity\n\n
"},{"location":"biological_process/subclass_of/","title":"Slot: subclass_of","text":"

the category to which this biological process belongs

URI: bp:subclass_of

"},{"location":"biological_process/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/subclass_of/#properties","title":"Properties","text":""},{"location":"biological_process/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\ndescription: the category to which this biological process belongs\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: subclass_of\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: BiologicalProcess\n\n
"},{"location":"biological_process/subject/","title":"Slot: subject","text":"

URI: bp:subject

"},{"location":"biological_process/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/subject/#properties","title":"Properties","text":""},{"location":"biological_process/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/subject/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biological_process/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: bp:subject_qualifier

"},{"location":"biological_process/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/subject_qualifier/#properties","title":"Properties","text":""},{"location":"biological_process/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biological_process/subject_text/","title":"Slot: subject_text","text":"

URI: bp:subject_text

"},{"location":"biological_process/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biological_process/subject_text/#properties","title":"Properties","text":""},{"location":"biological_process/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biological_process/synonyms/","title":"Slot: synonyms","text":"

alternative names of the biological process

URI: bp:synonyms

"},{"location":"biological_process/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/synonyms/#properties","title":"Properties","text":""},{"location":"biological_process/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\ndescription: alternative names of the biological process\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: string\n\n
"},{"location":"biological_process/title/","title":"Slot: title","text":"

The title of the publication

URI: bp:title

"},{"location":"biological_process/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biological_process/title/#properties","title":"Properties","text":""},{"location":"biological_process/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/title/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biological_process/triples/","title":"Slot: triples","text":"

URI: bp:triples

"},{"location":"biological_process/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"biological_process/triples/#properties","title":"Properties","text":""},{"location":"biological_process/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/triples/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biotic_interaction/","title":"Biotic Interaction Template","text":"

A template for biotic interactions

URI: https://w3id.org/ontogpt/biotic_interaction

Name: biotic-interaction-template

"},{"location":"biotic_interaction/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nContainer {\n\n}\nBioticInteraction {\n\n}\nInteractionType {\n    string id  \n    string label  \n}\nTaxon {\n    string id  \n    string label  \n}\n\nContainer ||--}o BioticInteraction : \"interactions\"\nBioticInteraction ||--|o Taxon : \"source_taxon\"\nBioticInteraction ||--|o Taxon : \"target_taxon\"\nBioticInteraction ||--|o InteractionType : \"interaction_type\"\n\n
"},{"location":"biotic_interaction/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None BioticInteraction None CompoundExpression None Triple Abstract parent for Relation Extraction tasks Container None ExtractionResult A result of extracting knowledge on text NamedEntity None InteractionType None RelationshipType None Taxon None Publication None TextWithTriples None"},{"location":"biotic_interaction/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title interaction_type the type of interaction interactions label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output source_taxon the taxon that is the subject of the interaction subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text target_taxon the taxon that is the object of the interaction title The title of the publication triples"},{"location":"biotic_interaction/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"biotic_interaction/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"biotic_interaction/#subsets","title":"Subsets","text":"Subset Description"},{"location":"biotic_interaction/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: bp:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"biotic_interaction/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"biotic_interaction/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:AnnotatorResult native bp:AnnotatorResult"},{"location":"biotic_interaction/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n\n
"},{"location":"biotic_interaction/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"biotic_interaction/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"biotic_interaction/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"biotic_interaction/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"biotic_interaction/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Any/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native bp:Any"},{"location":"biotic_interaction/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nclass_uri: linkml:Any\n\n
"},{"location":"biotic_interaction/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nclass_uri: linkml:Any\n\n
"},{"location":"biotic_interaction/BioticInteraction/","title":"Class: BioticInteraction","text":"

URI: bp:BioticInteraction

erDiagram\nBioticInteraction {\n\n}\nInteractionType {\n    string id  \n    string label  \n}\nTaxon {\n    string id  \n    string label  \n}\n\nBioticInteraction ||--|o Taxon : \"source_taxon\"\nBioticInteraction ||--|o Taxon : \"target_taxon\"\nBioticInteraction ||--|o InteractionType : \"interaction_type\"\n\n
"},{"location":"biotic_interaction/BioticInteraction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance source_taxon 0..1 Taxon the taxon that is the subject of the interaction direct target_taxon 0..1 Taxon the taxon that is the object of the interaction direct interaction_type 0..1 InteractionType the type of interaction direct"},{"location":"biotic_interaction/BioticInteraction/#usages","title":"Usages","text":"used by used in type used Container interactions range BioticInteraction"},{"location":"biotic_interaction/BioticInteraction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/BioticInteraction/#annotations","title":"Annotations","text":"property value prompt A semi-colon separated list of taxon to taxon relationships"},{"location":"biotic_interaction/BioticInteraction/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/BioticInteraction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:BioticInteraction native bp:BioticInteraction"},{"location":"biotic_interaction/BioticInteraction/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/BioticInteraction/#direct","title":"Direct","text":"
name: BioticInteraction\nannotations:\n  prompt:\n    tag: prompt\n    value: A semi-colon separated list of taxon to taxon relationships\n  prompt.example:\n    tag: prompt.example\n    value: Carcharodon carcharias eats elephant seal; Pandarus sinuatus parasitizes\n      Carcharodon carcharias; orca eats Carcharodon carcharias\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  source_taxon:\n    name: source_taxon\n    description: the taxon that is the subject of the interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: Taxon\n  target_taxon:\n    name: target_taxon\n    description: the taxon that is the object of the interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: Taxon\n  interaction_type:\n    name: interaction_type\n    description: the type of interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: InteractionType\n\n
"},{"location":"biotic_interaction/BioticInteraction/#induced","title":"Induced","text":"
name: BioticInteraction\nannotations:\n  prompt:\n    tag: prompt\n    value: A semi-colon separated list of taxon to taxon relationships\n  prompt.example:\n    tag: prompt.example\n    value: Carcharodon carcharias eats elephant seal; Pandarus sinuatus parasitizes\n      Carcharodon carcharias; orca eats Carcharodon carcharias\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  source_taxon:\n    name: source_taxon\n    description: the taxon that is the subject of the interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: source_taxon\n    owner: BioticInteraction\n    domain_of:\n    - BioticInteraction\n    range: Taxon\n  target_taxon:\n    name: target_taxon\n    description: the taxon that is the object of the interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: target_taxon\n    owner: BioticInteraction\n    domain_of:\n    - BioticInteraction\n    range: Taxon\n  interaction_type:\n    name: interaction_type\n    description: the type of interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: interaction_type\n    owner: BioticInteraction\n    domain_of:\n    - BioticInteraction\n    range: InteractionType\n\n
"},{"location":"biotic_interaction/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"biotic_interaction/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: bp:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"biotic_interaction/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"biotic_interaction/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:CompoundExpression native bp:CompoundExpression"},{"location":"biotic_interaction/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nabstract: true\n\n
"},{"location":"biotic_interaction/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nabstract: true\n\n
"},{"location":"biotic_interaction/Container/","title":"Class: Container","text":"

URI: bp:Container

erDiagram\nContainer {\n\n}\nBioticInteraction {\n\n}\nInteractionType {\n    string id  \n    string label  \n}\nTaxon {\n    string id  \n    string label  \n}\n\nContainer ||--}o BioticInteraction : \"interactions\"\nBioticInteraction ||--|o Taxon : \"source_taxon\"\nBioticInteraction ||--|o Taxon : \"target_taxon\"\nBioticInteraction ||--|o InteractionType : \"interaction_type\"\n\n
"},{"location":"biotic_interaction/Container/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance interactions 0..* BioticInteraction direct"},{"location":"biotic_interaction/Container/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Container/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Container/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Container native bp:Container"},{"location":"biotic_interaction/Container/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/Container/#direct","title":"Direct","text":"
name: Container\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  interactions:\n    name: interactions\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    range: BioticInteraction\n    inlined: true\n    inlined_as_list: true\ntree_root: true\n\n
"},{"location":"biotic_interaction/Container/#induced","title":"Induced","text":"
name: Container\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  interactions:\n    name: interactions\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    alias: interactions\n    owner: Container\n    domain_of:\n    - Container\n    range: BioticInteraction\n    inlined: true\n    inlined_as_list: true\ntree_root: true\n\n
"},{"location":"biotic_interaction/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"biotic_interaction/Curie/#comments","title":"Comments","text":""},{"location":"biotic_interaction/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Curie/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"biotic_interaction/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Date/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"biotic_interaction/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"biotic_interaction/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"biotic_interaction/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"biotic_interaction/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Double/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: bp:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"biotic_interaction/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"biotic_interaction/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ExtractionResult native bp:ExtractionResult"},{"location":"biotic_interaction/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biotic_interaction/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biotic_interaction/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"biotic_interaction/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Float/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"biotic_interaction/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Integer/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/InteractionType/","title":"Class: InteractionType","text":"

URI: bp:InteractionType

erDiagram\nInteractionType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biotic_interaction/InteractionType/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/InteractionType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biotic_interaction/InteractionType/#usages","title":"Usages","text":"used by used in type used BioticInteraction interaction_type range InteractionType"},{"location":"biotic_interaction/InteractionType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/InteractionType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biotic_interaction/InteractionType/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero"},{"location":"biotic_interaction/InteractionType/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/InteractionType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:InteractionType native bp:InteractionType"},{"location":"biotic_interaction/InteractionType/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/InteractionType/#direct","title":"Direct","text":"
name: InteractionType\nid_prefixes:\n- RO\n- MESH\n- ECOCORE\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\n\n
"},{"location":"biotic_interaction/InteractionType/#induced","title":"Induced","text":"
name: InteractionType\nid_prefixes:\n- RO\n- MESH\n- ECOCORE\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: InteractionType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: InteractionType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"biotic_interaction/NamedEntity/","title":"Class: NamedEntity","text":"

URI: bp:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biotic_interaction/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"biotic_interaction/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"biotic_interaction/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:NamedEntity native bp:NamedEntity"},{"location":"biotic_interaction/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"biotic_interaction/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"biotic_interaction/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"biotic_interaction/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"biotic_interaction/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"biotic_interaction/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"biotic_interaction/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"biotic_interaction/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"biotic_interaction/Objectidentifier/#comments","title":"Comments","text":""},{"location":"biotic_interaction/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Publication/","title":"Class: Publication","text":"

URI: bp:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"biotic_interaction/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"biotic_interaction/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"biotic_interaction/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Publication/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Publication native bp:Publication"},{"location":"biotic_interaction/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n\n
"},{"location":"biotic_interaction/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"biotic_interaction/RelationshipType/","title":"Class: RelationshipType","text":"

URI: bp:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biotic_interaction/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biotic_interaction/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"biotic_interaction/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biotic_interaction/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:RelationshipType native bp:RelationshipType"},{"location":"biotic_interaction/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\n\n
"},{"location":"biotic_interaction/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"biotic_interaction/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"biotic_interaction/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/String/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Taxon/","title":"Class: Taxon","text":"

URI: bp:Taxon

erDiagram\nTaxon {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biotic_interaction/Taxon/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/Taxon/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biotic_interaction/Taxon/#usages","title":"Usages","text":"used by used in type used BioticInteraction source_taxon range Taxon BioticInteraction target_taxon range Taxon"},{"location":"biotic_interaction/Taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Taxon/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biotic_interaction/Taxon/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ncbitaxon, bioportal:SNOMEDCT"},{"location":"biotic_interaction/Taxon/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Taxon/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Taxon native bp:Taxon"},{"location":"biotic_interaction/Taxon/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/Taxon/#direct","title":"Direct","text":"
name: Taxon\nid_prefixes:\n- NCBITaxon\n- SNOMEDCT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ncbitaxon, bioportal:SNOMEDCT\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\n\n
"},{"location":"biotic_interaction/Taxon/#induced","title":"Induced","text":"
name: Taxon\nid_prefixes:\n- NCBITaxon\n- SNOMEDCT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ncbitaxon, bioportal:SNOMEDCT\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Taxon\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Taxon\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"biotic_interaction/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: bp:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"biotic_interaction/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"biotic_interaction/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:TextWithTriples native bp:TextWithTriples"},{"location":"biotic_interaction/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biotic_interaction/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biotic_interaction/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"biotic_interaction/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Time/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: bp:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"biotic_interaction/Triple/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"biotic_interaction/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"biotic_interaction/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Triple/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Triple native bp:Triple"},{"location":"biotic_interaction/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"biotic_interaction/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"biotic_interaction/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"biotic_interaction/Uri/#comments","title":"Comments","text":""},{"location":"biotic_interaction/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Uri/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"biotic_interaction/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: bp:abstract

"},{"location":"biotic_interaction/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biotic_interaction/abstract/#properties","title":"Properties","text":""},{"location":"biotic_interaction/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/abstract/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biotic_interaction/biotic-interaction-template/","title":"biotic-interaction-template","text":"

A template for biotic interactions

URI: https://w3id.org/ontogpt/biotic_interaction

"},{"location":"biotic_interaction/combined_text/","title":"Slot: combined_text","text":"

URI: bp:combined_text

"},{"location":"biotic_interaction/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biotic_interaction/combined_text/#properties","title":"Properties","text":""},{"location":"biotic_interaction/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biotic_interaction/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: bp:extracted_object

"},{"location":"biotic_interaction/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/extracted_object/#properties","title":"Properties","text":""},{"location":"biotic_interaction/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"biotic_interaction/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: bp:full_text

"},{"location":"biotic_interaction/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biotic_interaction/full_text/#properties","title":"Properties","text":""},{"location":"biotic_interaction/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/full_text/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biotic_interaction/id/","title":"Slot: id","text":"

URI: bp:id

"},{"location":"biotic_interaction/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no InteractionType no NamedEntity no RelationshipType no Publication no"},{"location":"biotic_interaction/id/#properties","title":"Properties","text":""},{"location":"biotic_interaction/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"biotic_interaction/input_id/","title":"Slot: input_id","text":"

URI: bp:input_id

"},{"location":"biotic_interaction/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/input_id/#properties","title":"Properties","text":""},{"location":"biotic_interaction/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/input_id/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biotic_interaction/input_text/","title":"Slot: input_text","text":"

URI: bp:input_text

"},{"location":"biotic_interaction/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/input_text/#properties","title":"Properties","text":""},{"location":"biotic_interaction/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/input_text/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biotic_interaction/input_title/","title":"Slot: input_title","text":"

URI: bp:input_title

"},{"location":"biotic_interaction/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/input_title/#properties","title":"Properties","text":""},{"location":"biotic_interaction/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/input_title/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biotic_interaction/interaction_type/","title":"Slot: interaction_type","text":"

the type of interaction

URI: bp:interaction_type

"},{"location":"biotic_interaction/interaction_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BioticInteraction no"},{"location":"biotic_interaction/interaction_type/#properties","title":"Properties","text":""},{"location":"biotic_interaction/interaction_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/interaction_type/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/interaction_type/#linkml-source","title":"LinkML Source","text":"
name: interaction_type\ndescription: the type of interaction\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: interaction_type\nowner: BioticInteraction\ndomain_of:\n- BioticInteraction\nrange: InteractionType\n\n
"},{"location":"biotic_interaction/interactions/","title":"Slot: interactions","text":"

URI: bp:interactions

"},{"location":"biotic_interaction/interactions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Container no"},{"location":"biotic_interaction/interactions/#properties","title":"Properties","text":""},{"location":"biotic_interaction/interactions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/interactions/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/interactions/#linkml-source","title":"LinkML Source","text":"
name: interactions\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nmultivalued: true\nalias: interactions\nowner: Container\ndomain_of:\n- Container\nrange: BioticInteraction\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biotic_interaction/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"biotic_interaction/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no InteractionType no NamedEntity no RelationshipType no"},{"location":"biotic_interaction/label/#properties","title":"Properties","text":""},{"location":"biotic_interaction/label/#aliases","title":"Aliases","text":""},{"location":"biotic_interaction/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"biotic_interaction/label/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"biotic_interaction/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: bp:named_entities

"},{"location":"biotic_interaction/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/named_entities/#properties","title":"Properties","text":""},{"location":"biotic_interaction/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biotic_interaction/object/","title":"Slot: object","text":"

URI: bp:object

"},{"location":"biotic_interaction/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/object/#properties","title":"Properties","text":""},{"location":"biotic_interaction/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/object/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biotic_interaction/object_id/","title":"Slot: object_id","text":"

URI: bp:object_id

"},{"location":"biotic_interaction/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biotic_interaction/object_id/#properties","title":"Properties","text":""},{"location":"biotic_interaction/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/object_id/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biotic_interaction/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: bp:object_qualifier

"},{"location":"biotic_interaction/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/object_qualifier/#properties","title":"Properties","text":""},{"location":"biotic_interaction/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biotic_interaction/object_text/","title":"Slot: object_text","text":"

URI: bp:object_text

"},{"location":"biotic_interaction/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biotic_interaction/object_text/#properties","title":"Properties","text":""},{"location":"biotic_interaction/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/object_text/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biotic_interaction/predicate/","title":"Slot: predicate","text":"

URI: bp:predicate

"},{"location":"biotic_interaction/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/predicate/#properties","title":"Properties","text":""},{"location":"biotic_interaction/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/predicate/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"biotic_interaction/prompt/","title":"Slot: prompt","text":"

URI: bp:prompt

"},{"location":"biotic_interaction/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/prompt/#properties","title":"Properties","text":""},{"location":"biotic_interaction/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/prompt/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biotic_interaction/publication/","title":"Slot: publication","text":"

URI: bp:publication

"},{"location":"biotic_interaction/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"biotic_interaction/publication/#properties","title":"Properties","text":""},{"location":"biotic_interaction/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"biotic_interaction/publication/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"biotic_interaction/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: bp:qualifier

"},{"location":"biotic_interaction/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/qualifier/#properties","title":"Properties","text":""},{"location":"biotic_interaction/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"biotic_interaction/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: bp:raw_completion_output

"},{"location":"biotic_interaction/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/raw_completion_output/#properties","title":"Properties","text":""},{"location":"biotic_interaction/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biotic_interaction/source_taxon/","title":"Slot: source_taxon","text":"

the taxon that is the subject of the interaction

URI: bp:source_taxon

"},{"location":"biotic_interaction/source_taxon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BioticInteraction no"},{"location":"biotic_interaction/source_taxon/#properties","title":"Properties","text":""},{"location":"biotic_interaction/source_taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/source_taxon/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/source_taxon/#linkml-source","title":"LinkML Source","text":"
name: source_taxon\ndescription: the taxon that is the subject of the interaction\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: source_taxon\nowner: BioticInteraction\ndomain_of:\n- BioticInteraction\nrange: Taxon\n\n
"},{"location":"biotic_interaction/subject/","title":"Slot: subject","text":"

URI: bp:subject

"},{"location":"biotic_interaction/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/subject/#properties","title":"Properties","text":""},{"location":"biotic_interaction/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/subject/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biotic_interaction/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: bp:subject_qualifier

"},{"location":"biotic_interaction/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/subject_qualifier/#properties","title":"Properties","text":""},{"location":"biotic_interaction/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biotic_interaction/subject_text/","title":"Slot: subject_text","text":"

URI: bp:subject_text

"},{"location":"biotic_interaction/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biotic_interaction/subject_text/#properties","title":"Properties","text":""},{"location":"biotic_interaction/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biotic_interaction/target_taxon/","title":"Slot: target_taxon","text":"

the taxon that is the object of the interaction

URI: bp:target_taxon

"},{"location":"biotic_interaction/target_taxon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BioticInteraction no"},{"location":"biotic_interaction/target_taxon/#properties","title":"Properties","text":""},{"location":"biotic_interaction/target_taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/target_taxon/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/target_taxon/#linkml-source","title":"LinkML Source","text":"
name: target_taxon\ndescription: the taxon that is the object of the interaction\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: target_taxon\nowner: BioticInteraction\ndomain_of:\n- BioticInteraction\nrange: Taxon\n\n
"},{"location":"biotic_interaction/title/","title":"Slot: title","text":"

The title of the publication

URI: bp:title

"},{"location":"biotic_interaction/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biotic_interaction/title/#properties","title":"Properties","text":""},{"location":"biotic_interaction/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/title/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biotic_interaction/triples/","title":"Slot: triples","text":"

URI: bp:triples

"},{"location":"biotic_interaction/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"biotic_interaction/triples/#properties","title":"Properties","text":""},{"location":"biotic_interaction/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/triples/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"cell_type/","title":"Composite Disease","text":"

A template for representing cell types

URI: http://w3id.org/ontogpt/cell_type

Name: cell_type

"},{"location":"cell_type/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nCellType {\n    uriorcurie id  \n    string label  \n    string definition  \n}\nBiologicalProcess {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nAnatomicalStructure {\n    string id  \n    string label  \n}\nCellOntologyTerm {\n    string id  \n    string label  \n}\n\nCellType ||--|o CellOntologyTerm : \"equivalent_to\"\nCellType ||--}o CellOntologyTerm : \"parents\"\nCellType ||--}o CellOntologyTerm : \"subtypes\"\nCellType ||--}o AnatomicalStructure : \"localizations\"\nCellType ||--}o Gene : \"genes\"\nCellType ||--}o Disease : \"diseases\"\nCellType ||--}o BiologicalProcess : \"roles\"\n\n
"},{"location":"cell_type/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CellType Represents a cell type ImmuneCell None Neuron None Interneuron None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None AnatomicalStructure None BrainRegion None BiologicalProcess None CellOntologyTerm None ChemicalEntity None Neurotransmitter None Disease None Drug None Gene None Pathway None ProteinOrComplex None RelationshipType None Publication None TextWithTriples None"},{"location":"cell_type/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text definition diseases equivalent_to the the cell type described extracted_object The complex objects extracted from the text full_text The full text of the publication genes has_surface_markers id input_id input_text input_title label the concise name of the cell type localizations named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text parents categorization predicate projects_to_or_from Brain structures from which this cell type projects into or receives projecti... prompt publication qualifier A qualifier for the statements, e raw_completion_output releases_neurotransitter roles subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text subtypes title The title of the publication triples"},{"location":"cell_type/#enumerations","title":"Enumerations","text":"Enumeration Description BrainRegionIdentifier Brain region (or for now, any nervous system part) NeurotransmitterIdentifier NullDataOptions"},{"location":"cell_type/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"cell_type/#subsets","title":"Subsets","text":"Subset Description"},{"location":"cell_type/AnatomicalStructure/","title":"Class: AnatomicalStructure","text":"

URI: cell_type:AnatomicalStructure

erDiagram\nAnatomicalStructure {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/AnatomicalStructure/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/AnatomicalStructure/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/AnatomicalStructure/#usages","title":"Usages","text":"used by used in type used CellType localizations range AnatomicalStructure ImmuneCell localizations range AnatomicalStructure Neuron localizations range AnatomicalStructure Interneuron localizations range AnatomicalStructure"},{"location":"cell_type/AnatomicalStructure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/AnatomicalStructure/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/AnatomicalStructure/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt"},{"location":"cell_type/AnatomicalStructure/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/AnatomicalStructure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:AnatomicalStructure native cell_type:AnatomicalStructure"},{"location":"cell_type/AnatomicalStructure/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/AnatomicalStructure/#direct","title":"Direct","text":"
name: AnatomicalStructure\nid_prefixes:\n- UBERON\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/AnatomicalStructure/#induced","title":"Induced","text":"
name: AnatomicalStructure\nid_prefixes:\n- UBERON\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: AnatomicalStructure\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: AnatomicalStructure\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: cell_type:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"cell_type/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"cell_type/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:AnnotatorResult native cell_type:AnnotatorResult"},{"location":"cell_type/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n\n
"},{"location":"cell_type/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"cell_type/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"cell_type/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"cell_type/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"cell_type/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Any/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native cell_type:Any"},{"location":"cell_type/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/cell_type\nclass_uri: linkml:Any\n\n
"},{"location":"cell_type/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/cell_type\nclass_uri: linkml:Any\n\n
"},{"location":"cell_type/BiologicalProcess/","title":"Class: BiologicalProcess","text":"

URI: cell_type:BiologicalProcess

erDiagram\nBiologicalProcess {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/BiologicalProcess/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/BiologicalProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/BiologicalProcess/#usages","title":"Usages","text":"used by used in type used CellType roles range BiologicalProcess ImmuneCell roles range BiologicalProcess Neuron roles range BiologicalProcess Interneuron roles range BiologicalProcess"},{"location":"cell_type/BiologicalProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/BiologicalProcess/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/BiologicalProcess/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"cell_type/BiologicalProcess/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/BiologicalProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:BiologicalProcess native cell_type:BiologicalProcess"},{"location":"cell_type/BiologicalProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/BiologicalProcess/#direct","title":"Direct","text":"
name: BiologicalProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/BiologicalProcess/#induced","title":"Induced","text":"
name: BiologicalProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: BiologicalProcess\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: BiologicalProcess\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"cell_type/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/BrainRegion/","title":"Class: BrainRegion","text":"

URI: cell_type:BrainRegion

erDiagram\nBrainRegion {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/BrainRegion/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/BrainRegion/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/BrainRegion/#usages","title":"Usages","text":"used by used in type used Interneuron projects_to_or_from range BrainRegion"},{"location":"cell_type/BrainRegion/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/BrainRegion/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/BrainRegion/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt"},{"location":"cell_type/BrainRegion/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/BrainRegion/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:BrainRegion native cell_type:BrainRegion"},{"location":"cell_type/BrainRegion/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/BrainRegion/#direct","title":"Direct","text":"
name: BrainRegion\nid_prefixes:\n- UBERON\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: AnatomicalStructure\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - BrainRegionIdentifier\n    identifier: true\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n\n
"},{"location":"cell_type/BrainRegion/#induced","title":"Induced","text":"
name: BrainRegion\nid_prefixes:\n- UBERON\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: AnatomicalStructure\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - BrainRegionIdentifier\n    identifier: true\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/cell_type\n    values_from:\n    - BrainRegionIdentifier\n    identifier: true\n    alias: id\n    owner: BrainRegion\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: BrainRegion\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/BrainRegionIdentifier/","title":"Enum: BrainRegionIdentifier","text":"

Brain region (or for now, any nervous system part)

URI: BrainRegionIdentifier

This is a dynamic enum

"},{"location":"cell_type/BrainRegionIdentifier/#comments","title":"Comments","text":""},{"location":"cell_type/BrainRegionIdentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/BrainRegionIdentifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/BrainRegionIdentifier/#linkml-source","title":"LinkML Source","text":"
name: BrainRegionIdentifier\ndescription: Brain region (or for now, any nervous system part)\ncomments:\n- consider adding brain atlases here\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\ninclude:\n- reachable_from:\n    source_ontology: obo:uberon\n    source_nodes:\n    - UBERON:0001016\n    relationship_types:\n    - rdfs:subClassOf\n    - BFO:0000050\n- reachable_from:\n    source_ontology: obo:fbbt\n    source_nodes:\n    - FBbt:00005093\n    relationship_types:\n    - rdfs:subClassOf\n    - BFO:0000050\n- reachable_from:\n    source_ontology: obo:wbbt\n    source_nodes:\n    - WBbt:0005735\n    relationship_types:\n    - rdfs:subClassOf\n    - BFO:0000050\n\n
"},{"location":"cell_type/CellOntologyTerm/","title":"Class: CellOntologyTerm","text":"

URI: cell_type:CellOntologyTerm

erDiagram\nCellOntologyTerm {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/CellOntologyTerm/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/CellOntologyTerm/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/CellOntologyTerm/#usages","title":"Usages","text":"used by used in type used CellType equivalent_to range CellOntologyTerm CellType parents range CellOntologyTerm CellType subtypes range CellOntologyTerm ImmuneCell equivalent_to range CellOntologyTerm ImmuneCell parents range CellOntologyTerm ImmuneCell subtypes range CellOntologyTerm Neuron equivalent_to range CellOntologyTerm Neuron parents range CellOntologyTerm Neuron subtypes range CellOntologyTerm Interneuron equivalent_to range CellOntologyTerm Interneuron parents range CellOntologyTerm Interneuron subtypes range CellOntologyTerm"},{"location":"cell_type/CellOntologyTerm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/CellOntologyTerm/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/CellOntologyTerm/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:cl, sqlite:obo:fbbt, sqlite:obo:wbbt"},{"location":"cell_type/CellOntologyTerm/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/CellOntologyTerm/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:CellOntologyTerm native cell_type:CellOntologyTerm"},{"location":"cell_type/CellOntologyTerm/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/CellOntologyTerm/#direct","title":"Direct","text":"
name: CellOntologyTerm\nid_prefixes:\n- CL\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:cl, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/CellOntologyTerm/#induced","title":"Induced","text":"
name: CellOntologyTerm\nid_prefixes:\n- CL\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:cl, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: CellOntologyTerm\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: CellOntologyTerm\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/CellType/","title":"Class: CellType","text":"

Represents a cell type

URI: cell_type:CellType

erDiagram\nCellType {\n    uriorcurie id  \n    string label  \n    string definition  \n}\nBiologicalProcess {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nAnatomicalStructure {\n    string id  \n    string label  \n}\nCellOntologyTerm {\n    string id  \n    string label  \n}\n\nCellType ||--|o CellOntologyTerm : \"equivalent_to\"\nCellType ||--}o CellOntologyTerm : \"parents\"\nCellType ||--}o CellOntologyTerm : \"subtypes\"\nCellType ||--}o AnatomicalStructure : \"localizations\"\nCellType ||--}o Gene : \"genes\"\nCellType ||--}o Disease : \"diseases\"\nCellType ||--}o BiologicalProcess : \"roles\"\n\n
"},{"location":"cell_type/CellType/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/CellType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 Uriorcurie direct label 0..1 String the concise name of the cell type direct equivalent_to 0..1 CellOntologyTerm the the cell type described direct definition 0..1 String direct parents 0..* CellOntologyTerm categorization direct subtypes 0..* CellOntologyTerm direct localizations 0..* AnatomicalStructure direct genes 0..* Gene direct diseases 0..* Disease direct roles 0..* BiologicalProcess direct"},{"location":"cell_type/CellType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/CellType/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/CellType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:CellType native cell_type:CellType"},{"location":"cell_type/CellType/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/CellType/#direct","title":"Direct","text":"
name: CellType\ndescription: Represents a cell type\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the concise name of the cell type\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n  equivalent_to:\n    name: equivalent_to\n    annotations:\n      prompt:\n        tag: prompt\n        value: the cell type described in the text\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the the cell type described\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: skos:exactMatch\n    range: CellOntologyTerm\n  definition:\n    name: definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n          that <differentiating characteristics>'\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: IAO:0000115\n  parents:\n    name: parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent (broader) cell types\n      owl:\n        tag: owl\n        value: SubClassOf\n    description: categorization\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: CellOntologyTerm\n  subtypes:\n    name: subtypes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of the subtypes (subclasses) of this cell\n          type. Use concise terms, and separate elements in a list using semicolon\n          (;)\n      owl.template:\n        tag: owl.template\n        value: '{% for subtype in subtypes %}\n\n          SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: CellOntologyTerm\n  localizations:\n    name: localizations\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures in which this cell\n          type is localized\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: BFO:0000050\n    multivalued: true\n    range: AnatomicalStructure\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of genes expressed in cells of this type\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002292\n    multivalued: true\n    range: Gene\n  diseases:\n    name: diseases\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of diseases in which this cell type is implicated\n      owl.template:\n        tag: owl.template\n        value: '{% for disease in diseases %}\n\n          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}\n          ))\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: Disease\n  roles:\n    name: roles\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of roles (e.g. biological processes) that\n          this cell type plays. These should be short descriptive terms corresponding\n          to ontology terms in the GO biological process hierarchy.\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002215\n    multivalued: true\n    range: BiologicalProcess\ntree_root: true\n\n
"},{"location":"cell_type/CellType/#induced","title":"Induced","text":"
name: CellType\ndescription: Represents a cell type\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    alias: id\n    owner: CellType\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the concise name of the cell type\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: CellType\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n  equivalent_to:\n    name: equivalent_to\n    annotations:\n      prompt:\n        tag: prompt\n        value: the cell type described in the text\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the the cell type described\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: skos:exactMatch\n    alias: equivalent_to\n    owner: CellType\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  definition:\n    name: definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n          that <differentiating characteristics>'\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: IAO:0000115\n    alias: definition\n    owner: CellType\n    domain_of:\n    - CellType\n    range: string\n  parents:\n    name: parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent (broader) cell types\n      owl:\n        tag: owl\n        value: SubClassOf\n    description: categorization\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: parents\n    owner: CellType\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  subtypes:\n    name: subtypes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of the subtypes (subclasses) of this cell\n          type. Use concise terms, and separate elements in a list using semicolon\n          (;)\n      owl.template:\n        tag: owl.template\n        value: '{% for subtype in subtypes %}\n\n          SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: CellType\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  localizations:\n    name: localizations\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures in which this cell\n          type is localized\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: localizations\n    owner: CellType\n    domain_of:\n    - CellType\n    range: AnatomicalStructure\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of genes expressed in cells of this type\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002292\n    multivalued: true\n    alias: genes\n    owner: CellType\n    domain_of:\n    - CellType\n    range: Gene\n  diseases:\n    name: diseases\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of diseases in which this cell type is implicated\n      owl.template:\n        tag: owl.template\n        value: '{% for disease in diseases %}\n\n          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}\n          ))\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: diseases\n    owner: CellType\n    domain_of:\n    - CellType\n    range: Disease\n  roles:\n    name: roles\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of roles (e.g. biological processes) that\n          this cell type plays. These should be short descriptive terms corresponding\n          to ontology terms in the GO biological process hierarchy.\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002215\n    multivalued: true\n    alias: roles\n    owner: CellType\n    domain_of:\n    - CellType\n    range: BiologicalProcess\ntree_root: true\n\n
"},{"location":"cell_type/ChemicalEntity/","title":"Class: ChemicalEntity","text":"

URI: cell_type:ChemicalEntity

erDiagram\nChemicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/ChemicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"cell_type/ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:ChemicalEntity native cell_type:ChemicalEntity"},{"location":"cell_type/ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalEntity\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: cell_type:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"cell_type/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"cell_type/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:CompoundExpression native cell_type:CompoundExpression"},{"location":"cell_type/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/cell_type\nabstract: true\n\n
"},{"location":"cell_type/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/cell_type\nabstract: true\n\n
"},{"location":"cell_type/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"cell_type/Curie/#comments","title":"Comments","text":""},{"location":"cell_type/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Curie/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"cell_type/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Date/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"cell_type/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"cell_type/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"cell_type/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Disease/","title":"Class: Disease","text":"

URI: cell_type:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/Disease/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/Disease/#usages","title":"Usages","text":"used by used in type used CellType diseases range Disease ImmuneCell diseases range Disease Neuron diseases range Disease Interneuron diseases range Disease"},{"location":"cell_type/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Disease/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo, sqlite:obo:hp"},{"location":"cell_type/Disease/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Disease native cell_type:Disease"},{"location":"cell_type/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Disease/#direct","title":"Direct","text":"
name: Disease\nid_prefixes:\n- MONDO\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo, sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/Disease/#induced","title":"Induced","text":"
name: Disease\nid_prefixes:\n- MONDO\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo, sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"cell_type/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Double/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Drug/","title":"Class: Drug","text":"

URI: cell_type:Drug

erDiagram\nDrug {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/Drug/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Drug/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/Drug/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Drug/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi, sqlite:obo:drugbank"},{"location":"cell_type/Drug/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Drug/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Drug native cell_type:Drug"},{"location":"cell_type/Drug/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Drug/#direct","title":"Direct","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/Drug/#induced","title":"Induced","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: Drug\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Drug\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: cell_type:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"cell_type/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"cell_type/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:ExtractionResult native cell_type:ExtractionResult"},{"location":"cell_type/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"cell_type/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"cell_type/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"cell_type/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Float/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Gene/","title":"Class: Gene","text":"

URI: cell_type:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/Gene/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/Gene/#usages","title":"Usages","text":"used by used in type used CellType genes range Gene ImmuneCell genes range Gene Neuron genes range Gene Interneuron genes range Gene"},{"location":"cell_type/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/Gene/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hgnc, bioportal:hgnc-nr"},{"location":"cell_type/Gene/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Gene native cell_type:Gene"},{"location":"cell_type/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\n- MGI\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\n- MGI\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/ImmuneCell/","title":"Class: ImmuneCell","text":"

URI: cell_type:ImmuneCell

erDiagram\nImmuneCell {\n    uriorcurie id  \n    string label  \n    string definition  \n}\nBiologicalProcess {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nAnatomicalStructure {\n    string id  \n    string label  \n}\nCellOntologyTerm {\n    string id  \n    string label  \n}\nProteinOrComplex {\n    string id  \n    string label  \n}\n\nImmuneCell ||--}o ProteinOrComplex : \"has_surface_markers\"\nImmuneCell ||--|o CellOntologyTerm : \"equivalent_to\"\nImmuneCell ||--}o CellOntologyTerm : \"parents\"\nImmuneCell ||--}o CellOntologyTerm : \"subtypes\"\nImmuneCell ||--}o AnatomicalStructure : \"localizations\"\nImmuneCell ||--}o Gene : \"genes\"\nImmuneCell ||--}o Disease : \"diseases\"\nImmuneCell ||--}o BiologicalProcess : \"roles\"\n\n
"},{"location":"cell_type/ImmuneCell/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/ImmuneCell/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_surface_markers 0..* ProteinOrComplex direct id 1..1 Uriorcurie CellType label 0..1 String the concise name of the cell type CellType equivalent_to 0..1 CellOntologyTerm the the cell type described CellType definition 0..1 String CellType parents 0..* CellOntologyTerm categorization CellType subtypes 0..* CellOntologyTerm CellType localizations 0..* AnatomicalStructure CellType genes 0..* Gene CellType diseases 0..* Disease CellType roles 0..* BiologicalProcess CellType"},{"location":"cell_type/ImmuneCell/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/ImmuneCell/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/ImmuneCell/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:ImmuneCell native cell_type:ImmuneCell"},{"location":"cell_type/ImmuneCell/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/ImmuneCell/#direct","title":"Direct","text":"
name: ImmuneCell\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CellType\nattributes:\n  has_surface_markers:\n    name: has_surface_markers\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of proteins or complexes expressed on the\n          surface of the cell\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: ProteinOrComplex\n\n
"},{"location":"cell_type/ImmuneCell/#induced","title":"Induced","text":"
name: ImmuneCell\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CellType\nattributes:\n  has_surface_markers:\n    name: has_surface_markers\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of proteins or complexes expressed on the\n          surface of the cell\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: has_surface_markers\n    owner: ImmuneCell\n    domain_of:\n    - ImmuneCell\n    range: ProteinOrComplex\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    alias: id\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the concise name of the cell type\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n  equivalent_to:\n    name: equivalent_to\n    annotations:\n      prompt:\n        tag: prompt\n        value: the cell type described in the text\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the the cell type described\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: skos:exactMatch\n    alias: equivalent_to\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  definition:\n    name: definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n          that <differentiating characteristics>'\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: IAO:0000115\n    alias: definition\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: string\n  parents:\n    name: parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent (broader) cell types\n      owl:\n        tag: owl\n        value: SubClassOf\n    description: categorization\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: parents\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  subtypes:\n    name: subtypes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of the subtypes (subclasses) of this cell\n          type. Use concise terms, and separate elements in a list using semicolon\n          (;)\n      owl.template:\n        tag: owl.template\n        value: '{% for subtype in subtypes %}\n\n          SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  localizations:\n    name: localizations\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures in which this cell\n          type is localized\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: localizations\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: AnatomicalStructure\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of genes expressed in cells of this type\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002292\n    multivalued: true\n    alias: genes\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: Gene\n  diseases:\n    name: diseases\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of diseases in which this cell type is implicated\n      owl.template:\n        tag: owl.template\n        value: '{% for disease in diseases %}\n\n          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}\n          ))\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: diseases\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: Disease\n  roles:\n    name: roles\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of roles (e.g. biological processes) that\n          this cell type plays. These should be short descriptive terms corresponding\n          to ontology terms in the GO biological process hierarchy.\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002215\n    multivalued: true\n    alias: roles\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: BiologicalProcess\n\n
"},{"location":"cell_type/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"cell_type/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Integer/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Interneuron/","title":"Class: Interneuron","text":"

URI: cell_type:Interneuron

erDiagram\nInterneuron {\n    uriorcurie id  \n    string label  \n    string definition  \n}\nBiologicalProcess {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nAnatomicalStructure {\n    string id  \n    string label  \n}\nCellOntologyTerm {\n    string id  \n    string label  \n}\nNeurotransmitter {\n    string id  \n    string label  \n}\nBrainRegion {\n    string id  \n    string label  \n}\n\nInterneuron ||--}o BrainRegion : \"projects_to_or_from\"\nInterneuron ||--}o Neurotransmitter : \"releases_neurotransitter\"\nInterneuron ||--|o CellOntologyTerm : \"equivalent_to\"\nInterneuron ||--}o CellOntologyTerm : \"parents\"\nInterneuron ||--}o CellOntologyTerm : \"subtypes\"\nInterneuron ||--}o AnatomicalStructure : \"localizations\"\nInterneuron ||--}o Gene : \"genes\"\nInterneuron ||--}o Disease : \"diseases\"\nInterneuron ||--}o BiologicalProcess : \"roles\"\n\n
"},{"location":"cell_type/Interneuron/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Interneuron/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance projects_to_or_from 0..* BrainRegion Brain structures from which this cell type projects into or receives projecti... direct releases_neurotransitter 0..* Neurotransmitter Neuron id 1..1 Uriorcurie CellType label 0..1 String the concise name of the cell type CellType equivalent_to 0..1 CellOntologyTerm the the cell type described CellType definition 0..1 String CellType parents 0..* CellOntologyTerm categorization CellType subtypes 0..* CellOntologyTerm CellType localizations 0..* AnatomicalStructure CellType genes 0..* Gene CellType diseases 0..* Disease CellType roles 0..* BiologicalProcess CellType"},{"location":"cell_type/Interneuron/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Interneuron/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Interneuron/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Interneuron native cell_type:Interneuron"},{"location":"cell_type/Interneuron/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Interneuron/#direct","title":"Direct","text":"
name: Interneuron\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: Neuron\nattributes:\n  projects_to_or_from:\n    name: projects_to_or_from\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures from which this cell\n          type projects from or into\n    description: Brain structures from which this cell type projects into or receives\n      projections from\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002170\n    multivalued: true\n    range: BrainRegion\n\n
"},{"location":"cell_type/Interneuron/#induced","title":"Induced","text":"
name: Interneuron\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: Neuron\nattributes:\n  projects_to_or_from:\n    name: projects_to_or_from\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures from which this cell\n          type projects from or into\n    description: Brain structures from which this cell type projects into or receives\n      projections from\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002170\n    multivalued: true\n    alias: projects_to_or_from\n    owner: Interneuron\n    domain_of:\n    - Interneuron\n    range: BrainRegion\n  releases_neurotransitter:\n    name: releases_neurotransitter\n    annotations:\n      prompt:\n        tag: prompt\n        value: named of chemical entity that this neuron releases\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002111\n    multivalued: true\n    alias: releases_neurotransitter\n    owner: Interneuron\n    domain_of:\n    - Neuron\n    range: Neurotransmitter\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    alias: id\n    owner: Interneuron\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the concise name of the cell type\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Interneuron\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n  equivalent_to:\n    name: equivalent_to\n    annotations:\n      prompt:\n        tag: prompt\n        value: the cell type described in the text\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the the cell type described\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: skos:exactMatch\n    alias: equivalent_to\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  definition:\n    name: definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n          that <differentiating characteristics>'\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: IAO:0000115\n    alias: definition\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: string\n  parents:\n    name: parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent (broader) cell types\n      owl:\n        tag: owl\n        value: SubClassOf\n    description: categorization\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: parents\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  subtypes:\n    name: subtypes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of the subtypes (subclasses) of this cell\n          type. Use concise terms, and separate elements in a list using semicolon\n          (;)\n      owl.template:\n        tag: owl.template\n        value: '{% for subtype in subtypes %}\n\n          SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  localizations:\n    name: localizations\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures in which this cell\n          type is localized\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: localizations\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: AnatomicalStructure\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of genes expressed in cells of this type\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002292\n    multivalued: true\n    alias: genes\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: Gene\n  diseases:\n    name: diseases\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of diseases in which this cell type is implicated\n      owl.template:\n        tag: owl.template\n        value: '{% for disease in diseases %}\n\n          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}\n          ))\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: diseases\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: Disease\n  roles:\n    name: roles\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of roles (e.g. biological processes) that\n          this cell type plays. These should be short descriptive terms corresponding\n          to ontology terms in the GO biological process hierarchy.\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002215\n    multivalued: true\n    alias: roles\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: BiologicalProcess\n\n
"},{"location":"cell_type/NamedEntity/","title":"Class: NamedEntity","text":"

URI: cell_type:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"cell_type/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"cell_type/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:NamedEntity native cell_type:NamedEntity"},{"location":"cell_type/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/cell_type\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"cell_type/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/cell_type\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"cell_type/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Neuron/","title":"Class: Neuron","text":"

URI: cell_type:Neuron

erDiagram\nNeuron {\n    uriorcurie id  \n    string label  \n    string definition  \n}\nBiologicalProcess {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nAnatomicalStructure {\n    string id  \n    string label  \n}\nCellOntologyTerm {\n    string id  \n    string label  \n}\nNeurotransmitter {\n    string id  \n    string label  \n}\n\nNeuron ||--}o Neurotransmitter : \"releases_neurotransitter\"\nNeuron ||--|o CellOntologyTerm : \"equivalent_to\"\nNeuron ||--}o CellOntologyTerm : \"parents\"\nNeuron ||--}o CellOntologyTerm : \"subtypes\"\nNeuron ||--}o AnatomicalStructure : \"localizations\"\nNeuron ||--}o Gene : \"genes\"\nNeuron ||--}o Disease : \"diseases\"\nNeuron ||--}o BiologicalProcess : \"roles\"\n\n
"},{"location":"cell_type/Neuron/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Neuron/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance releases_neurotransitter 0..* Neurotransmitter direct id 1..1 Uriorcurie CellType label 0..1 String the concise name of the cell type CellType equivalent_to 0..1 CellOntologyTerm the the cell type described CellType definition 0..1 String CellType parents 0..* CellOntologyTerm categorization CellType subtypes 0..* CellOntologyTerm CellType localizations 0..* AnatomicalStructure CellType genes 0..* Gene CellType diseases 0..* Disease CellType roles 0..* BiologicalProcess CellType"},{"location":"cell_type/Neuron/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Neuron/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Neuron/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Neuron native cell_type:Neuron"},{"location":"cell_type/Neuron/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Neuron/#direct","title":"Direct","text":"
name: Neuron\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CellType\nattributes:\n  releases_neurotransitter:\n    name: releases_neurotransitter\n    annotations:\n      prompt:\n        tag: prompt\n        value: named of chemical entity that this neuron releases\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002111\n    multivalued: true\n    range: Neurotransmitter\n\n
"},{"location":"cell_type/Neuron/#induced","title":"Induced","text":"
name: Neuron\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CellType\nattributes:\n  releases_neurotransitter:\n    name: releases_neurotransitter\n    annotations:\n      prompt:\n        tag: prompt\n        value: named of chemical entity that this neuron releases\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002111\n    multivalued: true\n    alias: releases_neurotransitter\n    owner: Neuron\n    domain_of:\n    - Neuron\n    range: Neurotransmitter\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    alias: id\n    owner: Neuron\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the concise name of the cell type\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Neuron\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n  equivalent_to:\n    name: equivalent_to\n    annotations:\n      prompt:\n        tag: prompt\n        value: the cell type described in the text\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the the cell type described\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: skos:exactMatch\n    alias: equivalent_to\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  definition:\n    name: definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n          that <differentiating characteristics>'\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: IAO:0000115\n    alias: definition\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: string\n  parents:\n    name: parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent (broader) cell types\n      owl:\n        tag: owl\n        value: SubClassOf\n    description: categorization\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: parents\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  subtypes:\n    name: subtypes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of the subtypes (subclasses) of this cell\n          type. Use concise terms, and separate elements in a list using semicolon\n          (;)\n      owl.template:\n        tag: owl.template\n        value: '{% for subtype in subtypes %}\n\n          SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  localizations:\n    name: localizations\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures in which this cell\n          type is localized\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: localizations\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: AnatomicalStructure\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of genes expressed in cells of this type\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002292\n    multivalued: true\n    alias: genes\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: Gene\n  diseases:\n    name: diseases\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of diseases in which this cell type is implicated\n      owl.template:\n        tag: owl.template\n        value: '{% for disease in diseases %}\n\n          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}\n          ))\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: diseases\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: Disease\n  roles:\n    name: roles\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of roles (e.g. biological processes) that\n          this cell type plays. These should be short descriptive terms corresponding\n          to ontology terms in the GO biological process hierarchy.\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002215\n    multivalued: true\n    alias: roles\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: BiologicalProcess\n\n
"},{"location":"cell_type/Neurotransmitter/","title":"Class: Neurotransmitter","text":"

URI: cell_type:Neurotransmitter

erDiagram\nNeurotransmitter {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/Neurotransmitter/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Neurotransmitter/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/Neurotransmitter/#usages","title":"Usages","text":"used by used in type used Neuron releases_neurotransitter range Neurotransmitter Interneuron releases_neurotransitter range Neurotransmitter"},{"location":"cell_type/Neurotransmitter/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Neurotransmitter/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/Neurotransmitter/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"cell_type/Neurotransmitter/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Neurotransmitter/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Neurotransmitter native cell_type:Neurotransmitter"},{"location":"cell_type/Neurotransmitter/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Neurotransmitter/#direct","title":"Direct","text":"
name: Neurotransmitter\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: ChemicalEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - NeurotransmitterIdentifier\n    identifier: true\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n\n
"},{"location":"cell_type/Neurotransmitter/#induced","title":"Induced","text":"
name: Neurotransmitter\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: ChemicalEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - NeurotransmitterIdentifier\n    identifier: true\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/cell_type\n    values_from:\n    - NeurotransmitterIdentifier\n    identifier: true\n    alias: id\n    owner: Neurotransmitter\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Neurotransmitter\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/NeurotransmitterIdentifier/","title":"Enum: NeurotransmitterIdentifier","text":"

URI: NeurotransmitterIdentifier

This is a dynamic enum

"},{"location":"cell_type/NeurotransmitterIdentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/NeurotransmitterIdentifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/NeurotransmitterIdentifier/#linkml-source","title":"LinkML Source","text":"
name: NeurotransmitterIdentifier\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nreachable_from:\n  source_ontology: obo:chebi\n  source_nodes:\n  - CHEBI:35942\n  relationship_types:\n  - rdfs:subClassOf\n  - RO:0000087\n\n
"},{"location":"cell_type/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"cell_type/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"cell_type/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"cell_type/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"cell_type/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"cell_type/Objectidentifier/#comments","title":"Comments","text":""},{"location":"cell_type/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Pathway/","title":"Class: Pathway","text":"

URI: cell_type:Pathway

erDiagram\nPathway {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/Pathway/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Pathway/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/Pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Pathway/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/Pathway/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:pw"},{"location":"cell_type/Pathway/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Pathway/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Pathway native cell_type:Pathway"},{"location":"cell_type/Pathway/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Pathway/#direct","title":"Direct","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/Pathway/#induced","title":"Induced","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: Pathway\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Pathway\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/ProteinOrComplex/","title":"Class: ProteinOrComplex","text":"

URI: cell_type:ProteinOrComplex

erDiagram\nProteinOrComplex {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/ProteinOrComplex/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/ProteinOrComplex/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/ProteinOrComplex/#usages","title":"Usages","text":"used by used in type used ImmuneCell has_surface_markers range ProteinOrComplex"},{"location":"cell_type/ProteinOrComplex/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/ProteinOrComplex/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/ProteinOrComplex/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hgnc, bioportal:hgnc-nr, sqlite:obo:go, sqlite:obo:pr"},{"location":"cell_type/ProteinOrComplex/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/ProteinOrComplex/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:ProteinOrComplex native cell_type:ProteinOrComplex"},{"location":"cell_type/ProteinOrComplex/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/ProteinOrComplex/#direct","title":"Direct","text":"
name: ProteinOrComplex\nid_prefixes:\n- HGNC\n- MGI\n- PR\n- UniProtKB\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, bioportal:hgnc-nr, sqlite:obo:go, sqlite:obo:pr\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/ProteinOrComplex/#induced","title":"Induced","text":"
name: ProteinOrComplex\nid_prefixes:\n- HGNC\n- MGI\n- PR\n- UniProtKB\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, bioportal:hgnc-nr, sqlite:obo:go, sqlite:obo:pr\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: ProteinOrComplex\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ProteinOrComplex\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/Publication/","title":"Class: Publication","text":"

URI: cell_type:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"cell_type/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"cell_type/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"cell_type/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Publication/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Publication native cell_type:Publication"},{"location":"cell_type/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/cell_type\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n\n
"},{"location":"cell_type/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/cell_type\n    alias: id\n    owner: Publication\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"cell_type/RelationshipType/","title":"Class: RelationshipType","text":"

URI: cell_type:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"cell_type/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:RelationshipType native cell_type:RelationshipType"},{"location":"cell_type/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"cell_type/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/String/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: cell_type:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"cell_type/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"cell_type/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:TextWithTriples native cell_type:TextWithTriples"},{"location":"cell_type/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"cell_type/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"cell_type/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"cell_type/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Time/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: cell_type:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"cell_type/Triple/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"cell_type/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"cell_type/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Triple/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Triple native cell_type:Triple"},{"location":"cell_type/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"cell_type/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"cell_type/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"cell_type/Uri/#comments","title":"Comments","text":""},{"location":"cell_type/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Uri/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"cell_type/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: cell_type:abstract

"},{"location":"cell_type/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"cell_type/abstract/#properties","title":"Properties","text":""},{"location":"cell_type/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/abstract/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"cell_type/cell_type/","title":"cell_type","text":"

A template for representing cell types

URI: http://w3id.org/ontogpt/cell_type

"},{"location":"cell_type/combined_text/","title":"Slot: combined_text","text":"

URI: cell_type:combined_text

"},{"location":"cell_type/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"cell_type/combined_text/#properties","title":"Properties","text":""},{"location":"cell_type/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"cell_type/definition/","title":"Slot: definition","text":"

URI: IAO:0000115

"},{"location":"cell_type/definition/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/definition/#properties","title":"Properties","text":""},{"location":"cell_type/definition/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/definition/#annotations","title":"Annotations","text":"property value prompt A concise textual definition in genus-differentia form, i.e 'A that '"},{"location":"cell_type/definition/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/definition/#linkml-source","title":"LinkML Source","text":"
name: definition\nannotations:\n  prompt:\n    tag: prompt\n    value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n      that <differentiating characteristics>'\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: IAO:0000115\nalias: definition\nowner: CellType\ndomain_of:\n- CellType\nrange: string\n\n
"},{"location":"cell_type/diseases/","title":"Slot: diseases","text":"

URI: cell_type:diseases

"},{"location":"cell_type/diseases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/diseases/#properties","title":"Properties","text":""},{"location":"cell_type/diseases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/diseases/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of diseases in which this cell type is implicated SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }} )) {% endfor %}"},{"location":"cell_type/diseases/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/diseases/#linkml-source","title":"LinkML Source","text":"
name: diseases\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of diseases in which this cell type is implicated\n  owl.template:\n    tag: owl.template\n    value: '{% for disease in diseases %}\n\n      SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }} ))\n\n      {% endfor %}\n\n      '\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: diseases\nowner: CellType\ndomain_of:\n- CellType\nrange: Disease\n\n
"},{"location":"cell_type/equivalent_to/","title":"Slot: equivalent_to","text":"

the the cell type described

URI: skos:exactMatch

"},{"location":"cell_type/equivalent_to/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/equivalent_to/#properties","title":"Properties","text":""},{"location":"cell_type/equivalent_to/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/equivalent_to/#annotations","title":"Annotations","text":"property value prompt the cell type described in the text"},{"location":"cell_type/equivalent_to/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/equivalent_to/#linkml-source","title":"LinkML Source","text":"
name: equivalent_to\nannotations:\n  prompt:\n    tag: prompt\n    value: the cell type described in the text\n  owl:\n    tag: owl\n    value: AnnotationAssertion\ndescription: the the cell type described\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: skos:exactMatch\nalias: equivalent_to\nowner: CellType\ndomain_of:\n- CellType\nrange: CellOntologyTerm\n\n
"},{"location":"cell_type/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: cell_type:extracted_object

"},{"location":"cell_type/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/extracted_object/#properties","title":"Properties","text":""},{"location":"cell_type/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"cell_type/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: cell_type:full_text

"},{"location":"cell_type/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"cell_type/full_text/#properties","title":"Properties","text":""},{"location":"cell_type/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/full_text/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"cell_type/genes/","title":"Slot: genes","text":"

URI: RO:0002292

"},{"location":"cell_type/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/genes/#properties","title":"Properties","text":""},{"location":"cell_type/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/genes/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of genes expressed in cells of this type"},{"location":"cell_type/genes/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of genes expressed in cells of this type\n  owl:\n    tag: owl\n    value: SubClassOf, ObjectSomeValuesFrom\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: RO:0002292\nmultivalued: true\nalias: genes\nowner: CellType\ndomain_of:\n- CellType\nrange: Gene\n\n
"},{"location":"cell_type/has_surface_markers/","title":"Slot: has_surface_markers","text":"

URI: cell_type:has_surface_markers

"},{"location":"cell_type/has_surface_markers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ImmuneCell no"},{"location":"cell_type/has_surface_markers/#properties","title":"Properties","text":""},{"location":"cell_type/has_surface_markers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/has_surface_markers/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of proteins or complexes expressed on the surface of the cell"},{"location":"cell_type/has_surface_markers/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/has_surface_markers/#linkml-source","title":"LinkML Source","text":"
name: has_surface_markers\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of proteins or complexes expressed on the surface\n      of the cell\n  owl:\n    tag: owl\n    value: SubClassOf, ObjectSomeValuesFrom\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: has_surface_markers\nowner: ImmuneCell\ndomain_of:\n- ImmuneCell\nrange: ProteinOrComplex\n\n
"},{"location":"cell_type/id/","title":"Slot: id","text":"

URI: cell_type:id

"},{"location":"cell_type/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no Gene no ProteinOrComplex no BiologicalProcess no Pathway no AnatomicalStructure no ChemicalEntity no Neurotransmitter yes BrainRegion yes CellOntologyTerm no Disease no Drug no NamedEntity no RelationshipType no Publication no"},{"location":"cell_type/id/#properties","title":"Properties","text":""},{"location":"cell_type/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- CellType\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"cell_type/input_id/","title":"Slot: input_id","text":"

URI: cell_type:input_id

"},{"location":"cell_type/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/input_id/#properties","title":"Properties","text":""},{"location":"cell_type/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/input_id/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"cell_type/input_text/","title":"Slot: input_text","text":"

URI: cell_type:input_text

"},{"location":"cell_type/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/input_text/#properties","title":"Properties","text":""},{"location":"cell_type/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/input_text/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"cell_type/input_title/","title":"Slot: input_title","text":"

URI: cell_type:input_title

"},{"location":"cell_type/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/input_title/#properties","title":"Properties","text":""},{"location":"cell_type/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/input_title/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"cell_type/label/","title":"Slot: label","text":"

URI: cell_type:label

"},{"location":"cell_type/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no Gene no ProteinOrComplex no BiologicalProcess no Pathway no AnatomicalStructure no ChemicalEntity no Neurotransmitter no BrainRegion no CellOntologyTerm no Disease no Drug no NamedEntity no RelationshipType no"},{"location":"cell_type/label/#properties","title":"Properties","text":""},{"location":"cell_type/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- CellType\n- NamedEntity\nrange: string\n\n
"},{"location":"cell_type/localizations/","title":"Slot: localizations","text":"

URI: BFO:0000050

"},{"location":"cell_type/localizations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/localizations/#properties","title":"Properties","text":""},{"location":"cell_type/localizations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/localizations/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of anatomical structures in which this cell type is localized"},{"location":"cell_type/localizations/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/localizations/#linkml-source","title":"LinkML Source","text":"
name: localizations\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of anatomical structures in which this cell type\n      is localized\n  owl:\n    tag: owl\n    value: SubClassOf, ObjectSomeValuesFrom\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: BFO:0000050\nmultivalued: true\nalias: localizations\nowner: CellType\ndomain_of:\n- CellType\nrange: AnatomicalStructure\n\n
"},{"location":"cell_type/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: cell_type:named_entities

"},{"location":"cell_type/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/named_entities/#properties","title":"Properties","text":""},{"location":"cell_type/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"cell_type/object/","title":"Slot: object","text":"

URI: cell_type:object

"},{"location":"cell_type/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/object/#properties","title":"Properties","text":""},{"location":"cell_type/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/object/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"cell_type/object_id/","title":"Slot: object_id","text":"

URI: cell_type:object_id

"},{"location":"cell_type/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"cell_type/object_id/#properties","title":"Properties","text":""},{"location":"cell_type/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/object_id/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"cell_type/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: cell_type:object_qualifier

"},{"location":"cell_type/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/object_qualifier/#properties","title":"Properties","text":""},{"location":"cell_type/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"cell_type/object_text/","title":"Slot: object_text","text":"

URI: cell_type:object_text

"},{"location":"cell_type/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"cell_type/object_text/#properties","title":"Properties","text":""},{"location":"cell_type/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/object_text/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"cell_type/parents/","title":"Slot: parents","text":"

categorization

URI: cell_type:parents

"},{"location":"cell_type/parents/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/parents/#properties","title":"Properties","text":""},{"location":"cell_type/parents/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/parents/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of parent (broader) cell types"},{"location":"cell_type/parents/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/parents/#linkml-source","title":"LinkML Source","text":"
name: parents\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of parent (broader) cell types\n  owl:\n    tag: owl\n    value: SubClassOf\ndescription: categorization\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: parents\nowner: CellType\ndomain_of:\n- CellType\nrange: CellOntologyTerm\n\n
"},{"location":"cell_type/predicate/","title":"Slot: predicate","text":"

URI: cell_type:predicate

"},{"location":"cell_type/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/predicate/#properties","title":"Properties","text":""},{"location":"cell_type/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/predicate/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"cell_type/projects_to_or_from/","title":"Slot: projects_to_or_from","text":"

Brain structures from which this cell type projects into or receives projections from

URI: RO:0002170

"},{"location":"cell_type/projects_to_or_from/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Interneuron no"},{"location":"cell_type/projects_to_or_from/#properties","title":"Properties","text":""},{"location":"cell_type/projects_to_or_from/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/projects_to_or_from/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of anatomical structures from which this cell type projects from or into"},{"location":"cell_type/projects_to_or_from/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/projects_to_or_from/#linkml-source","title":"LinkML Source","text":"
name: projects_to_or_from\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of anatomical structures from which this cell\n      type projects from or into\ndescription: Brain structures from which this cell type projects into or receives\n  projections from\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: RO:0002170\nmultivalued: true\nalias: projects_to_or_from\nowner: Interneuron\ndomain_of:\n- Interneuron\nrange: BrainRegion\n\n
"},{"location":"cell_type/prompt/","title":"Slot: prompt","text":"

URI: cell_type:prompt

"},{"location":"cell_type/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/prompt/#properties","title":"Properties","text":""},{"location":"cell_type/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/prompt/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"cell_type/publication/","title":"Slot: publication","text":"

URI: cell_type:publication

"},{"location":"cell_type/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"cell_type/publication/#properties","title":"Properties","text":""},{"location":"cell_type/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"cell_type/publication/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"cell_type/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: cell_type:qualifier

"},{"location":"cell_type/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/qualifier/#properties","title":"Properties","text":""},{"location":"cell_type/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"cell_type/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: cell_type:raw_completion_output

"},{"location":"cell_type/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/raw_completion_output/#properties","title":"Properties","text":""},{"location":"cell_type/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"cell_type/releases_neurotransitter/","title":"Slot: releases_neurotransitter","text":"

URI: RO:0002111

"},{"location":"cell_type/releases_neurotransitter/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Neuron no Interneuron no"},{"location":"cell_type/releases_neurotransitter/#properties","title":"Properties","text":""},{"location":"cell_type/releases_neurotransitter/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/releases_neurotransitter/#annotations","title":"Annotations","text":"property value prompt named of chemical entity that this neuron releases"},{"location":"cell_type/releases_neurotransitter/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/releases_neurotransitter/#linkml-source","title":"LinkML Source","text":"
name: releases_neurotransitter\nannotations:\n  prompt:\n    tag: prompt\n    value: named of chemical entity that this neuron releases\n  owl:\n    tag: owl\n    value: SubClassOf, ObjectSomeValuesFrom\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: RO:0002111\nmultivalued: true\nalias: releases_neurotransitter\nowner: Neuron\ndomain_of:\n- Neuron\nrange: Neurotransmitter\n\n
"},{"location":"cell_type/roles/","title":"Slot: roles","text":"

URI: RO:0002215

"},{"location":"cell_type/roles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/roles/#properties","title":"Properties","text":""},{"location":"cell_type/roles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/roles/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of roles (e.g. biological processes) that this cell type plays. These should be short descriptive terms corresponding to ontology terms in the GO biological process hierarchy."},{"location":"cell_type/roles/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/roles/#linkml-source","title":"LinkML Source","text":"
name: roles\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of roles (e.g. biological processes) that this\n      cell type plays. These should be short descriptive terms corresponding to ontology\n      terms in the GO biological process hierarchy.\n  owl:\n    tag: owl\n    value: SubClassOf, ObjectSomeValuesFrom\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: RO:0002215\nmultivalued: true\nalias: roles\nowner: CellType\ndomain_of:\n- CellType\nrange: BiologicalProcess\n\n
"},{"location":"cell_type/subject/","title":"Slot: subject","text":"

URI: cell_type:subject

"},{"location":"cell_type/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/subject/#properties","title":"Properties","text":""},{"location":"cell_type/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/subject/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"cell_type/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: cell_type:subject_qualifier

"},{"location":"cell_type/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/subject_qualifier/#properties","title":"Properties","text":""},{"location":"cell_type/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"cell_type/subject_text/","title":"Slot: subject_text","text":"

URI: cell_type:subject_text

"},{"location":"cell_type/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"cell_type/subject_text/#properties","title":"Properties","text":""},{"location":"cell_type/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"cell_type/subtypes/","title":"Slot: subtypes","text":"

URI: cell_type:subtypes

"},{"location":"cell_type/subtypes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/subtypes/#properties","title":"Properties","text":""},{"location":"cell_type/subtypes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/subtypes/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of the subtypes (subclasses) of this cell type. Use concise terms, and separate elements in a list using semicolon (;) SubClassOf( {{ tr(subtype) }} {{ id }} ) {% endfor %}"},{"location":"cell_type/subtypes/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/subtypes/#linkml-source","title":"LinkML Source","text":"
name: subtypes\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of the subtypes (subclasses) of this cell type.\n      Use concise terms, and separate elements in a list using semicolon (;)\n  owl.template:\n    tag: owl.template\n    value: '{% for subtype in subtypes %}\n\n      SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n      {% endfor %}\n\n      '\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: subtypes\nowner: CellType\ndomain_of:\n- CellType\nrange: CellOntologyTerm\n\n
"},{"location":"cell_type/title/","title":"Slot: title","text":"

The title of the publication

URI: cell_type:title

"},{"location":"cell_type/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"cell_type/title/#properties","title":"Properties","text":""},{"location":"cell_type/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/title/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"cell_type/triples/","title":"Slot: triples","text":"

URI: cell_type:triples

"},{"location":"cell_type/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"cell_type/triples/#properties","title":"Properties","text":""},{"location":"cell_type/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/triples/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"class_enrichment/","title":"Class Enrichment Datamodel","text":"

A datamodel for representing the results of class enrichment on gene sets

URI: https://w3id.org/oak/class-enrichment

Name: class-enrichment

"},{"location":"class_enrichment/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nClassEnrichmentConfiguration {\n    float p_value_cutoff  \n}\nClassEnrichmentResultSet {\n\n}\nClassEnrichmentResult {\n    uriorcurie class_id  \n    string class_label  \n    integer rank  \n    float p_value  \n    float p_value_adjusted  \n    float false_discovery_rate  \n    float fold_enrichment  \n    float probability  \n    integer sample_count  \n    integer sample_total  \n    integer background_count  \n    integer background_total  \n    boolean ancestor_of_more_informative_result  \n    boolean descendant_of_more_informative_result  \n}\n\nClassEnrichmentResultSet ||--}o ClassEnrichmentResult : \"results\"\n\n
"},{"location":"class_enrichment/#classes","title":"Classes","text":"Class Description ClassEnrichmentConfiguration configuration for search ClassEnrichmentResult A single enrichment result ClassEnrichmentResultSet A collection of enrichemt results"},{"location":"class_enrichment/#slots","title":"Slots","text":"Slot Description ancestor_of_more_informative_result This term is more general than a previously reported result background_count The background count background_total The background total class_id The class id class_label The class label descendant_of_more_informative_result This term is more specific than a previously reported result false_discovery_rate The false discovery rate fold_enrichment The fold enrichment p_value The p-value p_value_adjusted The adjusted p-value p_value_cutoff p-value cutoff for enrichment probability The probability, as estimated by model-based approaches rank The rank of this result results The enrichment results sample_count The number of entities in the sample with this class sample_total The total number of entities in the sample"},{"location":"class_enrichment/#enumerations","title":"Enumerations","text":"Enumeration Description SortFieldEnum The field to sort by"},{"location":"class_enrichment/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Position String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"class_enrichment/#subsets","title":"Subsets","text":"Subset Description"},{"location":"class_enrichment/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"class_enrichment/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ClassEnrichmentConfiguration/","title":"Class: ClassEnrichmentConfiguration","text":"

configuration for search

URI: ontoenrich:ClassEnrichmentConfiguration

erDiagram\nClassEnrichmentConfiguration {\n    float p_value_cutoff  \n}\n\n\n\n
"},{"location":"class_enrichment/ClassEnrichmentConfiguration/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance p_value_cutoff 1..1 Float p-value cutoff for enrichment direct"},{"location":"class_enrichment/ClassEnrichmentConfiguration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/ClassEnrichmentConfiguration/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ClassEnrichmentConfiguration/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ontoenrich:ClassEnrichmentConfiguration native ontoenrich:ClassEnrichmentConfiguration"},{"location":"class_enrichment/ClassEnrichmentConfiguration/#linkml-source","title":"LinkML Source","text":""},{"location":"class_enrichment/ClassEnrichmentConfiguration/#direct","title":"Direct","text":"
name: ClassEnrichmentConfiguration\ndescription: configuration for search\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  p_value_cutoff:\n    name: p_value_cutoff\n    description: p-value cutoff for enrichment\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: float\n    required: true\n\n
"},{"location":"class_enrichment/ClassEnrichmentConfiguration/#induced","title":"Induced","text":"
name: ClassEnrichmentConfiguration\ndescription: configuration for search\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  p_value_cutoff:\n    name: p_value_cutoff\n    description: p-value cutoff for enrichment\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: p_value_cutoff\n    owner: ClassEnrichmentConfiguration\n    domain_of:\n    - ClassEnrichmentConfiguration\n    range: float\n    required: true\n\n
"},{"location":"class_enrichment/ClassEnrichmentResult/","title":"Class: ClassEnrichmentResult","text":"

A single enrichment result

URI: ontoenrich:ClassEnrichmentResult

erDiagram\nClassEnrichmentResult {\n    uriorcurie class_id  \n    string class_label  \n    integer rank  \n    float p_value  \n    float p_value_adjusted  \n    float false_discovery_rate  \n    float fold_enrichment  \n    float probability  \n    integer sample_count  \n    integer sample_total  \n    integer background_count  \n    integer background_total  \n    boolean ancestor_of_more_informative_result  \n    boolean descendant_of_more_informative_result  \n}\n\n\n\n
"},{"location":"class_enrichment/ClassEnrichmentResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance class_id 1..1 Uriorcurie The class id direct class_label 0..1 String The class label direct rank 0..1 Integer The rank of this result direct p_value 1..1 Float The p-value direct p_value_adjusted 0..1 Float The adjusted p-value direct false_discovery_rate 0..1 Float The false discovery rate direct fold_enrichment 0..1 Float The fold enrichment direct probability 0..1 Float The probability, as estimated by model-based approaches direct sample_count 0..1 Integer The number of entities in the sample with this class direct sample_total 0..1 Integer The total number of entities in the sample direct background_count 0..1 Integer The background count direct background_total 0..1 Integer The background total direct ancestor_of_more_informative_result 0..1 Boolean This term is more general than a previously reported result direct descendant_of_more_informative_result 0..1 Boolean This term is more specific than a previously reported result direct"},{"location":"class_enrichment/ClassEnrichmentResult/#usages","title":"Usages","text":"used by used in type used ClassEnrichmentResultSet results range ClassEnrichmentResult"},{"location":"class_enrichment/ClassEnrichmentResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/ClassEnrichmentResult/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ClassEnrichmentResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ontoenrich:ClassEnrichmentResult native ontoenrich:ClassEnrichmentResult"},{"location":"class_enrichment/ClassEnrichmentResult/#linkml-source","title":"LinkML Source","text":""},{"location":"class_enrichment/ClassEnrichmentResult/#direct","title":"Direct","text":"
name: ClassEnrichmentResult\ndescription: A single enrichment result\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  class_id:\n    name: class_id\n    description: The class id\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: uriorcurie\n    required: true\n  class_label:\n    name: class_label\n    description: The class label\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: string\n  rank:\n    name: rank\n    description: The rank of this result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: integer\n  p_value:\n    name: p_value\n    description: The p-value\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    slot_uri: OBI:0000175\n    range: float\n    required: true\n  p_value_adjusted:\n    name: p_value_adjusted\n    description: The adjusted p-value\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: float\n  false_discovery_rate:\n    name: false_discovery_rate\n    description: The false discovery rate\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: float\n  fold_enrichment:\n    name: fold_enrichment\n    description: The fold enrichment\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: float\n  probability:\n    name: probability\n    description: The probability, as estimated by model-based approaches\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: float\n    minimum_value: 0\n    maximum_value: 1\n  sample_count:\n    name: sample_count\n    description: The number of entities in the sample with this class\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: integer\n  sample_total:\n    name: sample_total\n    description: The total number of entities in the sample\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: integer\n  background_count:\n    name: background_count\n    description: The background count\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: integer\n  background_total:\n    name: background_total\n    description: The background total\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: integer\n  ancestor_of_more_informative_result:\n    name: ancestor_of_more_informative_result\n    description: This term is more general than a previously reported result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: boolean\n  descendant_of_more_informative_result:\n    name: descendant_of_more_informative_result\n    description: This term is more specific than a previously reported result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: boolean\n\n
"},{"location":"class_enrichment/ClassEnrichmentResult/#induced","title":"Induced","text":"
name: ClassEnrichmentResult\ndescription: A single enrichment result\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  class_id:\n    name: class_id\n    description: The class id\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: class_id\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: uriorcurie\n    required: true\n  class_label:\n    name: class_label\n    description: The class label\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: class_label\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: string\n  rank:\n    name: rank\n    description: The rank of this result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: rank\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: integer\n  p_value:\n    name: p_value\n    description: The p-value\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    slot_uri: OBI:0000175\n    alias: p_value\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: float\n    required: true\n  p_value_adjusted:\n    name: p_value_adjusted\n    description: The adjusted p-value\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: p_value_adjusted\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: float\n  false_discovery_rate:\n    name: false_discovery_rate\n    description: The false discovery rate\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: false_discovery_rate\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: float\n  fold_enrichment:\n    name: fold_enrichment\n    description: The fold enrichment\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: fold_enrichment\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: float\n  probability:\n    name: probability\n    description: The probability, as estimated by model-based approaches\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: probability\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: float\n    minimum_value: 0\n    maximum_value: 1\n  sample_count:\n    name: sample_count\n    description: The number of entities in the sample with this class\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: sample_count\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: integer\n  sample_total:\n    name: sample_total\n    description: The total number of entities in the sample\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: sample_total\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: integer\n  background_count:\n    name: background_count\n    description: The background count\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: background_count\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: integer\n  background_total:\n    name: background_total\n    description: The background total\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: background_total\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: integer\n  ancestor_of_more_informative_result:\n    name: ancestor_of_more_informative_result\n    description: This term is more general than a previously reported result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: ancestor_of_more_informative_result\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: boolean\n  descendant_of_more_informative_result:\n    name: descendant_of_more_informative_result\n    description: This term is more specific than a previously reported result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: descendant_of_more_informative_result\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: boolean\n\n
"},{"location":"class_enrichment/ClassEnrichmentResultSet/","title":"Class: ClassEnrichmentResultSet","text":"

A collection of enrichemt results

URI: ontoenrich:ClassEnrichmentResultSet

erDiagram\nClassEnrichmentResultSet {\n\n}\nClassEnrichmentResult {\n    uriorcurie class_id  \n    string class_label  \n    integer rank  \n    float p_value  \n    float p_value_adjusted  \n    float false_discovery_rate  \n    float fold_enrichment  \n    float probability  \n    integer sample_count  \n    integer sample_total  \n    integer background_count  \n    integer background_total  \n    boolean ancestor_of_more_informative_result  \n    boolean descendant_of_more_informative_result  \n}\n\nClassEnrichmentResultSet ||--}o ClassEnrichmentResult : \"results\"\n\n
"},{"location":"class_enrichment/ClassEnrichmentResultSet/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance results 0..* ClassEnrichmentResult The enrichment results direct"},{"location":"class_enrichment/ClassEnrichmentResultSet/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/ClassEnrichmentResultSet/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ClassEnrichmentResultSet/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ontoenrich:ClassEnrichmentResultSet native ontoenrich:ClassEnrichmentResultSet"},{"location":"class_enrichment/ClassEnrichmentResultSet/#linkml-source","title":"LinkML Source","text":""},{"location":"class_enrichment/ClassEnrichmentResultSet/#direct","title":"Direct","text":"
name: ClassEnrichmentResultSet\ndescription: A collection of enrichemt results\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  results:\n    name: results\n    description: The enrichment results\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    multivalued: true\n    range: ClassEnrichmentResult\n\n
"},{"location":"class_enrichment/ClassEnrichmentResultSet/#induced","title":"Induced","text":"
name: ClassEnrichmentResultSet\ndescription: A collection of enrichemt results\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  results:\n    name: results\n    description: The enrichment results\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    multivalued: true\n    alias: results\n    owner: ClassEnrichmentResultSet\n    domain_of:\n    - ClassEnrichmentResultSet\n    range: ClassEnrichmentResult\n\n
"},{"location":"class_enrichment/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"class_enrichment/Curie/#comments","title":"Comments","text":""},{"location":"class_enrichment/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Curie/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"class_enrichment/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Date/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"class_enrichment/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"class_enrichment/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"class_enrichment/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"class_enrichment/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Double/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"class_enrichment/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Float/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"class_enrichment/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Integer/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"class_enrichment/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"class_enrichment/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"class_enrichment/Objectidentifier/#comments","title":"Comments","text":""},{"location":"class_enrichment/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Position/","title":"Type: Position","text":"

URI: xsd:integer

"},{"location":"class_enrichment/Position/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Position/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/SortFieldEnum/","title":"Enum: SortFieldEnum","text":"

The field to sort by

URI: SortFieldEnum

"},{"location":"class_enrichment/SortFieldEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ANY None P_VALUE None"},{"location":"class_enrichment/SortFieldEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/SortFieldEnum/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/SortFieldEnum/#linkml-source","title":"LinkML Source","text":"
name: SortFieldEnum\ndescription: The field to sort by\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\npermissible_values:\n  ANY:\n    text: ANY\n  P_VALUE:\n    text: P_VALUE\n\n
"},{"location":"class_enrichment/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"class_enrichment/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/String/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"class_enrichment/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Time/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"class_enrichment/Uri/#comments","title":"Comments","text":""},{"location":"class_enrichment/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Uri/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"class_enrichment/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ancestor_of_more_informative_result/","title":"Slot: ancestor_of_more_informative_result","text":"

This term is more general than a previously reported result

URI: ontoenrich:ancestor_of_more_informative_result

"},{"location":"class_enrichment/ancestor_of_more_informative_result/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/ancestor_of_more_informative_result/#properties","title":"Properties","text":""},{"location":"class_enrichment/ancestor_of_more_informative_result/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/ancestor_of_more_informative_result/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ancestor_of_more_informative_result/#linkml-source","title":"LinkML Source","text":"
name: ancestor_of_more_informative_result\ndescription: This term is more general than a previously reported result\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: ancestor_of_more_informative_result\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: boolean\n\n
"},{"location":"class_enrichment/background_count/","title":"Slot: background_count","text":"

The background count

URI: ontoenrich:background_count

"},{"location":"class_enrichment/background_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/background_count/#properties","title":"Properties","text":""},{"location":"class_enrichment/background_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/background_count/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/background_count/#linkml-source","title":"LinkML Source","text":"
name: background_count\ndescription: The background count\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: background_count\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: integer\n\n
"},{"location":"class_enrichment/background_total/","title":"Slot: background_total","text":"

The background total

URI: ontoenrich:background_total

"},{"location":"class_enrichment/background_total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/background_total/#properties","title":"Properties","text":""},{"location":"class_enrichment/background_total/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/background_total/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/background_total/#linkml-source","title":"LinkML Source","text":"
name: background_total\ndescription: The background total\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: background_total\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: integer\n\n
"},{"location":"class_enrichment/class-enrichment/","title":"class-enrichment","text":"

A datamodel for representing the results of class enrichment on gene sets

URI: https://w3id.org/oak/class-enrichment

"},{"location":"class_enrichment/class_id/","title":"Slot: class_id","text":"

The class id

URI: ontoenrich:class_id

"},{"location":"class_enrichment/class_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/class_id/#properties","title":"Properties","text":""},{"location":"class_enrichment/class_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/class_id/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/class_id/#linkml-source","title":"LinkML Source","text":"
name: class_id\ndescription: The class id\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: class_id\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: uriorcurie\nrequired: true\n\n
"},{"location":"class_enrichment/class_label/","title":"Slot: class_label","text":"

The class label

URI: ontoenrich:class_label

"},{"location":"class_enrichment/class_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/class_label/#properties","title":"Properties","text":""},{"location":"class_enrichment/class_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/class_label/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/class_label/#linkml-source","title":"LinkML Source","text":"
name: class_label\ndescription: The class label\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: class_label\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: string\n\n
"},{"location":"class_enrichment/descendant_of_more_informative_result/","title":"Slot: descendant_of_more_informative_result","text":"

This term is more specific than a previously reported result

URI: ontoenrich:descendant_of_more_informative_result

"},{"location":"class_enrichment/descendant_of_more_informative_result/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/descendant_of_more_informative_result/#properties","title":"Properties","text":""},{"location":"class_enrichment/descendant_of_more_informative_result/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/descendant_of_more_informative_result/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/descendant_of_more_informative_result/#linkml-source","title":"LinkML Source","text":"
name: descendant_of_more_informative_result\ndescription: This term is more specific than a previously reported result\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: descendant_of_more_informative_result\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: boolean\n\n
"},{"location":"class_enrichment/false_discovery_rate/","title":"Slot: false_discovery_rate","text":"

The false discovery rate

URI: ontoenrich:false_discovery_rate

"},{"location":"class_enrichment/false_discovery_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/false_discovery_rate/#properties","title":"Properties","text":""},{"location":"class_enrichment/false_discovery_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/false_discovery_rate/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/false_discovery_rate/#linkml-source","title":"LinkML Source","text":"
name: false_discovery_rate\ndescription: The false discovery rate\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: false_discovery_rate\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: float\n\n
"},{"location":"class_enrichment/fold_enrichment/","title":"Slot: fold_enrichment","text":"

The fold enrichment

URI: ontoenrich:fold_enrichment

"},{"location":"class_enrichment/fold_enrichment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/fold_enrichment/#properties","title":"Properties","text":""},{"location":"class_enrichment/fold_enrichment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/fold_enrichment/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/fold_enrichment/#linkml-source","title":"LinkML Source","text":"
name: fold_enrichment\ndescription: The fold enrichment\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: fold_enrichment\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: float\n\n
"},{"location":"class_enrichment/p_value/","title":"Slot: p_value","text":"

The p-value

URI: OBI:0000175

"},{"location":"class_enrichment/p_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/p_value/#properties","title":"Properties","text":""},{"location":"class_enrichment/p_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/p_value/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/p_value/#linkml-source","title":"LinkML Source","text":"
name: p_value\ndescription: The p-value\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nslot_uri: OBI:0000175\nalias: p_value\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: float\nrequired: true\n\n
"},{"location":"class_enrichment/p_value_adjusted/","title":"Slot: p_value_adjusted","text":"

The adjusted p-value

URI: ontoenrich:p_value_adjusted

"},{"location":"class_enrichment/p_value_adjusted/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/p_value_adjusted/#properties","title":"Properties","text":""},{"location":"class_enrichment/p_value_adjusted/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/p_value_adjusted/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/p_value_adjusted/#linkml-source","title":"LinkML Source","text":"
name: p_value_adjusted\ndescription: The adjusted p-value\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: p_value_adjusted\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: float\n\n
"},{"location":"class_enrichment/p_value_cutoff/","title":"Slot: p_value_cutoff","text":"

p-value cutoff for enrichment

URI: ontoenrich:p_value_cutoff

"},{"location":"class_enrichment/p_value_cutoff/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentConfiguration configuration for search no"},{"location":"class_enrichment/p_value_cutoff/#properties","title":"Properties","text":""},{"location":"class_enrichment/p_value_cutoff/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/p_value_cutoff/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/p_value_cutoff/#linkml-source","title":"LinkML Source","text":"
name: p_value_cutoff\ndescription: p-value cutoff for enrichment\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: p_value_cutoff\nowner: ClassEnrichmentConfiguration\ndomain_of:\n- ClassEnrichmentConfiguration\nrange: float\nrequired: true\n\n
"},{"location":"class_enrichment/probability/","title":"Slot: probability","text":"

The probability, as estimated by model-based approaches

URI: ontoenrich:probability

"},{"location":"class_enrichment/probability/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/probability/#properties","title":"Properties","text":""},{"location":"class_enrichment/probability/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/probability/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/probability/#linkml-source","title":"LinkML Source","text":"
name: probability\ndescription: The probability, as estimated by model-based approaches\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: probability\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: float\nminimum_value: 0\nmaximum_value: 1\n\n
"},{"location":"class_enrichment/rank/","title":"Slot: rank","text":"

The rank of this result

URI: ontoenrich:rank

"},{"location":"class_enrichment/rank/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/rank/#properties","title":"Properties","text":""},{"location":"class_enrichment/rank/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/rank/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/rank/#linkml-source","title":"LinkML Source","text":"
name: rank\ndescription: The rank of this result\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: rank\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: integer\n\n
"},{"location":"class_enrichment/results/","title":"Slot: results","text":"

The enrichment results

URI: ontoenrich:results

"},{"location":"class_enrichment/results/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResultSet A collection of enrichemt results no"},{"location":"class_enrichment/results/#properties","title":"Properties","text":""},{"location":"class_enrichment/results/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/results/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/results/#linkml-source","title":"LinkML Source","text":"
name: results\ndescription: The enrichment results\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nmultivalued: true\nalias: results\nowner: ClassEnrichmentResultSet\ndomain_of:\n- ClassEnrichmentResultSet\nrange: ClassEnrichmentResult\n\n
"},{"location":"class_enrichment/sample_count/","title":"Slot: sample_count","text":"

The number of entities in the sample with this class

URI: ontoenrich:sample_count

"},{"location":"class_enrichment/sample_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/sample_count/#properties","title":"Properties","text":""},{"location":"class_enrichment/sample_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/sample_count/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/sample_count/#linkml-source","title":"LinkML Source","text":"
name: sample_count\ndescription: The number of entities in the sample with this class\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: sample_count\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: integer\n\n
"},{"location":"class_enrichment/sample_total/","title":"Slot: sample_total","text":"

The total number of entities in the sample

URI: ontoenrich:sample_total

"},{"location":"class_enrichment/sample_total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/sample_total/#properties","title":"Properties","text":""},{"location":"class_enrichment/sample_total/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/sample_total/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/sample_total/#linkml-source","title":"LinkML Source","text":"
name: sample_total\ndescription: The total number of entities in the sample\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: sample_total\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: integer\n\n
"},{"location":"coffee/","title":"Coffee Template","text":"

A template for extracting information about coffee beverages.

URI: http://w3id.org/ontogpt/coffee

Name: coffee-template

"},{"location":"coffee/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nBeverageSet {\n\n}\nBeverage {\n    string name  \n    stringList other_names  \n    string description  \n}\nIngredient {\n    string id  \n    string label  \n}\n\nBeverageSet ||--}o Beverage : \"beverages\"\nBeverage ||--}o Ingredient : \"ingredients\"\n\n
"},{"location":"coffee/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None Beverage None BeverageSet None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None Ingredient None RelationshipType None Publication None TextWithTriples None"},{"location":"coffee/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication beverages combined_text description A one sentence description of the beverage extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity ingredients A semicolon-separated list of ingredients in the beverage, without volumes or... input_id input_text input_title label The label (name) of the named thing name The common name of the beverage, for example, caff\u00e8 macchiato named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text other_names A semicolon-separated list of alternative names for the beverage, including E... predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"coffee/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"coffee/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"coffee/#subsets","title":"Subsets","text":"Subset Description"},{"location":"coffee/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: coffee:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"coffee/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"coffee/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"coffee/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:AnnotatorResult native coffee:AnnotatorResult"},{"location":"coffee/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n\n
"},{"location":"coffee/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"coffee/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"coffee/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"coffee/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"coffee/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Any/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native coffee:Any"},{"location":"coffee/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/coffee\nclass_uri: linkml:Any\n\n
"},{"location":"coffee/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/coffee\nclass_uri: linkml:Any\n\n
"},{"location":"coffee/Beverage/","title":"Class: Beverage","text":"

URI: coffee:Beverage

erDiagram\nBeverage {\n    string name  \n    stringList other_names  \n    string description  \n}\nIngredient {\n    string id  \n    string label  \n}\n\nBeverage ||--}o Ingredient : \"ingredients\"\n\n
"},{"location":"coffee/Beverage/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance name 0..1 String The common name of the beverage, for example, caff\u00e8 macchiato direct other_names 0..* String A semicolon-separated list of alternative names for the beverage, including E... direct description 0..1 String A one sentence description of the beverage direct ingredients 0..* Ingredient A semicolon-separated list of ingredients in the beverage, without volumes or... direct"},{"location":"coffee/Beverage/#usages","title":"Usages","text":"used by used in type used BeverageSet beverages range Beverage"},{"location":"coffee/Beverage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Beverage/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Beverage/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:Beverage native coffee:Beverage"},{"location":"coffee/Beverage/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/Beverage/#direct","title":"Direct","text":"
name: Beverage\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  name:\n    name: name\n    description: The common name of the beverage, for example, caff\u00e8 macchiato.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  other_names:\n    name: other_names\n    description: A semicolon-separated list of alternative names for the beverage,\n      including English names like 'stained coffee' or regional variations.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n  description:\n    name: description\n    description: A one sentence description of the beverage.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  ingredients:\n    name: ingredients\n    description: A semicolon-separated list of ingredients in the beverage, without\n      volumes or units.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    range: Ingredient\n\n
"},{"location":"coffee/Beverage/#induced","title":"Induced","text":"
name: Beverage\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  name:\n    name: name\n    description: The common name of the beverage, for example, caff\u00e8 macchiato.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: name\n    owner: Beverage\n    domain_of:\n    - Beverage\n    range: string\n  other_names:\n    name: other_names\n    description: A semicolon-separated list of alternative names for the beverage,\n      including English names like 'stained coffee' or regional variations.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    alias: other_names\n    owner: Beverage\n    domain_of:\n    - Beverage\n    range: string\n  description:\n    name: description\n    description: A one sentence description of the beverage.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: description\n    owner: Beverage\n    domain_of:\n    - Beverage\n    range: string\n  ingredients:\n    name: ingredients\n    description: A semicolon-separated list of ingredients in the beverage, without\n      volumes or units.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    alias: ingredients\n    owner: Beverage\n    domain_of:\n    - Beverage\n    range: Ingredient\n\n
"},{"location":"coffee/BeverageSet/","title":"Class: BeverageSet","text":"

URI: coffee:BeverageSet

erDiagram\nBeverageSet {\n\n}\nBeverage {\n    string name  \n    stringList other_names  \n    string description  \n}\nIngredient {\n    string id  \n    string label  \n}\n\nBeverageSet ||--}o Beverage : \"beverages\"\nBeverage ||--}o Ingredient : \"ingredients\"\n\n
"},{"location":"coffee/BeverageSet/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance beverages 0..* Beverage direct"},{"location":"coffee/BeverageSet/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/BeverageSet/#schema-source","title":"Schema Source","text":""},{"location":"coffee/BeverageSet/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:BeverageSet native coffee:BeverageSet"},{"location":"coffee/BeverageSet/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/BeverageSet/#direct","title":"Direct","text":"
name: BeverageSet\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  beverages:\n    name: beverages\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    range: Beverage\n    inlined: true\n    inlined_as_list: true\ntree_root: true\n\n
"},{"location":"coffee/BeverageSet/#induced","title":"Induced","text":"
name: BeverageSet\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  beverages:\n    name: beverages\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    alias: beverages\n    owner: BeverageSet\n    domain_of:\n    - BeverageSet\n    range: Beverage\n    inlined: true\n    inlined_as_list: true\ntree_root: true\n\n
"},{"location":"coffee/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"coffee/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"coffee/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: coffee:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"coffee/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"coffee/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"coffee/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"coffee/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:CompoundExpression native coffee:CompoundExpression"},{"location":"coffee/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/coffee\nabstract: true\n\n
"},{"location":"coffee/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/coffee\nabstract: true\n\n
"},{"location":"coffee/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"coffee/Curie/#comments","title":"Comments","text":""},{"location":"coffee/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Curie/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"coffee/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Date/#schema-source","title":"Schema Source","text":""},{"location":"coffee/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"coffee/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"coffee/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"coffee/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"coffee/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Double/#schema-source","title":"Schema Source","text":""},{"location":"coffee/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: coffee:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"coffee/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"coffee/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"coffee/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:ExtractionResult native coffee:ExtractionResult"},{"location":"coffee/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"coffee/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"coffee/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"coffee/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Float/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Ingredient/","title":"Class: Ingredient","text":"

URI: coffee:Ingredient

erDiagram\nIngredient {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"coffee/Ingredient/#inheritance","title":"Inheritance","text":""},{"location":"coffee/Ingredient/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"coffee/Ingredient/#usages","title":"Usages","text":"used by used in type used Beverage ingredients range Ingredient"},{"location":"coffee/Ingredient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Ingredient/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"coffee/Ingredient/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:foodon"},{"location":"coffee/Ingredient/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Ingredient/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:Ingredient native coffee:Ingredient"},{"location":"coffee/Ingredient/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/Ingredient/#direct","title":"Direct","text":"
name: Ingredient\nid_prefixes:\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: NamedEntity\n\n
"},{"location":"coffee/Ingredient/#induced","title":"Induced","text":"
name: Ingredient\nid_prefixes:\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Ingredient\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/coffee\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Ingredient\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"coffee/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"coffee/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Integer/#schema-source","title":"Schema Source","text":""},{"location":"coffee/NamedEntity/","title":"Class: NamedEntity","text":"

URI: coffee:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"coffee/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"coffee/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"coffee/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"coffee/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"coffee/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:NamedEntity native coffee:NamedEntity"},{"location":"coffee/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/coffee\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/coffee\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"coffee/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/coffee\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/coffee\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"coffee/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"coffee/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"coffee/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"coffee/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"coffee/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"coffee/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"coffee/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"coffee/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"coffee/Objectidentifier/#comments","title":"Comments","text":""},{"location":"coffee/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Publication/","title":"Class: Publication","text":"

URI: coffee:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"coffee/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"coffee/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"coffee/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Publication/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:Publication native coffee:Publication"},{"location":"coffee/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/coffee\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n\n
"},{"location":"coffee/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/coffee\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"coffee/RelationshipType/","title":"Class: RelationshipType","text":"

URI: coffee:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"coffee/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"coffee/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"coffee/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"coffee/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"coffee/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"coffee/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:RelationshipType native coffee:RelationshipType"},{"location":"coffee/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: NamedEntity\n\n
"},{"location":"coffee/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/coffee\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"coffee/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"coffee/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/String/#schema-source","title":"Schema Source","text":""},{"location":"coffee/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: coffee:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"coffee/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"coffee/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"coffee/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:TextWithTriples native coffee:TextWithTriples"},{"location":"coffee/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"coffee/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"coffee/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"coffee/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Time/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: coffee:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"coffee/Triple/#inheritance","title":"Inheritance","text":""},{"location":"coffee/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"coffee/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"coffee/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Triple/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:Triple native coffee:Triple"},{"location":"coffee/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"coffee/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"coffee/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"coffee/Uri/#comments","title":"Comments","text":""},{"location":"coffee/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Uri/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"coffee/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"coffee/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: coffee:abstract

"},{"location":"coffee/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"coffee/abstract/#properties","title":"Properties","text":""},{"location":"coffee/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/abstract/#schema-source","title":"Schema Source","text":""},{"location":"coffee/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"coffee/beverages/","title":"Slot: beverages","text":"

URI: coffee:beverages

"},{"location":"coffee/beverages/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BeverageSet no"},{"location":"coffee/beverages/#properties","title":"Properties","text":""},{"location":"coffee/beverages/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/beverages/#schema-source","title":"Schema Source","text":""},{"location":"coffee/beverages/#linkml-source","title":"LinkML Source","text":"
name: beverages\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nmultivalued: true\nalias: beverages\nowner: BeverageSet\ndomain_of:\n- BeverageSet\nrange: Beverage\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"coffee/coffee-template/","title":"coffee-template","text":"

A template for extracting information about coffee beverages.

URI: http://w3id.org/ontogpt/coffee

"},{"location":"coffee/combined_text/","title":"Slot: combined_text","text":"

URI: coffee:combined_text

"},{"location":"coffee/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"coffee/combined_text/#properties","title":"Properties","text":""},{"location":"coffee/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"coffee/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"coffee/description/","title":"Slot: description","text":"

A one sentence description of the beverage.

URI: coffee:description

"},{"location":"coffee/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Beverage no"},{"location":"coffee/description/#properties","title":"Properties","text":""},{"location":"coffee/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/description/#schema-source","title":"Schema Source","text":""},{"location":"coffee/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: A one sentence description of the beverage.\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: description\nowner: Beverage\ndomain_of:\n- Beverage\nrange: string\n\n
"},{"location":"coffee/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: coffee:extracted_object

"},{"location":"coffee/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/extracted_object/#properties","title":"Properties","text":""},{"location":"coffee/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"coffee/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"coffee/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: coffee:full_text

"},{"location":"coffee/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"coffee/full_text/#properties","title":"Properties","text":""},{"location":"coffee/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/full_text/#schema-source","title":"Schema Source","text":""},{"location":"coffee/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"coffee/id/","title":"Slot: id","text":"

URI: coffee:id

"},{"location":"coffee/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Ingredient no NamedEntity no RelationshipType no Publication no"},{"location":"coffee/id/#properties","title":"Properties","text":""},{"location":"coffee/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"coffee/ingredients/","title":"Slot: ingredients","text":"

A semicolon-separated list of ingredients in the beverage, without volumes or units.

URI: coffee:ingredients

"},{"location":"coffee/ingredients/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Beverage no"},{"location":"coffee/ingredients/#properties","title":"Properties","text":""},{"location":"coffee/ingredients/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/ingredients/#schema-source","title":"Schema Source","text":""},{"location":"coffee/ingredients/#linkml-source","title":"LinkML Source","text":"
name: ingredients\ndescription: A semicolon-separated list of ingredients in the beverage, without volumes\n  or units.\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nmultivalued: true\nalias: ingredients\nowner: Beverage\ndomain_of:\n- Beverage\nrange: Ingredient\n\n
"},{"location":"coffee/input_id/","title":"Slot: input_id","text":"

URI: coffee:input_id

"},{"location":"coffee/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/input_id/#properties","title":"Properties","text":""},{"location":"coffee/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/input_id/#schema-source","title":"Schema Source","text":""},{"location":"coffee/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"coffee/input_text/","title":"Slot: input_text","text":"

URI: coffee:input_text

"},{"location":"coffee/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/input_text/#properties","title":"Properties","text":""},{"location":"coffee/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/input_text/#schema-source","title":"Schema Source","text":""},{"location":"coffee/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"coffee/input_title/","title":"Slot: input_title","text":"

URI: coffee:input_title

"},{"location":"coffee/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/input_title/#properties","title":"Properties","text":""},{"location":"coffee/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/input_title/#schema-source","title":"Schema Source","text":""},{"location":"coffee/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"coffee/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"coffee/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Ingredient no NamedEntity no RelationshipType no"},{"location":"coffee/label/#properties","title":"Properties","text":""},{"location":"coffee/label/#aliases","title":"Aliases","text":""},{"location":"coffee/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"coffee/label/#schema-source","title":"Schema Source","text":""},{"location":"coffee/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/coffee\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"coffee/name/","title":"Slot: name","text":"

The common name of the beverage, for example, caff\u00e8 macchiato.

URI: coffee:name

"},{"location":"coffee/name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Beverage no"},{"location":"coffee/name/#properties","title":"Properties","text":""},{"location":"coffee/name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/name/#schema-source","title":"Schema Source","text":""},{"location":"coffee/name/#linkml-source","title":"LinkML Source","text":"
name: name\ndescription: The common name of the beverage, for example, caff\u00e8 macchiato.\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: name\nowner: Beverage\ndomain_of:\n- Beverage\nrange: string\n\n
"},{"location":"coffee/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: coffee:named_entities

"},{"location":"coffee/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/named_entities/#properties","title":"Properties","text":""},{"location":"coffee/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"coffee/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"coffee/object/","title":"Slot: object","text":"

URI: coffee:object

"},{"location":"coffee/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/object/#properties","title":"Properties","text":""},{"location":"coffee/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/object/#schema-source","title":"Schema Source","text":""},{"location":"coffee/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"coffee/object_id/","title":"Slot: object_id","text":"

URI: coffee:object_id

"},{"location":"coffee/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"coffee/object_id/#properties","title":"Properties","text":""},{"location":"coffee/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/object_id/#schema-source","title":"Schema Source","text":""},{"location":"coffee/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"coffee/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: coffee:object_qualifier

"},{"location":"coffee/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/object_qualifier/#properties","title":"Properties","text":""},{"location":"coffee/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"coffee/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"coffee/object_text/","title":"Slot: object_text","text":"

URI: coffee:object_text

"},{"location":"coffee/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"coffee/object_text/#properties","title":"Properties","text":""},{"location":"coffee/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/object_text/#schema-source","title":"Schema Source","text":""},{"location":"coffee/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"coffee/other_names/","title":"Slot: other_names","text":"

A semicolon-separated list of alternative names for the beverage, including English names like 'stained coffee' or regional variations.

URI: coffee:other_names

"},{"location":"coffee/other_names/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Beverage no"},{"location":"coffee/other_names/#properties","title":"Properties","text":""},{"location":"coffee/other_names/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/other_names/#schema-source","title":"Schema Source","text":""},{"location":"coffee/other_names/#linkml-source","title":"LinkML Source","text":"
name: other_names\ndescription: A semicolon-separated list of alternative names for the beverage, including\n  English names like 'stained coffee' or regional variations.\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nmultivalued: true\nalias: other_names\nowner: Beverage\ndomain_of:\n- Beverage\nrange: string\n\n
"},{"location":"coffee/predicate/","title":"Slot: predicate","text":"

URI: coffee:predicate

"},{"location":"coffee/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/predicate/#properties","title":"Properties","text":""},{"location":"coffee/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/predicate/#schema-source","title":"Schema Source","text":""},{"location":"coffee/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"coffee/prompt/","title":"Slot: prompt","text":"

URI: coffee:prompt

"},{"location":"coffee/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/prompt/#properties","title":"Properties","text":""},{"location":"coffee/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/prompt/#schema-source","title":"Schema Source","text":""},{"location":"coffee/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"coffee/publication/","title":"Slot: publication","text":"

URI: coffee:publication

"},{"location":"coffee/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"coffee/publication/#properties","title":"Properties","text":""},{"location":"coffee/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"coffee/publication/#schema-source","title":"Schema Source","text":""},{"location":"coffee/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"coffee/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: coffee:qualifier

"},{"location":"coffee/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/qualifier/#properties","title":"Properties","text":""},{"location":"coffee/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"coffee/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"coffee/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: coffee:raw_completion_output

"},{"location":"coffee/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/raw_completion_output/#properties","title":"Properties","text":""},{"location":"coffee/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"coffee/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"coffee/subject/","title":"Slot: subject","text":"

URI: coffee:subject

"},{"location":"coffee/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/subject/#properties","title":"Properties","text":""},{"location":"coffee/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/subject/#schema-source","title":"Schema Source","text":""},{"location":"coffee/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"coffee/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: coffee:subject_qualifier

"},{"location":"coffee/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/subject_qualifier/#properties","title":"Properties","text":""},{"location":"coffee/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"coffee/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"coffee/subject_text/","title":"Slot: subject_text","text":"

URI: coffee:subject_text

"},{"location":"coffee/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"coffee/subject_text/#properties","title":"Properties","text":""},{"location":"coffee/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"coffee/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"coffee/title/","title":"Slot: title","text":"

The title of the publication

URI: coffee:title

"},{"location":"coffee/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"coffee/title/#properties","title":"Properties","text":""},{"location":"coffee/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/title/#schema-source","title":"Schema Source","text":""},{"location":"coffee/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"coffee/triples/","title":"Slot: triples","text":"

URI: coffee:triples

"},{"location":"coffee/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"coffee/triples/#properties","title":"Properties","text":""},{"location":"coffee/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/triples/#schema-source","title":"Schema Source","text":""},{"location":"coffee/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"composite_disease/","title":"Composite Disease","text":"

A template for representing composite disease concepts

URI: http://w3id.org/ontogpt/composite_disease

Name: composite_disease

"},{"location":"composite_disease/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nCompositeDisease {\n\n}\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nCompositeDisease ||--|o Disease : \"main_disease\"\nCompositeDisease ||--}o Drug : \"drugs\"\nCompositeDisease ||--}o Treatment : \"treatments\"\nCompositeDisease ||--}o Treatment : \"contraindications\"\nCompositeDisease ||--}o TreatmentMechanism : \"treatment_mechanisms\"\nCompositeDisease ||--}o TreatmentEfficacy : \"treatment_efficacies\"\nCompositeDisease ||--}o TreatmentAdverseEffect : \"treatment_adverse_effects\"\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"composite_disease/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompositeDisease None CompoundExpression None TreatmentAdverseEffect None TreatmentEfficacy None TreatmentMechanism None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None AdverseEffect None Disease None Drug None Gene None Mechanism None RelationshipType None Symptom None Treatment None Publication None TextWithTriples None"},{"location":"composite_disease/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication adverse_effects combined_text contraindications semicolon-separated list of therapies and treatments that are contra-indicate... drugs semicolon-separated list of named small molecule drugs efficacy extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing main_disease the name of the disease that is treated mechanism named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication treatment treatment_adverse_effects semicolon-separated list of treatment to adverse effect associations, e treatment_efficacies semicolon-separated list of treatment to efficacy associations, e treatment_mechanisms semicolon-separated list of treatment to asterisk-separated mechanism associa... treatments semicolon-separated list of therapies and treatments are indicated for treati... triples"},{"location":"composite_disease/#enumerations","title":"Enumerations","text":"Enumeration Description CHEBIDrugType MAXOActionType MESHTherapeuticType NCITDrugType NCITTActivityType NCITTreatmentType NullDataOptions"},{"location":"composite_disease/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"composite_disease/#subsets","title":"Subsets","text":"Subset Description"},{"location":"composite_disease/AdverseEffect/","title":"Class: AdverseEffect","text":"

URI: composite_disease:AdverseEffect

erDiagram\nAdverseEffect {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/AdverseEffect/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/AdverseEffect/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/AdverseEffect/#usages","title":"Usages","text":"used by used in type used TreatmentAdverseEffect adverse_effects range AdverseEffect"},{"location":"composite_disease/AdverseEffect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/AdverseEffect/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:ncit"},{"location":"composite_disease/AdverseEffect/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/AdverseEffect/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:AdverseEffect native composite_disease:AdverseEffect"},{"location":"composite_disease/AdverseEffect/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/AdverseEffect/#direct","title":"Direct","text":"
name: AdverseEffect\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/AdverseEffect/#induced","title":"Induced","text":"
name: AdverseEffect\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: AdverseEffect\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: AdverseEffect\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: composite_disease:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"composite_disease/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"composite_disease/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:AnnotatorResult native composite_disease:AnnotatorResult"},{"location":"composite_disease/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n\n
"},{"location":"composite_disease/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"composite_disease/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"composite_disease/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"composite_disease/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"composite_disease/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Any/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native composite_disease:Any"},{"location":"composite_disease/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nclass_uri: linkml:Any\n\n
"},{"location":"composite_disease/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nclass_uri: linkml:Any\n\n
"},{"location":"composite_disease/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"composite_disease/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/CHEBIDrugType/","title":"Enum: CHEBIDrugType","text":"

URI: CHEBIDrugType

This is a dynamic enum

"},{"location":"composite_disease/CHEBIDrugType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/CHEBIDrugType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/CHEBIDrugType/#linkml-source","title":"LinkML Source","text":"
name: CHEBIDrugType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:chebi\n  source_nodes:\n  - CHEBI:23888\n  relationship_types:\n  - rdfs:subClassOf\n  - RO:0000087\n\n
"},{"location":"composite_disease/CompositeDisease/","title":"Class: CompositeDisease","text":"

URI: composite_disease:CompositeDisease

erDiagram\nCompositeDisease {\n\n}\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nCompositeDisease ||--|o Disease : \"main_disease\"\nCompositeDisease ||--}o Drug : \"drugs\"\nCompositeDisease ||--}o Treatment : \"treatments\"\nCompositeDisease ||--}o Treatment : \"contraindications\"\nCompositeDisease ||--}o TreatmentMechanism : \"treatment_mechanisms\"\nCompositeDisease ||--}o TreatmentEfficacy : \"treatment_efficacies\"\nCompositeDisease ||--}o TreatmentAdverseEffect : \"treatment_adverse_effects\"\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"composite_disease/CompositeDisease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance main_disease 0..1 Disease the name of the disease that is treated direct drugs 0..* Drug semicolon-separated list of named small molecule drugs direct treatments 0..* Treatment semicolon-separated list of therapies and treatments are indicated for treati... direct contraindications 0..* Treatment semicolon-separated list of therapies and treatments that are contra-indicate... direct treatment_mechanisms 0..* TreatmentMechanism semicolon-separated list of treatment to asterisk-separated mechanism associa... direct treatment_efficacies 0..* TreatmentEfficacy semicolon-separated list of treatment to efficacy associations, e direct treatment_adverse_effects 0..* TreatmentAdverseEffect semicolon-separated list of treatment to adverse effect associations, e direct"},{"location":"composite_disease/CompositeDisease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/CompositeDisease/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/CompositeDisease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:CompositeDisease native composite_disease:CompositeDisease"},{"location":"composite_disease/CompositeDisease/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/CompositeDisease/#direct","title":"Direct","text":"
name: CompositeDisease\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  main_disease:\n    name: main_disease\n    description: the name of the disease that is treated.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: Disease\n  drugs:\n    name: drugs\n    description: semicolon-separated list of named small molecule drugs\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: Drug\n  treatments:\n    name: treatments\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Imatinib, exercise, surgery\n    description: semicolon-separated list of therapies and treatments are indicated\n      for treating the disease.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: Treatment\n  contraindications:\n    name: contraindications\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Beta-blockers, exercise, surgery\n    description: semicolon-separated list of therapies and treatments that are contra-indicated\n      for the disease, and should not be used, due to risk of adverse effects.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: Treatment\n  treatment_mechanisms:\n    name: treatment_mechanisms\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to asterisk-separated mechanism\n      associations\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: TreatmentMechanism\n  treatment_efficacies:\n    name: treatment_efficacies\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to efficacy associations, e.g.\n      Imatinib*effective\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: TreatmentEfficacy\n  treatment_adverse_effects:\n    name: treatment_adverse_effects\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to adverse effect associations,\n      e.g. Imatinib*nausea\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: TreatmentAdverseEffect\ntree_root: true\n\n
"},{"location":"composite_disease/CompositeDisease/#induced","title":"Induced","text":"
name: CompositeDisease\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  main_disease:\n    name: main_disease\n    description: the name of the disease that is treated.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: main_disease\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: Disease\n  drugs:\n    name: drugs\n    description: semicolon-separated list of named small molecule drugs\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: drugs\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: Drug\n  treatments:\n    name: treatments\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Imatinib, exercise, surgery\n    description: semicolon-separated list of therapies and treatments are indicated\n      for treating the disease.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: treatments\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: Treatment\n  contraindications:\n    name: contraindications\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Beta-blockers, exercise, surgery\n    description: semicolon-separated list of therapies and treatments that are contra-indicated\n      for the disease, and should not be used, due to risk of adverse effects.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: contraindications\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: Treatment\n  treatment_mechanisms:\n    name: treatment_mechanisms\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to asterisk-separated mechanism\n      associations\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: treatment_mechanisms\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: TreatmentMechanism\n  treatment_efficacies:\n    name: treatment_efficacies\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to efficacy associations, e.g.\n      Imatinib*effective\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: treatment_efficacies\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: TreatmentEfficacy\n  treatment_adverse_effects:\n    name: treatment_adverse_effects\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to adverse effect associations,\n      e.g. Imatinib*nausea\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: treatment_adverse_effects\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: TreatmentAdverseEffect\ntree_root: true\n\n
"},{"location":"composite_disease/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: composite_disease:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"composite_disease/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"composite_disease/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:CompoundExpression native composite_disease:CompoundExpression"},{"location":"composite_disease/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nabstract: true\n\n
"},{"location":"composite_disease/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nabstract: true\n\n
"},{"location":"composite_disease/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"composite_disease/Curie/#comments","title":"Comments","text":""},{"location":"composite_disease/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Curie/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"composite_disease/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Date/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"composite_disease/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"composite_disease/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"composite_disease/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Disease/","title":"Class: Disease","text":"

URI: composite_disease:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Disease/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Disease/#usages","title":"Usages","text":"used by used in type used CompositeDisease main_disease range Disease"},{"location":"composite_disease/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo"},{"location":"composite_disease/Disease/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Disease native composite_disease:Disease"},{"location":"composite_disease/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Disease/#direct","title":"Direct","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/Disease/#induced","title":"Induced","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"composite_disease/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Double/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Drug/","title":"Class: Drug","text":"

URI: composite_disease:Drug

erDiagram\nDrug {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Drug/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Drug/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Drug/#usages","title":"Usages","text":"used by used in type used CompositeDisease drugs range Drug"},{"location":"composite_disease/Drug/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Drug/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi, sqlite:obo:drugbank"},{"location":"composite_disease/Drug/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Drug/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Drug native composite_disease:Drug"},{"location":"composite_disease/Drug/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Drug/#direct","title":"Direct","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/Drug/#induced","title":"Induced","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: composite_disease:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"composite_disease/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"composite_disease/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:ExtractionResult native composite_disease:ExtractionResult"},{"location":"composite_disease/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"composite_disease/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"composite_disease/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"composite_disease/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Float/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Gene/","title":"Class: Gene","text":"

URI: composite_disease:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Gene/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"composite_disease/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, obo:sql:hgnc, bioportal:hgnc-nr"},{"location":"composite_disease/Gene/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Gene native composite_disease:Gene"},{"location":"composite_disease/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, obo:sql:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, obo:sql:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"composite_disease/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Integer/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/MAXOActionType/","title":"Enum: MAXOActionType","text":"

URI: MAXOActionType

This is a dynamic enum

"},{"location":"composite_disease/MAXOActionType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/MAXOActionType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/MAXOActionType/#linkml-source","title":"LinkML Source","text":"
name: MAXOActionType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:maxo\n  source_nodes:\n  - MAXO:0000001\n\n
"},{"location":"composite_disease/MESHTherapeuticType/","title":"Enum: MESHTherapeuticType","text":"

URI: MESHTherapeuticType

This is a dynamic enum

"},{"location":"composite_disease/MESHTherapeuticType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/MESHTherapeuticType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/MESHTherapeuticType/#linkml-source","title":"LinkML Source","text":"
name: MESHTherapeuticType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:mesh\n  source_nodes:\n  - MESH:D013812\n\n
"},{"location":"composite_disease/Mechanism/","title":"Class: Mechanism","text":"

URI: composite_disease:Mechanism

erDiagram\nMechanism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Mechanism/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Mechanism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Mechanism/#usages","title":"Usages","text":"used by used in type used TreatmentMechanism mechanism range Mechanism"},{"location":"composite_disease/Mechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Mechanism/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh"},{"location":"composite_disease/Mechanism/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Mechanism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Mechanism native composite_disease:Mechanism"},{"location":"composite_disease/Mechanism/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Mechanism/#direct","title":"Direct","text":"
name: Mechanism\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/Mechanism/#induced","title":"Induced","text":"
name: Mechanism\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Mechanism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Mechanism\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/NCITDrugType/","title":"Enum: NCITDrugType","text":"

URI: NCITDrugType

This is a dynamic enum

"},{"location":"composite_disease/NCITDrugType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/NCITDrugType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NCITDrugType/#linkml-source","title":"LinkML Source","text":"
name: NCITDrugType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C1908\n\n
"},{"location":"composite_disease/NCITTActivityType/","title":"Enum: NCITTActivityType","text":"

URI: NCITTActivityType

This is a dynamic enum

"},{"location":"composite_disease/NCITTActivityType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/NCITTActivityType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NCITTActivityType/#linkml-source","title":"LinkML Source","text":"
name: NCITTActivityType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C43431\n\n
"},{"location":"composite_disease/NCITTreatmentType/","title":"Enum: NCITTreatmentType","text":"

URI: NCITTreatmentType

This is a dynamic enum

"},{"location":"composite_disease/NCITTreatmentType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/NCITTreatmentType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NCITTreatmentType/#linkml-source","title":"LinkML Source","text":"
name: NCITTreatmentType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C25218\n\n
"},{"location":"composite_disease/NamedEntity/","title":"Class: NamedEntity","text":"

URI: composite_disease:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"composite_disease/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"composite_disease/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:NamedEntity native composite_disease:NamedEntity"},{"location":"composite_disease/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"composite_disease/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"composite_disease/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"composite_disease/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"composite_disease/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"composite_disease/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"composite_disease/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"composite_disease/Objectidentifier/#comments","title":"Comments","text":""},{"location":"composite_disease/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Publication/","title":"Class: Publication","text":"

URI: composite_disease:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"composite_disease/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"composite_disease/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"composite_disease/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Publication/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Publication native composite_disease:Publication"},{"location":"composite_disease/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/composite_disease\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n\n
"},{"location":"composite_disease/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"composite_disease/RelationshipType/","title":"Class: RelationshipType","text":"

URI: composite_disease:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"composite_disease/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"composite_disease/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:RelationshipType native composite_disease:RelationshipType"},{"location":"composite_disease/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"composite_disease/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/String/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Symptom/","title":"Class: Symptom","text":"

URI: composite_disease:Symptom

erDiagram\nSymptom {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Symptom/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Symptom/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Symptom/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"composite_disease/Symptom/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp"},{"location":"composite_disease/Symptom/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Symptom/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Symptom native composite_disease:Symptom"},{"location":"composite_disease/Symptom/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Symptom/#direct","title":"Direct","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/Symptom/#induced","title":"Induced","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: composite_disease:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"composite_disease/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"composite_disease/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:TextWithTriples native composite_disease:TextWithTriples"},{"location":"composite_disease/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"composite_disease/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"composite_disease/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"composite_disease/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Time/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Treatment/","title":"Class: Treatment","text":"

URI: composite_disease:Treatment

erDiagram\nTreatment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Treatment/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Treatment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Treatment/#usages","title":"Usages","text":"used by used in type used CompositeDisease treatments range Treatment CompositeDisease contraindications range Treatment TreatmentMechanism treatment range Treatment TreatmentAdverseEffect treatment range Treatment TreatmentEfficacy treatment range Treatment"},{"location":"composite_disease/Treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Treatment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi"},{"location":"composite_disease/Treatment/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Treatment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Treatment native composite_disease:Treatment"},{"location":"composite_disease/Treatment/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Treatment/#direct","title":"Direct","text":"
name: Treatment\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nvalues_from:\n- NCITDrugType\n- NCITTreatmentType\n- NCITActivityType\n- MAXOTreatmentType\n- MESHTherapeuticType\n- CHEBIDrugType\n\n
"},{"location":"composite_disease/Treatment/#induced","title":"Induced","text":"
name: Treatment\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nvalues_from:\n- NCITDrugType\n- NCITTreatmentType\n- NCITActivityType\n- MAXOTreatmentType\n- MESHTherapeuticType\n- CHEBIDrugType\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/TreatmentAdverseEffect/","title":"Class: TreatmentAdverseEffect","text":"

URI: composite_disease:TreatmentAdverseEffect

erDiagram\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\n\n
"},{"location":"composite_disease/TreatmentAdverseEffect/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/TreatmentAdverseEffect/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct adverse_effects 0..* AdverseEffect direct"},{"location":"composite_disease/TreatmentAdverseEffect/#usages","title":"Usages","text":"used by used in type used CompositeDisease treatment_adverse_effects range TreatmentAdverseEffect"},{"location":"composite_disease/TreatmentAdverseEffect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/TreatmentAdverseEffect/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/TreatmentAdverseEffect/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:TreatmentAdverseEffect native composite_disease:TreatmentAdverseEffect"},{"location":"composite_disease/TreatmentAdverseEffect/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/TreatmentAdverseEffect/#direct","title":"Direct","text":"
name: TreatmentAdverseEffect\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    range: Treatment\n  adverse_effects:\n    name: adverse_effects\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: AdverseEffect\n\n
"},{"location":"composite_disease/TreatmentAdverseEffect/#induced","title":"Induced","text":"
name: TreatmentAdverseEffect\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    alias: treatment\n    owner: TreatmentAdverseEffect\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  adverse_effects:\n    name: adverse_effects\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: adverse_effects\n    owner: TreatmentAdverseEffect\n    domain_of:\n    - TreatmentAdverseEffect\n    range: AdverseEffect\n\n
"},{"location":"composite_disease/TreatmentEfficacy/","title":"Class: TreatmentEfficacy","text":"

URI: composite_disease:TreatmentEfficacy

erDiagram\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\n\n
"},{"location":"composite_disease/TreatmentEfficacy/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/TreatmentEfficacy/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct efficacy 0..1 String direct"},{"location":"composite_disease/TreatmentEfficacy/#usages","title":"Usages","text":"used by used in type used CompositeDisease treatment_efficacies range TreatmentEfficacy"},{"location":"composite_disease/TreatmentEfficacy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/TreatmentEfficacy/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/TreatmentEfficacy/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:TreatmentEfficacy native composite_disease:TreatmentEfficacy"},{"location":"composite_disease/TreatmentEfficacy/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/TreatmentEfficacy/#direct","title":"Direct","text":"
name: TreatmentEfficacy\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    range: Treatment\n  efficacy:\n    name: efficacy\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: string\n\n
"},{"location":"composite_disease/TreatmentEfficacy/#induced","title":"Induced","text":"
name: TreatmentEfficacy\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    alias: treatment\n    owner: TreatmentEfficacy\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  efficacy:\n    name: efficacy\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: efficacy\n    owner: TreatmentEfficacy\n    domain_of:\n    - TreatmentEfficacy\n    range: string\n\n
"},{"location":"composite_disease/TreatmentMechanism/","title":"Class: TreatmentMechanism","text":"

URI: composite_disease:TreatmentMechanism

erDiagram\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"composite_disease/TreatmentMechanism/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/TreatmentMechanism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct mechanism 0..1 Mechanism direct"},{"location":"composite_disease/TreatmentMechanism/#usages","title":"Usages","text":"used by used in type used CompositeDisease treatment_mechanisms range TreatmentMechanism"},{"location":"composite_disease/TreatmentMechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/TreatmentMechanism/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/TreatmentMechanism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:TreatmentMechanism native composite_disease:TreatmentMechanism"},{"location":"composite_disease/TreatmentMechanism/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/TreatmentMechanism/#direct","title":"Direct","text":"
name: TreatmentMechanism\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: Treatment\n  mechanism:\n    name: mechanism\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: Mechanism\n\n
"},{"location":"composite_disease/TreatmentMechanism/#induced","title":"Induced","text":"
name: TreatmentMechanism\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: treatment\n    owner: TreatmentMechanism\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  mechanism:\n    name: mechanism\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: mechanism\n    owner: TreatmentMechanism\n    domain_of:\n    - TreatmentMechanism\n    range: Mechanism\n\n
"},{"location":"composite_disease/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: composite_disease:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"composite_disease/Triple/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"composite_disease/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"composite_disease/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Triple/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Triple native composite_disease:Triple"},{"location":"composite_disease/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"composite_disease/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"composite_disease/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"composite_disease/Uri/#comments","title":"Comments","text":""},{"location":"composite_disease/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Uri/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"composite_disease/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: composite_disease:abstract

"},{"location":"composite_disease/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"composite_disease/abstract/#properties","title":"Properties","text":""},{"location":"composite_disease/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/abstract/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"composite_disease/adverse_effects/","title":"Slot: adverse_effects","text":"

URI: composite_disease:adverse_effects

"},{"location":"composite_disease/adverse_effects/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentAdverseEffect no"},{"location":"composite_disease/adverse_effects/#properties","title":"Properties","text":""},{"location":"composite_disease/adverse_effects/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/adverse_effects/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/adverse_effects/#linkml-source","title":"LinkML Source","text":"
name: adverse_effects\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: adverse_effects\nowner: TreatmentAdverseEffect\ndomain_of:\n- TreatmentAdverseEffect\nrange: AdverseEffect\n\n
"},{"location":"composite_disease/combined_text/","title":"Slot: combined_text","text":"

URI: composite_disease:combined_text

"},{"location":"composite_disease/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"composite_disease/combined_text/#properties","title":"Properties","text":""},{"location":"composite_disease/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"composite_disease/composite_disease/","title":"composite_disease","text":"

A template for representing composite disease concepts

URI: http://w3id.org/ontogpt/composite_disease

"},{"location":"composite_disease/contraindications/","title":"Slot: contraindications","text":"

semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.

URI: composite_disease:contraindications

"},{"location":"composite_disease/contraindications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/contraindications/#properties","title":"Properties","text":""},{"location":"composite_disease/contraindications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/contraindications/#annotations","title":"Annotations","text":"property value prompt.examples Beta-blockers, exercise, surgery"},{"location":"composite_disease/contraindications/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/contraindications/#linkml-source","title":"LinkML Source","text":"
name: contraindications\nannotations:\n  prompt.examples:\n    tag: prompt.examples\n    value: Beta-blockers, exercise, surgery\ndescription: semicolon-separated list of therapies and treatments that are contra-indicated\n  for the disease, and should not be used, due to risk of adverse effects.\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: contraindications\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: Treatment\n\n
"},{"location":"composite_disease/drugs/","title":"Slot: drugs","text":"

semicolon-separated list of named small molecule drugs

URI: composite_disease:drugs

"},{"location":"composite_disease/drugs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/drugs/#properties","title":"Properties","text":""},{"location":"composite_disease/drugs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/drugs/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/drugs/#linkml-source","title":"LinkML Source","text":"
name: drugs\ndescription: semicolon-separated list of named small molecule drugs\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: drugs\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: Drug\n\n
"},{"location":"composite_disease/efficacy/","title":"Slot: efficacy","text":"

URI: composite_disease:efficacy

"},{"location":"composite_disease/efficacy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentEfficacy no"},{"location":"composite_disease/efficacy/#properties","title":"Properties","text":""},{"location":"composite_disease/efficacy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/efficacy/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/efficacy/#linkml-source","title":"LinkML Source","text":"
name: efficacy\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: efficacy\nowner: TreatmentEfficacy\ndomain_of:\n- TreatmentEfficacy\nrange: string\n\n
"},{"location":"composite_disease/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: composite_disease:extracted_object

"},{"location":"composite_disease/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/extracted_object/#properties","title":"Properties","text":""},{"location":"composite_disease/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"composite_disease/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: composite_disease:full_text

"},{"location":"composite_disease/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"composite_disease/full_text/#properties","title":"Properties","text":""},{"location":"composite_disease/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/full_text/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"composite_disease/id/","title":"Slot: id","text":"

URI: composite_disease:id

"},{"location":"composite_disease/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Symptom no Disease no AdverseEffect no Treatment no Mechanism no Drug no NamedEntity no RelationshipType no Publication no"},{"location":"composite_disease/id/#properties","title":"Properties","text":""},{"location":"composite_disease/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"composite_disease/input_id/","title":"Slot: input_id","text":"

URI: composite_disease:input_id

"},{"location":"composite_disease/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/input_id/#properties","title":"Properties","text":""},{"location":"composite_disease/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/input_id/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"composite_disease/input_text/","title":"Slot: input_text","text":"

URI: composite_disease:input_text

"},{"location":"composite_disease/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/input_text/#properties","title":"Properties","text":""},{"location":"composite_disease/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/input_text/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"composite_disease/input_title/","title":"Slot: input_title","text":"

URI: composite_disease:input_title

"},{"location":"composite_disease/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/input_title/#properties","title":"Properties","text":""},{"location":"composite_disease/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/input_title/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"composite_disease/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"composite_disease/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Symptom no Disease no AdverseEffect no Treatment no Mechanism no Drug no NamedEntity no RelationshipType no"},{"location":"composite_disease/label/#properties","title":"Properties","text":""},{"location":"composite_disease/label/#aliases","title":"Aliases","text":""},{"location":"composite_disease/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"composite_disease/label/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/composite_disease\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"composite_disease/main_disease/","title":"Slot: main_disease","text":"

the name of the disease that is treated.

URI: composite_disease:main_disease

"},{"location":"composite_disease/main_disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/main_disease/#properties","title":"Properties","text":""},{"location":"composite_disease/main_disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/main_disease/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/main_disease/#linkml-source","title":"LinkML Source","text":"
name: main_disease\ndescription: the name of the disease that is treated.\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: main_disease\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: Disease\n\n
"},{"location":"composite_disease/mechanism/","title":"Slot: mechanism","text":"

URI: composite_disease:mechanism

"},{"location":"composite_disease/mechanism/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentMechanism no"},{"location":"composite_disease/mechanism/#properties","title":"Properties","text":""},{"location":"composite_disease/mechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/mechanism/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/mechanism/#linkml-source","title":"LinkML Source","text":"
name: mechanism\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: mechanism\nowner: TreatmentMechanism\ndomain_of:\n- TreatmentMechanism\nrange: Mechanism\n\n
"},{"location":"composite_disease/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: composite_disease:named_entities

"},{"location":"composite_disease/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/named_entities/#properties","title":"Properties","text":""},{"location":"composite_disease/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"composite_disease/object/","title":"Slot: object","text":"

URI: composite_disease:object

"},{"location":"composite_disease/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/object/#properties","title":"Properties","text":""},{"location":"composite_disease/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/object/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"composite_disease/object_id/","title":"Slot: object_id","text":"

URI: composite_disease:object_id

"},{"location":"composite_disease/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"composite_disease/object_id/#properties","title":"Properties","text":""},{"location":"composite_disease/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/object_id/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"composite_disease/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: composite_disease:object_qualifier

"},{"location":"composite_disease/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/object_qualifier/#properties","title":"Properties","text":""},{"location":"composite_disease/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"composite_disease/object_text/","title":"Slot: object_text","text":"

URI: composite_disease:object_text

"},{"location":"composite_disease/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"composite_disease/object_text/#properties","title":"Properties","text":""},{"location":"composite_disease/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/object_text/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"composite_disease/predicate/","title":"Slot: predicate","text":"

URI: composite_disease:predicate

"},{"location":"composite_disease/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/predicate/#properties","title":"Properties","text":""},{"location":"composite_disease/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/predicate/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"composite_disease/prompt/","title":"Slot: prompt","text":"

URI: composite_disease:prompt

"},{"location":"composite_disease/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/prompt/#properties","title":"Properties","text":""},{"location":"composite_disease/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/prompt/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"composite_disease/publication/","title":"Slot: publication","text":"

URI: composite_disease:publication

"},{"location":"composite_disease/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"composite_disease/publication/#properties","title":"Properties","text":""},{"location":"composite_disease/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"composite_disease/publication/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"composite_disease/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: composite_disease:qualifier

"},{"location":"composite_disease/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/qualifier/#properties","title":"Properties","text":""},{"location":"composite_disease/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"composite_disease/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: composite_disease:raw_completion_output

"},{"location":"composite_disease/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/raw_completion_output/#properties","title":"Properties","text":""},{"location":"composite_disease/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"composite_disease/subject/","title":"Slot: subject","text":"

URI: composite_disease:subject

"},{"location":"composite_disease/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/subject/#properties","title":"Properties","text":""},{"location":"composite_disease/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/subject/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"composite_disease/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: composite_disease:subject_qualifier

"},{"location":"composite_disease/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/subject_qualifier/#properties","title":"Properties","text":""},{"location":"composite_disease/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"composite_disease/subject_text/","title":"Slot: subject_text","text":"

URI: composite_disease:subject_text

"},{"location":"composite_disease/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"composite_disease/subject_text/#properties","title":"Properties","text":""},{"location":"composite_disease/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"composite_disease/title/","title":"Slot: title","text":"

The title of the publication

URI: composite_disease:title

"},{"location":"composite_disease/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"composite_disease/title/#properties","title":"Properties","text":""},{"location":"composite_disease/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/title/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"composite_disease/treatment/","title":"Slot: treatment","text":"

URI: composite_disease:treatment

"},{"location":"composite_disease/treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentMechanism no TreatmentAdverseEffect no TreatmentEfficacy no"},{"location":"composite_disease/treatment/#properties","title":"Properties","text":""},{"location":"composite_disease/treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/treatment/#linkml-source","title":"LinkML Source","text":"
name: treatment\nalias: treatment\ndomain_of:\n- TreatmentMechanism\n- TreatmentAdverseEffect\n- TreatmentEfficacy\nrange: string\n\n
"},{"location":"composite_disease/treatment_adverse_effects/","title":"Slot: treatment_adverse_effects","text":"

semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea

URI: composite_disease:treatment_adverse_effects

"},{"location":"composite_disease/treatment_adverse_effects/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/treatment_adverse_effects/#properties","title":"Properties","text":""},{"location":"composite_disease/treatment_adverse_effects/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/treatment_adverse_effects/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"composite_disease/treatment_adverse_effects/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/treatment_adverse_effects/#linkml-source","title":"LinkML Source","text":"
name: treatment_adverse_effects\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to adverse effect associations,\n  e.g. Imatinib*nausea\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: treatment_adverse_effects\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: TreatmentAdverseEffect\n\n
"},{"location":"composite_disease/treatment_efficacies/","title":"Slot: treatment_efficacies","text":"

semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective

URI: composite_disease:treatment_efficacies

"},{"location":"composite_disease/treatment_efficacies/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/treatment_efficacies/#properties","title":"Properties","text":""},{"location":"composite_disease/treatment_efficacies/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/treatment_efficacies/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"composite_disease/treatment_efficacies/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/treatment_efficacies/#linkml-source","title":"LinkML Source","text":"
name: treatment_efficacies\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to efficacy associations, e.g.\n  Imatinib*effective\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: treatment_efficacies\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: TreatmentEfficacy\n\n
"},{"location":"composite_disease/treatment_mechanisms/","title":"Slot: treatment_mechanisms","text":"

semicolon-separated list of treatment to asterisk-separated mechanism associations

URI: composite_disease:treatment_mechanisms

"},{"location":"composite_disease/treatment_mechanisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/treatment_mechanisms/#properties","title":"Properties","text":""},{"location":"composite_disease/treatment_mechanisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/treatment_mechanisms/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"composite_disease/treatment_mechanisms/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/treatment_mechanisms/#linkml-source","title":"LinkML Source","text":"
name: treatment_mechanisms\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to asterisk-separated mechanism\n  associations\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: treatment_mechanisms\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: TreatmentMechanism\n\n
"},{"location":"composite_disease/treatments/","title":"Slot: treatments","text":"

semicolon-separated list of therapies and treatments are indicated for treating the disease.

URI: composite_disease:treatments

"},{"location":"composite_disease/treatments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/treatments/#properties","title":"Properties","text":""},{"location":"composite_disease/treatments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/treatments/#annotations","title":"Annotations","text":"property value prompt.examples Imatinib, exercise, surgery"},{"location":"composite_disease/treatments/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/treatments/#linkml-source","title":"LinkML Source","text":"
name: treatments\nannotations:\n  prompt.examples:\n    tag: prompt.examples\n    value: Imatinib, exercise, surgery\ndescription: semicolon-separated list of therapies and treatments are indicated for\n  treating the disease.\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: treatments\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: Treatment\n\n
"},{"location":"composite_disease/triples/","title":"Slot: triples","text":"

URI: composite_disease:triples

"},{"location":"composite_disease/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"composite_disease/triples/#properties","title":"Properties","text":""},{"location":"composite_disease/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/triples/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"core/","title":"AI core Template","text":"

Core upper level

URI: http://w3id.org/ontogpt/core

Name: core

"},{"location":"core/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"core/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None RelationshipType None Publication None TextWithTriples None"},{"location":"core/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"core/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"core/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"core/#subsets","title":"Subsets","text":"Subset Description"},{"location":"core/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: core:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"core/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"core/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"core/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:AnnotatorResult native core:AnnotatorResult"},{"location":"core/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"core/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n\n
"},{"location":"core/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"core/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"core/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"core/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"core/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Any/#schema-source","title":"Schema Source","text":""},{"location":"core/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native core:Any"},{"location":"core/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"core/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/core\nclass_uri: linkml:Any\n\n
"},{"location":"core/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/core\nclass_uri: linkml:Any\n\n
"},{"location":"core/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"core/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"core/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: core:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"core/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"core/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"core/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"core/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:CompoundExpression native core:CompoundExpression"},{"location":"core/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"core/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/core\nabstract: true\n\n
"},{"location":"core/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/core\nabstract: true\n\n
"},{"location":"core/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"core/Curie/#comments","title":"Comments","text":""},{"location":"core/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Curie/#schema-source","title":"Schema Source","text":""},{"location":"core/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"core/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Date/#schema-source","title":"Schema Source","text":""},{"location":"core/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"core/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"core/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"core/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"core/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"core/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"core/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"core/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Double/#schema-source","title":"Schema Source","text":""},{"location":"core/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: core:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"core/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"core/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"core/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:ExtractionResult native core:ExtractionResult"},{"location":"core/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"core/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"core/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"core/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"core/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Float/#schema-source","title":"Schema Source","text":""},{"location":"core/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"core/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Integer/#schema-source","title":"Schema Source","text":""},{"location":"core/NamedEntity/","title":"Class: NamedEntity","text":"

URI: core:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"core/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"core/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"core/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"core/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"core/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:NamedEntity native core:NamedEntity"},{"location":"core/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"core/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/core\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/core\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"core/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/core\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/core\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"core/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"core/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"core/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"core/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"core/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"core/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"core/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"core/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"core/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"core/Objectidentifier/#comments","title":"Comments","text":""},{"location":"core/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"core/Publication/","title":"Class: Publication","text":"

URI: core:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"core/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"core/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"core/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Publication/#schema-source","title":"Schema Source","text":""},{"location":"core/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:Publication native core:Publication"},{"location":"core/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"core/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/core\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n\n
"},{"location":"core/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/core\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"core/RelationshipType/","title":"Class: RelationshipType","text":"

URI: core:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"core/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"core/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"core/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"core/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"core/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"core/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:RelationshipType native core:RelationshipType"},{"location":"core/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"core/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/core\nis_a: NamedEntity\n\n
"},{"location":"core/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/core\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/core\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"core/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"core/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/String/#schema-source","title":"Schema Source","text":""},{"location":"core/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: core:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"core/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"core/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"core/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:TextWithTriples native core:TextWithTriples"},{"location":"core/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"core/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"core/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"core/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"core/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Time/#schema-source","title":"Schema Source","text":""},{"location":"core/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: core:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"core/Triple/#inheritance","title":"Inheritance","text":""},{"location":"core/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"core/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"core/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Triple/#schema-source","title":"Schema Source","text":""},{"location":"core/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:Triple native core:Triple"},{"location":"core/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"core/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/core\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"core/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/core\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"core/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"core/Uri/#comments","title":"Comments","text":""},{"location":"core/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Uri/#schema-source","title":"Schema Source","text":""},{"location":"core/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"core/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"core/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: core:abstract

"},{"location":"core/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"core/abstract/#properties","title":"Properties","text":""},{"location":"core/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/abstract/#schema-source","title":"Schema Source","text":""},{"location":"core/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"core/combined_text/","title":"Slot: combined_text","text":"

URI: core:combined_text

"},{"location":"core/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"core/combined_text/#properties","title":"Properties","text":""},{"location":"core/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"core/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"core/core/","title":"core","text":"

Core upper level

URI: http://w3id.org/ontogpt/core

"},{"location":"core/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: core:extracted_object

"},{"location":"core/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/extracted_object/#properties","title":"Properties","text":""},{"location":"core/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"core/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"core/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: core:full_text

"},{"location":"core/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"core/full_text/#properties","title":"Properties","text":""},{"location":"core/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/full_text/#schema-source","title":"Schema Source","text":""},{"location":"core/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"core/id/","title":"Slot: id","text":"

URI: core:id

"},{"location":"core/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NamedEntity no RelationshipType no Publication no"},{"location":"core/id/#properties","title":"Properties","text":""},{"location":"core/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"core/input_id/","title":"Slot: input_id","text":"

URI: core:input_id

"},{"location":"core/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/input_id/#properties","title":"Properties","text":""},{"location":"core/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/input_id/#schema-source","title":"Schema Source","text":""},{"location":"core/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"core/input_text/","title":"Slot: input_text","text":"

URI: core:input_text

"},{"location":"core/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/input_text/#properties","title":"Properties","text":""},{"location":"core/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/input_text/#schema-source","title":"Schema Source","text":""},{"location":"core/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"core/input_title/","title":"Slot: input_title","text":"

URI: core:input_title

"},{"location":"core/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/input_title/#properties","title":"Properties","text":""},{"location":"core/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/input_title/#schema-source","title":"Schema Source","text":""},{"location":"core/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"core/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"core/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NamedEntity no RelationshipType no"},{"location":"core/label/#properties","title":"Properties","text":""},{"location":"core/label/#aliases","title":"Aliases","text":""},{"location":"core/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"core/label/#schema-source","title":"Schema Source","text":""},{"location":"core/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/core\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"core/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: core:named_entities

"},{"location":"core/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/named_entities/#properties","title":"Properties","text":""},{"location":"core/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"core/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"core/object/","title":"Slot: object","text":"

URI: core:object

"},{"location":"core/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/object/#properties","title":"Properties","text":""},{"location":"core/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/object/#schema-source","title":"Schema Source","text":""},{"location":"core/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"core/object_id/","title":"Slot: object_id","text":"

URI: core:object_id

"},{"location":"core/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"core/object_id/#properties","title":"Properties","text":""},{"location":"core/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/object_id/#schema-source","title":"Schema Source","text":""},{"location":"core/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"core/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: core:object_qualifier

"},{"location":"core/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/object_qualifier/#properties","title":"Properties","text":""},{"location":"core/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"core/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"core/object_text/","title":"Slot: object_text","text":"

URI: core:object_text

"},{"location":"core/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"core/object_text/#properties","title":"Properties","text":""},{"location":"core/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/object_text/#schema-source","title":"Schema Source","text":""},{"location":"core/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"core/predicate/","title":"Slot: predicate","text":"

URI: core:predicate

"},{"location":"core/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/predicate/#properties","title":"Properties","text":""},{"location":"core/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/predicate/#schema-source","title":"Schema Source","text":""},{"location":"core/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"core/prompt/","title":"Slot: prompt","text":"

URI: core:prompt

"},{"location":"core/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/prompt/#properties","title":"Properties","text":""},{"location":"core/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/prompt/#schema-source","title":"Schema Source","text":""},{"location":"core/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"core/publication/","title":"Slot: publication","text":"

URI: core:publication

"},{"location":"core/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"core/publication/#properties","title":"Properties","text":""},{"location":"core/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"core/publication/#schema-source","title":"Schema Source","text":""},{"location":"core/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"core/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: core:qualifier

"},{"location":"core/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/qualifier/#properties","title":"Properties","text":""},{"location":"core/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"core/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"core/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: core:raw_completion_output

"},{"location":"core/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/raw_completion_output/#properties","title":"Properties","text":""},{"location":"core/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"core/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"core/subject/","title":"Slot: subject","text":"

URI: core:subject

"},{"location":"core/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/subject/#properties","title":"Properties","text":""},{"location":"core/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/subject/#schema-source","title":"Schema Source","text":""},{"location":"core/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"core/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: core:subject_qualifier

"},{"location":"core/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/subject_qualifier/#properties","title":"Properties","text":""},{"location":"core/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"core/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"core/subject_text/","title":"Slot: subject_text","text":"

URI: core:subject_text

"},{"location":"core/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"core/subject_text/#properties","title":"Properties","text":""},{"location":"core/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"core/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"core/title/","title":"Slot: title","text":"

The title of the publication

URI: core:title

"},{"location":"core/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"core/title/#properties","title":"Properties","text":""},{"location":"core/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/title/#schema-source","title":"Schema Source","text":""},{"location":"core/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"core/triples/","title":"Slot: triples","text":"

URI: core:triples

"},{"location":"core/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"core/triples/#properties","title":"Properties","text":""},{"location":"core/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/triples/#schema-source","title":"Schema Source","text":""},{"location":"core/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ctd/","title":"Chemical to Disease Template","text":"

A template for Chemical to Disease associations. This template is intended to represent associations between chemicals and diseases, and for evaluating Semantic Llama against BioCreative V Chemical Disease Relation (CDR) Task (BC5CDR).

URI: http://w3id.org/ontogpt/ctd

Name: ctd

"},{"location":"ctd/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nChemicalToDiseaseDocument {\n\n}\nChemicalToDiseaseRelationship {\n    string qualifier  \n}\nDisease {\n    string id  \n    string label  \n}\nChemical {\n    string id  \n    string label  \n}\nChemicalToDiseasePredicate {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nChemicalToDiseaseDocument ||--|o Publication : \"publication\"\nChemicalToDiseaseDocument ||--}o ChemicalToDiseaseRelationship : \"triples\"\nChemicalToDiseaseRelationship ||--|o Chemical : \"subject\"\nChemicalToDiseaseRelationship ||--|o ChemicalToDiseasePredicate : \"predicate\"\nChemicalToDiseaseRelationship ||--|o Disease : \"object\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"ctd/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease. ExtractionResult A result of extracting knowledge on text NamedEntity None Chemical None Disease None RelationshipType None ChemicalToDiseasePredicate A predicate for chemical to disease relationships Publication None TextWithTriples None ChemicalToDiseaseDocument A document that contains chemical to disease relations."},{"location":"ctd/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"ctd/#enumerations","title":"Enumerations","text":"Enumeration Description MeshChemicalIdentifier MeshDiseaseIdentifier NullDataOptions"},{"location":"ctd/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"ctd/#subsets","title":"Subsets","text":"Subset Description"},{"location":"ctd/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: drug:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"ctd/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"ctd/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"ctd/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:AnnotatorResult native drug:AnnotatorResult"},{"location":"ctd/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n\n
"},{"location":"ctd/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"ctd/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"ctd/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ctd/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"ctd/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Any/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native drug:Any"},{"location":"ctd/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/ctd\nclass_uri: linkml:Any\n\n
"},{"location":"ctd/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/ctd\nclass_uri: linkml:Any\n\n
"},{"location":"ctd/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"ctd/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Chemical/","title":"Class: Chemical","text":"

URI: drug:Chemical

erDiagram\nChemical {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ctd/Chemical/#inheritance","title":"Inheritance","text":""},{"location":"ctd/Chemical/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ctd/Chemical/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseRelationship subject range Chemical"},{"location":"ctd/Chemical/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Chemical/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ctd/Chemical/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:"},{"location":"ctd/Chemical/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Chemical/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Chemical native drug:Chemical"},{"location":"ctd/Chemical/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/Chemical/#direct","title":"Direct","text":"
name: Chemical\nid_prefixes:\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: 'sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank,\n      gilda:'\n  prompt.examples:\n    tag: prompt.examples\n    value: Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - MeshChemicalIdentifier\n    domain_of:\n    - NamedEntity\n    - Publication\n    pattern: ^MESH:[CD][0-9]{6}$\n\n
"},{"location":"ctd/Chemical/#induced","title":"Induced","text":"
name: Chemical\nid_prefixes:\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: 'sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank,\n      gilda:'\n  prompt.examples:\n    tag: prompt.examples\n    value: Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - MeshChemicalIdentifier\n    domain_of:\n    - NamedEntity\n    - Publication\n    pattern: ^MESH:[CD][0-9]{6}$\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    values_from:\n    - MeshChemicalIdentifier\n    identifier: true\n    alias: id\n    owner: Chemical\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n    pattern: ^MESH:[CD][0-9]{6}$\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Chemical\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ctd/ChemicalToDiseaseDocument/","title":"Class: ChemicalToDiseaseDocument","text":"

A document that contains chemical to disease relations.

URI: drug:ChemicalToDiseaseDocument

erDiagram\nChemicalToDiseaseDocument {\n\n}\nChemicalToDiseaseRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nChemicalToDiseasePredicate {\n    string id  \n    string label  \n}\nChemical {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nChemicalToDiseaseDocument ||--|o Publication : \"publication\"\nChemicalToDiseaseDocument ||--}o ChemicalToDiseaseRelationship : \"triples\"\nChemicalToDiseaseRelationship ||--|o Chemical : \"subject\"\nChemicalToDiseaseRelationship ||--|o ChemicalToDiseasePredicate : \"predicate\"\nChemicalToDiseaseRelationship ||--|o Disease : \"object\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ctd/ChemicalToDiseaseDocument/#inheritance","title":"Inheritance","text":""},{"location":"ctd/ChemicalToDiseaseDocument/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication TextWithTriples triples 0..* ChemicalToDiseaseRelationship TextWithTriples"},{"location":"ctd/ChemicalToDiseaseDocument/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/ChemicalToDiseaseDocument/#schema-source","title":"Schema Source","text":""},{"location":"ctd/ChemicalToDiseaseDocument/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:ChemicalToDiseaseDocument native drug:ChemicalToDiseaseDocument"},{"location":"ctd/ChemicalToDiseaseDocument/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/ChemicalToDiseaseDocument/#direct","title":"Direct","text":"
name: ChemicalToDiseaseDocument\ndescription: A document that contains chemical to disease relations.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: TextWithTriples\nslot_usage:\n  triples:\n    name: triples\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'A semi-colon separated list of chemical to disease relationships,\n          where the relationship is either INDUCES or TREATS. for example: Lidocaine\n          INDUCES cardiac asystole;  Hydroxychloroquine NOT TREATS COVID-19; Methyldopa\n          INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib\n          TREATS cancer'\n      exclude:\n        tag: exclude\n        value: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa,\n          Headache, Imatinib, cancer\n    domain_of:\n    - TextWithTriples\n    range: ChemicalToDiseaseRelationship\n\n
"},{"location":"ctd/ChemicalToDiseaseDocument/#induced","title":"Induced","text":"
name: ChemicalToDiseaseDocument\ndescription: A document that contains chemical to disease relations.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: TextWithTriples\nslot_usage:\n  triples:\n    name: triples\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'A semi-colon separated list of chemical to disease relationships,\n          where the relationship is either INDUCES or TREATS. for example: Lidocaine\n          INDUCES cardiac asystole;  Hydroxychloroquine NOT TREATS COVID-19; Methyldopa\n          INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib\n          TREATS cancer'\n      exclude:\n        tag: exclude\n        value: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa,\n          Headache, Imatinib, cancer\n    domain_of:\n    - TextWithTriples\n    range: ChemicalToDiseaseRelationship\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: publication\n    owner: ChemicalToDiseaseDocument\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'A semi-colon separated list of chemical to disease relationships,\n          where the relationship is either INDUCES or TREATS. for example: Lidocaine\n          INDUCES cardiac asystole;  Hydroxychloroquine NOT TREATS COVID-19; Methyldopa\n          INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib\n          TREATS cancer'\n      exclude:\n        tag: exclude\n        value: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa,\n          Headache, Imatinib, cancer\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: ChemicalToDiseaseDocument\n    domain_of:\n    - TextWithTriples\n    range: ChemicalToDiseaseRelationship\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ctd/ChemicalToDiseasePredicate/","title":"Class: ChemicalToDiseasePredicate","text":"

A predicate for chemical to disease relationships

URI: drug:ChemicalToDiseasePredicate

erDiagram\nChemicalToDiseasePredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ctd/ChemicalToDiseasePredicate/#inheritance","title":"Inheritance","text":""},{"location":"ctd/ChemicalToDiseasePredicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ctd/ChemicalToDiseasePredicate/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseRelationship predicate range ChemicalToDiseasePredicate"},{"location":"ctd/ChemicalToDiseasePredicate/#comments","title":"Comments","text":""},{"location":"ctd/ChemicalToDiseasePredicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/ChemicalToDiseasePredicate/#schema-source","title":"Schema Source","text":""},{"location":"ctd/ChemicalToDiseasePredicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:ChemicalToDiseasePredicate native drug:ChemicalToDiseasePredicate"},{"location":"ctd/ChemicalToDiseasePredicate/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/ChemicalToDiseasePredicate/#direct","title":"Direct","text":"
name: ChemicalToDiseasePredicate\ndescription: A predicate for chemical to disease relationships\ncomments:\n- for the purposes of evaluation against BC5CDR, any predicate other than INDUCES\n  is ignored.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: RelationshipType\n\n
"},{"location":"ctd/ChemicalToDiseasePredicate/#induced","title":"Induced","text":"
name: ChemicalToDiseasePredicate\ndescription: A predicate for chemical to disease relationships\ncomments:\n- for the purposes of evaluation against BC5CDR, any predicate other than INDUCES\n  is ignored.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: RelationshipType\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalToDiseasePredicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalToDiseasePredicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ctd/ChemicalToDiseaseRelationship/","title":"Class: ChemicalToDiseaseRelationship","text":"

A triple where the subject is a chemical and the object is a disease.

URI: drug:ChemicalToDiseaseRelationship

erDiagram\nChemicalToDiseaseRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nChemicalToDiseasePredicate {\n    string id  \n    string label  \n}\nChemical {\n    string id  \n    string label  \n}\n\nChemicalToDiseaseRelationship ||--|o Chemical : \"subject\"\nChemicalToDiseaseRelationship ||--|o ChemicalToDiseasePredicate : \"predicate\"\nChemicalToDiseaseRelationship ||--|o Disease : \"object\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ctd/ChemicalToDiseaseRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ctd/ChemicalToDiseaseRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 Chemical The chemical substance, drug, or small molecule Triple predicate 0..1 ChemicalToDiseasePredicate The relationship type, e Triple object 0..1 Disease The disease or condition that is being treated or induced by the chemical Triple qualifier 0..1 String A qualifier for the statements, e Triple subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the chemical, e Triple object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the disease, e Triple"},{"location":"ctd/ChemicalToDiseaseRelationship/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseDocument triples range ChemicalToDiseaseRelationship"},{"location":"ctd/ChemicalToDiseaseRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/ChemicalToDiseaseRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ctd/ChemicalToDiseaseRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:ChemicalToDiseaseRelationship native drug:ChemicalToDiseaseRelationship"},{"location":"ctd/ChemicalToDiseaseRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/ChemicalToDiseaseRelationship/#direct","title":"Direct","text":"
name: ChemicalToDiseaseRelationship\ndescription: A triple where the subject is a chemical and the object is a disease.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: 'The chemical substance, drug, or small molecule.  For example: Lidocaine,\n      Monosodium Glutamate, Imatinib.'\n    domain_of:\n    - Triple\n    range: Chemical\n  object:\n    name: object\n    description: The disease or condition that is being treated or induced by the\n      chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension,\n      Headache.\n    domain_of:\n    - Triple\n    range: Disease\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. INDUCES, TREATS.\n    domain_of:\n    - Triple\n    range: ChemicalToDiseasePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the chemical, e.g. \"high dose\"\n      or \"intravenously administered\"\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease, e.g. \"severe\"\n      or \"with additional complications\"\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ctd/ChemicalToDiseaseRelationship/#induced","title":"Induced","text":"
name: ChemicalToDiseaseRelationship\ndescription: A triple where the subject is a chemical and the object is a disease.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: 'The chemical substance, drug, or small molecule.  For example: Lidocaine,\n      Monosodium Glutamate, Imatinib.'\n    domain_of:\n    - Triple\n    range: Chemical\n  object:\n    name: object\n    description: The disease or condition that is being treated or induced by the\n      chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension,\n      Headache.\n    domain_of:\n    - Triple\n    range: Disease\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. INDUCES, TREATS.\n    domain_of:\n    - Triple\n    range: ChemicalToDiseasePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the chemical, e.g. \"high dose\"\n      or \"intravenously administered\"\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease, e.g. \"severe\"\n      or \"with additional complications\"\n    domain_of:\n    - Triple\n    range: NamedEntity\nattributes:\n  subject:\n    name: subject\n    description: 'The chemical substance, drug, or small molecule.  For example: Lidocaine,\n      Monosodium Glutamate, Imatinib.'\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: subject\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: Chemical\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. INDUCES, TREATS.\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: predicate\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: ChemicalToDiseasePredicate\n  object:\n    name: object\n    description: The disease or condition that is being treated or induced by the\n      chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension,\n      Headache.\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: Disease\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: qualifier\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the chemical, e.g. \"high dose\"\n      or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: subject_qualifier\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease, e.g. \"severe\"\n      or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object_qualifier\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ctd/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: drug:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"ctd/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"ctd/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ctd/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"ctd/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:CompoundExpression native drug:CompoundExpression"},{"location":"ctd/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/ctd\nabstract: true\n\n
"},{"location":"ctd/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/ctd\nabstract: true\n\n
"},{"location":"ctd/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"ctd/Curie/#comments","title":"Comments","text":""},{"location":"ctd/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Curie/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"ctd/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Date/#schema-source","title":"Schema Source","text":""},{"location":"ctd/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"ctd/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"ctd/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"ctd/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Disease/","title":"Class: Disease","text":"

URI: drug:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ctd/Disease/#inheritance","title":"Inheritance","text":""},{"location":"ctd/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ctd/Disease/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseRelationship object range Disease"},{"location":"ctd/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Disease/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ctd/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra"},{"location":"ctd/Disease/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Disease native drug:Disease"},{"location":"ctd/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/Disease/#direct","title":"Direct","text":"
name: Disease\nid_prefixes:\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid,\n      bioportal:meddra\n  prompt.examples:\n    tag: prompt.examples\n    value: cardiac asystole, COVID-19, Headache, cancer\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - MeshDiseaseIdentifier\n    domain_of:\n    - NamedEntity\n    - Publication\n    pattern: ^MESH:[CD][0-9]{6}$\n\n
"},{"location":"ctd/Disease/#induced","title":"Induced","text":"
name: Disease\nid_prefixes:\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid,\n      bioportal:meddra\n  prompt.examples:\n    tag: prompt.examples\n    value: cardiac asystole, COVID-19, Headache, cancer\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - MeshDiseaseIdentifier\n    domain_of:\n    - NamedEntity\n    - Publication\n    pattern: ^MESH:[CD][0-9]{6}$\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    values_from:\n    - MeshDiseaseIdentifier\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n    pattern: ^MESH:[CD][0-9]{6}$\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ctd/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"ctd/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Double/#schema-source","title":"Schema Source","text":""},{"location":"ctd/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: drug:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"ctd/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"ctd/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"ctd/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:ExtractionResult native drug:ExtractionResult"},{"location":"ctd/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ctd/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ctd/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"ctd/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Float/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"ctd/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Integer/#schema-source","title":"Schema Source","text":""},{"location":"ctd/MeshChemicalIdentifier/","title":"Enum: MeshChemicalIdentifier","text":"

URI: MeshChemicalIdentifier

This is a dynamic enum

"},{"location":"ctd/MeshChemicalIdentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/MeshChemicalIdentifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/MeshChemicalIdentifier/#linkml-source","title":"LinkML Source","text":"
name: MeshChemicalIdentifier\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nreachable_from:\n  source_ontology: obo:mesh\n  source_nodes:\n  - MESH:D000602\n  - MESH:D001685\n  - MESH:D002241\n  - MESH:D004364\n  - MESH:D006571\n  - MESH:D007287\n  - MESH:D008055\n  - MESH:D009706\n  - MESH:D009930\n  - MESH:D011083\n  - MESH:D013812\n  - MESH:D019602\n  - MESH:D045424\n  - MESH:D045762\n  - MESH:D046911\n\n
"},{"location":"ctd/MeshDiseaseIdentifier/","title":"Enum: MeshDiseaseIdentifier","text":"

URI: MeshDiseaseIdentifier

This is a dynamic enum

"},{"location":"ctd/MeshDiseaseIdentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/MeshDiseaseIdentifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/MeshDiseaseIdentifier/#linkml-source","title":"LinkML Source","text":"
name: MeshDiseaseIdentifier\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nreachable_from:\n  source_ontology: obo:mesh\n  source_nodes:\n  - MESH:D001423\n  - MESH:D001523\n  - MESH:D002318\n  - MESH:D002943\n  - MESH:D004066\n  - MESH:D004700\n  - MESH:D005128\n  - MESH:D005261\n  - MESH:D006425\n  - MESH:D007154\n  - MESH:D007280\n  - MESH:D009057\n  - MESH:D009140\n  - MESH:D009358\n  - MESH:D009369\n  - MESH:D009422\n  - MESH:D009750\n  - MESH:D009784\n  - MESH:D010038\n  - MESH:D010272\n  - MESH:D012140\n  - MESH:D013568\n  - MESH:D014777\n  - MESH:D014947\n  - MESH:D017437\n  - MESH:D052801\n  - MESH:D064419\n\n
"},{"location":"ctd/NamedEntity/","title":"Class: NamedEntity","text":"

URI: drug:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ctd/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"ctd/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"ctd/NamedEntity/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseRelationship subject_qualifier range NamedEntity ChemicalToDiseaseRelationship object_qualifier range NamedEntity Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"ctd/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"ctd/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:NamedEntity native drug:NamedEntity"},{"location":"ctd/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/ctd\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"ctd/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/ctd\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ctd/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"ctd/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"ctd/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"ctd/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"ctd/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"ctd/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"ctd/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"ctd/Objectidentifier/#comments","title":"Comments","text":""},{"location":"ctd/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Publication/","title":"Class: Publication","text":"

URI: drug:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"ctd/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"ctd/Publication/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseDocument publication range Publication TextWithTriples publication range Publication"},{"location":"ctd/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Publication/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Publication native drug:Publication"},{"location":"ctd/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/ctd\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n\n
"},{"location":"ctd/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/ctd\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"ctd/RelationshipType/","title":"Class: RelationshipType","text":"

URI: drug:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ctd/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"ctd/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ctd/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"ctd/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ctd/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"ctd/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:RelationshipType native drug:RelationshipType"},{"location":"ctd/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\n\n
"},{"location":"ctd/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ctd/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"ctd/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/String/#schema-source","title":"Schema Source","text":""},{"location":"ctd/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: drug:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ctd/TextWithTriples/#inheritance","title":"Inheritance","text":""},{"location":"ctd/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"ctd/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"ctd/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:TextWithTriples native drug:TextWithTriples"},{"location":"ctd/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ctd/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ctd/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"ctd/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Time/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: drug:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ctd/Triple/#inheritance","title":"Inheritance","text":""},{"location":"ctd/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"ctd/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"ctd/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Triple/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Triple native drug:Triple"},{"location":"ctd/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"ctd/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ctd/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"ctd/Uri/#comments","title":"Comments","text":""},{"location":"ctd/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Uri/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"ctd/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"ctd/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: drug:abstract

"},{"location":"ctd/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ctd/abstract/#properties","title":"Properties","text":""},{"location":"ctd/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/abstract/#schema-source","title":"Schema Source","text":""},{"location":"ctd/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ctd/combined_text/","title":"Slot: combined_text","text":"

URI: drug:combined_text

"},{"location":"ctd/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ctd/combined_text/#properties","title":"Properties","text":""},{"location":"ctd/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"ctd/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ctd/ctd/","title":"ctd","text":"

A template for Chemical to Disease associations. This template is intended to represent associations between chemicals and diseases, and for evaluating Semantic Llama against BioCreative V Chemical Disease Relation (CDR) Task (BC5CDR).

URI: http://w3id.org/ontogpt/ctd

"},{"location":"ctd/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: drug:extracted_object

"},{"location":"ctd/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/extracted_object/#properties","title":"Properties","text":""},{"location":"ctd/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"ctd/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"ctd/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: drug:full_text

"},{"location":"ctd/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ctd/full_text/#properties","title":"Properties","text":""},{"location":"ctd/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/full_text/#schema-source","title":"Schema Source","text":""},{"location":"ctd/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ctd/id/","title":"Slot: id","text":"

URI: drug:id

"},{"location":"ctd/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Disease yes Chemical yes ChemicalToDiseasePredicate A predicate for chemical to disease relationships no NamedEntity no RelationshipType no Publication no"},{"location":"ctd/id/#properties","title":"Properties","text":""},{"location":"ctd/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"ctd/input_id/","title":"Slot: input_id","text":"

URI: drug:input_id

"},{"location":"ctd/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/input_id/#properties","title":"Properties","text":""},{"location":"ctd/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/input_id/#schema-source","title":"Schema Source","text":""},{"location":"ctd/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ctd/input_text/","title":"Slot: input_text","text":"

URI: drug:input_text

"},{"location":"ctd/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/input_text/#properties","title":"Properties","text":""},{"location":"ctd/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/input_text/#schema-source","title":"Schema Source","text":""},{"location":"ctd/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ctd/input_title/","title":"Slot: input_title","text":"

URI: drug:input_title

"},{"location":"ctd/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/input_title/#properties","title":"Properties","text":""},{"location":"ctd/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/input_title/#schema-source","title":"Schema Source","text":""},{"location":"ctd/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ctd/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"ctd/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Disease no Chemical no ChemicalToDiseasePredicate A predicate for chemical to disease relationships no NamedEntity no RelationshipType no"},{"location":"ctd/label/#properties","title":"Properties","text":""},{"location":"ctd/label/#aliases","title":"Aliases","text":""},{"location":"ctd/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"ctd/label/#schema-source","title":"Schema Source","text":""},{"location":"ctd/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/ctd\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"ctd/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: drug:named_entities

"},{"location":"ctd/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/named_entities/#properties","title":"Properties","text":""},{"location":"ctd/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"ctd/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ctd/object/","title":"Slot: object","text":"

URI: drug:object

"},{"location":"ctd/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/object/#properties","title":"Properties","text":""},{"location":"ctd/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/object/#schema-source","title":"Schema Source","text":""},{"location":"ctd/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ctd/object_id/","title":"Slot: object_id","text":"

URI: drug:object_id

"},{"location":"ctd/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ctd/object_id/#properties","title":"Properties","text":""},{"location":"ctd/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/object_id/#schema-source","title":"Schema Source","text":""},{"location":"ctd/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ctd/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: drug:object_qualifier

"},{"location":"ctd/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/object_qualifier/#properties","title":"Properties","text":""},{"location":"ctd/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ctd/object_text/","title":"Slot: object_text","text":"

URI: drug:object_text

"},{"location":"ctd/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ctd/object_text/#properties","title":"Properties","text":""},{"location":"ctd/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/object_text/#schema-source","title":"Schema Source","text":""},{"location":"ctd/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ctd/predicate/","title":"Slot: predicate","text":"

URI: drug:predicate

"},{"location":"ctd/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/predicate/#properties","title":"Properties","text":""},{"location":"ctd/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/predicate/#schema-source","title":"Schema Source","text":""},{"location":"ctd/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"ctd/prompt/","title":"Slot: prompt","text":"

URI: drug:prompt

"},{"location":"ctd/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/prompt/#properties","title":"Properties","text":""},{"location":"ctd/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/prompt/#schema-source","title":"Schema Source","text":""},{"location":"ctd/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ctd/publication/","title":"Slot: publication","text":"

URI: drug:publication

"},{"location":"ctd/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseDocument A document that contains chemical to disease relations no TextWithTriples no"},{"location":"ctd/publication/#properties","title":"Properties","text":""},{"location":"ctd/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"ctd/publication/#schema-source","title":"Schema Source","text":""},{"location":"ctd/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"ctd/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: drug:qualifier

"},{"location":"ctd/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/qualifier/#properties","title":"Properties","text":""},{"location":"ctd/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"ctd/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: drug:raw_completion_output

"},{"location":"ctd/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/raw_completion_output/#properties","title":"Properties","text":""},{"location":"ctd/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"ctd/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ctd/subject/","title":"Slot: subject","text":"

URI: drug:subject

"},{"location":"ctd/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/subject/#properties","title":"Properties","text":""},{"location":"ctd/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/subject/#schema-source","title":"Schema Source","text":""},{"location":"ctd/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ctd/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: drug:subject_qualifier

"},{"location":"ctd/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/subject_qualifier/#properties","title":"Properties","text":""},{"location":"ctd/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ctd/subject_text/","title":"Slot: subject_text","text":"

URI: drug:subject_text

"},{"location":"ctd/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ctd/subject_text/#properties","title":"Properties","text":""},{"location":"ctd/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"ctd/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ctd/title/","title":"Slot: title","text":"

The title of the publication

URI: drug:title

"},{"location":"ctd/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ctd/title/#properties","title":"Properties","text":""},{"location":"ctd/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/title/#schema-source","title":"Schema Source","text":""},{"location":"ctd/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ctd/triples/","title":"Slot: triples","text":"

URI: drug:triples

"},{"location":"ctd/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseDocument A document that contains chemical to disease relations yes TextWithTriples no"},{"location":"ctd/triples/#properties","title":"Properties","text":""},{"location":"ctd/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/triples/#schema-source","title":"Schema Source","text":""},{"location":"ctd/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/","title":"Diagnostic Procedure Template","text":"

A template for clinical diagnostic procedures and the phenotypes they may contribute to.

URI: http://w3id.org/ontogpt/diagnostic_procedure

Name: diagnostic_procedure

"},{"location":"diagnostic_procedure/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nDiagnosticProceduretoPhenotypeAssociation {\n    string qualifier  \n}\nDiagnosticProceduretoAttributeAssociation {\n    string qualifier  \n}\nDiagnosticProcedure {\n    string id  \n    string label  \n}\nPhenotype {\n    string id  \n    string label  \n}\nClinicalAttribute {\n    string id  \n    string label  \n}\nQuality {\n    string id  \n    string label  \n}\nProcedureToPhenotypePredicate {\n    string id  \n    string label  \n}\nProcedureToAttributePredicate {\n    string id  \n    string label  \n}\nUnit {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nDiagnosticProceduretoPhenotypeAssociation ||--|o DiagnosticProcedure : \"subject\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o ProcedureToPhenotypePredicate : \"predicate\"\nDiagnosticProceduretoPhenotypeAssociation ||--}o Phenotype : \"object\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o NamedEntity : \"subject_qualifier\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o NamedEntity : \"object_qualifier\"\nDiagnosticProceduretoAttributeAssociation ||--|o DiagnosticProcedure : \"subject\"\nDiagnosticProceduretoAttributeAssociation ||--|o ProcedureToAttributePredicate : \"predicate\"\nDiagnosticProceduretoAttributeAssociation ||--}o ClinicalAttribute : \"object\"\nDiagnosticProceduretoAttributeAssociation ||--|o NamedEntity : \"subject_qualifier\"\nDiagnosticProceduretoAttributeAssociation ||--|o Quality : \"object_qualifier\"\nClinicalAttribute ||--|o Unit : \"unit\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"diagnostic_procedure/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\"). DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\". ExtractionResult A result of extracting knowledge on text NamedEntity None ClinicalAttribute None DiagnosticProcedure None Phenotype None Quality None RelationshipType None ProcedureToAttributePredicate A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\". ProcedureToPhenotypePredicate A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\". Unit None Publication None TextWithTriples None"},{"location":"diagnostic_procedure/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples unit the unit used to measure the attribute"},{"location":"diagnostic_procedure/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"diagnostic_procedure/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"diagnostic_procedure/#subsets","title":"Subsets","text":"Subset Description"},{"location":"diagnostic_procedure/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: diag:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"diagnostic_procedure/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:AnnotatorResult native diag:AnnotatorResult"},{"location":"diagnostic_procedure/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n\n
"},{"location":"diagnostic_procedure/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"diagnostic_procedure/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"diagnostic_procedure/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"diagnostic_procedure/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"diagnostic_procedure/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Any/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native diag:Any"},{"location":"diagnostic_procedure/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nclass_uri: linkml:Any\n\n
"},{"location":"diagnostic_procedure/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nclass_uri: linkml:Any\n\n
"},{"location":"diagnostic_procedure/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"diagnostic_procedure/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ClinicalAttribute/","title":"Class: ClinicalAttribute","text":"

URI: diag:ClinicalAttribute

erDiagram\nClinicalAttribute {\n    string id  \n    string label  \n}\nUnit {\n    string id  \n    string label  \n}\n\nClinicalAttribute ||--|o Unit : \"unit\"\n\n
"},{"location":"diagnostic_procedure/ClinicalAttribute/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/ClinicalAttribute/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance unit 0..1 Unit the unit used to measure the attribute direct id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/ClinicalAttribute/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoAttributeAssociation object range ClinicalAttribute"},{"location":"diagnostic_procedure/ClinicalAttribute/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/ClinicalAttribute/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/ClinicalAttribute/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:oba, sqlite:obo:ncit"},{"location":"diagnostic_procedure/ClinicalAttribute/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ClinicalAttribute/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:ClinicalAttribute native diag:ClinicalAttribute"},{"location":"diagnostic_procedure/ClinicalAttribute/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/ClinicalAttribute/#direct","title":"Direct","text":"
name: ClinicalAttribute\nid_prefixes:\n- OBA\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:oba, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  unit:\n    name: unit\n    description: the unit used to measure the attribute\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: Unit\n\n
"},{"location":"diagnostic_procedure/ClinicalAttribute/#induced","title":"Induced","text":"
name: ClinicalAttribute\nid_prefixes:\n- OBA\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:oba, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  unit:\n    name: unit\n    description: the unit used to measure the attribute\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: unit\n    owner: ClinicalAttribute\n    domain_of:\n    - ClinicalAttribute\n    range: Unit\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ClinicalAttribute\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ClinicalAttribute\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: diag:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"diagnostic_procedure/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"diagnostic_procedure/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:CompoundExpression native diag:CompoundExpression"},{"location":"diagnostic_procedure/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nabstract: true\n\n
"},{"location":"diagnostic_procedure/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nabstract: true\n\n
"},{"location":"diagnostic_procedure/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"diagnostic_procedure/Curie/#comments","title":"Comments","text":""},{"location":"diagnostic_procedure/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Curie/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"diagnostic_procedure/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Date/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"diagnostic_procedure/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"diagnostic_procedure/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"diagnostic_procedure/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/DiagnosticProcedure/","title":"Class: DiagnosticProcedure","text":"

URI: diag:DiagnosticProcedure

erDiagram\nDiagnosticProcedure {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/DiagnosticProcedure/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/DiagnosticProcedure/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/DiagnosticProcedure/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoPhenotypeAssociation subject range DiagnosticProcedure DiagnosticProceduretoAttributeAssociation subject range DiagnosticProcedure"},{"location":"diagnostic_procedure/DiagnosticProcedure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/DiagnosticProcedure/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/DiagnosticProcedure/#annotations","title":"Annotations","text":"property value annotators bioportal:loinc, sqlite:obo:ncit"},{"location":"diagnostic_procedure/DiagnosticProcedure/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/DiagnosticProcedure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:DiagnosticProcedure native diag:DiagnosticProcedure"},{"location":"diagnostic_procedure/DiagnosticProcedure/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/DiagnosticProcedure/#direct","title":"Direct","text":"
name: DiagnosticProcedure\nid_prefixes:\n- LOINC\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:loinc, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\n\n
"},{"location":"diagnostic_procedure/DiagnosticProcedure/#induced","title":"Induced","text":"
name: DiagnosticProcedure\nid_prefixes:\n- LOINC\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:loinc, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DiagnosticProcedure\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: DiagnosticProcedure\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/","title":"Class: DiagnosticProceduretoAttributeAssociation","text":"

A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").

URI: diag:DiagnosticProceduretoAttributeAssociation

erDiagram\nDiagnosticProceduretoAttributeAssociation {\n    string qualifier  \n}\nQuality {\n    string id  \n    string label  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nClinicalAttribute {\n    string id  \n    string label  \n}\nUnit {\n    string id  \n    string label  \n}\nProcedureToAttributePredicate {\n    string id  \n    string label  \n}\nDiagnosticProcedure {\n    string id  \n    string label  \n}\n\nDiagnosticProceduretoAttributeAssociation ||--|o DiagnosticProcedure : \"subject\"\nDiagnosticProceduretoAttributeAssociation ||--|o ProcedureToAttributePredicate : \"predicate\"\nDiagnosticProceduretoAttributeAssociation ||--}o ClinicalAttribute : \"object\"\nDiagnosticProceduretoAttributeAssociation ||--|o NamedEntity : \"subject_qualifier\"\nDiagnosticProceduretoAttributeAssociation ||--|o Quality : \"object_qualifier\"\nClinicalAttribute ||--|o Unit : \"unit\"\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 DiagnosticProcedure A diagnostic procedure yielding a result, which in turn may be interpreted as... Triple predicate 0..1 ProcedureToAttributePredicate The relationship type, e Triple object 0..* ClinicalAttribute Any measurable clinical attribute Triple qualifier 0..1 String A qualifier for the statements, e Triple subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the procedure Triple object_qualifier 0..1 Quality An optional qualifier or modifier for the phenotype Triple"},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:DiagnosticProceduretoAttributeAssociation native diag:DiagnosticProceduretoAttributeAssociation"},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#direct","title":"Direct","text":"
name: DiagnosticProceduretoAttributeAssociation\ndescription: A triple representing a relationship between a diagnostic procedure and\n  a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood\n  pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  object:\n    name: object\n    description: Any measurable clinical attribute.\n    multivalued: true\n    domain_of:\n    - Triple\n    range: ClinicalAttribute\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    domain_of:\n    - Triple\n    range: ProcedureToAttributePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    domain_of:\n    - Triple\n    range: Quality\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#induced","title":"Induced","text":"
name: DiagnosticProceduretoAttributeAssociation\ndescription: A triple representing a relationship between a diagnostic procedure and\n  a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood\n  pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  object:\n    name: object\n    description: Any measurable clinical attribute.\n    multivalued: true\n    domain_of:\n    - Triple\n    range: ClinicalAttribute\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    domain_of:\n    - Triple\n    range: ProcedureToAttributePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    domain_of:\n    - Triple\n    range: Quality\nattributes:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: predicate\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: ProcedureToAttributePredicate\n  object:\n    name: object\n    description: Any measurable clinical attribute.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    alias: object\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: ClinicalAttribute\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: qualifier\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject_qualifier\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object_qualifier\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: Quality\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/","title":"Class: DiagnosticProceduretoPhenotypeAssociation","text":"

A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\".

URI: diag:DiagnosticProceduretoPhenotypeAssociation

erDiagram\nDiagnosticProceduretoPhenotypeAssociation {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nPhenotype {\n    string id  \n    string label  \n}\nProcedureToPhenotypePredicate {\n    string id  \n    string label  \n}\nDiagnosticProcedure {\n    string id  \n    string label  \n}\n\nDiagnosticProceduretoPhenotypeAssociation ||--|o DiagnosticProcedure : \"subject\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o ProcedureToPhenotypePredicate : \"predicate\"\nDiagnosticProceduretoPhenotypeAssociation ||--}o Phenotype : \"object\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o NamedEntity : \"subject_qualifier\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 DiagnosticProcedure A diagnostic procedure yielding a result, which in turn may be interpreted as... Triple predicate 0..1 ProcedureToPhenotypePredicate The relationship type, e Triple object 0..* Phenotype The observable physical or biochemical characteristics of a patient Triple qualifier 0..1 String A qualifier for the statements, e Triple subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the procedure Triple object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the phenotype Triple"},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:DiagnosticProceduretoPhenotypeAssociation native diag:DiagnosticProceduretoPhenotypeAssociation"},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#direct","title":"Direct","text":"
name: DiagnosticProceduretoPhenotypeAssociation\ndescription: A triple representing a relationship between a diagnostic procedure and\n  an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high\n  blood pressure\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  object:\n    name: object\n    description: The observable physical or biochemical characteristics of a patient.\n      Not equivalent to a disease state, but may contribute to a diagnosis.\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Phenotype\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    domain_of:\n    - Triple\n    range: ProcedureToPhenotypePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#induced","title":"Induced","text":"
name: DiagnosticProceduretoPhenotypeAssociation\ndescription: A triple representing a relationship between a diagnostic procedure and\n  an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high\n  blood pressure\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  object:\n    name: object\n    description: The observable physical or biochemical characteristics of a patient.\n      Not equivalent to a disease state, but may contribute to a diagnosis.\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Phenotype\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    domain_of:\n    - Triple\n    range: ProcedureToPhenotypePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    domain_of:\n    - Triple\n    range: NamedEntity\nattributes:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: predicate\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: ProcedureToPhenotypePredicate\n  object:\n    name: object\n    description: The observable physical or biochemical characteristics of a patient.\n      Not equivalent to a disease state, but may contribute to a diagnosis.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    alias: object\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: Phenotype\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: qualifier\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject_qualifier\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object_qualifier\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"diagnostic_procedure/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Double/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: diag:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"diagnostic_procedure/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"diagnostic_procedure/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:ExtractionResult native diag:ExtractionResult"},{"location":"diagnostic_procedure/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"diagnostic_procedure/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Float/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"diagnostic_procedure/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Integer/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/NamedEntity/","title":"Class: NamedEntity","text":"

URI: diag:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"diagnostic_procedure/NamedEntity/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoPhenotypeAssociation subject_qualifier range NamedEntity DiagnosticProceduretoPhenotypeAssociation object_qualifier range NamedEntity DiagnosticProceduretoAttributeAssociation subject_qualifier range NamedEntity Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"diagnostic_procedure/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:NamedEntity native diag:NamedEntity"},{"location":"diagnostic_procedure/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"diagnostic_procedure/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"diagnostic_procedure/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"diagnostic_procedure/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"diagnostic_procedure/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"diagnostic_procedure/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"diagnostic_procedure/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"diagnostic_procedure/Objectidentifier/#comments","title":"Comments","text":""},{"location":"diagnostic_procedure/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Phenotype/","title":"Class: Phenotype","text":"

URI: diag:Phenotype

erDiagram\nPhenotype {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/Phenotype/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/Phenotype/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/Phenotype/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoPhenotypeAssociation object range Phenotype"},{"location":"diagnostic_procedure/Phenotype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Phenotype/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/Phenotype/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp"},{"location":"diagnostic_procedure/Phenotype/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Phenotype/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:Phenotype native diag:Phenotype"},{"location":"diagnostic_procedure/Phenotype/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Phenotype/#direct","title":"Direct","text":"
name: Phenotype\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Phenotype/#induced","title":"Induced","text":"
name: Phenotype\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Phenotype\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Phenotype\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/","title":"Class: ProcedureToAttributePredicate","text":"

A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\".

URI: diag:ProcedureToAttributePredicate

erDiagram\nProcedureToAttributePredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoAttributeAssociation predicate range ProcedureToAttributePredicate"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:ProcedureToAttributePredicate native diag:ProcedureToAttributePredicate"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#direct","title":"Direct","text":"
name: ProcedureToAttributePredicate\ndescription: A predicate for procedure to attribute relationships, defining \"this\n  procedure is a measurement of this attribute\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: RelationshipType\n\n
"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#induced","title":"Induced","text":"
name: ProcedureToAttributePredicate\ndescription: A predicate for procedure to attribute relationships, defining \"this\n  procedure is a measurement of this attribute\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: RelationshipType\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ProcedureToAttributePredicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ProcedureToAttributePredicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/","title":"Class: ProcedureToPhenotypePredicate","text":"

A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\".

URI: diag:ProcedureToPhenotypePredicate

erDiagram\nProcedureToPhenotypePredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoPhenotypeAssociation predicate range ProcedureToPhenotypePredicate"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:ProcedureToPhenotypePredicate native diag:ProcedureToPhenotypePredicate"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#direct","title":"Direct","text":"
name: ProcedureToPhenotypePredicate\ndescription: A predicate for procedure to phenotype relationships, defining \"this\n  procedure is intended to provide support for/against this phenotype\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: RelationshipType\n\n
"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#induced","title":"Induced","text":"
name: ProcedureToPhenotypePredicate\ndescription: A predicate for procedure to phenotype relationships, defining \"this\n  procedure is intended to provide support for/against this phenotype\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: RelationshipType\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ProcedureToPhenotypePredicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ProcedureToPhenotypePredicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/Publication/","title":"Class: Publication","text":"

URI: diag:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"diagnostic_procedure/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"diagnostic_procedure/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Publication/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:Publication native diag:Publication"},{"location":"diagnostic_procedure/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n\n
"},{"location":"diagnostic_procedure/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"diagnostic_procedure/Quality/","title":"Class: Quality","text":"

URI: diag:Quality

erDiagram\nQuality {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/Quality/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/Quality/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/Quality/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoAttributeAssociation object_qualifier range Quality"},{"location":"diagnostic_procedure/Quality/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Quality/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/Quality/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:pato"},{"location":"diagnostic_procedure/Quality/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Quality/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:Quality native diag:Quality"},{"location":"diagnostic_procedure/Quality/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Quality/#direct","title":"Direct","text":"
name: Quality\nid_prefixes:\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:pato\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Quality/#induced","title":"Induced","text":"
name: Quality\nid_prefixes:\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:pato\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Quality\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Quality\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/RelationshipType/","title":"Class: RelationshipType","text":"

URI: diag:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"diagnostic_procedure/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:RelationshipType native diag:RelationshipType"},{"location":"diagnostic_procedure/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\n\n
"},{"location":"diagnostic_procedure/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"diagnostic_procedure/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/String/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: diag:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"diagnostic_procedure/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"diagnostic_procedure/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:TextWithTriples native diag:TextWithTriples"},{"location":"diagnostic_procedure/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"diagnostic_procedure/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Time/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: diag:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"diagnostic_procedure/Triple/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"diagnostic_procedure/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"diagnostic_procedure/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Triple/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:Triple native diag:Triple"},{"location":"diagnostic_procedure/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Unit/","title":"Class: Unit","text":"

URI: diag:Unit

erDiagram\nUnit {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/Unit/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/Unit/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/Unit/#usages","title":"Usages","text":"used by used in type used ClinicalAttribute unit range Unit"},{"location":"diagnostic_procedure/Unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Unit/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/Unit/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uo"},{"location":"diagnostic_procedure/Unit/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Unit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:Unit native diag:Unit"},{"location":"diagnostic_procedure/Unit/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Unit/#direct","title":"Direct","text":"
name: Unit\nid_prefixes:\n- UO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Unit/#induced","title":"Induced","text":"
name: Unit\nid_prefixes:\n- UO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"diagnostic_procedure/Uri/#comments","title":"Comments","text":""},{"location":"diagnostic_procedure/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Uri/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"diagnostic_procedure/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: diag:abstract

"},{"location":"diagnostic_procedure/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"diagnostic_procedure/abstract/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/abstract/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"diagnostic_procedure/combined_text/","title":"Slot: combined_text","text":"

URI: diag:combined_text

"},{"location":"diagnostic_procedure/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"diagnostic_procedure/combined_text/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"diagnostic_procedure/diagnostic_procedure/","title":"diagnostic_procedure","text":"

A template for clinical diagnostic procedures and the phenotypes they may contribute to.

URI: http://w3id.org/ontogpt/diagnostic_procedure

"},{"location":"diagnostic_procedure/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: diag:extracted_object

"},{"location":"diagnostic_procedure/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/extracted_object/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"diagnostic_procedure/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: diag:full_text

"},{"location":"diagnostic_procedure/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"diagnostic_procedure/full_text/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/full_text/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"diagnostic_procedure/id/","title":"Slot: id","text":"

URI: diag:id

"},{"location":"diagnostic_procedure/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProcedure no Phenotype no ClinicalAttribute no Quality no ProcedureToPhenotypePredicate A predicate for procedure to phenotype relationships, defining \"this procedur... no ProcedureToAttributePredicate A predicate for procedure to attribute relationships, defining \"this procedur... no Unit no NamedEntity no RelationshipType no Publication no"},{"location":"diagnostic_procedure/id/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"diagnostic_procedure/input_id/","title":"Slot: input_id","text":"

URI: diag:input_id

"},{"location":"diagnostic_procedure/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/input_id/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/input_id/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/input_text/","title":"Slot: input_text","text":"

URI: diag:input_text

"},{"location":"diagnostic_procedure/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/input_text/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/input_text/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/input_title/","title":"Slot: input_title","text":"

URI: diag:input_title

"},{"location":"diagnostic_procedure/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/input_title/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/input_title/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"diagnostic_procedure/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProcedure no Phenotype no ClinicalAttribute no Quality no ProcedureToPhenotypePredicate A predicate for procedure to phenotype relationships, defining \"this procedur... no ProcedureToAttributePredicate A predicate for procedure to attribute relationships, defining \"this procedur... no Unit no NamedEntity no RelationshipType no"},{"location":"diagnostic_procedure/label/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/label/#aliases","title":"Aliases","text":""},{"location":"diagnostic_procedure/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"diagnostic_procedure/label/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"diagnostic_procedure/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: diag:named_entities

"},{"location":"diagnostic_procedure/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/named_entities/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/object/","title":"Slot: object","text":"

URI: diag:object

"},{"location":"diagnostic_procedure/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... yes DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/object/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/object/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"diagnostic_procedure/object_id/","title":"Slot: object_id","text":"

URI: diag:object_id

"},{"location":"diagnostic_procedure/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"diagnostic_procedure/object_id/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/object_id/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: diag:object_qualifier

"},{"location":"diagnostic_procedure/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... yes DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/object_qualifier/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"diagnostic_procedure/object_text/","title":"Slot: object_text","text":"

URI: diag:object_text

"},{"location":"diagnostic_procedure/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"diagnostic_procedure/object_text/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/object_text/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/predicate/","title":"Slot: predicate","text":"

URI: diag:predicate

"},{"location":"diagnostic_procedure/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... yes DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/predicate/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/predicate/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"diagnostic_procedure/prompt/","title":"Slot: prompt","text":"

URI: diag:prompt

"},{"location":"diagnostic_procedure/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/prompt/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/prompt/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/publication/","title":"Slot: publication","text":"

URI: diag:publication

"},{"location":"diagnostic_procedure/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"diagnostic_procedure/publication/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"diagnostic_procedure/publication/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"diagnostic_procedure/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: diag:qualifier

"},{"location":"diagnostic_procedure/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... no DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... no Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/qualifier/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"diagnostic_procedure/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: diag:raw_completion_output

"},{"location":"diagnostic_procedure/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/raw_completion_output/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/subject/","title":"Slot: subject","text":"

URI: diag:subject

"},{"location":"diagnostic_procedure/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... yes DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/subject/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/subject/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"diagnostic_procedure/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: diag:subject_qualifier

"},{"location":"diagnostic_procedure/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... yes DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/subject_qualifier/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"diagnostic_procedure/subject_text/","title":"Slot: subject_text","text":"

URI: diag:subject_text

"},{"location":"diagnostic_procedure/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"diagnostic_procedure/subject_text/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/title/","title":"Slot: title","text":"

The title of the publication

URI: diag:title

"},{"location":"diagnostic_procedure/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"diagnostic_procedure/title/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/title/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"diagnostic_procedure/triples/","title":"Slot: triples","text":"

URI: diag:triples

"},{"location":"diagnostic_procedure/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"diagnostic_procedure/triples/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/triples/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/unit/","title":"Slot: unit","text":"

the unit used to measure the attribute

URI: diag:unit

"},{"location":"diagnostic_procedure/unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClinicalAttribute no"},{"location":"diagnostic_procedure/unit/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/unit/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/unit/#linkml-source","title":"LinkML Source","text":"
name: unit\ndescription: the unit used to measure the attribute\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: unit\nowner: ClinicalAttribute\ndomain_of:\n- ClinicalAttribute\nrange: Unit\n\n
"},{"location":"drug/","title":"Drug Template","text":"

A template for Drugs and drug mechanism

URI: http://w3id.org/ontogpt/drug

Name: drug

"},{"location":"drug/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nDrugMechanism {\n    stringList references  \n    string source_text  \n}\nMechanismLink {\n\n}\nMechanismElement {\n    string id  \n    string label  \n}\nPredicate {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nDrugMechanism ||--|o Disease : \"disease\"\nDrugMechanism ||--|o Drug : \"drug\"\nDrugMechanism ||--}o MechanismLink : \"mechanism_links\"\nMechanismLink ||--|o MechanismElement : \"subject\"\nMechanismLink ||--|o Predicate : \"predicate\"\nMechanismLink ||--|o MechanismElement : \"object\"\n\n
"},{"location":"drug/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None MechanismLink None Triple Abstract parent for Relation Extraction tasks DrugMechanism None ExtractionResult A result of extracting knowledge on text NamedEntity None Disease None Drug None MechanismElement None Predicate None RelationshipType None Publication None TextWithTriples None"},{"location":"drug/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text disease the name of the disease that is treated drug the name of the drug that treats the disease extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing mechanism_links semicolon-separated list of links, where each link is a triple connecting two... named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output references source_text subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"drug/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"drug/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"drug/#subsets","title":"Subsets","text":"Subset Description"},{"location":"drug/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: drug:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"drug/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"drug/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"drug/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:AnnotatorResult native drug:AnnotatorResult"},{"location":"drug/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n\n
"},{"location":"drug/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"drug/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"drug/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"drug/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"drug/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Any/#schema-source","title":"Schema Source","text":""},{"location":"drug/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native drug:Any"},{"location":"drug/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/drug\nclass_uri: linkml:Any\n\n
"},{"location":"drug/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/drug\nclass_uri: linkml:Any\n\n
"},{"location":"drug/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"drug/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"drug/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: drug:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"drug/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"drug/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"drug/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"drug/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:CompoundExpression native drug:CompoundExpression"},{"location":"drug/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/drug\nabstract: true\n\n
"},{"location":"drug/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/drug\nabstract: true\n\n
"},{"location":"drug/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"drug/Curie/#comments","title":"Comments","text":""},{"location":"drug/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Curie/#schema-source","title":"Schema Source","text":""},{"location":"drug/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"drug/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Date/#schema-source","title":"Schema Source","text":""},{"location":"drug/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"drug/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"drug/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"drug/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"drug/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"drug/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"drug/Disease/","title":"Class: Disease","text":"

URI: drug:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/Disease/#inheritance","title":"Inheritance","text":""},{"location":"drug/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"drug/Disease/#usages","title":"Usages","text":"used by used in type used DrugMechanism disease range Disease"},{"location":"drug/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mesh, sqlite:obo:mondo"},{"location":"drug/Disease/#schema-source","title":"Schema Source","text":""},{"location":"drug/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Disease native drug:Disease"},{"location":"drug/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Disease/#direct","title":"Direct","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mesh, sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\n\n
"},{"location":"drug/Disease/#induced","title":"Induced","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mesh, sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"drug/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Double/#schema-source","title":"Schema Source","text":""},{"location":"drug/Drug/","title":"Class: Drug","text":"

URI: drug:Drug

erDiagram\nDrug {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/Drug/#inheritance","title":"Inheritance","text":""},{"location":"drug/Drug/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"drug/Drug/#usages","title":"Usages","text":"used by used in type used DrugMechanism drug range Drug"},{"location":"drug/Drug/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Drug/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh"},{"location":"drug/Drug/#schema-source","title":"Schema Source","text":""},{"location":"drug/Drug/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Drug native drug:Drug"},{"location":"drug/Drug/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Drug/#direct","title":"Direct","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\n\n
"},{"location":"drug/Drug/#induced","title":"Induced","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/DrugMechanism/","title":"Class: DrugMechanism","text":"

URI: drug:DrugMechanism

erDiagram\nDrugMechanism {\n    stringList references  \n    string source_text  \n}\nMechanismLink {\n\n}\nMechanismElement {\n    string id  \n    string label  \n}\nPredicate {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nDrugMechanism ||--|o Disease : \"disease\"\nDrugMechanism ||--|o Drug : \"drug\"\nDrugMechanism ||--}o MechanismLink : \"mechanism_links\"\nMechanismLink ||--|o MechanismElement : \"subject\"\nMechanismLink ||--|o Predicate : \"predicate\"\nMechanismLink ||--|o MechanismElement : \"object\"\n\n
"},{"location":"drug/DrugMechanism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance disease 0..1 Disease the name of the disease that is treated direct drug 0..1 Drug the name of the drug that treats the disease direct mechanism_links 0..* MechanismLink semicolon-separated list of links, where each link is a triple connecting two... direct references 0..* String direct source_text 0..1 String direct"},{"location":"drug/DrugMechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/DrugMechanism/#schema-source","title":"Schema Source","text":""},{"location":"drug/DrugMechanism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:DrugMechanism native drug:DrugMechanism"},{"location":"drug/DrugMechanism/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/DrugMechanism/#direct","title":"Direct","text":"
name: DrugMechanism\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  disease:\n    name: disease\n    description: the name of the disease that is treated\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: Disease\n  drug:\n    name: drug\n    description: the name of the drug that treats the disease\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: Drug\n  mechanism_links:\n    name: mechanism_links\n    description: semicolon-separated list of links, where each link is a triple connecting\n      two entities via a relationship type\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    range: MechanismLink\n  references:\n    name: references\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    range: string\n  source_text:\n    name: source_text\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: string\ntree_root: true\n\n
"},{"location":"drug/DrugMechanism/#induced","title":"Induced","text":"
name: DrugMechanism\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  disease:\n    name: disease\n    description: the name of the disease that is treated\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: disease\n    owner: DrugMechanism\n    domain_of:\n    - DrugMechanism\n    range: Disease\n  drug:\n    name: drug\n    description: the name of the drug that treats the disease\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: drug\n    owner: DrugMechanism\n    domain_of:\n    - DrugMechanism\n    range: Drug\n  mechanism_links:\n    name: mechanism_links\n    description: semicolon-separated list of links, where each link is a triple connecting\n      two entities via a relationship type\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    alias: mechanism_links\n    owner: DrugMechanism\n    domain_of:\n    - DrugMechanism\n    range: MechanismLink\n  references:\n    name: references\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    alias: references\n    owner: DrugMechanism\n    domain_of:\n    - DrugMechanism\n    range: string\n  source_text:\n    name: source_text\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: source_text\n    owner: DrugMechanism\n    domain_of:\n    - DrugMechanism\n    range: string\ntree_root: true\n\n
"},{"location":"drug/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: drug:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"drug/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"drug/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"drug/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:ExtractionResult native drug:ExtractionResult"},{"location":"drug/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"drug/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"drug/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"drug/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Float/#schema-source","title":"Schema Source","text":""},{"location":"drug/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"drug/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Integer/#schema-source","title":"Schema Source","text":""},{"location":"drug/MechanismElement/","title":"Class: MechanismElement","text":"

URI: drug:MechanismElement

erDiagram\nMechanismElement {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/MechanismElement/#inheritance","title":"Inheritance","text":""},{"location":"drug/MechanismElement/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"drug/MechanismElement/#usages","title":"Usages","text":"used by used in type used MechanismLink subject range MechanismElement MechanismLink object range MechanismElement"},{"location":"drug/MechanismElement/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/MechanismElement/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"drug/MechanismElement/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon, sqlite:obo:cl"},{"location":"drug/MechanismElement/#schema-source","title":"Schema Source","text":""},{"location":"drug/MechanismElement/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:MechanismElement native drug:MechanismElement"},{"location":"drug/MechanismElement/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/MechanismElement/#direct","title":"Direct","text":"
name: MechanismElement\nid_prefixes:\n- HGNC\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon,\n      sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\n\n
"},{"location":"drug/MechanismElement/#induced","title":"Induced","text":"
name: MechanismElement\nid_prefixes:\n- HGNC\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon,\n      sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MechanismElement\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: MechanismElement\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/MechanismLink/","title":"Class: MechanismLink","text":"

URI: drug:MechanismLink

erDiagram\nMechanismLink {\n\n}\nMechanismElement {\n    string id  \n    string label  \n}\nPredicate {\n    string id  \n    string label  \n}\n\nMechanismLink ||--|o MechanismElement : \"subject\"\nMechanismLink ||--|o Predicate : \"predicate\"\nMechanismLink ||--|o MechanismElement : \"object\"\n\n
"},{"location":"drug/MechanismLink/#inheritance","title":"Inheritance","text":""},{"location":"drug/MechanismLink/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 MechanismElement direct predicate 0..1 Predicate direct object 0..1 MechanismElement direct"},{"location":"drug/MechanismLink/#usages","title":"Usages","text":"used by used in type used DrugMechanism mechanism_links range MechanismLink"},{"location":"drug/MechanismLink/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/MechanismLink/#schema-source","title":"Schema Source","text":""},{"location":"drug/MechanismLink/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:MechanismLink native drug:MechanismLink"},{"location":"drug/MechanismLink/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/MechanismLink/#direct","title":"Direct","text":"
name: MechanismLink\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: MechanismElement\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: Predicate\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: MechanismElement\n\n
"},{"location":"drug/MechanismLink/#induced","title":"Induced","text":"
name: MechanismLink\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: subject\n    owner: MechanismLink\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: MechanismElement\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: predicate\n    owner: MechanismLink\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: Predicate\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: object\n    owner: MechanismLink\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: MechanismElement\n\n
"},{"location":"drug/NamedEntity/","title":"Class: NamedEntity","text":"

URI: drug:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"drug/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"drug/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"drug/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"drug/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:NamedEntity native drug:NamedEntity"},{"location":"drug/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/drug\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"drug/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/drug\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"drug/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"drug/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"drug/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"drug/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"drug/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"drug/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"drug/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"drug/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"drug/Objectidentifier/#comments","title":"Comments","text":""},{"location":"drug/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"drug/Predicate/","title":"Class: Predicate","text":"

URI: drug:Predicate

erDiagram\nPredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/Predicate/#inheritance","title":"Inheritance","text":""},{"location":"drug/Predicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"drug/Predicate/#usages","title":"Usages","text":"used by used in type used MechanismLink predicate range Predicate"},{"location":"drug/Predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Predicate/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:biolink, sqlite:obo:ro"},{"location":"drug/Predicate/#schema-source","title":"Schema Source","text":""},{"location":"drug/Predicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Predicate native drug:Predicate"},{"location":"drug/Predicate/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Predicate/#direct","title":"Direct","text":"
name: Predicate\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:biolink, sqlite:obo:ro\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\n\n
"},{"location":"drug/Predicate/#induced","title":"Induced","text":"
name: Predicate\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:biolink, sqlite:obo:ro\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Predicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Predicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/Publication/","title":"Class: Publication","text":"

URI: drug:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"drug/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"drug/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"drug/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Publication/#schema-source","title":"Schema Source","text":""},{"location":"drug/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Publication native drug:Publication"},{"location":"drug/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/drug\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n\n
"},{"location":"drug/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/drug\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"drug/RelationshipType/","title":"Class: RelationshipType","text":"

URI: drug:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"drug/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"drug/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"drug/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"drug/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"drug/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:RelationshipType native drug:RelationshipType"},{"location":"drug/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\n\n
"},{"location":"drug/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"drug/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/String/#schema-source","title":"Schema Source","text":""},{"location":"drug/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: drug:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"drug/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"drug/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"drug/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:TextWithTriples native drug:TextWithTriples"},{"location":"drug/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"drug/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"drug/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"drug/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Time/#schema-source","title":"Schema Source","text":""},{"location":"drug/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: drug:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"drug/Triple/#inheritance","title":"Inheritance","text":""},{"location":"drug/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"drug/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"drug/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Triple/#schema-source","title":"Schema Source","text":""},{"location":"drug/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Triple native drug:Triple"},{"location":"drug/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/drug\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/drug\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/drug\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"drug/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/drug\n    alias: subject\n    owner: Triple\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/drug\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/drug\n    alias: object\n    owner: Triple\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"drug/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"drug/Uri/#comments","title":"Comments","text":""},{"location":"drug/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Uri/#schema-source","title":"Schema Source","text":""},{"location":"drug/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"drug/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"drug/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: drug:abstract

"},{"location":"drug/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"drug/abstract/#properties","title":"Properties","text":""},{"location":"drug/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/abstract/#schema-source","title":"Schema Source","text":""},{"location":"drug/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"drug/combined_text/","title":"Slot: combined_text","text":"

URI: drug:combined_text

"},{"location":"drug/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"drug/combined_text/#properties","title":"Properties","text":""},{"location":"drug/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"drug/disease/","title":"Slot: disease","text":"

the name of the disease that is treated

URI: drug:disease

"},{"location":"drug/disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DrugMechanism no"},{"location":"drug/disease/#properties","title":"Properties","text":""},{"location":"drug/disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/disease/#schema-source","title":"Schema Source","text":""},{"location":"drug/disease/#linkml-source","title":"LinkML Source","text":"
name: disease\ndescription: the name of the disease that is treated\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: disease\nowner: DrugMechanism\ndomain_of:\n- DrugMechanism\nrange: Disease\n\n
"},{"location":"drug/drug/","title":"Slot: drug","text":"

the name of the drug that treats the disease

URI: drug:drug

"},{"location":"drug/drug/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DrugMechanism no"},{"location":"drug/drug/#properties","title":"Properties","text":""},{"location":"drug/drug/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/drug/#schema-source","title":"Schema Source","text":""},{"location":"drug/drug/#linkml-source","title":"LinkML Source","text":"
name: drug\ndescription: the name of the drug that treats the disease\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: drug\nowner: DrugMechanism\ndomain_of:\n- DrugMechanism\nrange: Drug\n\n
"},{"location":"drug/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: drug:extracted_object

"},{"location":"drug/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/extracted_object/#properties","title":"Properties","text":""},{"location":"drug/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"drug/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"drug/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: drug:full_text

"},{"location":"drug/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"drug/full_text/#properties","title":"Properties","text":""},{"location":"drug/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/full_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"drug/id/","title":"Slot: id","text":"

URI: drug:id

"},{"location":"drug/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MechanismElement no Disease no Drug no Predicate no NamedEntity no RelationshipType no Publication no"},{"location":"drug/id/#properties","title":"Properties","text":""},{"location":"drug/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"drug/input_id/","title":"Slot: input_id","text":"

URI: drug:input_id

"},{"location":"drug/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/input_id/#properties","title":"Properties","text":""},{"location":"drug/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/input_id/#schema-source","title":"Schema Source","text":""},{"location":"drug/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"drug/input_text/","title":"Slot: input_text","text":"

URI: drug:input_text

"},{"location":"drug/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/input_text/#properties","title":"Properties","text":""},{"location":"drug/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/input_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"drug/input_title/","title":"Slot: input_title","text":"

URI: drug:input_title

"},{"location":"drug/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/input_title/#properties","title":"Properties","text":""},{"location":"drug/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/input_title/#schema-source","title":"Schema Source","text":""},{"location":"drug/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"drug/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"drug/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MechanismElement no Disease no Drug no Predicate no NamedEntity no RelationshipType no"},{"location":"drug/label/#properties","title":"Properties","text":""},{"location":"drug/label/#aliases","title":"Aliases","text":""},{"location":"drug/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"drug/label/#schema-source","title":"Schema Source","text":""},{"location":"drug/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/drug\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"drug/mechanism_links/","title":"Slot: mechanism_links","text":"

semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type

URI: drug:mechanism_links

"},{"location":"drug/mechanism_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DrugMechanism no"},{"location":"drug/mechanism_links/#properties","title":"Properties","text":""},{"location":"drug/mechanism_links/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/mechanism_links/#schema-source","title":"Schema Source","text":""},{"location":"drug/mechanism_links/#linkml-source","title":"LinkML Source","text":"
name: mechanism_links\ndescription: semicolon-separated list of links, where each link is a triple connecting\n  two entities via a relationship type\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nmultivalued: true\nalias: mechanism_links\nowner: DrugMechanism\ndomain_of:\n- DrugMechanism\nrange: MechanismLink\n\n
"},{"location":"drug/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: drug:named_entities

"},{"location":"drug/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/named_entities/#properties","title":"Properties","text":""},{"location":"drug/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"drug/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"drug/object/","title":"Slot: object","text":"

URI: drug:object

"},{"location":"drug/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MechanismLink no Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/object/#properties","title":"Properties","text":""},{"location":"drug/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/object/#linkml-source","title":"LinkML Source","text":"
name: object\nalias: object\ndomain_of:\n- MechanismLink\n- Triple\nrange: string\n\n
"},{"location":"drug/object_id/","title":"Slot: object_id","text":"

URI: drug:object_id

"},{"location":"drug/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"drug/object_id/#properties","title":"Properties","text":""},{"location":"drug/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/object_id/#schema-source","title":"Schema Source","text":""},{"location":"drug/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"drug/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: drug:object_qualifier

"},{"location":"drug/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/object_qualifier/#properties","title":"Properties","text":""},{"location":"drug/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"drug/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"drug/object_text/","title":"Slot: object_text","text":"

URI: drug:object_text

"},{"location":"drug/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"drug/object_text/#properties","title":"Properties","text":""},{"location":"drug/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/object_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"drug/predicate/","title":"Slot: predicate","text":"

URI: drug:predicate

"},{"location":"drug/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MechanismLink no Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/predicate/#properties","title":"Properties","text":""},{"location":"drug/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nalias: predicate\ndomain_of:\n- MechanismLink\n- Triple\nrange: string\n\n
"},{"location":"drug/prompt/","title":"Slot: prompt","text":"

URI: drug:prompt

"},{"location":"drug/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/prompt/#properties","title":"Properties","text":""},{"location":"drug/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/prompt/#schema-source","title":"Schema Source","text":""},{"location":"drug/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"drug/publication/","title":"Slot: publication","text":"

URI: drug:publication

"},{"location":"drug/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"drug/publication/#properties","title":"Properties","text":""},{"location":"drug/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"drug/publication/#schema-source","title":"Schema Source","text":""},{"location":"drug/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"drug/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: drug:qualifier

"},{"location":"drug/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/qualifier/#properties","title":"Properties","text":""},{"location":"drug/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"drug/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"drug/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: drug:raw_completion_output

"},{"location":"drug/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/raw_completion_output/#properties","title":"Properties","text":""},{"location":"drug/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"drug/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"drug/references/","title":"Slot: references","text":"

URI: drug:references

"},{"location":"drug/references/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DrugMechanism no"},{"location":"drug/references/#properties","title":"Properties","text":""},{"location":"drug/references/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/references/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"drug/references/#schema-source","title":"Schema Source","text":""},{"location":"drug/references/#linkml-source","title":"LinkML Source","text":"
name: references\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nmultivalued: true\nalias: references\nowner: DrugMechanism\ndomain_of:\n- DrugMechanism\nrange: string\n\n
"},{"location":"drug/source_text/","title":"Slot: source_text","text":"

URI: drug:source_text

"},{"location":"drug/source_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DrugMechanism no"},{"location":"drug/source_text/#properties","title":"Properties","text":""},{"location":"drug/source_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/source_text/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"drug/source_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/source_text/#linkml-source","title":"LinkML Source","text":"
name: source_text\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: source_text\nowner: DrugMechanism\ndomain_of:\n- DrugMechanism\nrange: string\n\n
"},{"location":"drug/subject/","title":"Slot: subject","text":"

URI: drug:subject

"},{"location":"drug/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MechanismLink no Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/subject/#properties","title":"Properties","text":""},{"location":"drug/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nalias: subject\ndomain_of:\n- MechanismLink\n- Triple\nrange: string\n\n
"},{"location":"drug/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: drug:subject_qualifier

"},{"location":"drug/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/subject_qualifier/#properties","title":"Properties","text":""},{"location":"drug/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"drug/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"drug/subject_text/","title":"Slot: subject_text","text":"

URI: drug:subject_text

"},{"location":"drug/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"drug/subject_text/#properties","title":"Properties","text":""},{"location":"drug/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"drug/title/","title":"Slot: title","text":"

The title of the publication

URI: drug:title

"},{"location":"drug/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"drug/title/#properties","title":"Properties","text":""},{"location":"drug/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/title/#schema-source","title":"Schema Source","text":""},{"location":"drug/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"drug/triples/","title":"Slot: triples","text":"

URI: drug:triples

"},{"location":"drug/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"drug/triples/#properties","title":"Properties","text":""},{"location":"drug/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/triples/#schema-source","title":"Schema Source","text":""},{"location":"drug/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"environmental_metadata/","title":"Environmental sample metadata","text":"

A template for categorizing Environmental Data Initiative data entries. See https://github.com/EDIorg/EDIorg-repository-index

URI: http://w3id.org/ontogpt/environmental-metadata

Name: environmental-metadata

"},{"location":"environmental_metadata/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nDataset {\n    string packageid  \n}\nMethod {\n    string id  \n    string label  \n}\nEnvironment {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nLocation {\n    string id  \n    string label  \n}\nTopic {\n    string id  \n    string label  \n}\n\nDataset ||--}o Topic : \"topic\"\nDataset ||--}o Location : \"location\"\nDataset ||--}o EnvironmentalMaterial : \"environmental_material\"\nDataset ||--}o Environment : \"environments\"\nDataset ||--}o Method : \"methods\"\n\n
"},{"location":"environmental_metadata/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks Dataset None ExtractionResult A result of extracting knowledge on text NamedEntity None Environment None EnvironmentalMaterial None Location None Method None RelationshipType None Topic None Publication None TextWithTriples None"},{"location":"environmental_metadata/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text environmental_material the environmental material that was sampled environments the environmental context in which the study was conducted extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing location the geographic location where the sample was isolated methods named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text packageid The internal identifier for the dataset predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication topic the general scientific area of study concerning the sample(s) triples"},{"location":"environmental_metadata/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"environmental_metadata/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"environmental_metadata/#subsets","title":"Subsets","text":"Subset Description"},{"location":"environmental_metadata/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: envmd:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"environmental_metadata/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"environmental_metadata/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:AnnotatorResult native envmd:AnnotatorResult"},{"location":"environmental_metadata/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n\n
"},{"location":"environmental_metadata/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"environmental_metadata/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"environmental_metadata/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"environmental_metadata/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"environmental_metadata/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Any/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native envmd:Any"},{"location":"environmental_metadata/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nclass_uri: linkml:Any\n\n
"},{"location":"environmental_metadata/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nclass_uri: linkml:Any\n\n
"},{"location":"environmental_metadata/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"environmental_metadata/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: envmd:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"environmental_metadata/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"environmental_metadata/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:CompoundExpression native envmd:CompoundExpression"},{"location":"environmental_metadata/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nabstract: true\n\n
"},{"location":"environmental_metadata/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nabstract: true\n\n
"},{"location":"environmental_metadata/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"environmental_metadata/Curie/#comments","title":"Comments","text":""},{"location":"environmental_metadata/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Curie/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Dataset/","title":"Class: Dataset","text":"

URI: envmd:Dataset

erDiagram\nDataset {\n    string packageid  \n}\nMethod {\n    string id  \n    string label  \n}\nEnvironment {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nLocation {\n    string id  \n    string label  \n}\nTopic {\n    string id  \n    string label  \n}\n\nDataset ||--}o Topic : \"topic\"\nDataset ||--}o Location : \"location\"\nDataset ||--}o EnvironmentalMaterial : \"environmental_material\"\nDataset ||--}o Environment : \"environments\"\nDataset ||--}o Method : \"methods\"\n\n
"},{"location":"environmental_metadata/Dataset/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance packageid 0..1 String The internal identifier for the dataset direct topic 0..* Topic the general scientific area of study concerning the sample(s) direct location 0..* Location the geographic location where the sample was isolated direct environmental_material 0..* EnvironmentalMaterial the environmental material that was sampled direct environments 0..* Environment the environmental context in which the study was conducted direct methods 0..* Method direct"},{"location":"environmental_metadata/Dataset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Dataset/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Dataset/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Dataset native envmd:Dataset"},{"location":"environmental_metadata/Dataset/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Dataset/#direct","title":"Direct","text":"
name: Dataset\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  packageid:\n    name: packageid\n    annotations:\n      prompt:\n        tag: prompt\n        value: single unique identifier for the dataset\n    description: The internal identifier for the dataset\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: false\n    range: string\n  topic:\n    name: topic\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of scientific areas of study concerning the\n          sample(s)\n    description: the general scientific area of study concerning the sample(s)\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Topic\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of geographic locations of sample isolations\n    description: the geographic location where the sample was isolated\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: EnvironmentalMaterial\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental contexts in which the study\n          was conducted\n    description: the environmental context in which the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Environment\n  methods:\n    name: methods\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of methods used in measuring sample variables\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Method\ntree_root: true\n\n
"},{"location":"environmental_metadata/Dataset/#induced","title":"Induced","text":"
name: Dataset\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  packageid:\n    name: packageid\n    annotations:\n      prompt:\n        tag: prompt\n        value: single unique identifier for the dataset\n    description: The internal identifier for the dataset\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: false\n    alias: packageid\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: string\n  topic:\n    name: topic\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of scientific areas of study concerning the\n          sample(s)\n    description: the general scientific area of study concerning the sample(s)\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: topic\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: Topic\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of geographic locations of sample isolations\n    description: the geographic location where the sample was isolated\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: location\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: environmental_material\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: EnvironmentalMaterial\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental contexts in which the study\n          was conducted\n    description: the environmental context in which the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: environments\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: Environment\n  methods:\n    name: methods\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of methods used in measuring sample variables\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: methods\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: Method\ntree_root: true\n\n
"},{"location":"environmental_metadata/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"environmental_metadata/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Date/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"environmental_metadata/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"environmental_metadata/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"environmental_metadata/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"environmental_metadata/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Double/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Environment/","title":"Class: Environment","text":"

URI: envmd:Environment

erDiagram\nEnvironment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/Environment/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/Environment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/Environment/#usages","title":"Usages","text":"used by used in type used Dataset environments range Environment"},{"location":"environmental_metadata/Environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Environment/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/Environment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:ENVTHES"},{"location":"environmental_metadata/Environment/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Environment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Environment native envmd:Environment"},{"location":"environmental_metadata/Environment/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Environment/#direct","title":"Direct","text":"
name: Environment\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/Environment/#induced","title":"Induced","text":"
name: Environment\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/EnvironmentalMaterial/","title":"Class: EnvironmentalMaterial","text":"

URI: envmd:EnvironmentalMaterial

erDiagram\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/EnvironmentalMaterial/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/EnvironmentalMaterial/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/EnvironmentalMaterial/#usages","title":"Usages","text":"used by used in type used Dataset environmental_material range EnvironmentalMaterial"},{"location":"environmental_metadata/EnvironmentalMaterial/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/EnvironmentalMaterial/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/EnvironmentalMaterial/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:ENVTHES"},{"location":"environmental_metadata/EnvironmentalMaterial/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/EnvironmentalMaterial/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:EnvironmentalMaterial native envmd:EnvironmentalMaterial"},{"location":"environmental_metadata/EnvironmentalMaterial/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/EnvironmentalMaterial/#direct","title":"Direct","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/EnvironmentalMaterial/#induced","title":"Induced","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: envmd:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"environmental_metadata/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"environmental_metadata/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:ExtractionResult native envmd:ExtractionResult"},{"location":"environmental_metadata/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_metadata/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_metadata/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"environmental_metadata/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Float/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"environmental_metadata/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Integer/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Location/","title":"Class: Location","text":"

URI: envmd:Location

erDiagram\nLocation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/Location/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/Location/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/Location/#usages","title":"Usages","text":"used by used in type used Dataset location range Location"},{"location":"environmental_metadata/Location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Location/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/Location/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:GAZ"},{"location":"environmental_metadata/Location/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Location/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Location native envmd:Location"},{"location":"environmental_metadata/Location/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Location/#direct","title":"Direct","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:GAZ\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/Location/#induced","title":"Induced","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:GAZ\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Location\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Location\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/Method/","title":"Class: Method","text":"

URI: envmd:Method

erDiagram\nMethod {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/Method/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/Method/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/Method/#usages","title":"Usages","text":"used by used in type used Dataset methods range Method"},{"location":"environmental_metadata/Method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Method/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/Method/#annotations","title":"Annotations","text":"property value annotators bioportal:ENVTHES"},{"location":"environmental_metadata/Method/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Method/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Method native envmd:Method"},{"location":"environmental_metadata/Method/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Method/#direct","title":"Direct","text":"
name: Method\nid_prefixes:\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/Method/#induced","title":"Induced","text":"
name: Method\nid_prefixes:\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Method\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Method\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/NamedEntity/","title":"Class: NamedEntity","text":"

URI: envmd:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"environmental_metadata/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"environmental_metadata/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:NamedEntity native envmd:NamedEntity"},{"location":"environmental_metadata/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"environmental_metadata/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"environmental_metadata/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"environmental_metadata/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"environmental_metadata/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"environmental_metadata/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"environmental_metadata/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"environmental_metadata/Objectidentifier/#comments","title":"Comments","text":""},{"location":"environmental_metadata/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Publication/","title":"Class: Publication","text":"

URI: envmd:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"environmental_metadata/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"environmental_metadata/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"environmental_metadata/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Publication/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Publication native envmd:Publication"},{"location":"environmental_metadata/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n\n
"},{"location":"environmental_metadata/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"environmental_metadata/RelationshipType/","title":"Class: RelationshipType","text":"

URI: envmd:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"environmental_metadata/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:RelationshipType native envmd:RelationshipType"},{"location":"environmental_metadata/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"environmental_metadata/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/String/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: envmd:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"environmental_metadata/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"environmental_metadata/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:TextWithTriples native envmd:TextWithTriples"},{"location":"environmental_metadata/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_metadata/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_metadata/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"environmental_metadata/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Time/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Topic/","title":"Class: Topic","text":"

URI: envmd:Topic

erDiagram\nTopic {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/Topic/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/Topic/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/Topic/#usages","title":"Usages","text":"used by used in type used Dataset topic range Topic"},{"location":"environmental_metadata/Topic/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Topic/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/Topic/#annotations","title":"Annotations","text":"property value annotators bioportal:ENVTHES"},{"location":"environmental_metadata/Topic/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Topic/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Topic native envmd:Topic"},{"location":"environmental_metadata/Topic/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Topic/#direct","title":"Direct","text":"
name: Topic\nid_prefixes:\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/Topic/#induced","title":"Induced","text":"
name: Topic\nid_prefixes:\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Topic\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Topic\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: envmd:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"environmental_metadata/Triple/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"environmental_metadata/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"environmental_metadata/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Triple/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Triple native envmd:Triple"},{"location":"environmental_metadata/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"environmental_metadata/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"environmental_metadata/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"environmental_metadata/Uri/#comments","title":"Comments","text":""},{"location":"environmental_metadata/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Uri/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"environmental_metadata/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: envmd:abstract

"},{"location":"environmental_metadata/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_metadata/abstract/#properties","title":"Properties","text":""},{"location":"environmental_metadata/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/abstract/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_metadata/combined_text/","title":"Slot: combined_text","text":"

URI: envmd:combined_text

"},{"location":"environmental_metadata/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_metadata/combined_text/#properties","title":"Properties","text":""},{"location":"environmental_metadata/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_metadata/environmental-metadata/","title":"environmental-metadata","text":"

A template for categorizing Environmental Data Initiative data entries. See https://github.com/EDIorg/EDIorg-repository-index

URI: http://w3id.org/ontogpt/environmental-metadata

"},{"location":"environmental_metadata/environmental_material/","title":"Slot: environmental_material","text":"

the environmental material that was sampled

URI: envmd:environmental_material

"},{"location":"environmental_metadata/environmental_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/environmental_material/#properties","title":"Properties","text":""},{"location":"environmental_metadata/environmental_material/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/environmental_material/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental materials"},{"location":"environmental_metadata/environmental_material/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/environmental_material/#linkml-source","title":"LinkML Source","text":"
name: environmental_material\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental materials\ndescription: the environmental material that was sampled\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: environmental_material\nowner: Dataset\ndomain_of:\n- Dataset\nrange: EnvironmentalMaterial\n\n
"},{"location":"environmental_metadata/environments/","title":"Slot: environments","text":"

the environmental context in which the study was conducted

URI: envmd:environments

"},{"location":"environmental_metadata/environments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/environments/#properties","title":"Properties","text":""},{"location":"environmental_metadata/environments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/environments/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental contexts in which the study was conducted"},{"location":"environmental_metadata/environments/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/environments/#linkml-source","title":"LinkML Source","text":"
name: environments\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental contexts in which the study was\n      conducted\ndescription: the environmental context in which the study was conducted\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: environments\nowner: Dataset\ndomain_of:\n- Dataset\nrange: Environment\n\n
"},{"location":"environmental_metadata/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: envmd:extracted_object

"},{"location":"environmental_metadata/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/extracted_object/#properties","title":"Properties","text":""},{"location":"environmental_metadata/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"environmental_metadata/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: envmd:full_text

"},{"location":"environmental_metadata/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_metadata/full_text/#properties","title":"Properties","text":""},{"location":"environmental_metadata/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/full_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_metadata/id/","title":"Slot: id","text":"

URI: envmd:id

"},{"location":"environmental_metadata/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Topic no Location no EnvironmentalMaterial no Environment no Method no NamedEntity no RelationshipType no Publication no"},{"location":"environmental_metadata/id/#properties","title":"Properties","text":""},{"location":"environmental_metadata/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"environmental_metadata/input_id/","title":"Slot: input_id","text":"

URI: envmd:input_id

"},{"location":"environmental_metadata/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/input_id/#properties","title":"Properties","text":""},{"location":"environmental_metadata/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/input_id/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_metadata/input_text/","title":"Slot: input_text","text":"

URI: envmd:input_text

"},{"location":"environmental_metadata/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/input_text/#properties","title":"Properties","text":""},{"location":"environmental_metadata/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/input_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_metadata/input_title/","title":"Slot: input_title","text":"

URI: envmd:input_title

"},{"location":"environmental_metadata/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/input_title/#properties","title":"Properties","text":""},{"location":"environmental_metadata/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/input_title/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_metadata/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"environmental_metadata/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Topic no Location no EnvironmentalMaterial no Environment no Method no NamedEntity no RelationshipType no"},{"location":"environmental_metadata/label/#properties","title":"Properties","text":""},{"location":"environmental_metadata/label/#aliases","title":"Aliases","text":""},{"location":"environmental_metadata/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"environmental_metadata/label/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"environmental_metadata/location/","title":"Slot: location","text":"

the geographic location where the sample was isolated

URI: envmd:location

"},{"location":"environmental_metadata/location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/location/#properties","title":"Properties","text":""},{"location":"environmental_metadata/location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/location/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of geographic locations of sample isolations"},{"location":"environmental_metadata/location/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/location/#linkml-source","title":"LinkML Source","text":"
name: location\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of geographic locations of sample isolations\ndescription: the geographic location where the sample was isolated\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: location\nowner: Dataset\ndomain_of:\n- Dataset\nrange: Location\n\n
"},{"location":"environmental_metadata/methods/","title":"Slot: methods","text":"

URI: envmd:methods

"},{"location":"environmental_metadata/methods/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/methods/#properties","title":"Properties","text":""},{"location":"environmental_metadata/methods/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/methods/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of methods used in measuring sample variables"},{"location":"environmental_metadata/methods/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/methods/#linkml-source","title":"LinkML Source","text":"
name: methods\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of methods used in measuring sample variables\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: methods\nowner: Dataset\ndomain_of:\n- Dataset\nrange: Method\n\n
"},{"location":"environmental_metadata/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: envmd:named_entities

"},{"location":"environmental_metadata/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/named_entities/#properties","title":"Properties","text":""},{"location":"environmental_metadata/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"environmental_metadata/object/","title":"Slot: object","text":"

URI: envmd:object

"},{"location":"environmental_metadata/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/object/#properties","title":"Properties","text":""},{"location":"environmental_metadata/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/object/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_metadata/object_id/","title":"Slot: object_id","text":"

URI: envmd:object_id

"},{"location":"environmental_metadata/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_metadata/object_id/#properties","title":"Properties","text":""},{"location":"environmental_metadata/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/object_id/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_metadata/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: envmd:object_qualifier

"},{"location":"environmental_metadata/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/object_qualifier/#properties","title":"Properties","text":""},{"location":"environmental_metadata/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_metadata/object_text/","title":"Slot: object_text","text":"

URI: envmd:object_text

"},{"location":"environmental_metadata/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_metadata/object_text/#properties","title":"Properties","text":""},{"location":"environmental_metadata/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/object_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_metadata/packageid/","title":"Slot: packageid","text":"

The internal identifier for the dataset

URI: envmd:packageid

"},{"location":"environmental_metadata/packageid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/packageid/#properties","title":"Properties","text":""},{"location":"environmental_metadata/packageid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/packageid/#annotations","title":"Annotations","text":"property value prompt single unique identifier for the dataset"},{"location":"environmental_metadata/packageid/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/packageid/#linkml-source","title":"LinkML Source","text":"
name: packageid\nannotations:\n  prompt:\n    tag: prompt\n    value: single unique identifier for the dataset\ndescription: The internal identifier for the dataset\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: false\nalias: packageid\nowner: Dataset\ndomain_of:\n- Dataset\nrange: string\n\n
"},{"location":"environmental_metadata/predicate/","title":"Slot: predicate","text":"

URI: envmd:predicate

"},{"location":"environmental_metadata/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/predicate/#properties","title":"Properties","text":""},{"location":"environmental_metadata/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/predicate/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"environmental_metadata/prompt/","title":"Slot: prompt","text":"

URI: envmd:prompt

"},{"location":"environmental_metadata/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/prompt/#properties","title":"Properties","text":""},{"location":"environmental_metadata/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/prompt/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_metadata/publication/","title":"Slot: publication","text":"

URI: envmd:publication

"},{"location":"environmental_metadata/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"environmental_metadata/publication/#properties","title":"Properties","text":""},{"location":"environmental_metadata/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"environmental_metadata/publication/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"environmental_metadata/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: envmd:qualifier

"},{"location":"environmental_metadata/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/qualifier/#properties","title":"Properties","text":""},{"location":"environmental_metadata/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"environmental_metadata/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: envmd:raw_completion_output

"},{"location":"environmental_metadata/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/raw_completion_output/#properties","title":"Properties","text":""},{"location":"environmental_metadata/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_metadata/subject/","title":"Slot: subject","text":"

URI: envmd:subject

"},{"location":"environmental_metadata/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/subject/#properties","title":"Properties","text":""},{"location":"environmental_metadata/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/subject/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_metadata/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: envmd:subject_qualifier

"},{"location":"environmental_metadata/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/subject_qualifier/#properties","title":"Properties","text":""},{"location":"environmental_metadata/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_metadata/subject_text/","title":"Slot: subject_text","text":"

URI: envmd:subject_text

"},{"location":"environmental_metadata/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_metadata/subject_text/#properties","title":"Properties","text":""},{"location":"environmental_metadata/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_metadata/title/","title":"Slot: title","text":"

The title of the publication

URI: envmd:title

"},{"location":"environmental_metadata/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_metadata/title/#properties","title":"Properties","text":""},{"location":"environmental_metadata/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/title/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_metadata/topic/","title":"Slot: topic","text":"

the general scientific area of study concerning the sample(s)

URI: envmd:topic

"},{"location":"environmental_metadata/topic/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/topic/#properties","title":"Properties","text":""},{"location":"environmental_metadata/topic/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/topic/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of scientific areas of study concerning the sample(s)"},{"location":"environmental_metadata/topic/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/topic/#linkml-source","title":"LinkML Source","text":"
name: topic\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of scientific areas of study concerning the sample(s)\ndescription: the general scientific area of study concerning the sample(s)\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: topic\nowner: Dataset\ndomain_of:\n- Dataset\nrange: Topic\n\n
"},{"location":"environmental_metadata/triples/","title":"Slot: triples","text":"

URI: envmd:triples

"},{"location":"environmental_metadata/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"environmental_metadata/triples/#properties","title":"Properties","text":""},{"location":"environmental_metadata/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/triples/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"environmental_sample/","title":"Environmental Sample Template","text":"

A template for Environmental Samples

URI: http://w3id.org/ontogpt/environmental-sample

Name: environmental-sample

"},{"location":"environmental_sample/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nStudy {\n\n}\nMeasurement {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\nVariable {\n    string id  \n    string label  \n}\nCausalRelationship {\n\n}\nEnvironment {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nLocation {\n    string id  \n    string label  \n}\n\nStudy ||--}o Location : \"location\"\nStudy ||--}o EnvironmentalMaterial : \"environmental_material\"\nStudy ||--}o Environment : \"environments\"\nStudy ||--}o CausalRelationship : \"causal_relationships\"\nStudy ||--}o Variable : \"variables\"\nStudy ||--}o Measurement : \"measurements\"\nMeasurement ||--|o Unit : \"unit\"\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\n\n
"},{"location":"environmental_sample/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None CausalRelationship None Measurement None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None Environment None EnvironmentalMaterial None Location None RelationshipType None Unit None Variable None Publication None Study None TextWithTriples None"},{"location":"environmental_sample/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication causal_relationships cause the variable that is the cause of the effect combined_text effect the things that is affected environmental_material the environmental material that was sampled environments extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing location the sites at which the study was conducted measurements named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples unit the unit of the measurement value the value of the measurement variables"},{"location":"environmental_sample/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"environmental_sample/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"environmental_sample/#subsets","title":"Subsets","text":"Subset Description"},{"location":"environmental_sample/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: sample:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"environmental_sample/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"environmental_sample/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:AnnotatorResult native sample:AnnotatorResult"},{"location":"environmental_sample/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n\n
"},{"location":"environmental_sample/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"environmental_sample/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"environmental_sample/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"environmental_sample/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"environmental_sample/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Any/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native sample:Any"},{"location":"environmental_sample/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nclass_uri: linkml:Any\n\n
"},{"location":"environmental_sample/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nclass_uri: linkml:Any\n\n
"},{"location":"environmental_sample/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"environmental_sample/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/CausalRelationship/","title":"Class: CausalRelationship","text":"

URI: sample:CausalRelationship

erDiagram\nCausalRelationship {\n\n}\nVariable {\n    string id  \n    string label  \n}\n\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\n\n
"},{"location":"environmental_sample/CausalRelationship/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/CausalRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance cause 0..1 Variable the variable that is the cause of the effect direct effect 0..1 Variable the things that is affected direct"},{"location":"environmental_sample/CausalRelationship/#usages","title":"Usages","text":"used by used in type used Study causal_relationships range CausalRelationship"},{"location":"environmental_sample/CausalRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/CausalRelationship/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/CausalRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:CausalRelationship native sample:CausalRelationship"},{"location":"environmental_sample/CausalRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/CausalRelationship/#direct","title":"Direct","text":"
name: CausalRelationship\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nattributes:\n  cause:\n    name: cause\n    description: the variable that is the cause of the effect\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: Variable\n  effect:\n    name: effect\n    description: the things that is affected\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: Variable\n\n
"},{"location":"environmental_sample/CausalRelationship/#induced","title":"Induced","text":"
name: CausalRelationship\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nattributes:\n  cause:\n    name: cause\n    description: the variable that is the cause of the effect\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: cause\n    owner: CausalRelationship\n    domain_of:\n    - CausalRelationship\n    range: Variable\n  effect:\n    name: effect\n    description: the things that is affected\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: effect\n    owner: CausalRelationship\n    domain_of:\n    - CausalRelationship\n    range: Variable\n\n
"},{"location":"environmental_sample/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: sample:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"environmental_sample/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"environmental_sample/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:CompoundExpression native sample:CompoundExpression"},{"location":"environmental_sample/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nabstract: true\n\n
"},{"location":"environmental_sample/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nabstract: true\n\n
"},{"location":"environmental_sample/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"environmental_sample/Curie/#comments","title":"Comments","text":""},{"location":"environmental_sample/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Curie/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"environmental_sample/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Date/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"environmental_sample/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"environmental_sample/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"environmental_sample/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"environmental_sample/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Double/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Environment/","title":"Class: Environment","text":"

URI: sample:Environment

erDiagram\nEnvironment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/Environment/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Environment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/Environment/#usages","title":"Usages","text":"used by used in type used Study environments range Environment"},{"location":"environmental_sample/Environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Environment/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/Environment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:envthes"},{"location":"environmental_sample/Environment/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Environment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Environment native sample:Environment"},{"location":"environmental_sample/Environment/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Environment/#direct","title":"Direct","text":"
name: Environment\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/Environment/#induced","title":"Induced","text":"
name: Environment\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/EnvironmentalMaterial/","title":"Class: EnvironmentalMaterial","text":"

URI: sample:EnvironmentalMaterial

erDiagram\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/EnvironmentalMaterial/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/EnvironmentalMaterial/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/EnvironmentalMaterial/#usages","title":"Usages","text":"used by used in type used Study environmental_material range EnvironmentalMaterial"},{"location":"environmental_sample/EnvironmentalMaterial/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/EnvironmentalMaterial/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/EnvironmentalMaterial/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:envthes"},{"location":"environmental_sample/EnvironmentalMaterial/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/EnvironmentalMaterial/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:EnvironmentalMaterial native sample:EnvironmentalMaterial"},{"location":"environmental_sample/EnvironmentalMaterial/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/EnvironmentalMaterial/#direct","title":"Direct","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/EnvironmentalMaterial/#induced","title":"Induced","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: sample:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"environmental_sample/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"environmental_sample/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:ExtractionResult native sample:ExtractionResult"},{"location":"environmental_sample/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_sample/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_sample/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"environmental_sample/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Float/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"environmental_sample/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Integer/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Location/","title":"Class: Location","text":"

URI: sample:Location

erDiagram\nLocation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/Location/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Location/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/Location/#usages","title":"Usages","text":"used by used in type used Study location range Location"},{"location":"environmental_sample/Location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Location/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/Location/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:gaz, bioportal:envthes"},{"location":"environmental_sample/Location/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Location/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Location native sample:Location"},{"location":"environmental_sample/Location/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Location/#direct","title":"Direct","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:gaz, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/Location/#induced","title":"Induced","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:gaz, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Location\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Location\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/Measurement/","title":"Class: Measurement","text":"

URI: sample:Measurement

erDiagram\nMeasurement {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\n\nMeasurement ||--|o Unit : \"unit\"\n\n
"},{"location":"environmental_sample/Measurement/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Measurement/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance value 0..1 String the value of the measurement direct unit 0..1 Unit the unit of the measurement direct"},{"location":"environmental_sample/Measurement/#usages","title":"Usages","text":"used by used in type used Study measurements range Measurement"},{"location":"environmental_sample/Measurement/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Measurement/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Measurement/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Measurement native sample:Measurement"},{"location":"environmental_sample/Measurement/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Measurement/#direct","title":"Direct","text":"
name: Measurement\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    description: the value of the measurement\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  unit:\n    name: unit\n    description: the unit of the measurement\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: Unit\n\n
"},{"location":"environmental_sample/Measurement/#induced","title":"Induced","text":"
name: Measurement\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    description: the value of the measurement\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: value\n    owner: Measurement\n    domain_of:\n    - Measurement\n    range: string\n  unit:\n    name: unit\n    description: the unit of the measurement\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: unit\n    owner: Measurement\n    domain_of:\n    - Measurement\n    range: Unit\n\n
"},{"location":"environmental_sample/NamedEntity/","title":"Class: NamedEntity","text":"

URI: sample:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"environmental_sample/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"environmental_sample/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:NamedEntity native sample:NamedEntity"},{"location":"environmental_sample/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"environmental_sample/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"environmental_sample/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"environmental_sample/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"environmental_sample/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"environmental_sample/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"environmental_sample/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"environmental_sample/Objectidentifier/#comments","title":"Comments","text":""},{"location":"environmental_sample/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Publication/","title":"Class: Publication","text":"

URI: sample:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"environmental_sample/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"environmental_sample/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"environmental_sample/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Publication/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Publication native sample:Publication"},{"location":"environmental_sample/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n\n
"},{"location":"environmental_sample/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"environmental_sample/RelationshipType/","title":"Class: RelationshipType","text":"

URI: sample:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"environmental_sample/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:RelationshipType native sample:RelationshipType"},{"location":"environmental_sample/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"environmental_sample/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/String/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Study/","title":"Class: Study","text":"

URI: sample:Study

erDiagram\nStudy {\n\n}\nMeasurement {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\nVariable {\n    string id  \n    string label  \n}\nCausalRelationship {\n\n}\nEnvironment {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nLocation {\n    string id  \n    string label  \n}\n\nStudy ||--}o Location : \"location\"\nStudy ||--}o EnvironmentalMaterial : \"environmental_material\"\nStudy ||--}o Environment : \"environments\"\nStudy ||--}o CausalRelationship : \"causal_relationships\"\nStudy ||--}o Variable : \"variables\"\nStudy ||--}o Measurement : \"measurements\"\nMeasurement ||--|o Unit : \"unit\"\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\n\n
"},{"location":"environmental_sample/Study/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance location 0..* Location the sites at which the study was conducted direct environmental_material 0..* EnvironmentalMaterial the environmental material that was sampled direct environments 0..* Environment direct causal_relationships 0..* CausalRelationship direct variables 0..* Variable direct measurements 0..* Measurement direct"},{"location":"environmental_sample/Study/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Study/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Study/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Study native sample:Study"},{"location":"environmental_sample/Study/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Study/#direct","title":"Direct","text":"
name: Study\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of sites at which the study was conducted.\n          give specific place names. if you cannot find a specific place name leave\n          the field as empty.\n    description: the sites at which the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: EnvironmentalMaterial\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environment terms for the location in which\n          the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Environment\n  causal_relationships:\n    name: causal_relationships\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of cause-effect pairs, for example, effect\n          of temperature on growth\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: CausalRelationship\n  variables:\n    name: variables\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of study variables\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Variable\n  measurements:\n    name: measurements\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of value-measurement pairs\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Measurement\ntree_root: true\n\n
"},{"location":"environmental_sample/Study/#induced","title":"Induced","text":"
name: Study\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of sites at which the study was conducted.\n          give specific place names. if you cannot find a specific place name leave\n          the field as empty.\n    description: the sites at which the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: location\n    owner: Study\n    domain_of:\n    - Study\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: environmental_material\n    owner: Study\n    domain_of:\n    - Study\n    range: EnvironmentalMaterial\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environment terms for the location in which\n          the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: environments\n    owner: Study\n    domain_of:\n    - Study\n    range: Environment\n  causal_relationships:\n    name: causal_relationships\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of cause-effect pairs, for example, effect\n          of temperature on growth\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: causal_relationships\n    owner: Study\n    domain_of:\n    - Study\n    range: CausalRelationship\n  variables:\n    name: variables\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of study variables\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: variables\n    owner: Study\n    domain_of:\n    - Study\n    range: Variable\n  measurements:\n    name: measurements\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of value-measurement pairs\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: measurements\n    owner: Study\n    domain_of:\n    - Study\n    range: Measurement\ntree_root: true\n\n
"},{"location":"environmental_sample/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: sample:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"environmental_sample/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"environmental_sample/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:TextWithTriples native sample:TextWithTriples"},{"location":"environmental_sample/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_sample/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_sample/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"environmental_sample/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Time/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: sample:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"environmental_sample/Triple/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"environmental_sample/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"environmental_sample/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Triple/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Triple native sample:Triple"},{"location":"environmental_sample/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"environmental_sample/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"environmental_sample/Unit/","title":"Class: Unit","text":"

URI: sample:Unit

erDiagram\nUnit {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/Unit/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Unit/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/Unit/#usages","title":"Usages","text":"used by used in type used Measurement unit range Unit"},{"location":"environmental_sample/Unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Unit/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/Unit/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uo, bioportal:ncit"},{"location":"environmental_sample/Unit/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Unit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Unit native sample:Unit"},{"location":"environmental_sample/Unit/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Unit/#direct","title":"Direct","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, bioportal:ncit\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/Unit/#induced","title":"Induced","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, bioportal:ncit\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"environmental_sample/Uri/#comments","title":"Comments","text":""},{"location":"environmental_sample/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Uri/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"environmental_sample/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Variable/","title":"Class: Variable","text":"

URI: sample:Variable

erDiagram\nVariable {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/Variable/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Variable/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/Variable/#usages","title":"Usages","text":"used by used in type used Study variables range Variable CausalRelationship cause range Variable CausalRelationship effect range Variable"},{"location":"environmental_sample/Variable/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Variable/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/Variable/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:bero, bioportal:envthes"},{"location":"environmental_sample/Variable/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Variable/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Variable native sample:Variable"},{"location":"environmental_sample/Variable/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Variable/#direct","title":"Direct","text":"
name: Variable\nid_prefixes:\n- ENVO\n- MIXS\n- PATO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:bero, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/Variable/#induced","title":"Induced","text":"
name: Variable\nid_prefixes:\n- ENVO\n- MIXS\n- PATO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:bero, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Variable\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Variable\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: sample:abstract

"},{"location":"environmental_sample/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_sample/abstract/#properties","title":"Properties","text":""},{"location":"environmental_sample/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/abstract/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_sample/causal_relationships/","title":"Slot: causal_relationships","text":"

URI: sample:causal_relationships

"},{"location":"environmental_sample/causal_relationships/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/causal_relationships/#properties","title":"Properties","text":""},{"location":"environmental_sample/causal_relationships/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/causal_relationships/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth"},{"location":"environmental_sample/causal_relationships/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/causal_relationships/#linkml-source","title":"LinkML Source","text":"
name: causal_relationships\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of cause-effect pairs, for example, effect of\n      temperature on growth\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: causal_relationships\nowner: Study\ndomain_of:\n- Study\nrange: CausalRelationship\n\n
"},{"location":"environmental_sample/cause/","title":"Slot: cause","text":"

the variable that is the cause of the effect

URI: sample:cause

"},{"location":"environmental_sample/cause/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CausalRelationship no"},{"location":"environmental_sample/cause/#properties","title":"Properties","text":""},{"location":"environmental_sample/cause/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/cause/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/cause/#linkml-source","title":"LinkML Source","text":"
name: cause\ndescription: the variable that is the cause of the effect\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: cause\nowner: CausalRelationship\ndomain_of:\n- CausalRelationship\nrange: Variable\n\n
"},{"location":"environmental_sample/combined_text/","title":"Slot: combined_text","text":"

URI: sample:combined_text

"},{"location":"environmental_sample/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_sample/combined_text/#properties","title":"Properties","text":""},{"location":"environmental_sample/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_sample/effect/","title":"Slot: effect","text":"

the things that is affected

URI: sample:effect

"},{"location":"environmental_sample/effect/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CausalRelationship no"},{"location":"environmental_sample/effect/#properties","title":"Properties","text":""},{"location":"environmental_sample/effect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/effect/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/effect/#linkml-source","title":"LinkML Source","text":"
name: effect\ndescription: the things that is affected\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: effect\nowner: CausalRelationship\ndomain_of:\n- CausalRelationship\nrange: Variable\n\n
"},{"location":"environmental_sample/environmental-sample/","title":"environmental-sample","text":"

A template for Environmental Samples

URI: http://w3id.org/ontogpt/environmental-sample

"},{"location":"environmental_sample/environmental_material/","title":"Slot: environmental_material","text":"

the environmental material that was sampled

URI: sample:environmental_material

"},{"location":"environmental_sample/environmental_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/environmental_material/#properties","title":"Properties","text":""},{"location":"environmental_sample/environmental_material/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/environmental_material/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental materials"},{"location":"environmental_sample/environmental_material/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/environmental_material/#linkml-source","title":"LinkML Source","text":"
name: environmental_material\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental materials\ndescription: the environmental material that was sampled\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: environmental_material\nowner: Study\ndomain_of:\n- Study\nrange: EnvironmentalMaterial\n\n
"},{"location":"environmental_sample/environments/","title":"Slot: environments","text":"

URI: sample:environments

"},{"location":"environmental_sample/environments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/environments/#properties","title":"Properties","text":""},{"location":"environmental_sample/environments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/environments/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environment terms for the location in which the study was conducted"},{"location":"environmental_sample/environments/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/environments/#linkml-source","title":"LinkML Source","text":"
name: environments\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environment terms for the location in which\n      the study was conducted\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: environments\nowner: Study\ndomain_of:\n- Study\nrange: Environment\n\n
"},{"location":"environmental_sample/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: sample:extracted_object

"},{"location":"environmental_sample/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/extracted_object/#properties","title":"Properties","text":""},{"location":"environmental_sample/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"environmental_sample/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: sample:full_text

"},{"location":"environmental_sample/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_sample/full_text/#properties","title":"Properties","text":""},{"location":"environmental_sample/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/full_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_sample/id/","title":"Slot: id","text":"

URI: sample:id

"},{"location":"environmental_sample/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Location no EnvironmentalMaterial no Environment no Variable no Unit no NamedEntity no RelationshipType no Publication no"},{"location":"environmental_sample/id/#properties","title":"Properties","text":""},{"location":"environmental_sample/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"environmental_sample/input_id/","title":"Slot: input_id","text":"

URI: sample:input_id

"},{"location":"environmental_sample/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/input_id/#properties","title":"Properties","text":""},{"location":"environmental_sample/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/input_id/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_sample/input_text/","title":"Slot: input_text","text":"

URI: sample:input_text

"},{"location":"environmental_sample/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/input_text/#properties","title":"Properties","text":""},{"location":"environmental_sample/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/input_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_sample/input_title/","title":"Slot: input_title","text":"

URI: sample:input_title

"},{"location":"environmental_sample/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/input_title/#properties","title":"Properties","text":""},{"location":"environmental_sample/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/input_title/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_sample/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"environmental_sample/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Location no EnvironmentalMaterial no Environment no Variable no Unit no NamedEntity no RelationshipType no"},{"location":"environmental_sample/label/#properties","title":"Properties","text":""},{"location":"environmental_sample/label/#aliases","title":"Aliases","text":""},{"location":"environmental_sample/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"environmental_sample/label/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"environmental_sample/location/","title":"Slot: location","text":"

the sites at which the study was conducted

URI: sample:location

"},{"location":"environmental_sample/location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/location/#properties","title":"Properties","text":""},{"location":"environmental_sample/location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/location/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty."},{"location":"environmental_sample/location/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/location/#linkml-source","title":"LinkML Source","text":"
name: location\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of sites at which the study was conducted. give\n      specific place names. if you cannot find a specific place name leave the field\n      as empty.\ndescription: the sites at which the study was conducted\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: location\nowner: Study\ndomain_of:\n- Study\nrange: Location\n\n
"},{"location":"environmental_sample/measurements/","title":"Slot: measurements","text":"

URI: sample:measurements

"},{"location":"environmental_sample/measurements/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/measurements/#properties","title":"Properties","text":""},{"location":"environmental_sample/measurements/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/measurements/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of value-measurement pairs"},{"location":"environmental_sample/measurements/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/measurements/#linkml-source","title":"LinkML Source","text":"
name: measurements\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of value-measurement pairs\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: measurements\nowner: Study\ndomain_of:\n- Study\nrange: Measurement\n\n
"},{"location":"environmental_sample/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: sample:named_entities

"},{"location":"environmental_sample/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/named_entities/#properties","title":"Properties","text":""},{"location":"environmental_sample/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"environmental_sample/object/","title":"Slot: object","text":"

URI: sample:object

"},{"location":"environmental_sample/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/object/#properties","title":"Properties","text":""},{"location":"environmental_sample/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/object/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_sample/object_id/","title":"Slot: object_id","text":"

URI: sample:object_id

"},{"location":"environmental_sample/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_sample/object_id/#properties","title":"Properties","text":""},{"location":"environmental_sample/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/object_id/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_sample/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: sample:object_qualifier

"},{"location":"environmental_sample/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/object_qualifier/#properties","title":"Properties","text":""},{"location":"environmental_sample/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_sample/object_text/","title":"Slot: object_text","text":"

URI: sample:object_text

"},{"location":"environmental_sample/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_sample/object_text/#properties","title":"Properties","text":""},{"location":"environmental_sample/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/object_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_sample/predicate/","title":"Slot: predicate","text":"

URI: sample:predicate

"},{"location":"environmental_sample/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/predicate/#properties","title":"Properties","text":""},{"location":"environmental_sample/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/predicate/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"environmental_sample/prompt/","title":"Slot: prompt","text":"

URI: sample:prompt

"},{"location":"environmental_sample/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/prompt/#properties","title":"Properties","text":""},{"location":"environmental_sample/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/prompt/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_sample/publication/","title":"Slot: publication","text":"

URI: sample:publication

"},{"location":"environmental_sample/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"environmental_sample/publication/#properties","title":"Properties","text":""},{"location":"environmental_sample/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"environmental_sample/publication/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"environmental_sample/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: sample:qualifier

"},{"location":"environmental_sample/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/qualifier/#properties","title":"Properties","text":""},{"location":"environmental_sample/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"environmental_sample/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: sample:raw_completion_output

"},{"location":"environmental_sample/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/raw_completion_output/#properties","title":"Properties","text":""},{"location":"environmental_sample/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_sample/subject/","title":"Slot: subject","text":"

URI: sample:subject

"},{"location":"environmental_sample/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/subject/#properties","title":"Properties","text":""},{"location":"environmental_sample/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/subject/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_sample/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: sample:subject_qualifier

"},{"location":"environmental_sample/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/subject_qualifier/#properties","title":"Properties","text":""},{"location":"environmental_sample/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_sample/subject_text/","title":"Slot: subject_text","text":"

URI: sample:subject_text

"},{"location":"environmental_sample/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_sample/subject_text/#properties","title":"Properties","text":""},{"location":"environmental_sample/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_sample/title/","title":"Slot: title","text":"

The title of the publication

URI: sample:title

"},{"location":"environmental_sample/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_sample/title/#properties","title":"Properties","text":""},{"location":"environmental_sample/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/title/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_sample/triples/","title":"Slot: triples","text":"

URI: sample:triples

"},{"location":"environmental_sample/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"environmental_sample/triples/#properties","title":"Properties","text":""},{"location":"environmental_sample/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/triples/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"environmental_sample/unit/","title":"Slot: unit","text":"

the unit of the measurement

URI: sample:unit

"},{"location":"environmental_sample/unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Measurement no"},{"location":"environmental_sample/unit/#properties","title":"Properties","text":""},{"location":"environmental_sample/unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/unit/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/unit/#linkml-source","title":"LinkML Source","text":"
name: unit\ndescription: the unit of the measurement\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: unit\nowner: Measurement\ndomain_of:\n- Measurement\nrange: Unit\n\n
"},{"location":"environmental_sample/value/","title":"Slot: value","text":"

the value of the measurement

URI: sample:value

"},{"location":"environmental_sample/value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Measurement no"},{"location":"environmental_sample/value/#properties","title":"Properties","text":""},{"location":"environmental_sample/value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/value/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/value/#linkml-source","title":"LinkML Source","text":"
name: value\ndescription: the value of the measurement\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: value\nowner: Measurement\ndomain_of:\n- Measurement\nrange: string\n\n
"},{"location":"environmental_sample/variables/","title":"Slot: variables","text":"

URI: sample:variables

"},{"location":"environmental_sample/variables/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/variables/#properties","title":"Properties","text":""},{"location":"environmental_sample/variables/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/variables/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of study variables"},{"location":"environmental_sample/variables/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/variables/#linkml-source","title":"LinkML Source","text":"
name: variables\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of study variables\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: variables\nowner: Study\ndomain_of:\n- Study\nrange: Variable\n\n
"},{"location":"gene_description_term/","title":"GO Term Template","text":"

A simple GO term template for NER

URI: https://w3id.org/ontogpt/go_term

Name: go-term-template

"},{"location":"gene_description_term/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nGeneDescriptionTerm {\n    string label  \n    string id  \n}\n\n\n\n
"},{"location":"gene_description_term/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text GeneDescription A summarization of an individual gene NamedEntity None Gene None GeneDescriptionTerm None RelationshipType None Publication None TextWithTriples None"},{"location":"gene_description_term/#slots","title":"Slots","text":"Slot Description about The official symbol of the gene that is described abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label the name of the GO term named_entities Named entities extracted from the text narrative_summary A free text summary describing the function of the gene object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text terms A semicolon separated list of controlled terms drawn from the Gene Ontology t... title The title of the publication triples"},{"location":"gene_description_term/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"gene_description_term/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"gene_description_term/#subsets","title":"Subsets","text":"Subset Description"},{"location":"gene_description_term/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: bp:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"gene_description_term/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"gene_description_term/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:AnnotatorResult native bp:AnnotatorResult"},{"location":"gene_description_term/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n\n
"},{"location":"gene_description_term/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"gene_description_term/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"gene_description_term/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"gene_description_term/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"gene_description_term/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Any/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native bp:Any"},{"location":"gene_description_term/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/go_term\nclass_uri: linkml:Any\n\n
"},{"location":"gene_description_term/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/go_term\nclass_uri: linkml:Any\n\n
"},{"location":"gene_description_term/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"gene_description_term/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: bp:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"gene_description_term/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"gene_description_term/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:CompoundExpression native bp:CompoundExpression"},{"location":"gene_description_term/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/go_term\nabstract: true\n\n
"},{"location":"gene_description_term/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/go_term\nabstract: true\n\n
"},{"location":"gene_description_term/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"gene_description_term/Curie/#comments","title":"Comments","text":""},{"location":"gene_description_term/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Curie/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"gene_description_term/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Date/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"gene_description_term/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"gene_description_term/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"gene_description_term/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"gene_description_term/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Double/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: bp:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"gene_description_term/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"gene_description_term/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ExtractionResult native bp:ExtractionResult"},{"location":"gene_description_term/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gene_description_term/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gene_description_term/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"gene_description_term/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Float/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Gene/","title":"Class: Gene","text":"

URI: bp:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gene_description_term/Gene/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gene_description_term/Gene/#usages","title":"Usages","text":"used by used in type used GeneDescription about range Gene"},{"location":"gene_description_term/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gene_description_term/Gene/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hgnc"},{"location":"gene_description_term/Gene/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Gene native bp:Gene"},{"location":"gene_description_term/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\n\n
"},{"location":"gene_description_term/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/go_term\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - GeneDescriptionTerm\n    - NamedEntity\n    range: string\n\n
"},{"location":"gene_description_term/GeneDescription/","title":"Class: GeneDescription","text":"

A summarization of an individual gene

URI: bp:GeneDescription

erDiagram\nGeneDescription {\n    string narrative_summary  \n}\nGeneDescriptionTerm {\n    string label  \n    string id  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneDescription ||--|o Gene : \"about\"\nGeneDescription ||--}o GeneDescriptionTerm : \"terms\"\n\n
"},{"location":"gene_description_term/GeneDescription/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance about 0..1 Gene The official symbol of the gene that is described direct narrative_summary 0..1 String A free text summary describing the function of the gene direct terms 0..* GeneDescriptionTerm A semicolon separated list of controlled terms drawn from the Gene Ontology t... direct"},{"location":"gene_description_term/GeneDescription/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/GeneDescription/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/GeneDescription/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:GeneDescription native bp:GeneDescription"},{"location":"gene_description_term/GeneDescription/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/GeneDescription/#direct","title":"Direct","text":"
name: GeneDescription\ndescription: A summarization of an individual gene\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  about:\n    name: about\n    description: The official symbol of the gene that is described. For example \"TP53\".\n      Do not include the word \"gene\" in the answer.\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: Gene\n  narrative_summary:\n    name: narrative_summary\n    description: A free text summary describing the function of the gene\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: string\n  terms:\n    name: terms\n    description: A semicolon separated list of controlled terms drawn from the Gene\n      Ontology that describe the function of the gene\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    range: GeneDescriptionTerm\n\n
"},{"location":"gene_description_term/GeneDescription/#induced","title":"Induced","text":"
name: GeneDescription\ndescription: A summarization of an individual gene\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  about:\n    name: about\n    description: The official symbol of the gene that is described. For example \"TP53\".\n      Do not include the word \"gene\" in the answer.\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: about\n    owner: GeneDescription\n    domain_of:\n    - GeneDescription\n    range: Gene\n  narrative_summary:\n    name: narrative_summary\n    description: A free text summary describing the function of the gene\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: narrative_summary\n    owner: GeneDescription\n    domain_of:\n    - GeneDescription\n    range: string\n  terms:\n    name: terms\n    description: A semicolon separated list of controlled terms drawn from the Gene\n      Ontology that describe the function of the gene\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    alias: terms\n    owner: GeneDescription\n    domain_of:\n    - GeneDescription\n    range: GeneDescriptionTerm\n\n
"},{"location":"gene_description_term/GeneDescriptionTerm/","title":"Class: GeneDescriptionTerm","text":"

URI: bp:GeneDescriptionTerm

erDiagram\nGeneDescriptionTerm {\n    string label  \n    string id  \n}\n\n\n\n
"},{"location":"gene_description_term/GeneDescriptionTerm/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/GeneDescriptionTerm/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 0..1 String the name of the GO term direct id 1..1 String A unique identifier for the named entity NamedEntity"},{"location":"gene_description_term/GeneDescriptionTerm/#usages","title":"Usages","text":"used by used in type used GeneDescription terms range GeneDescriptionTerm"},{"location":"gene_description_term/GeneDescriptionTerm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/GeneDescriptionTerm/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gene_description_term/GeneDescriptionTerm/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh"},{"location":"gene_description_term/GeneDescriptionTerm/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/GeneDescriptionTerm/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:GeneDescriptionTerm native bp:GeneDescriptionTerm"},{"location":"gene_description_term/GeneDescriptionTerm/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/GeneDescriptionTerm/#direct","title":"Direct","text":"
name: GeneDescriptionTerm\nid_prefixes:\n- GO\n- MONDO\n- UBERON\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the GO term\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\ntree_root: true\n\n
"},{"location":"gene_description_term/GeneDescriptionTerm/#induced","title":"Induced","text":"
name: GeneDescriptionTerm\nid_prefixes:\n- GO\n- MONDO\n- UBERON\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the GO term\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: label\n    owner: GeneDescriptionTerm\n    domain_of:\n    - GeneDescriptionTerm\n    - NamedEntity\n    range: string\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: GeneDescriptionTerm\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\ntree_root: true\n\n
"},{"location":"gene_description_term/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"gene_description_term/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Integer/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/NamedEntity/","title":"Class: NamedEntity","text":"

URI: bp:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gene_description_term/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"gene_description_term/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"gene_description_term/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:NamedEntity native bp:NamedEntity"},{"location":"gene_description_term/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/go_term\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/go_term\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"gene_description_term/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/go_term\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/go_term\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - GeneDescriptionTerm\n    - NamedEntity\n    range: string\n\n
"},{"location":"gene_description_term/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"gene_description_term/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"gene_description_term/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"gene_description_term/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"gene_description_term/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"gene_description_term/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"gene_description_term/Objectidentifier/#comments","title":"Comments","text":""},{"location":"gene_description_term/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Publication/","title":"Class: Publication","text":"

URI: bp:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"gene_description_term/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"gene_description_term/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"gene_description_term/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Publication/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Publication native bp:Publication"},{"location":"gene_description_term/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/go_term\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n\n
"},{"location":"gene_description_term/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/go_term\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"gene_description_term/RelationshipType/","title":"Class: RelationshipType","text":"

URI: bp:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gene_description_term/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gene_description_term/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"gene_description_term/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gene_description_term/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:RelationshipType native bp:RelationshipType"},{"location":"gene_description_term/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\n\n
"},{"location":"gene_description_term/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/go_term\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - GeneDescriptionTerm\n    - NamedEntity\n    range: string\n\n
"},{"location":"gene_description_term/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"gene_description_term/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/String/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: bp:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"gene_description_term/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"gene_description_term/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:TextWithTriples native bp:TextWithTriples"},{"location":"gene_description_term/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gene_description_term/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gene_description_term/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"gene_description_term/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Time/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: bp:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"gene_description_term/Triple/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"gene_description_term/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"gene_description_term/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Triple/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Triple native bp:Triple"},{"location":"gene_description_term/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"gene_description_term/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"gene_description_term/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"gene_description_term/Uri/#comments","title":"Comments","text":""},{"location":"gene_description_term/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Uri/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"gene_description_term/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/about/","title":"Slot: about","text":"

The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.

URI: bp:about

"},{"location":"gene_description_term/about/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneDescription A summarization of an individual gene no"},{"location":"gene_description_term/about/#properties","title":"Properties","text":""},{"location":"gene_description_term/about/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/about/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/about/#linkml-source","title":"LinkML Source","text":"
name: about\ndescription: The official symbol of the gene that is described. For example \"TP53\".\n  Do not include the word \"gene\" in the answer.\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: about\nowner: GeneDescription\ndomain_of:\n- GeneDescription\nrange: Gene\n\n
"},{"location":"gene_description_term/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: bp:abstract

"},{"location":"gene_description_term/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gene_description_term/abstract/#properties","title":"Properties","text":""},{"location":"gene_description_term/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/abstract/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gene_description_term/combined_text/","title":"Slot: combined_text","text":"

URI: bp:combined_text

"},{"location":"gene_description_term/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gene_description_term/combined_text/#properties","title":"Properties","text":""},{"location":"gene_description_term/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gene_description_term/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: bp:extracted_object

"},{"location":"gene_description_term/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/extracted_object/#properties","title":"Properties","text":""},{"location":"gene_description_term/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"gene_description_term/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: bp:full_text

"},{"location":"gene_description_term/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gene_description_term/full_text/#properties","title":"Properties","text":""},{"location":"gene_description_term/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/full_text/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gene_description_term/go-term-template/","title":"go-term-template","text":"

A simple GO term template for NER

URI: https://w3id.org/ontogpt/go_term

"},{"location":"gene_description_term/id/","title":"Slot: id","text":"

URI: bp:id

"},{"location":"gene_description_term/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no GeneDescriptionTerm no NamedEntity no RelationshipType no Publication no"},{"location":"gene_description_term/id/#properties","title":"Properties","text":""},{"location":"gene_description_term/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"gene_description_term/input_id/","title":"Slot: input_id","text":"

URI: bp:input_id

"},{"location":"gene_description_term/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/input_id/#properties","title":"Properties","text":""},{"location":"gene_description_term/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/input_id/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gene_description_term/input_text/","title":"Slot: input_text","text":"

URI: bp:input_text

"},{"location":"gene_description_term/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/input_text/#properties","title":"Properties","text":""},{"location":"gene_description_term/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/input_text/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gene_description_term/input_title/","title":"Slot: input_title","text":"

URI: bp:input_title

"},{"location":"gene_description_term/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/input_title/#properties","title":"Properties","text":""},{"location":"gene_description_term/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/input_title/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gene_description_term/label/","title":"Slot: label","text":"

URI: bp:label

"},{"location":"gene_description_term/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no GeneDescriptionTerm no NamedEntity no RelationshipType no"},{"location":"gene_description_term/label/#properties","title":"Properties","text":""},{"location":"gene_description_term/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- GeneDescriptionTerm\n- NamedEntity\nrange: string\n\n
"},{"location":"gene_description_term/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: bp:named_entities

"},{"location":"gene_description_term/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/named_entities/#properties","title":"Properties","text":""},{"location":"gene_description_term/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gene_description_term/narrative_summary/","title":"Slot: narrative_summary","text":"

A free text summary describing the function of the gene

URI: bp:narrative_summary

"},{"location":"gene_description_term/narrative_summary/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneDescription A summarization of an individual gene no"},{"location":"gene_description_term/narrative_summary/#properties","title":"Properties","text":""},{"location":"gene_description_term/narrative_summary/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/narrative_summary/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/narrative_summary/#linkml-source","title":"LinkML Source","text":"
name: narrative_summary\ndescription: A free text summary describing the function of the gene\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: narrative_summary\nowner: GeneDescription\ndomain_of:\n- GeneDescription\nrange: string\n\n
"},{"location":"gene_description_term/object/","title":"Slot: object","text":"

URI: bp:object

"},{"location":"gene_description_term/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/object/#properties","title":"Properties","text":""},{"location":"gene_description_term/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/object/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gene_description_term/object_id/","title":"Slot: object_id","text":"

URI: bp:object_id

"},{"location":"gene_description_term/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gene_description_term/object_id/#properties","title":"Properties","text":""},{"location":"gene_description_term/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/object_id/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gene_description_term/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: bp:object_qualifier

"},{"location":"gene_description_term/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/object_qualifier/#properties","title":"Properties","text":""},{"location":"gene_description_term/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gene_description_term/object_text/","title":"Slot: object_text","text":"

URI: bp:object_text

"},{"location":"gene_description_term/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gene_description_term/object_text/#properties","title":"Properties","text":""},{"location":"gene_description_term/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/object_text/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gene_description_term/predicate/","title":"Slot: predicate","text":"

URI: bp:predicate

"},{"location":"gene_description_term/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/predicate/#properties","title":"Properties","text":""},{"location":"gene_description_term/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/predicate/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"gene_description_term/prompt/","title":"Slot: prompt","text":"

URI: bp:prompt

"},{"location":"gene_description_term/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/prompt/#properties","title":"Properties","text":""},{"location":"gene_description_term/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/prompt/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gene_description_term/publication/","title":"Slot: publication","text":"

URI: bp:publication

"},{"location":"gene_description_term/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"gene_description_term/publication/#properties","title":"Properties","text":""},{"location":"gene_description_term/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"gene_description_term/publication/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"gene_description_term/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: bp:qualifier

"},{"location":"gene_description_term/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/qualifier/#properties","title":"Properties","text":""},{"location":"gene_description_term/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"gene_description_term/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: bp:raw_completion_output

"},{"location":"gene_description_term/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/raw_completion_output/#properties","title":"Properties","text":""},{"location":"gene_description_term/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gene_description_term/subject/","title":"Slot: subject","text":"

URI: bp:subject

"},{"location":"gene_description_term/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/subject/#properties","title":"Properties","text":""},{"location":"gene_description_term/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/subject/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gene_description_term/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: bp:subject_qualifier

"},{"location":"gene_description_term/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/subject_qualifier/#properties","title":"Properties","text":""},{"location":"gene_description_term/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gene_description_term/subject_text/","title":"Slot: subject_text","text":"

URI: bp:subject_text

"},{"location":"gene_description_term/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gene_description_term/subject_text/#properties","title":"Properties","text":""},{"location":"gene_description_term/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gene_description_term/terms/","title":"Slot: terms","text":"

A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene

URI: bp:terms

"},{"location":"gene_description_term/terms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneDescription A summarization of an individual gene no"},{"location":"gene_description_term/terms/#properties","title":"Properties","text":""},{"location":"gene_description_term/terms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/terms/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/terms/#linkml-source","title":"LinkML Source","text":"
name: terms\ndescription: A semicolon separated list of controlled terms drawn from the Gene Ontology\n  that describe the function of the gene\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nmultivalued: true\nalias: terms\nowner: GeneDescription\ndomain_of:\n- GeneDescription\nrange: GeneDescriptionTerm\n\n
"},{"location":"gene_description_term/title/","title":"Slot: title","text":"

The title of the publication

URI: bp:title

"},{"location":"gene_description_term/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gene_description_term/title/#properties","title":"Properties","text":""},{"location":"gene_description_term/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/title/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gene_description_term/triples/","title":"Slot: triples","text":"

URI: bp:triples

"},{"location":"gene_description_term/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"gene_description_term/triples/#properties","title":"Properties","text":""},{"location":"gene_description_term/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/triples/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gocam/","title":"GO-CAM Template","text":"

A template for GO-CAMs

URI: http://w3id.org/ontogpt/gocam

Name: gocam-template

"},{"location":"gocam/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nGoCamAnnotations {\n\n}\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nGeneGeneInteraction {\n\n}\nPathway {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\n\nGoCamAnnotations ||--}o Gene : \"genes\"\nGoCamAnnotations ||--}o Organism : \"organisms\"\nGoCamAnnotations ||--}o GeneOrganismRelationship : \"gene_organisms\"\nGoCamAnnotations ||--}o MolecularActivity : \"activities\"\nGoCamAnnotations ||--}o GeneMolecularActivityRelationship : \"gene_functions\"\nGoCamAnnotations ||--}o CellularProcess : \"cellular_processes\"\nGoCamAnnotations ||--}o Pathway : \"pathways\"\nGoCamAnnotations ||--}o GeneGeneInteraction : \"gene_gene_interactions\"\nGoCamAnnotations ||--}o GeneSubcellularLocalizationRelationship : \"gene_localizations\"\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"gocam/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None GeneGeneInteraction None GeneMolecularActivityRelationship None GeneMolecularActivityRelationship2 None GeneOrganismRelationship None GeneSubcellularLocalizationRelationship None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text GoCamAnnotations None NamedEntity None CellularProcess None Gene None GeneLocation None MolecularActivity None Molecule None Organism None Pathway None RelationshipType None Publication None TextWithTriples None"},{"location":"gocam/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication activities semicolon-separated list of molecular activities cellular_processes semicolon-separated list of cellular processes combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication gene gene1 gene2 gene_functions semicolon-separated list of gene to molecular activity relationships gene_gene_interactions semicolon-separated list of gene to gene interactions gene_localizations semicolon-separated list of genes plus their location in the cell; for exampl... gene_organisms genes semicolon-separated list of genes id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing location molecular_activity named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text organism organisms semicolon-separated list of organism taxons pathways semicolon-separated list of pathways predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text target title The title of the publication triples"},{"location":"gocam/#enumerations","title":"Enumerations","text":"Enumeration Description CellType GeneLocationEnum GOCellComponentType NullDataOptions"},{"location":"gocam/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"gocam/#subsets","title":"Subsets","text":"Subset Description"},{"location":"gocam/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: gocam:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"gocam/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"gocam/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"gocam/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:AnnotatorResult native gocam:AnnotatorResult"},{"location":"gocam/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n\n
"},{"location":"gocam/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"gocam/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"gocam/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"gocam/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"gocam/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Any/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native gocam:Any"},{"location":"gocam/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/gocam\nclass_uri: linkml:Any\n\n
"},{"location":"gocam/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/gocam\nclass_uri: linkml:Any\n\n
"},{"location":"gocam/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"gocam/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"gocam/CellType/","title":"Enum: CellType","text":"

URI: CellType

This is a dynamic enum

"},{"location":"gocam/CellType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/CellType/#schema-source","title":"Schema Source","text":""},{"location":"gocam/CellType/#linkml-source","title":"LinkML Source","text":"
name: CellType\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nreachable_from:\n  source_ontology: obo:cl\n  source_nodes:\n  - CL:0000000\n\n
"},{"location":"gocam/CellularProcess/","title":"Class: CellularProcess","text":"

URI: gocam:CellularProcess

erDiagram\nCellularProcess {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/CellularProcess/#inheritance","title":"Inheritance","text":""},{"location":"gocam/CellularProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/CellularProcess/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations cellular_processes range CellularProcess"},{"location":"gocam/CellularProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/CellularProcess/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/CellularProcess/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"gocam/CellularProcess/#schema-source","title":"Schema Source","text":""},{"location":"gocam/CellularProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:CellularProcess native gocam:CellularProcess"},{"location":"gocam/CellularProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/CellularProcess/#direct","title":"Direct","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/CellularProcess/#induced","title":"Induced","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: gocam:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"gocam/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"gocam/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"gocam/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"gocam/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:CompoundExpression native gocam:CompoundExpression"},{"location":"gocam/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\n\n
"},{"location":"gocam/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\n\n
"},{"location":"gocam/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"gocam/Curie/#comments","title":"Comments","text":""},{"location":"gocam/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Curie/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"gocam/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Date/#schema-source","title":"Schema Source","text":""},{"location":"gocam/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"gocam/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"gocam/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"gocam/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"gocam/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Double/#schema-source","title":"Schema Source","text":""},{"location":"gocam/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: gocam:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"gocam/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"gocam/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"gocam/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:ExtractionResult native gocam:ExtractionResult"},{"location":"gocam/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gocam/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gocam/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"gocam/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Float/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GOCellComponentType/","title":"Enum: GOCellComponentType","text":"

URI: GOCellComponentType

This is a dynamic enum

"},{"location":"gocam/GOCellComponentType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GOCellComponentType/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GOCellComponentType/#linkml-source","title":"LinkML Source","text":"
name: GOCellComponentType\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nreachable_from:\n  source_ontology: obo:go\n  source_nodes:\n  - GO:0005575\n\n
"},{"location":"gocam/Gene/","title":"Class: Gene","text":"

URI: gocam:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/Gene/#inheritance","title":"Inheritance","text":""},{"location":"gocam/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/Gene/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations genes range Gene GeneOrganismRelationship gene range Gene GeneMolecularActivityRelationship gene range Gene GeneMolecularActivityRelationship2 gene range Gene GeneSubcellularLocalizationRelationship gene range Gene GeneGeneInteraction gene1 range Gene GeneGeneInteraction gene2 range Gene"},{"location":"gocam/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, bioportal:hgnc-nr"},{"location":"gocam/Gene/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Gene native gocam:Gene"},{"location":"gocam/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/GeneGeneInteraction/","title":"Class: GeneGeneInteraction","text":"

URI: gocam:GeneGeneInteraction

erDiagram\nGeneGeneInteraction {\n\n}\nGene {\n    string id  \n    string label  \n}\n\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\n\n
"},{"location":"gocam/GeneGeneInteraction/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneGeneInteraction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene1 0..1 Gene direct gene2 0..1 Gene direct"},{"location":"gocam/GeneGeneInteraction/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations gene_gene_interactions range GeneGeneInteraction"},{"location":"gocam/GeneGeneInteraction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneGeneInteraction/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneGeneInteraction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneGeneInteraction native gocam:GeneGeneInteraction"},{"location":"gocam/GeneGeneInteraction/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneGeneInteraction/#direct","title":"Direct","text":"
name: GeneGeneInteraction\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene1:\n    name: gene1\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n  gene2:\n    name: gene2\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n\n
"},{"location":"gocam/GeneGeneInteraction/#induced","title":"Induced","text":"
name: GeneGeneInteraction\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene1:\n    name: gene1\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene1\n    owner: GeneGeneInteraction\n    domain_of:\n    - GeneGeneInteraction\n    range: Gene\n  gene2:\n    name: gene2\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene2\n    owner: GeneGeneInteraction\n    domain_of:\n    - GeneGeneInteraction\n    range: Gene\n\n
"},{"location":"gocam/GeneLocation/","title":"Class: GeneLocation","text":"

URI: gocam:GeneLocation

erDiagram\nGeneLocation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/GeneLocation/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneLocation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/GeneLocation/#usages","title":"Usages","text":"used by used in type used GeneSubcellularLocalizationRelationship location range GeneLocation"},{"location":"gocam/GeneLocation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneLocation/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/GeneLocation/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:cl"},{"location":"gocam/GeneLocation/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneLocation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneLocation native gocam:GeneLocation"},{"location":"gocam/GeneLocation/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneLocation/#direct","title":"Direct","text":"
name: GeneLocation\nid_prefixes:\n- GO\n- CL\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - GOCellComponentType\n    - CellType\n    domain_of:\n    - NamedEntity\n    - Publication\n\n
"},{"location":"gocam/GeneLocation/#induced","title":"Induced","text":"
name: GeneLocation\nid_prefixes:\n- GO\n- CL\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - GOCellComponentType\n    - CellType\n    domain_of:\n    - NamedEntity\n    - Publication\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    values_from:\n    - GOCellComponentType\n    - CellType\n    identifier: true\n    alias: id\n    owner: GeneLocation\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: GeneLocation\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/GeneLocationEnum/","title":"Enum: GeneLocationEnum","text":"

URI: GeneLocationEnum

This is a dynamic enum

"},{"location":"gocam/GeneLocationEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneLocationEnum/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneLocationEnum/#linkml-source","title":"LinkML Source","text":"
name: GeneLocationEnum\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\ninherits:\n- GOCellComponent\n- CellType\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship/","title":"Class: GeneMolecularActivityRelationship","text":"

URI: gocam:GeneMolecularActivityRelationship

erDiagram\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneMolecularActivityRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct molecular_activity 0..1 MolecularActivity direct"},{"location":"gocam/GeneMolecularActivityRelationship/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations gene_functions range GeneMolecularActivityRelationship"},{"location":"gocam/GeneMolecularActivityRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneMolecularActivityRelationship/#annotations","title":"Annotations","text":"property value prompt.example TODO

gene: HGNC:1234 molecular_activity: GO:0003674 |

"},{"location":"gocam/GeneMolecularActivityRelationship/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneMolecularActivityRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneMolecularActivityRelationship native gocam:GeneMolecularActivityRelationship"},{"location":"gocam/GeneMolecularActivityRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneMolecularActivityRelationship/#direct","title":"Direct","text":"
name: GeneMolecularActivityRelationship\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: 'TODO\n\n\n      gene: HGNC:1234\n\n      molecular_activity: GO:0003674'\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene in the pair. This comes first.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular function in the pair. This comes second.\n          May be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: MolecularActivity\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship/#induced","title":"Induced","text":"
name: GeneMolecularActivityRelationship\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: 'TODO\n\n\n      gene: HGNC:1234\n\n      molecular_activity: GO:0003674'\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene in the pair. This comes first.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular function in the pair. This comes second.\n          May be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: molecular_activity\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    range: MolecularActivity\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship2/","title":"Class: GeneMolecularActivityRelationship2","text":"

URI: gocam:GeneMolecularActivityRelationship2

erDiagram\nGeneMolecularActivityRelationship2 {\n\n}\nMolecule {\n    string id  \n    string label  \n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneMolecularActivityRelationship2 ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship2 ||--|o MolecularActivity : \"molecular_activity\"\nGeneMolecularActivityRelationship2 ||--|o Molecule : \"target\"\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship2/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneMolecularActivityRelationship2/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct molecular_activity 0..1 MolecularActivity direct target 0..1 Molecule direct"},{"location":"gocam/GeneMolecularActivityRelationship2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneMolecularActivityRelationship2/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneMolecularActivityRelationship2/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneMolecularActivityRelationship2 native gocam:GeneMolecularActivityRelationship2"},{"location":"gocam/GeneMolecularActivityRelationship2/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneMolecularActivityRelationship2/#direct","title":"Direct","text":"
name: GeneMolecularActivityRelationship2\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular activity, for example, ubiquitination. May\n          be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: MolecularActivity\n  target:\n    name: target\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular entity that is the target of the molecular\n          activity.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Molecule\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship2/#induced","title":"Induced","text":"
name: GeneMolecularActivityRelationship2\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular activity, for example, ubiquitination. May\n          be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: molecular_activity\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    range: MolecularActivity\n  target:\n    name: target\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular entity that is the target of the molecular\n          activity.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: target\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneMolecularActivityRelationship2\n    range: Molecule\n\n
"},{"location":"gocam/GeneOrganismRelationship/","title":"Class: GeneOrganismRelationship","text":"

URI: gocam:GeneOrganismRelationship

erDiagram\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"gocam/GeneOrganismRelationship/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneOrganismRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct organism 0..1 Organism direct"},{"location":"gocam/GeneOrganismRelationship/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations gene_organisms range GeneOrganismRelationship"},{"location":"gocam/GeneOrganismRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneOrganismRelationship/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneOrganismRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneOrganismRelationship native gocam:GeneOrganismRelationship"},{"location":"gocam/GeneOrganismRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneOrganismRelationship/#direct","title":"Direct","text":"
name: GeneOrganismRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n  organism:\n    name: organism\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Organism\n\n
"},{"location":"gocam/GeneOrganismRelationship/#induced","title":"Induced","text":"
name: GeneOrganismRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene\n    owner: GeneOrganismRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  organism:\n    name: organism\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: organism\n    owner: GeneOrganismRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    range: Organism\n\n
"},{"location":"gocam/GeneSubcellularLocalizationRelationship/","title":"Class: GeneSubcellularLocalizationRelationship","text":"

URI: gocam:GeneSubcellularLocalizationRelationship

erDiagram\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\n\n
"},{"location":"gocam/GeneSubcellularLocalizationRelationship/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneSubcellularLocalizationRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct location 0..1 GeneLocation direct"},{"location":"gocam/GeneSubcellularLocalizationRelationship/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations gene_localizations range GeneSubcellularLocalizationRelationship"},{"location":"gocam/GeneSubcellularLocalizationRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneSubcellularLocalizationRelationship/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneSubcellularLocalizationRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneSubcellularLocalizationRelationship native gocam:GeneSubcellularLocalizationRelationship"},{"location":"gocam/GeneSubcellularLocalizationRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneSubcellularLocalizationRelationship/#direct","title":"Direct","text":"
name: GeneSubcellularLocalizationRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  location:\n    name: location\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: GeneLocation\n\n
"},{"location":"gocam/GeneSubcellularLocalizationRelationship/#induced","title":"Induced","text":"
name: GeneSubcellularLocalizationRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneSubcellularLocalizationRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  location:\n    name: location\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: location\n    owner: GeneSubcellularLocalizationRelationship\n    domain_of:\n    - GeneSubcellularLocalizationRelationship\n    range: GeneLocation\n\n
"},{"location":"gocam/GoCamAnnotations/","title":"Class: GoCamAnnotations","text":"

URI: gocam:GoCamAnnotations

erDiagram\nGoCamAnnotations {\n\n}\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nGeneGeneInteraction {\n\n}\nPathway {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\n\nGoCamAnnotations ||--}o Gene : \"genes\"\nGoCamAnnotations ||--}o Organism : \"organisms\"\nGoCamAnnotations ||--}o GeneOrganismRelationship : \"gene_organisms\"\nGoCamAnnotations ||--}o MolecularActivity : \"activities\"\nGoCamAnnotations ||--}o GeneMolecularActivityRelationship : \"gene_functions\"\nGoCamAnnotations ||--}o CellularProcess : \"cellular_processes\"\nGoCamAnnotations ||--}o Pathway : \"pathways\"\nGoCamAnnotations ||--}o GeneGeneInteraction : \"gene_gene_interactions\"\nGoCamAnnotations ||--}o GeneSubcellularLocalizationRelationship : \"gene_localizations\"\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"gocam/GoCamAnnotations/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance genes 0..* Gene semicolon-separated list of genes direct organisms 0..* Organism semicolon-separated list of organism taxons direct gene_organisms 0..* GeneOrganismRelationship direct activities 0..* MolecularActivity semicolon-separated list of molecular activities direct gene_functions 0..* GeneMolecularActivityRelationship semicolon-separated list of gene to molecular activity relationships direct cellular_processes 0..* CellularProcess semicolon-separated list of cellular processes direct pathways 0..* Pathway semicolon-separated list of pathways direct gene_gene_interactions 0..* GeneGeneInteraction semicolon-separated list of gene to gene interactions direct gene_localizations 0..* GeneSubcellularLocalizationRelationship semicolon-separated list of genes plus their location in the cell; for exampl... direct"},{"location":"gocam/GoCamAnnotations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GoCamAnnotations/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GoCamAnnotations/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GoCamAnnotations native gocam:GoCamAnnotations"},{"location":"gocam/GoCamAnnotations/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GoCamAnnotations/#direct","title":"Direct","text":"
name: GoCamAnnotations\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Gene\n  organisms:\n    name: organisms\n    description: semicolon-separated list of organism taxons\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Organism\n  gene_organisms:\n    name: gene_organisms\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of asterisk separated gene to organism relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneOrganismRelationship\n  activities:\n    name: activities\n    description: semicolon-separated list of molecular activities\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: MolecularActivity\n  gene_functions:\n    name: gene_functions\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneMolecularActivityRelationship\n  cellular_processes:\n    name: cellular_processes\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: CellularProcess\n  pathways:\n    name: pathways\n    description: semicolon-separated list of pathways\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Pathway\n  gene_gene_interactions:\n    name: gene_gene_interactions\n    description: semicolon-separated list of gene to gene interactions\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneGeneInteraction\n  gene_localizations:\n    name: gene_localizations\n    description: semicolon-separated list of genes plus their location in the cell;\n      for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneSubcellularLocalizationRelationship\ntree_root: true\n\n
"},{"location":"gocam/GoCamAnnotations/#induced","title":"Induced","text":"
name: GoCamAnnotations\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: Gene\n  organisms:\n    name: organisms\n    description: semicolon-separated list of organism taxons\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: organisms\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: Organism\n  gene_organisms:\n    name: gene_organisms\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of asterisk separated gene to organism relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_organisms\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: GeneOrganismRelationship\n  activities:\n    name: activities\n    description: semicolon-separated list of molecular activities\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: activities\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: MolecularActivity\n  gene_functions:\n    name: gene_functions\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_functions\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: GeneMolecularActivityRelationship\n  cellular_processes:\n    name: cellular_processes\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: cellular_processes\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: CellularProcess\n  pathways:\n    name: pathways\n    description: semicolon-separated list of pathways\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: pathways\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: Pathway\n  gene_gene_interactions:\n    name: gene_gene_interactions\n    description: semicolon-separated list of gene to gene interactions\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_gene_interactions\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: GeneGeneInteraction\n  gene_localizations:\n    name: gene_localizations\n    description: semicolon-separated list of genes plus their location in the cell;\n      for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_localizations\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: GeneSubcellularLocalizationRelationship\ntree_root: true\n\n
"},{"location":"gocam/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"gocam/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Integer/#schema-source","title":"Schema Source","text":""},{"location":"gocam/MolecularActivity/","title":"Class: MolecularActivity","text":"

URI: gocam:MolecularActivity

erDiagram\nMolecularActivity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/MolecularActivity/#inheritance","title":"Inheritance","text":""},{"location":"gocam/MolecularActivity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/MolecularActivity/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations activities range MolecularActivity GeneMolecularActivityRelationship molecular_activity range MolecularActivity GeneMolecularActivityRelationship2 molecular_activity range MolecularActivity"},{"location":"gocam/MolecularActivity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/MolecularActivity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/MolecularActivity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"gocam/MolecularActivity/#schema-source","title":"Schema Source","text":""},{"location":"gocam/MolecularActivity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:MolecularActivity native gocam:MolecularActivity"},{"location":"gocam/MolecularActivity/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/MolecularActivity/#direct","title":"Direct","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/MolecularActivity/#induced","title":"Induced","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MolecularActivity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: MolecularActivity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/Molecule/","title":"Class: Molecule","text":"

URI: gocam:Molecule

erDiagram\nMolecule {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/Molecule/#inheritance","title":"Inheritance","text":""},{"location":"gocam/Molecule/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/Molecule/#usages","title":"Usages","text":"used by used in type used GeneMolecularActivityRelationship2 target range Molecule"},{"location":"gocam/Molecule/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Molecule/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/Molecule/#annotations","title":"Annotations","text":"property value annotators gilda:, sqlite:obo:chebi"},{"location":"gocam/Molecule/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Molecule/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Molecule native gocam:Molecule"},{"location":"gocam/Molecule/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Molecule/#direct","title":"Direct","text":"
name: Molecule\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/Molecule/#induced","title":"Induced","text":"
name: Molecule\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Molecule\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Molecule\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/NamedEntity/","title":"Class: NamedEntity","text":"

URI: gocam:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"gocam/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"gocam/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"gocam/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"gocam/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:NamedEntity native gocam:NamedEntity"},{"location":"gocam/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"gocam/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"gocam/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"gocam/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"gocam/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"gocam/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"gocam/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"gocam/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"gocam/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"gocam/Objectidentifier/#comments","title":"Comments","text":""},{"location":"gocam/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Organism/","title":"Class: Organism","text":"

URI: gocam:Organism

erDiagram\nOrganism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/Organism/#inheritance","title":"Inheritance","text":""},{"location":"gocam/Organism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/Organism/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations organisms range Organism GeneOrganismRelationship organism range Organism"},{"location":"gocam/Organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Organism/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/Organism/#annotations","title":"Annotations","text":"property value annotators gilda:, sqlite:obo:ncbitaxon"},{"location":"gocam/Organism/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Organism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Organism native gocam:Organism"},{"location":"gocam/Organism/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Organism/#direct","title":"Direct","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/Organism/#induced","title":"Induced","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/Pathway/","title":"Class: Pathway","text":"

URI: gocam:Pathway

erDiagram\nPathway {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/Pathway/#inheritance","title":"Inheritance","text":""},{"location":"gocam/Pathway/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/Pathway/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations pathways range Pathway"},{"location":"gocam/Pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Pathway/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/Pathway/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:pw"},{"location":"gocam/Pathway/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Pathway/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Pathway native gocam:Pathway"},{"location":"gocam/Pathway/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Pathway/#direct","title":"Direct","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/Pathway/#induced","title":"Induced","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Pathway\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Pathway\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/Publication/","title":"Class: Publication","text":"

URI: gocam:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"gocam/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"gocam/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"gocam/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Publication/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Publication native gocam:Publication"},{"location":"gocam/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/gocam\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n\n
"},{"location":"gocam/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"gocam/RelationshipType/","title":"Class: RelationshipType","text":"

URI: gocam:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"gocam/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"gocam/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"gocam/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:RelationshipType native gocam:RelationshipType"},{"location":"gocam/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"gocam/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/String/#schema-source","title":"Schema Source","text":""},{"location":"gocam/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: gocam:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"gocam/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"gocam/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"gocam/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:TextWithTriples native gocam:TextWithTriples"},{"location":"gocam/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gocam/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gocam/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"gocam/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Time/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: gocam:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"gocam/Triple/#inheritance","title":"Inheritance","text":""},{"location":"gocam/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"gocam/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"gocam/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Triple/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Triple native gocam:Triple"},{"location":"gocam/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"gocam/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"gocam/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"gocam/Uri/#comments","title":"Comments","text":""},{"location":"gocam/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Uri/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"gocam/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"gocam/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: gocam:abstract

"},{"location":"gocam/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gocam/abstract/#properties","title":"Properties","text":""},{"location":"gocam/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/abstract/#schema-source","title":"Schema Source","text":""},{"location":"gocam/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gocam/activities/","title":"Slot: activities","text":"

semicolon-separated list of molecular activities

URI: gocam:activities

"},{"location":"gocam/activities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/activities/#properties","title":"Properties","text":""},{"location":"gocam/activities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/activities/#schema-source","title":"Schema Source","text":""},{"location":"gocam/activities/#linkml-source","title":"LinkML Source","text":"
name: activities\ndescription: semicolon-separated list of molecular activities\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: activities\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: MolecularActivity\n\n
"},{"location":"gocam/cellular_processes/","title":"Slot: cellular_processes","text":"

semicolon-separated list of cellular processes

URI: gocam:cellular_processes

"},{"location":"gocam/cellular_processes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/cellular_processes/#properties","title":"Properties","text":""},{"location":"gocam/cellular_processes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/cellular_processes/#schema-source","title":"Schema Source","text":""},{"location":"gocam/cellular_processes/#linkml-source","title":"LinkML Source","text":"
name: cellular_processes\ndescription: semicolon-separated list of cellular processes\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: cellular_processes\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: CellularProcess\n\n
"},{"location":"gocam/combined_text/","title":"Slot: combined_text","text":"

URI: gocam:combined_text

"},{"location":"gocam/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gocam/combined_text/#properties","title":"Properties","text":""},{"location":"gocam/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"gocam/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gocam/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: gocam:extracted_object

"},{"location":"gocam/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/extracted_object/#properties","title":"Properties","text":""},{"location":"gocam/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"gocam/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"gocam/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: gocam:full_text

"},{"location":"gocam/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gocam/full_text/#properties","title":"Properties","text":""},{"location":"gocam/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/full_text/#schema-source","title":"Schema Source","text":""},{"location":"gocam/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gocam/gene/","title":"Slot: gene","text":"

URI: gocam:gene

"},{"location":"gocam/gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneOrganismRelationship no GeneMolecularActivityRelationship no GeneMolecularActivityRelationship2 no GeneSubcellularLocalizationRelationship no"},{"location":"gocam/gene/#properties","title":"Properties","text":""},{"location":"gocam/gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene/#linkml-source","title":"LinkML Source","text":"
name: gene\nalias: gene\ndomain_of:\n- GeneOrganismRelationship\n- GeneMolecularActivityRelationship\n- GeneMolecularActivityRelationship2\n- GeneSubcellularLocalizationRelationship\nrange: string\n\n
"},{"location":"gocam/gene1/","title":"Slot: gene1","text":"

URI: gocam:gene1

"},{"location":"gocam/gene1/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneGeneInteraction no"},{"location":"gocam/gene1/#properties","title":"Properties","text":""},{"location":"gocam/gene1/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene1/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene1/#linkml-source","title":"LinkML Source","text":"
name: gene1\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: gene1\nowner: GeneGeneInteraction\ndomain_of:\n- GeneGeneInteraction\nrange: Gene\n\n
"},{"location":"gocam/gene2/","title":"Slot: gene2","text":"

URI: gocam:gene2

"},{"location":"gocam/gene2/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneGeneInteraction no"},{"location":"gocam/gene2/#properties","title":"Properties","text":""},{"location":"gocam/gene2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene2/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene2/#linkml-source","title":"LinkML Source","text":"
name: gene2\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: gene2\nowner: GeneGeneInteraction\ndomain_of:\n- GeneGeneInteraction\nrange: Gene\n\n
"},{"location":"gocam/gene_functions/","title":"Slot: gene_functions","text":"

semicolon-separated list of gene to molecular activity relationships

URI: gocam:gene_functions

"},{"location":"gocam/gene_functions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/gene_functions/#properties","title":"Properties","text":""},{"location":"gocam/gene_functions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene_functions/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene_functions/#linkml-source","title":"LinkML Source","text":"
name: gene_functions\ndescription: semicolon-separated list of gene to molecular activity relationships\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_functions\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: GeneMolecularActivityRelationship\n\n
"},{"location":"gocam/gene_gene_interactions/","title":"Slot: gene_gene_interactions","text":"

semicolon-separated list of gene to gene interactions

URI: gocam:gene_gene_interactions

"},{"location":"gocam/gene_gene_interactions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/gene_gene_interactions/#properties","title":"Properties","text":""},{"location":"gocam/gene_gene_interactions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene_gene_interactions/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene_gene_interactions/#linkml-source","title":"LinkML Source","text":"
name: gene_gene_interactions\ndescription: semicolon-separated list of gene to gene interactions\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_gene_interactions\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: GeneGeneInteraction\n\n
"},{"location":"gocam/gene_localizations/","title":"Slot: gene_localizations","text":"

semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"

URI: gocam:gene_localizations

"},{"location":"gocam/gene_localizations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/gene_localizations/#properties","title":"Properties","text":""},{"location":"gocam/gene_localizations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene_localizations/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene_localizations/#linkml-source","title":"LinkML Source","text":"
name: gene_localizations\ndescription: semicolon-separated list of genes plus their location in the cell; for\n  example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_localizations\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: GeneSubcellularLocalizationRelationship\n\n
"},{"location":"gocam/gene_organisms/","title":"Slot: gene_organisms","text":"

URI: gocam:gene_organisms

"},{"location":"gocam/gene_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/gene_organisms/#properties","title":"Properties","text":""},{"location":"gocam/gene_organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene_organisms/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of asterisk separated gene to organism relationships"},{"location":"gocam/gene_organisms/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene_organisms/#linkml-source","title":"LinkML Source","text":"
name: gene_organisms\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of asterisk separated gene to organism relationships\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_organisms\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: GeneOrganismRelationship\n\n
"},{"location":"gocam/genes/","title":"Slot: genes","text":"

semicolon-separated list of genes

URI: gocam:genes

"},{"location":"gocam/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/genes/#properties","title":"Properties","text":""},{"location":"gocam/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/genes/#schema-source","title":"Schema Source","text":""},{"location":"gocam/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\ndescription: semicolon-separated list of genes\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: genes\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: Gene\n\n
"},{"location":"gocam/gocam-template/","title":"gocam-template","text":"

A template for GO-CAMs

URI: http://w3id.org/ontogpt/gocam

"},{"location":"gocam/id/","title":"Slot: id","text":"

URI: gocam:id

"},{"location":"gocam/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Pathway no CellularProcess no MolecularActivity no GeneLocation yes Organism no Molecule no NamedEntity no RelationshipType no Publication no"},{"location":"gocam/id/#properties","title":"Properties","text":""},{"location":"gocam/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"gocam/input_id/","title":"Slot: input_id","text":"

URI: gocam:input_id

"},{"location":"gocam/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/input_id/#properties","title":"Properties","text":""},{"location":"gocam/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/input_id/#schema-source","title":"Schema Source","text":""},{"location":"gocam/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gocam/input_text/","title":"Slot: input_text","text":"

URI: gocam:input_text

"},{"location":"gocam/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/input_text/#properties","title":"Properties","text":""},{"location":"gocam/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/input_text/#schema-source","title":"Schema Source","text":""},{"location":"gocam/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gocam/input_title/","title":"Slot: input_title","text":"

URI: gocam:input_title

"},{"location":"gocam/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/input_title/#properties","title":"Properties","text":""},{"location":"gocam/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/input_title/#schema-source","title":"Schema Source","text":""},{"location":"gocam/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gocam/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"gocam/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Pathway no CellularProcess no MolecularActivity no GeneLocation no Organism no Molecule no NamedEntity no RelationshipType no"},{"location":"gocam/label/#properties","title":"Properties","text":""},{"location":"gocam/label/#aliases","title":"Aliases","text":""},{"location":"gocam/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"gocam/label/#schema-source","title":"Schema Source","text":""},{"location":"gocam/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/gocam\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"gocam/location/","title":"Slot: location","text":"

URI: gocam:location

"},{"location":"gocam/location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneSubcellularLocalizationRelationship no"},{"location":"gocam/location/#properties","title":"Properties","text":""},{"location":"gocam/location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/location/#schema-source","title":"Schema Source","text":""},{"location":"gocam/location/#linkml-source","title":"LinkML Source","text":"
name: location\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: location\nowner: GeneSubcellularLocalizationRelationship\ndomain_of:\n- GeneSubcellularLocalizationRelationship\nrange: GeneLocation\n\n
"},{"location":"gocam/molecular_activity/","title":"Slot: molecular_activity","text":"

URI: gocam:molecular_activity

"},{"location":"gocam/molecular_activity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship no GeneMolecularActivityRelationship2 no"},{"location":"gocam/molecular_activity/#properties","title":"Properties","text":""},{"location":"gocam/molecular_activity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/molecular_activity/#linkml-source","title":"LinkML Source","text":"
name: molecular_activity\nalias: molecular_activity\ndomain_of:\n- GeneMolecularActivityRelationship\n- GeneMolecularActivityRelationship2\nrange: string\n\n
"},{"location":"gocam/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: gocam:named_entities

"},{"location":"gocam/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/named_entities/#properties","title":"Properties","text":""},{"location":"gocam/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"gocam/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gocam/object/","title":"Slot: object","text":"

URI: gocam:object

"},{"location":"gocam/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/object/#properties","title":"Properties","text":""},{"location":"gocam/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/object/#schema-source","title":"Schema Source","text":""},{"location":"gocam/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gocam/object_id/","title":"Slot: object_id","text":"

URI: gocam:object_id

"},{"location":"gocam/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gocam/object_id/#properties","title":"Properties","text":""},{"location":"gocam/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/object_id/#schema-source","title":"Schema Source","text":""},{"location":"gocam/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gocam/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: gocam:object_qualifier

"},{"location":"gocam/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/object_qualifier/#properties","title":"Properties","text":""},{"location":"gocam/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gocam/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gocam/object_text/","title":"Slot: object_text","text":"

URI: gocam:object_text

"},{"location":"gocam/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gocam/object_text/#properties","title":"Properties","text":""},{"location":"gocam/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/object_text/#schema-source","title":"Schema Source","text":""},{"location":"gocam/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gocam/organism/","title":"Slot: organism","text":"

URI: gocam:organism

"},{"location":"gocam/organism/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneOrganismRelationship no"},{"location":"gocam/organism/#properties","title":"Properties","text":""},{"location":"gocam/organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/organism/#schema-source","title":"Schema Source","text":""},{"location":"gocam/organism/#linkml-source","title":"LinkML Source","text":"
name: organism\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: organism\nowner: GeneOrganismRelationship\ndomain_of:\n- GeneOrganismRelationship\nrange: Organism\n\n
"},{"location":"gocam/organisms/","title":"Slot: organisms","text":"

semicolon-separated list of organism taxons

URI: gocam:organisms

"},{"location":"gocam/organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/organisms/#properties","title":"Properties","text":""},{"location":"gocam/organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/organisms/#schema-source","title":"Schema Source","text":""},{"location":"gocam/organisms/#linkml-source","title":"LinkML Source","text":"
name: organisms\ndescription: semicolon-separated list of organism taxons\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: organisms\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: Organism\n\n
"},{"location":"gocam/pathways/","title":"Slot: pathways","text":"

semicolon-separated list of pathways

URI: gocam:pathways

"},{"location":"gocam/pathways/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/pathways/#properties","title":"Properties","text":""},{"location":"gocam/pathways/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/pathways/#schema-source","title":"Schema Source","text":""},{"location":"gocam/pathways/#linkml-source","title":"LinkML Source","text":"
name: pathways\ndescription: semicolon-separated list of pathways\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: pathways\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: Pathway\n\n
"},{"location":"gocam/predicate/","title":"Slot: predicate","text":"

URI: gocam:predicate

"},{"location":"gocam/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/predicate/#properties","title":"Properties","text":""},{"location":"gocam/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/predicate/#schema-source","title":"Schema Source","text":""},{"location":"gocam/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"gocam/prompt/","title":"Slot: prompt","text":"

URI: gocam:prompt

"},{"location":"gocam/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/prompt/#properties","title":"Properties","text":""},{"location":"gocam/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/prompt/#schema-source","title":"Schema Source","text":""},{"location":"gocam/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gocam/publication/","title":"Slot: publication","text":"

URI: gocam:publication

"},{"location":"gocam/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"gocam/publication/#properties","title":"Properties","text":""},{"location":"gocam/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"gocam/publication/#schema-source","title":"Schema Source","text":""},{"location":"gocam/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"gocam/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: gocam:qualifier

"},{"location":"gocam/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/qualifier/#properties","title":"Properties","text":""},{"location":"gocam/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gocam/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"gocam/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: gocam:raw_completion_output

"},{"location":"gocam/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/raw_completion_output/#properties","title":"Properties","text":""},{"location":"gocam/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"gocam/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gocam/subject/","title":"Slot: subject","text":"

URI: gocam:subject

"},{"location":"gocam/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/subject/#properties","title":"Properties","text":""},{"location":"gocam/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/subject/#schema-source","title":"Schema Source","text":""},{"location":"gocam/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gocam/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: gocam:subject_qualifier

"},{"location":"gocam/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/subject_qualifier/#properties","title":"Properties","text":""},{"location":"gocam/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gocam/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gocam/subject_text/","title":"Slot: subject_text","text":"

URI: gocam:subject_text

"},{"location":"gocam/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gocam/subject_text/#properties","title":"Properties","text":""},{"location":"gocam/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"gocam/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gocam/target/","title":"Slot: target","text":"

URI: gocam:target

"},{"location":"gocam/target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship2 no"},{"location":"gocam/target/#properties","title":"Properties","text":""},{"location":"gocam/target/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/target/#annotations","title":"Annotations","text":"property value prompt the name of the molecular entity that is the target of the molecular activity."},{"location":"gocam/target/#schema-source","title":"Schema Source","text":""},{"location":"gocam/target/#linkml-source","title":"LinkML Source","text":"
name: target\nannotations:\n  prompt:\n    tag: prompt\n    value: the name of the molecular entity that is the target of the molecular activity.\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: target\nowner: GeneMolecularActivityRelationship2\ndomain_of:\n- GeneMolecularActivityRelationship2\nrange: Molecule\n\n
"},{"location":"gocam/title/","title":"Slot: title","text":"

The title of the publication

URI: gocam:title

"},{"location":"gocam/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gocam/title/#properties","title":"Properties","text":""},{"location":"gocam/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/title/#schema-source","title":"Schema Source","text":""},{"location":"gocam/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gocam/triples/","title":"Slot: triples","text":"

URI: gocam:triples

"},{"location":"gocam/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"gocam/triples/#properties","title":"Properties","text":""},{"location":"gocam/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/triples/#schema-source","title":"Schema Source","text":""},{"location":"gocam/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"halo/","title":"Ontology Class Template","text":"

A template for Ontology Classes

URI: https://w3id.org/ontogpt/halo

Name: ontology-class

"},{"location":"halo/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nOntology {\n\n}\nOntologyElement {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\nCategory {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nOntology ||--}o OntologyElement : \"elements\"\nOntologyElement ||--}o Category : \"categories\"\nOntologyElement ||--}o OntologyElement : \"subclass_of\"\nOntologyElement ||--}o OntologyElement : \"part_of\"\nOntologyElement ||--}o OntologyElement : \"subtypes\"\nOntologyElement ||--}o OntologyElement : \"parts\"\nCategory ||--}o Category : \"categories\"\nCategory ||--}o OntologyElement : \"subclass_of\"\nCategory ||--}o OntologyElement : \"part_of\"\nCategory ||--}o OntologyElement : \"subtypes\"\nCategory ||--}o OntologyElement : \"parts\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"halo/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None RelationshipType None Ontology None OntologyElement None Category None Publication None TextWithTriples None"},{"location":"halo/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication categories a list of the categories to which this entity belongs combined_text context the ontology to which this belongs (single-valued) description a textual description of the entity (single-valued) elements equivalent_to an OWL class expression with the necessary and sufficient conditions for this... extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing name the name of the entity named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text part_of a list of things this element is part of parts a list of names of things this element has as parts (components) predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subclass_of a list of parent class (superclasses) of this entity subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text subtypes a list of child classes (subclasses) of this entity synonyms a list of alternative names of the entity title The title of the publication triples"},{"location":"halo/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"halo/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"halo/#subsets","title":"Subsets","text":"Subset Description"},{"location":"halo/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: oc:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"halo/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"halo/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"halo/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:AnnotatorResult native oc:AnnotatorResult"},{"location":"halo/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n\n
"},{"location":"halo/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"halo/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"halo/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"halo/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"halo/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Any/#schema-source","title":"Schema Source","text":""},{"location":"halo/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native oc:Any"},{"location":"halo/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/halo\nclass_uri: linkml:Any\n\n
"},{"location":"halo/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/halo\nclass_uri: linkml:Any\n\n
"},{"location":"halo/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"halo/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"halo/Category/","title":"Class: Category","text":"

URI: oc:Category

erDiagram\nCategory {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\nOntologyElement {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\n\nCategory ||--}o Category : \"categories\"\nCategory ||--}o OntologyElement : \"subclass_of\"\nCategory ||--}o OntologyElement : \"part_of\"\nCategory ||--}o OntologyElement : \"subtypes\"\nCategory ||--}o OntologyElement : \"parts\"\nOntologyElement ||--}o Category : \"categories\"\nOntologyElement ||--}o OntologyElement : \"subclass_of\"\nOntologyElement ||--}o OntologyElement : \"part_of\"\nOntologyElement ||--}o OntologyElement : \"subtypes\"\nOntologyElement ||--}o OntologyElement : \"parts\"\n\n
"},{"location":"halo/Category/#inheritance","title":"Inheritance","text":""},{"location":"halo/Category/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance name 1..1 String the name of the entity OntologyElement context 0..1 String the ontology to which this belongs (single-valued) OntologyElement description 0..1 String a textual description of the entity (single-valued) OntologyElement synonyms 0..* String a list of alternative names of the entity OntologyElement categories 0..* Category a list of the categories to which this entity belongs OntologyElement subclass_of 0..* OntologyElement a list of parent class (superclasses) of this entity OntologyElement part_of 0..* OntologyElement a list of things this element is part of OntologyElement subtypes 0..* OntologyElement a list of child classes (subclasses) of this entity OntologyElement parts 0..* OntologyElement a list of names of things this element has as parts (components) OntologyElement equivalent_to 0..1 String an OWL class expression with the necessary and sufficient conditions for this... OntologyElement"},{"location":"halo/Category/#usages","title":"Usages","text":"used by used in type used OntologyElement categories range Category Category categories range Category"},{"location":"halo/Category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Category/#schema-source","title":"Schema Source","text":""},{"location":"halo/Category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Category native oc:Category"},{"location":"halo/Category/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/Category/#direct","title":"Direct","text":"
name: Category\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: OntologyElement\n\n
"},{"location":"halo/Category/#induced","title":"Induced","text":"
name: Category\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: OntologyElement\nattributes:\n  name:\n    name: name\n    description: the name of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    alias: name\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: string\n    required: true\n  context:\n    name: context\n    description: the ontology to which this belongs (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: context\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: string\n  description:\n    name: description\n    description: a textual description of the entity (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: description\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: string\n  synonyms:\n    name: synonyms\n    description: a list of alternative names of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: string\n  categories:\n    name: categories\n    description: a list of the categories to which this entity belongs\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: categories\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: Category\n  subclass_of:\n    name: subclass_of\n    description: a list of parent class (superclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: rdfs:subClassOf\n    multivalued: true\n    alias: subclass_of\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: OntologyElement\n  part_of:\n    name: part_of\n    description: a list of things this element is part of\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: part_of\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: OntologyElement\n  subtypes:\n    name: subtypes\n    description: a list of child classes (subclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: Category\n    domain_of:\n    - OntologyElement\n    inverse: subclass_of\n    range: OntologyElement\n  parts:\n    name: parts\n    description: a list of names of things this element has as parts (components)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: parts\n    owner: Category\n    domain_of:\n    - OntologyElement\n    inverse: part_of\n    range: OntologyElement\n  equivalent_to:\n    name: equivalent_to\n    description: an OWL class expression with the necessary and sufficient conditions\n      for this entity to be an instance of this class\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: equivalent_to\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: string\n\n
"},{"location":"halo/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: oc:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"halo/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"halo/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"halo/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"halo/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:CompoundExpression native oc:CompoundExpression"},{"location":"halo/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/halo\nabstract: true\n\n
"},{"location":"halo/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/halo\nabstract: true\n\n
"},{"location":"halo/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"halo/Curie/#comments","title":"Comments","text":""},{"location":"halo/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Curie/#schema-source","title":"Schema Source","text":""},{"location":"halo/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"halo/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Date/#schema-source","title":"Schema Source","text":""},{"location":"halo/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"halo/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"halo/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"halo/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"halo/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"halo/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"halo/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"halo/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Double/#schema-source","title":"Schema Source","text":""},{"location":"halo/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: oc:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"halo/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"halo/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"halo/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:ExtractionResult native oc:ExtractionResult"},{"location":"halo/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"halo/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Float/#schema-source","title":"Schema Source","text":""},{"location":"halo/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"halo/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Integer/#schema-source","title":"Schema Source","text":""},{"location":"halo/NamedEntity/","title":"Class: NamedEntity","text":"

URI: oc:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"halo/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"halo/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"halo/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"halo/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"halo/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:NamedEntity native oc:NamedEntity"},{"location":"halo/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/halo\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/halo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"halo/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/halo\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/halo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"halo/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"halo/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"halo/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"halo/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"halo/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"halo/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"halo/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"halo/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"halo/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"halo/Objectidentifier/#comments","title":"Comments","text":""},{"location":"halo/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"halo/Ontology/","title":"Class: Ontology","text":"

URI: oc:Ontology

erDiagram\nOntology {\n\n}\nOntologyElement {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\nCategory {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\n\nOntology ||--}o OntologyElement : \"elements\"\nOntologyElement ||--}o Category : \"categories\"\nOntologyElement ||--}o OntologyElement : \"subclass_of\"\nOntologyElement ||--}o OntologyElement : \"part_of\"\nOntologyElement ||--}o OntologyElement : \"subtypes\"\nOntologyElement ||--}o OntologyElement : \"parts\"\nCategory ||--}o Category : \"categories\"\nCategory ||--}o OntologyElement : \"subclass_of\"\nCategory ||--}o OntologyElement : \"part_of\"\nCategory ||--}o OntologyElement : \"subtypes\"\nCategory ||--}o OntologyElement : \"parts\"\n\n
"},{"location":"halo/Ontology/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance elements 0..* OntologyElement direct"},{"location":"halo/Ontology/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Ontology/#schema-source","title":"Schema Source","text":""},{"location":"halo/Ontology/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Ontology native oc:Ontology"},{"location":"halo/Ontology/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/Ontology/#direct","title":"Direct","text":"
name: Ontology\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  elements:\n    name: elements\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    range: OntologyElement\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/Ontology/#induced","title":"Induced","text":"
name: Ontology\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  elements:\n    name: elements\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: elements\n    owner: Ontology\n    domain_of:\n    - Ontology\n    range: OntologyElement\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/OntologyElement/","title":"Class: OntologyElement","text":"

URI: oc:OntologyElement

erDiagram\nOntologyElement {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\nCategory {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\n\nOntologyElement ||--}o Category : \"categories\"\nOntologyElement ||--}o OntologyElement : \"subclass_of\"\nOntologyElement ||--}o OntologyElement : \"part_of\"\nOntologyElement ||--}o OntologyElement : \"subtypes\"\nOntologyElement ||--}o OntologyElement : \"parts\"\nCategory ||--}o Category : \"categories\"\nCategory ||--}o OntologyElement : \"subclass_of\"\nCategory ||--}o OntologyElement : \"part_of\"\nCategory ||--}o OntologyElement : \"subtypes\"\nCategory ||--}o OntologyElement : \"parts\"\n\n
"},{"location":"halo/OntologyElement/#inheritance","title":"Inheritance","text":""},{"location":"halo/OntologyElement/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance name 1..1 String the name of the entity direct context 0..1 String the ontology to which this belongs (single-valued) direct description 0..1 String a textual description of the entity (single-valued) direct synonyms 0..* String a list of alternative names of the entity direct categories 0..* Category a list of the categories to which this entity belongs direct subclass_of 0..* OntologyElement a list of parent class (superclasses) of this entity direct part_of 0..* OntologyElement a list of things this element is part of direct subtypes 0..* OntologyElement a list of child classes (subclasses) of this entity direct parts 0..* OntologyElement a list of names of things this element has as parts (components) direct equivalent_to 0..1 String an OWL class expression with the necessary and sufficient conditions for this... direct"},{"location":"halo/OntologyElement/#usages","title":"Usages","text":"used by used in type used Ontology elements range OntologyElement OntologyElement subclass_of range OntologyElement OntologyElement part_of range OntologyElement OntologyElement subtypes range OntologyElement OntologyElement parts range OntologyElement Category subclass_of range OntologyElement Category part_of range OntologyElement Category subtypes range OntologyElement Category parts range OntologyElement"},{"location":"halo/OntologyElement/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/OntologyElement/#schema-source","title":"Schema Source","text":""},{"location":"halo/OntologyElement/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyElement native oc:OntologyElement"},{"location":"halo/OntologyElement/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/OntologyElement/#direct","title":"Direct","text":"
name: OntologyElement\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  name:\n    name: name\n    description: the name of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    required: true\n  context:\n    name: context\n    description: the ontology to which this belongs (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  description:\n    name: description\n    description: a textual description of the entity (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  synonyms:\n    name: synonyms\n    description: a list of alternative names of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n  categories:\n    name: categories\n    description: a list of the categories to which this entity belongs\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    range: Category\n  subclass_of:\n    name: subclass_of\n    description: a list of parent class (superclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: rdfs:subClassOf\n    multivalued: true\n    range: OntologyElement\n  part_of:\n    name: part_of\n    description: a list of things this element is part of\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: BFO:0000050\n    multivalued: true\n    range: OntologyElement\n  subtypes:\n    name: subtypes\n    description: a list of child classes (subclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    inverse: subclass_of\n    range: OntologyElement\n  parts:\n    name: parts\n    description: a list of names of things this element has as parts (components)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    inverse: part_of\n    range: OntologyElement\n  equivalent_to:\n    name: equivalent_to\n    description: an OWL class expression with the necessary and sufficient conditions\n      for this entity to be an instance of this class\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: string\n\n
"},{"location":"halo/OntologyElement/#induced","title":"Induced","text":"
name: OntologyElement\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  name:\n    name: name\n    description: the name of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    alias: name\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: string\n    required: true\n  context:\n    name: context\n    description: the ontology to which this belongs (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: context\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: string\n  description:\n    name: description\n    description: a textual description of the entity (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: description\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: string\n  synonyms:\n    name: synonyms\n    description: a list of alternative names of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: string\n  categories:\n    name: categories\n    description: a list of the categories to which this entity belongs\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: categories\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: Category\n  subclass_of:\n    name: subclass_of\n    description: a list of parent class (superclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: rdfs:subClassOf\n    multivalued: true\n    alias: subclass_of\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: OntologyElement\n  part_of:\n    name: part_of\n    description: a list of things this element is part of\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: part_of\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: OntologyElement\n  subtypes:\n    name: subtypes\n    description: a list of child classes (subclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    inverse: subclass_of\n    range: OntologyElement\n  parts:\n    name: parts\n    description: a list of names of things this element has as parts (components)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: parts\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    inverse: part_of\n    range: OntologyElement\n  equivalent_to:\n    name: equivalent_to\n    description: an OWL class expression with the necessary and sufficient conditions\n      for this entity to be an instance of this class\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: equivalent_to\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: string\n\n
"},{"location":"halo/Publication/","title":"Class: Publication","text":"

URI: oc:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"halo/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"halo/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"halo/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Publication/#schema-source","title":"Schema Source","text":""},{"location":"halo/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Publication native oc:Publication"},{"location":"halo/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/halo\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n\n
"},{"location":"halo/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/halo\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"halo/RelationshipType/","title":"Class: RelationshipType","text":"

URI: oc:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"halo/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"halo/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"halo/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"halo/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"halo/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"halo/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:RelationshipType native oc:RelationshipType"},{"location":"halo/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: NamedEntity\n\n
"},{"location":"halo/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/halo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"halo/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"halo/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/String/#schema-source","title":"Schema Source","text":""},{"location":"halo/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: oc:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"halo/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"halo/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"halo/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:TextWithTriples native oc:TextWithTriples"},{"location":"halo/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"halo/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Time/#schema-source","title":"Schema Source","text":""},{"location":"halo/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: oc:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"halo/Triple/#inheritance","title":"Inheritance","text":""},{"location":"halo/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"halo/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"halo/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Triple/#schema-source","title":"Schema Source","text":""},{"location":"halo/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Triple native oc:Triple"},{"location":"halo/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"halo/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"halo/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"halo/Uri/#comments","title":"Comments","text":""},{"location":"halo/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Uri/#schema-source","title":"Schema Source","text":""},{"location":"halo/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"halo/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"halo/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: oc:abstract

"},{"location":"halo/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"halo/abstract/#properties","title":"Properties","text":""},{"location":"halo/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/abstract/#schema-source","title":"Schema Source","text":""},{"location":"halo/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"halo/categories/","title":"Slot: categories","text":"

a list of the categories to which this entity belongs

URI: oc:categories

"},{"location":"halo/categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/categories/#properties","title":"Properties","text":""},{"location":"halo/categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/categories/#schema-source","title":"Schema Source","text":""},{"location":"halo/categories/#linkml-source","title":"LinkML Source","text":"
name: categories\ndescription: a list of the categories to which this entity belongs\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: categories\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: Category\n\n
"},{"location":"halo/combined_text/","title":"Slot: combined_text","text":"

URI: oc:combined_text

"},{"location":"halo/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"halo/combined_text/#properties","title":"Properties","text":""},{"location":"halo/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"halo/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"halo/context/","title":"Slot: context","text":"

the ontology to which this belongs (single-valued)

URI: oc:context

"},{"location":"halo/context/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/context/#properties","title":"Properties","text":""},{"location":"halo/context/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/context/#schema-source","title":"Schema Source","text":""},{"location":"halo/context/#linkml-source","title":"LinkML Source","text":"
name: context\ndescription: the ontology to which this belongs (single-valued)\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: context\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: string\n\n
"},{"location":"halo/description/","title":"Slot: description","text":"

a textual description of the entity (single-valued)

URI: oc:description

"},{"location":"halo/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/description/#properties","title":"Properties","text":""},{"location":"halo/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/description/#schema-source","title":"Schema Source","text":""},{"location":"halo/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a textual description of the entity (single-valued)\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: description\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: string\n\n
"},{"location":"halo/elements/","title":"Slot: elements","text":"

URI: oc:elements

"},{"location":"halo/elements/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Ontology no"},{"location":"halo/elements/#properties","title":"Properties","text":""},{"location":"halo/elements/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/elements/#schema-source","title":"Schema Source","text":""},{"location":"halo/elements/#linkml-source","title":"LinkML Source","text":"
name: elements\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: elements\nowner: Ontology\ndomain_of:\n- Ontology\nrange: OntologyElement\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"halo/equivalent_to/","title":"Slot: equivalent_to","text":"

an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class

URI: oc:equivalent_to

"},{"location":"halo/equivalent_to/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/equivalent_to/#properties","title":"Properties","text":""},{"location":"halo/equivalent_to/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/equivalent_to/#schema-source","title":"Schema Source","text":""},{"location":"halo/equivalent_to/#linkml-source","title":"LinkML Source","text":"
name: equivalent_to\ndescription: an OWL class expression with the necessary and sufficient conditions\n  for this entity to be an instance of this class\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: equivalent_to\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: string\n\n
"},{"location":"halo/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: oc:extracted_object

"},{"location":"halo/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/extracted_object/#properties","title":"Properties","text":""},{"location":"halo/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"halo/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"halo/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: oc:full_text

"},{"location":"halo/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"halo/full_text/#properties","title":"Properties","text":""},{"location":"halo/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/full_text/#schema-source","title":"Schema Source","text":""},{"location":"halo/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"halo/id/","title":"Slot: id","text":"

URI: oc:id

"},{"location":"halo/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NamedEntity no RelationshipType no Publication no"},{"location":"halo/id/#properties","title":"Properties","text":""},{"location":"halo/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"halo/input_id/","title":"Slot: input_id","text":"

URI: oc:input_id

"},{"location":"halo/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/input_id/#properties","title":"Properties","text":""},{"location":"halo/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/input_id/#schema-source","title":"Schema Source","text":""},{"location":"halo/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"halo/input_text/","title":"Slot: input_text","text":"

URI: oc:input_text

"},{"location":"halo/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/input_text/#properties","title":"Properties","text":""},{"location":"halo/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/input_text/#schema-source","title":"Schema Source","text":""},{"location":"halo/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"halo/input_title/","title":"Slot: input_title","text":"

URI: oc:input_title

"},{"location":"halo/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/input_title/#properties","title":"Properties","text":""},{"location":"halo/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/input_title/#schema-source","title":"Schema Source","text":""},{"location":"halo/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"halo/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"halo/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NamedEntity no RelationshipType no"},{"location":"halo/label/#properties","title":"Properties","text":""},{"location":"halo/label/#aliases","title":"Aliases","text":""},{"location":"halo/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"halo/label/#schema-source","title":"Schema Source","text":""},{"location":"halo/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: https://w3id.org/ontogpt/halo\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"halo/name/","title":"Slot: name","text":"

the name of the entity

URI: oc:name

"},{"location":"halo/name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/name/#properties","title":"Properties","text":""},{"location":"halo/name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/name/#schema-source","title":"Schema Source","text":""},{"location":"halo/name/#linkml-source","title":"LinkML Source","text":"
name: name\ndescription: the name of the entity\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nidentifier: true\nalias: name\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: string\nrequired: true\n\n
"},{"location":"halo/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: oc:named_entities

"},{"location":"halo/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/named_entities/#properties","title":"Properties","text":""},{"location":"halo/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"halo/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"halo/object/","title":"Slot: object","text":"

URI: oc:object

"},{"location":"halo/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/object/#properties","title":"Properties","text":""},{"location":"halo/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/object/#schema-source","title":"Schema Source","text":""},{"location":"halo/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"halo/object_id/","title":"Slot: object_id","text":"

URI: oc:object_id

"},{"location":"halo/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"halo/object_id/#properties","title":"Properties","text":""},{"location":"halo/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/object_id/#schema-source","title":"Schema Source","text":""},{"location":"halo/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"halo/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: oc:object_qualifier

"},{"location":"halo/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/object_qualifier/#properties","title":"Properties","text":""},{"location":"halo/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"halo/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"halo/object_text/","title":"Slot: object_text","text":"

URI: oc:object_text

"},{"location":"halo/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"halo/object_text/#properties","title":"Properties","text":""},{"location":"halo/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/object_text/#schema-source","title":"Schema Source","text":""},{"location":"halo/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"halo/ontology-class/","title":"ontology-class","text":"

A template for Ontology Classes

URI: https://w3id.org/ontogpt/halo

"},{"location":"halo/part_of/","title":"Slot: part_of","text":"

a list of things this element is part of

URI: BFO:0000050

"},{"location":"halo/part_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/part_of/#properties","title":"Properties","text":""},{"location":"halo/part_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/part_of/#schema-source","title":"Schema Source","text":""},{"location":"halo/part_of/#linkml-source","title":"LinkML Source","text":"
name: part_of\ndescription: a list of things this element is part of\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nslot_uri: BFO:0000050\nmultivalued: true\nalias: part_of\ndomain_of:\n- OntologyElement\nrange: OntologyElement\n\n
"},{"location":"halo/parts/","title":"Slot: parts","text":"

a list of names of things this element has as parts (components)

URI: oc:parts

"},{"location":"halo/parts/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/parts/#properties","title":"Properties","text":""},{"location":"halo/parts/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/parts/#schema-source","title":"Schema Source","text":""},{"location":"halo/parts/#linkml-source","title":"LinkML Source","text":"
name: parts\ndescription: a list of names of things this element has as parts (components)\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: parts\nowner: OntologyElement\ndomain_of:\n- OntologyElement\ninverse: part_of\nrange: OntologyElement\n\n
"},{"location":"halo/predicate/","title":"Slot: predicate","text":"

URI: oc:predicate

"},{"location":"halo/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/predicate/#properties","title":"Properties","text":""},{"location":"halo/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/predicate/#schema-source","title":"Schema Source","text":""},{"location":"halo/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"halo/prompt/","title":"Slot: prompt","text":"

URI: oc:prompt

"},{"location":"halo/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/prompt/#properties","title":"Properties","text":""},{"location":"halo/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/prompt/#schema-source","title":"Schema Source","text":""},{"location":"halo/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"halo/publication/","title":"Slot: publication","text":"

URI: oc:publication

"},{"location":"halo/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"halo/publication/#properties","title":"Properties","text":""},{"location":"halo/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"halo/publication/#schema-source","title":"Schema Source","text":""},{"location":"halo/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"halo/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: oc:qualifier

"},{"location":"halo/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/qualifier/#properties","title":"Properties","text":""},{"location":"halo/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"halo/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"halo/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: oc:raw_completion_output

"},{"location":"halo/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/raw_completion_output/#properties","title":"Properties","text":""},{"location":"halo/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"halo/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"halo/subclass_of/","title":"Slot: subclass_of","text":"

a list of parent class (superclasses) of this entity

URI: rdfs:subClassOf

"},{"location":"halo/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/subclass_of/#properties","title":"Properties","text":""},{"location":"halo/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"halo/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\ndescription: a list of parent class (superclasses) of this entity\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nslot_uri: rdfs:subClassOf\nmultivalued: true\nalias: subclass_of\ndomain_of:\n- OntologyElement\nrange: OntologyElement\n\n
"},{"location":"halo/subject/","title":"Slot: subject","text":"

URI: oc:subject

"},{"location":"halo/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/subject/#properties","title":"Properties","text":""},{"location":"halo/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/subject/#schema-source","title":"Schema Source","text":""},{"location":"halo/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"halo/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: oc:subject_qualifier

"},{"location":"halo/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/subject_qualifier/#properties","title":"Properties","text":""},{"location":"halo/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"halo/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"halo/subject_text/","title":"Slot: subject_text","text":"

URI: oc:subject_text

"},{"location":"halo/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"halo/subject_text/#properties","title":"Properties","text":""},{"location":"halo/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"halo/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"halo/subtypes/","title":"Slot: subtypes","text":"

a list of child classes (subclasses) of this entity

URI: oc:subtypes

"},{"location":"halo/subtypes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/subtypes/#properties","title":"Properties","text":""},{"location":"halo/subtypes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/subtypes/#schema-source","title":"Schema Source","text":""},{"location":"halo/subtypes/#linkml-source","title":"LinkML Source","text":"
name: subtypes\ndescription: a list of child classes (subclasses) of this entity\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: subtypes\nowner: OntologyElement\ndomain_of:\n- OntologyElement\ninverse: subclass_of\nrange: OntologyElement\n\n
"},{"location":"halo/synonyms/","title":"Slot: synonyms","text":"

a list of alternative names of the entity

URI: oc:synonyms

"},{"location":"halo/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/synonyms/#properties","title":"Properties","text":""},{"location":"halo/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"halo/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\ndescription: a list of alternative names of the entity\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: string\n\n
"},{"location":"halo/title/","title":"Slot: title","text":"

The title of the publication

URI: oc:title

"},{"location":"halo/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"halo/title/#properties","title":"Properties","text":""},{"location":"halo/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/title/#schema-source","title":"Schema Source","text":""},{"location":"halo/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"halo/triples/","title":"Slot: triples","text":"

URI: oc:triples

"},{"location":"halo/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"halo/triples/#properties","title":"Properties","text":""},{"location":"halo/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/triples/#schema-source","title":"Schema Source","text":""},{"location":"halo/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"human_phenotype/","title":"Human Phenotype Extraction Template","text":"

A template for extracting human phenotypes to HPO terms

URI: http://w3id.org/ontogpt/human_phenotype

Name: human_phenotype-template

"},{"location":"human_phenotype/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nHumanPhenotypeSet {\n    string id  \n    string label  \n}\nHumanPhenotype {\n    string id  \n    string label  \n}\n\nHumanPhenotypeSet ||--}o HumanPhenotype : \"phenotypes\"\n\n
"},{"location":"human_phenotype/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None HumanPhenotype None HumanPhenotypeSet None RelationshipType None Publication None TextWithTriples None"},{"location":"human_phenotype/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text phenotypes A semicolon-separated list of human phenotypes, including symptoms of disease predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"human_phenotype/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"human_phenotype/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"human_phenotype/#subsets","title":"Subsets","text":"Subset Description"},{"location":"human_phenotype/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: human_phenotype:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"human_phenotype/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"human_phenotype/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:AnnotatorResult native human_phenotype:AnnotatorResult"},{"location":"human_phenotype/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n\n
"},{"location":"human_phenotype/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"human_phenotype/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"human_phenotype/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"human_phenotype/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"human_phenotype/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Any/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native human_phenotype:Any"},{"location":"human_phenotype/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nclass_uri: linkml:Any\n\n
"},{"location":"human_phenotype/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nclass_uri: linkml:Any\n\n
"},{"location":"human_phenotype/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"human_phenotype/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: human_phenotype:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"human_phenotype/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"human_phenotype/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:CompoundExpression native human_phenotype:CompoundExpression"},{"location":"human_phenotype/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nabstract: true\n\n
"},{"location":"human_phenotype/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nabstract: true\n\n
"},{"location":"human_phenotype/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"human_phenotype/Curie/#comments","title":"Comments","text":""},{"location":"human_phenotype/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Curie/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"human_phenotype/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Date/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"human_phenotype/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"human_phenotype/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"human_phenotype/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"human_phenotype/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Double/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: human_phenotype:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"human_phenotype/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"human_phenotype/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:ExtractionResult native human_phenotype:ExtractionResult"},{"location":"human_phenotype/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"human_phenotype/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"human_phenotype/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"human_phenotype/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Float/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/HumanPhenotype/","title":"Class: HumanPhenotype","text":"

URI: human_phenotype:HumanPhenotype

erDiagram\nHumanPhenotype {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"human_phenotype/HumanPhenotype/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/HumanPhenotype/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"human_phenotype/HumanPhenotype/#usages","title":"Usages","text":"used by used in type used HumanPhenotypeSet phenotypes range HumanPhenotype"},{"location":"human_phenotype/HumanPhenotype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/HumanPhenotype/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"human_phenotype/HumanPhenotype/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:mondo, sqlite:obo:mesh, sqlite:obo:ncit Examples are ascites, fever, pain, seizure, increased intracranial pressure, lactic acidosis."},{"location":"human_phenotype/HumanPhenotype/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/HumanPhenotype/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:HumanPhenotype native human_phenotype:HumanPhenotype"},{"location":"human_phenotype/HumanPhenotype/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/HumanPhenotype/#direct","title":"Direct","text":"
name: HumanPhenotype\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:mondo, sqlite:obo:mesh, sqlite:obo:ncit\n  prompt:\n    tag: prompt\n    value: \"the name of a human phenotype or symptom.\\n Examples are ascites, fever,\\\n      \\ pain, seizure, increased intracranial pressure, lactic acidosis.\"\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\n\n
"},{"location":"human_phenotype/HumanPhenotype/#induced","title":"Induced","text":"
name: HumanPhenotype\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:mondo, sqlite:obo:mesh, sqlite:obo:ncit\n  prompt:\n    tag: prompt\n    value: \"the name of a human phenotype or symptom.\\n Examples are ascites, fever,\\\n      \\ pain, seizure, increased intracranial pressure, lactic acidosis.\"\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: HumanPhenotype\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: HumanPhenotype\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"human_phenotype/HumanPhenotypeSet/","title":"Class: HumanPhenotypeSet","text":"

URI: human_phenotype:HumanPhenotypeSet

erDiagram\nHumanPhenotypeSet {\n    string id  \n    string label  \n}\nHumanPhenotype {\n    string id  \n    string label  \n}\n\nHumanPhenotypeSet ||--}o HumanPhenotype : \"phenotypes\"\n\n
"},{"location":"human_phenotype/HumanPhenotypeSet/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/HumanPhenotypeSet/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance phenotypes 0..* HumanPhenotype A semicolon-separated list of human phenotypes, including symptoms of disease direct id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"human_phenotype/HumanPhenotypeSet/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/HumanPhenotypeSet/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/HumanPhenotypeSet/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:HumanPhenotypeSet native human_phenotype:HumanPhenotypeSet"},{"location":"human_phenotype/HumanPhenotypeSet/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/HumanPhenotypeSet/#direct","title":"Direct","text":"
name: HumanPhenotypeSet\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\nattributes:\n  phenotypes:\n    name: phenotypes\n    description: A semicolon-separated list of human phenotypes, including symptoms\n      of disease. It must be semicolon-separated. Labels containing the word 'with'\n      should be split into multiple phenotypes.\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    range: HumanPhenotype\ntree_root: true\n\n
"},{"location":"human_phenotype/HumanPhenotypeSet/#induced","title":"Induced","text":"
name: HumanPhenotypeSet\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\nattributes:\n  phenotypes:\n    name: phenotypes\n    description: A semicolon-separated list of human phenotypes, including symptoms\n      of disease. It must be semicolon-separated. Labels containing the word 'with'\n      should be split into multiple phenotypes.\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    alias: phenotypes\n    owner: HumanPhenotypeSet\n    domain_of:\n    - HumanPhenotypeSet\n    range: HumanPhenotype\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: HumanPhenotypeSet\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: HumanPhenotypeSet\n    domain_of:\n    - NamedEntity\n    range: string\ntree_root: true\n\n
"},{"location":"human_phenotype/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"human_phenotype/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Integer/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/NamedEntity/","title":"Class: NamedEntity","text":"

URI: human_phenotype:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"human_phenotype/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"human_phenotype/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"human_phenotype/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:NamedEntity native human_phenotype:NamedEntity"},{"location":"human_phenotype/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"human_phenotype/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"human_phenotype/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"human_phenotype/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"human_phenotype/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"human_phenotype/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"human_phenotype/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"human_phenotype/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"human_phenotype/Objectidentifier/#comments","title":"Comments","text":""},{"location":"human_phenotype/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Publication/","title":"Class: Publication","text":"

URI: human_phenotype:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"human_phenotype/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"human_phenotype/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"human_phenotype/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Publication/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:Publication native human_phenotype:Publication"},{"location":"human_phenotype/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n\n
"},{"location":"human_phenotype/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"human_phenotype/RelationshipType/","title":"Class: RelationshipType","text":"

URI: human_phenotype:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"human_phenotype/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"human_phenotype/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"human_phenotype/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"human_phenotype/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:RelationshipType native human_phenotype:RelationshipType"},{"location":"human_phenotype/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\n\n
"},{"location":"human_phenotype/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"human_phenotype/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"human_phenotype/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/String/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: human_phenotype:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"human_phenotype/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"human_phenotype/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:TextWithTriples native human_phenotype:TextWithTriples"},{"location":"human_phenotype/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"human_phenotype/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"human_phenotype/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"human_phenotype/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Time/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: human_phenotype:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"human_phenotype/Triple/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"human_phenotype/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"human_phenotype/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Triple/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:Triple native human_phenotype:Triple"},{"location":"human_phenotype/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"human_phenotype/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"human_phenotype/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"human_phenotype/Uri/#comments","title":"Comments","text":""},{"location":"human_phenotype/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Uri/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"human_phenotype/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: human_phenotype:abstract

"},{"location":"human_phenotype/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"human_phenotype/abstract/#properties","title":"Properties","text":""},{"location":"human_phenotype/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/abstract/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"human_phenotype/combined_text/","title":"Slot: combined_text","text":"

URI: human_phenotype:combined_text

"},{"location":"human_phenotype/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"human_phenotype/combined_text/#properties","title":"Properties","text":""},{"location":"human_phenotype/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"human_phenotype/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: human_phenotype:extracted_object

"},{"location":"human_phenotype/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/extracted_object/#properties","title":"Properties","text":""},{"location":"human_phenotype/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"human_phenotype/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: human_phenotype:full_text

"},{"location":"human_phenotype/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"human_phenotype/full_text/#properties","title":"Properties","text":""},{"location":"human_phenotype/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/full_text/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"human_phenotype/human_phenotype-template/","title":"human_phenotype-template","text":"

A template for extracting human phenotypes to HPO terms

URI: http://w3id.org/ontogpt/human_phenotype

"},{"location":"human_phenotype/id/","title":"Slot: id","text":"

URI: human_phenotype:id

"},{"location":"human_phenotype/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot HumanPhenotypeSet no HumanPhenotype no NamedEntity no RelationshipType no Publication no"},{"location":"human_phenotype/id/#properties","title":"Properties","text":""},{"location":"human_phenotype/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"human_phenotype/input_id/","title":"Slot: input_id","text":"

URI: human_phenotype:input_id

"},{"location":"human_phenotype/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/input_id/#properties","title":"Properties","text":""},{"location":"human_phenotype/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/input_id/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"human_phenotype/input_text/","title":"Slot: input_text","text":"

URI: human_phenotype:input_text

"},{"location":"human_phenotype/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/input_text/#properties","title":"Properties","text":""},{"location":"human_phenotype/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/input_text/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"human_phenotype/input_title/","title":"Slot: input_title","text":"

URI: human_phenotype:input_title

"},{"location":"human_phenotype/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/input_title/#properties","title":"Properties","text":""},{"location":"human_phenotype/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/input_title/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"human_phenotype/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"human_phenotype/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot HumanPhenotypeSet no HumanPhenotype no NamedEntity no RelationshipType no"},{"location":"human_phenotype/label/#properties","title":"Properties","text":""},{"location":"human_phenotype/label/#aliases","title":"Aliases","text":""},{"location":"human_phenotype/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"human_phenotype/label/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"human_phenotype/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: human_phenotype:named_entities

"},{"location":"human_phenotype/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/named_entities/#properties","title":"Properties","text":""},{"location":"human_phenotype/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"human_phenotype/object/","title":"Slot: object","text":"

URI: human_phenotype:object

"},{"location":"human_phenotype/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/object/#properties","title":"Properties","text":""},{"location":"human_phenotype/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/object/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"human_phenotype/object_id/","title":"Slot: object_id","text":"

URI: human_phenotype:object_id

"},{"location":"human_phenotype/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"human_phenotype/object_id/#properties","title":"Properties","text":""},{"location":"human_phenotype/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/object_id/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"human_phenotype/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: human_phenotype:object_qualifier

"},{"location":"human_phenotype/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/object_qualifier/#properties","title":"Properties","text":""},{"location":"human_phenotype/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"human_phenotype/object_text/","title":"Slot: object_text","text":"

URI: human_phenotype:object_text

"},{"location":"human_phenotype/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"human_phenotype/object_text/#properties","title":"Properties","text":""},{"location":"human_phenotype/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/object_text/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"human_phenotype/phenotypes/","title":"Slot: phenotypes","text":"

A semicolon-separated list of human phenotypes, including symptoms of disease. It must be semicolon-separated. Labels containing the word 'with' should be split into multiple phenotypes.

URI: human_phenotype:phenotypes

"},{"location":"human_phenotype/phenotypes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot HumanPhenotypeSet no"},{"location":"human_phenotype/phenotypes/#properties","title":"Properties","text":""},{"location":"human_phenotype/phenotypes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/phenotypes/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/phenotypes/#linkml-source","title":"LinkML Source","text":"
name: phenotypes\ndescription: A semicolon-separated list of human phenotypes, including symptoms of\n  disease. It must be semicolon-separated. Labels containing the word 'with' should\n  be split into multiple phenotypes.\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nmultivalued: true\nalias: phenotypes\nowner: HumanPhenotypeSet\ndomain_of:\n- HumanPhenotypeSet\nrange: HumanPhenotype\n\n
"},{"location":"human_phenotype/predicate/","title":"Slot: predicate","text":"

URI: human_phenotype:predicate

"},{"location":"human_phenotype/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/predicate/#properties","title":"Properties","text":""},{"location":"human_phenotype/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/predicate/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"human_phenotype/prompt/","title":"Slot: prompt","text":"

URI: human_phenotype:prompt

"},{"location":"human_phenotype/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/prompt/#properties","title":"Properties","text":""},{"location":"human_phenotype/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/prompt/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"human_phenotype/publication/","title":"Slot: publication","text":"

URI: human_phenotype:publication

"},{"location":"human_phenotype/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"human_phenotype/publication/#properties","title":"Properties","text":""},{"location":"human_phenotype/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"human_phenotype/publication/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"human_phenotype/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: human_phenotype:qualifier

"},{"location":"human_phenotype/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/qualifier/#properties","title":"Properties","text":""},{"location":"human_phenotype/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"human_phenotype/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: human_phenotype:raw_completion_output

"},{"location":"human_phenotype/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/raw_completion_output/#properties","title":"Properties","text":""},{"location":"human_phenotype/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"human_phenotype/subject/","title":"Slot: subject","text":"

URI: human_phenotype:subject

"},{"location":"human_phenotype/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/subject/#properties","title":"Properties","text":""},{"location":"human_phenotype/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/subject/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"human_phenotype/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: human_phenotype:subject_qualifier

"},{"location":"human_phenotype/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/subject_qualifier/#properties","title":"Properties","text":""},{"location":"human_phenotype/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"human_phenotype/subject_text/","title":"Slot: subject_text","text":"

URI: human_phenotype:subject_text

"},{"location":"human_phenotype/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"human_phenotype/subject_text/#properties","title":"Properties","text":""},{"location":"human_phenotype/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"human_phenotype/title/","title":"Slot: title","text":"

The title of the publication

URI: human_phenotype:title

"},{"location":"human_phenotype/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"human_phenotype/title/#properties","title":"Properties","text":""},{"location":"human_phenotype/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/title/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"human_phenotype/triples/","title":"Slot: triples","text":"

URI: human_phenotype:triples

"},{"location":"human_phenotype/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"human_phenotype/triples/#properties","title":"Properties","text":""},{"location":"human_phenotype/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/triples/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ibd/","title":"GO-CAM Template","text":"

A template for GO-CAMs

URI: http://w3id.org/ontogpt/gocam

Name: gocam-template

"},{"location":"ibd/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nIBDAnnotations {\n\n}\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nGeneGeneInteraction {\n\n}\nPathway {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\n\nIBDAnnotations ||--}o Gene : \"genes\"\nIBDAnnotations ||--}o Organism : \"organisms\"\nIBDAnnotations ||--}o GeneOrganismRelationship : \"gene_organisms\"\nIBDAnnotations ||--}o MolecularActivity : \"activities\"\nIBDAnnotations ||--}o GeneMolecularActivityRelationship : \"gene_functions\"\nIBDAnnotations ||--}o CellularProcess : \"cellular_processes\"\nIBDAnnotations ||--}o Pathway : \"pathways\"\nIBDAnnotations ||--}o GeneGeneInteraction : \"gene_gene_interactions\"\nIBDAnnotations ||--}o GeneSubcellularLocalizationRelationship : \"gene_localizations\"\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"ibd/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None GeneGeneInteraction None GeneMolecularActivityRelationship None GeneMolecularActivityRelationship2 None GeneOrganismRelationship None GeneSubcellularLocalizationRelationship None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text IBDAnnotations None NamedEntity None CellularProcess None Gene None GeneLocation None MolecularActivity None Molecule None Organism None Pathway None RelationshipType None Publication None TextWithTriples None"},{"location":"ibd/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication activities semicolon-separated list of molecular activities cellular_processes semicolon-separated list of cellular processes combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication gene gene1 gene2 gene_functions semicolon-separated list of gene to molecular activity relationships gene_gene_interactions semicolon-separated list of gene to gene interactions gene_localizations semicolon-separated list of genes plus their location in the cell; for exampl... gene_organisms genes semicolon-separated list of genes id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing location molecular_activity named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text organism organisms semicolon-separated list of organism taxons pathways semicolon-separated list of pathways predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text target title The title of the publication triples"},{"location":"ibd/#enumerations","title":"Enumerations","text":"Enumeration Description CellType GeneLocationEnum GOCellComponentType NullDataOptions"},{"location":"ibd/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"ibd/#subsets","title":"Subsets","text":"Subset Description"},{"location":"ibd/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: gocam:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"ibd/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"ibd/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"ibd/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:AnnotatorResult native gocam:AnnotatorResult"},{"location":"ibd/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n\n
"},{"location":"ibd/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"ibd/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"ibd/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ibd/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"ibd/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Any/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native gocam:Any"},{"location":"ibd/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/gocam\nclass_uri: linkml:Any\n\n
"},{"location":"ibd/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/gocam\nclass_uri: linkml:Any\n\n
"},{"location":"ibd/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"ibd/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"ibd/CellType/","title":"Enum: CellType","text":"

URI: CellType

This is a dynamic enum

"},{"location":"ibd/CellType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/CellType/#schema-source","title":"Schema Source","text":""},{"location":"ibd/CellType/#linkml-source","title":"LinkML Source","text":"
name: CellType\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nreachable_from:\n  source_ontology: obo:cl\n  source_nodes:\n  - CL:0000000\n\n
"},{"location":"ibd/CellularProcess/","title":"Class: CellularProcess","text":"

URI: gocam:CellularProcess

erDiagram\nCellularProcess {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/CellularProcess/#inheritance","title":"Inheritance","text":""},{"location":"ibd/CellularProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/CellularProcess/#usages","title":"Usages","text":"used by used in type used IBDAnnotations cellular_processes range CellularProcess"},{"location":"ibd/CellularProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/CellularProcess/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/CellularProcess/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"ibd/CellularProcess/#schema-source","title":"Schema Source","text":""},{"location":"ibd/CellularProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:CellularProcess native gocam:CellularProcess"},{"location":"ibd/CellularProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/CellularProcess/#direct","title":"Direct","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/CellularProcess/#induced","title":"Induced","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: gocam:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"ibd/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"ibd/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ibd/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"ibd/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:CompoundExpression native gocam:CompoundExpression"},{"location":"ibd/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\n\n
"},{"location":"ibd/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\n\n
"},{"location":"ibd/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"ibd/Curie/#comments","title":"Comments","text":""},{"location":"ibd/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Curie/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"ibd/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Date/#schema-source","title":"Schema Source","text":""},{"location":"ibd/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"ibd/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"ibd/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"ibd/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"ibd/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Double/#schema-source","title":"Schema Source","text":""},{"location":"ibd/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: gocam:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"ibd/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"ibd/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"ibd/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:ExtractionResult native gocam:ExtractionResult"},{"location":"ibd/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"ibd/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Float/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GOCellComponentType/","title":"Enum: GOCellComponentType","text":"

URI: GOCellComponentType

This is a dynamic enum

"},{"location":"ibd/GOCellComponentType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GOCellComponentType/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GOCellComponentType/#linkml-source","title":"LinkML Source","text":"
name: GOCellComponentType\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nreachable_from:\n  source_ontology: obo:go\n  source_nodes:\n  - GO:0005575\n\n
"},{"location":"ibd/Gene/","title":"Class: Gene","text":"

URI: gocam:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/Gene/#inheritance","title":"Inheritance","text":""},{"location":"ibd/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/Gene/#usages","title":"Usages","text":"used by used in type used IBDAnnotations genes range Gene GeneOrganismRelationship gene range Gene GeneMolecularActivityRelationship gene range Gene GeneMolecularActivityRelationship2 gene range Gene GeneSubcellularLocalizationRelationship gene range Gene GeneGeneInteraction gene1 range Gene GeneGeneInteraction gene2 range Gene"},{"location":"ibd/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, bioportal:hgnc-nr"},{"location":"ibd/Gene/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Gene native gocam:Gene"},{"location":"ibd/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/GeneGeneInteraction/","title":"Class: GeneGeneInteraction","text":"

URI: gocam:GeneGeneInteraction

erDiagram\nGeneGeneInteraction {\n\n}\nGene {\n    string id  \n    string label  \n}\n\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\n\n
"},{"location":"ibd/GeneGeneInteraction/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneGeneInteraction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene1 0..1 Gene direct gene2 0..1 Gene direct"},{"location":"ibd/GeneGeneInteraction/#usages","title":"Usages","text":"used by used in type used IBDAnnotations gene_gene_interactions range GeneGeneInteraction"},{"location":"ibd/GeneGeneInteraction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneGeneInteraction/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneGeneInteraction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneGeneInteraction native gocam:GeneGeneInteraction"},{"location":"ibd/GeneGeneInteraction/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneGeneInteraction/#direct","title":"Direct","text":"
name: GeneGeneInteraction\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene1:\n    name: gene1\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n  gene2:\n    name: gene2\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n\n
"},{"location":"ibd/GeneGeneInteraction/#induced","title":"Induced","text":"
name: GeneGeneInteraction\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene1:\n    name: gene1\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene1\n    owner: GeneGeneInteraction\n    domain_of:\n    - GeneGeneInteraction\n    range: Gene\n  gene2:\n    name: gene2\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene2\n    owner: GeneGeneInteraction\n    domain_of:\n    - GeneGeneInteraction\n    range: Gene\n\n
"},{"location":"ibd/GeneLocation/","title":"Class: GeneLocation","text":"

URI: gocam:GeneLocation

erDiagram\nGeneLocation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/GeneLocation/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneLocation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/GeneLocation/#usages","title":"Usages","text":"used by used in type used GeneSubcellularLocalizationRelationship location range GeneLocation"},{"location":"ibd/GeneLocation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneLocation/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/GeneLocation/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:cl"},{"location":"ibd/GeneLocation/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneLocation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneLocation native gocam:GeneLocation"},{"location":"ibd/GeneLocation/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneLocation/#direct","title":"Direct","text":"
name: GeneLocation\nid_prefixes:\n- GO\n- CL\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - GOCellComponentType\n    - CellType\n    domain_of:\n    - NamedEntity\n    - Publication\n\n
"},{"location":"ibd/GeneLocation/#induced","title":"Induced","text":"
name: GeneLocation\nid_prefixes:\n- GO\n- CL\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - GOCellComponentType\n    - CellType\n    domain_of:\n    - NamedEntity\n    - Publication\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    values_from:\n    - GOCellComponentType\n    - CellType\n    identifier: true\n    alias: id\n    owner: GeneLocation\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: GeneLocation\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/GeneLocationEnum/","title":"Enum: GeneLocationEnum","text":"

URI: GeneLocationEnum

This is a dynamic enum

"},{"location":"ibd/GeneLocationEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneLocationEnum/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneLocationEnum/#linkml-source","title":"LinkML Source","text":"
name: GeneLocationEnum\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\ninherits:\n- GOCellComponent\n- CellType\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship/","title":"Class: GeneMolecularActivityRelationship","text":"

URI: gocam:GeneMolecularActivityRelationship

erDiagram\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneMolecularActivityRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct molecular_activity 0..1 MolecularActivity direct"},{"location":"ibd/GeneMolecularActivityRelationship/#usages","title":"Usages","text":"used by used in type used IBDAnnotations gene_functions range GeneMolecularActivityRelationship"},{"location":"ibd/GeneMolecularActivityRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneMolecularActivityRelationship/#annotations","title":"Annotations","text":"property value prompt.example TODO

gene: HGNC:1234 molecular_activity: GO:0003674 |

"},{"location":"ibd/GeneMolecularActivityRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneMolecularActivityRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneMolecularActivityRelationship native gocam:GeneMolecularActivityRelationship"},{"location":"ibd/GeneMolecularActivityRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneMolecularActivityRelationship/#direct","title":"Direct","text":"
name: GeneMolecularActivityRelationship\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: 'TODO\n\n\n      gene: HGNC:1234\n\n      molecular_activity: GO:0003674'\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene in the pair. This comes first.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular function in the pair. This comes second.\n          May be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: MolecularActivity\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship/#induced","title":"Induced","text":"
name: GeneMolecularActivityRelationship\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: 'TODO\n\n\n      gene: HGNC:1234\n\n      molecular_activity: GO:0003674'\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene in the pair. This comes first.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular function in the pair. This comes second.\n          May be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: molecular_activity\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    range: MolecularActivity\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship2/","title":"Class: GeneMolecularActivityRelationship2","text":"

URI: gocam:GeneMolecularActivityRelationship2

erDiagram\nGeneMolecularActivityRelationship2 {\n\n}\nMolecule {\n    string id  \n    string label  \n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneMolecularActivityRelationship2 ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship2 ||--|o MolecularActivity : \"molecular_activity\"\nGeneMolecularActivityRelationship2 ||--|o Molecule : \"target\"\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship2/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneMolecularActivityRelationship2/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct molecular_activity 0..1 MolecularActivity direct target 0..1 Molecule direct"},{"location":"ibd/GeneMolecularActivityRelationship2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneMolecularActivityRelationship2/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneMolecularActivityRelationship2/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneMolecularActivityRelationship2 native gocam:GeneMolecularActivityRelationship2"},{"location":"ibd/GeneMolecularActivityRelationship2/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneMolecularActivityRelationship2/#direct","title":"Direct","text":"
name: GeneMolecularActivityRelationship2\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular activity, for example, ubiquitination. May\n          be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: MolecularActivity\n  target:\n    name: target\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular entity that is the target of the molecular\n          activity.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Molecule\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship2/#induced","title":"Induced","text":"
name: GeneMolecularActivityRelationship2\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular activity, for example, ubiquitination. May\n          be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: molecular_activity\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    range: MolecularActivity\n  target:\n    name: target\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular entity that is the target of the molecular\n          activity.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: target\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneMolecularActivityRelationship2\n    range: Molecule\n\n
"},{"location":"ibd/GeneOrganismRelationship/","title":"Class: GeneOrganismRelationship","text":"

URI: gocam:GeneOrganismRelationship

erDiagram\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"ibd/GeneOrganismRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneOrganismRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct organism 0..1 Organism direct"},{"location":"ibd/GeneOrganismRelationship/#usages","title":"Usages","text":"used by used in type used IBDAnnotations gene_organisms range GeneOrganismRelationship"},{"location":"ibd/GeneOrganismRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneOrganismRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneOrganismRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneOrganismRelationship native gocam:GeneOrganismRelationship"},{"location":"ibd/GeneOrganismRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneOrganismRelationship/#direct","title":"Direct","text":"
name: GeneOrganismRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n  organism:\n    name: organism\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Organism\n\n
"},{"location":"ibd/GeneOrganismRelationship/#induced","title":"Induced","text":"
name: GeneOrganismRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene\n    owner: GeneOrganismRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  organism:\n    name: organism\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: organism\n    owner: GeneOrganismRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    range: Organism\n\n
"},{"location":"ibd/GeneSubcellularLocalizationRelationship/","title":"Class: GeneSubcellularLocalizationRelationship","text":"

URI: gocam:GeneSubcellularLocalizationRelationship

erDiagram\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\n\n
"},{"location":"ibd/GeneSubcellularLocalizationRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneSubcellularLocalizationRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct location 0..1 GeneLocation direct"},{"location":"ibd/GeneSubcellularLocalizationRelationship/#usages","title":"Usages","text":"used by used in type used IBDAnnotations gene_localizations range GeneSubcellularLocalizationRelationship"},{"location":"ibd/GeneSubcellularLocalizationRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneSubcellularLocalizationRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneSubcellularLocalizationRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneSubcellularLocalizationRelationship native gocam:GeneSubcellularLocalizationRelationship"},{"location":"ibd/GeneSubcellularLocalizationRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneSubcellularLocalizationRelationship/#direct","title":"Direct","text":"
name: GeneSubcellularLocalizationRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  location:\n    name: location\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: GeneLocation\n\n
"},{"location":"ibd/GeneSubcellularLocalizationRelationship/#induced","title":"Induced","text":"
name: GeneSubcellularLocalizationRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneSubcellularLocalizationRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  location:\n    name: location\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: location\n    owner: GeneSubcellularLocalizationRelationship\n    domain_of:\n    - GeneSubcellularLocalizationRelationship\n    range: GeneLocation\n\n
"},{"location":"ibd/IBDAnnotations/","title":"Class: IBDAnnotations","text":"

URI: gocam:IBDAnnotations

erDiagram\nIBDAnnotations {\n\n}\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nGeneGeneInteraction {\n\n}\nPathway {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\n\nIBDAnnotations ||--}o Gene : \"genes\"\nIBDAnnotations ||--}o Organism : \"organisms\"\nIBDAnnotations ||--}o GeneOrganismRelationship : \"gene_organisms\"\nIBDAnnotations ||--}o MolecularActivity : \"activities\"\nIBDAnnotations ||--}o GeneMolecularActivityRelationship : \"gene_functions\"\nIBDAnnotations ||--}o CellularProcess : \"cellular_processes\"\nIBDAnnotations ||--}o Pathway : \"pathways\"\nIBDAnnotations ||--}o GeneGeneInteraction : \"gene_gene_interactions\"\nIBDAnnotations ||--}o GeneSubcellularLocalizationRelationship : \"gene_localizations\"\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"ibd/IBDAnnotations/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance genes 0..* Gene semicolon-separated list of genes direct organisms 0..* Organism semicolon-separated list of organism taxons direct gene_organisms 0..* GeneOrganismRelationship direct activities 0..* MolecularActivity semicolon-separated list of molecular activities direct gene_functions 0..* GeneMolecularActivityRelationship semicolon-separated list of gene to molecular activity relationships direct cellular_processes 0..* CellularProcess semicolon-separated list of cellular processes direct pathways 0..* Pathway semicolon-separated list of pathways direct gene_gene_interactions 0..* GeneGeneInteraction semicolon-separated list of gene to gene interactions direct gene_localizations 0..* GeneSubcellularLocalizationRelationship semicolon-separated list of genes plus their location in the cell; for exampl... direct"},{"location":"ibd/IBDAnnotations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/IBDAnnotations/#schema-source","title":"Schema Source","text":""},{"location":"ibd/IBDAnnotations/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:IBDAnnotations native gocam:IBDAnnotations"},{"location":"ibd/IBDAnnotations/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/IBDAnnotations/#direct","title":"Direct","text":"
name: IBDAnnotations\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Gene\n  organisms:\n    name: organisms\n    description: semicolon-separated list of organism taxons\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Organism\n  gene_organisms:\n    name: gene_organisms\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of asterisk separated gene to organism relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneOrganismRelationship\n  activities:\n    name: activities\n    description: semicolon-separated list of molecular activities\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: MolecularActivity\n  gene_functions:\n    name: gene_functions\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneMolecularActivityRelationship\n  cellular_processes:\n    name: cellular_processes\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: CellularProcess\n  pathways:\n    name: pathways\n    description: semicolon-separated list of pathways\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Pathway\n  gene_gene_interactions:\n    name: gene_gene_interactions\n    description: semicolon-separated list of gene to gene interactions\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneGeneInteraction\n  gene_localizations:\n    name: gene_localizations\n    description: semicolon-separated list of genes plus their location in the cell;\n      for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneSubcellularLocalizationRelationship\ntree_root: true\n\n
"},{"location":"ibd/IBDAnnotations/#induced","title":"Induced","text":"
name: IBDAnnotations\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: Gene\n  organisms:\n    name: organisms\n    description: semicolon-separated list of organism taxons\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: organisms\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: Organism\n  gene_organisms:\n    name: gene_organisms\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of asterisk separated gene to organism relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_organisms\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: GeneOrganismRelationship\n  activities:\n    name: activities\n    description: semicolon-separated list of molecular activities\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: activities\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: MolecularActivity\n  gene_functions:\n    name: gene_functions\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_functions\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: GeneMolecularActivityRelationship\n  cellular_processes:\n    name: cellular_processes\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: cellular_processes\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: CellularProcess\n  pathways:\n    name: pathways\n    description: semicolon-separated list of pathways\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: pathways\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: Pathway\n  gene_gene_interactions:\n    name: gene_gene_interactions\n    description: semicolon-separated list of gene to gene interactions\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_gene_interactions\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: GeneGeneInteraction\n  gene_localizations:\n    name: gene_localizations\n    description: semicolon-separated list of genes plus their location in the cell;\n      for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_localizations\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: GeneSubcellularLocalizationRelationship\ntree_root: true\n\n
"},{"location":"ibd/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"ibd/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Integer/#schema-source","title":"Schema Source","text":""},{"location":"ibd/MolecularActivity/","title":"Class: MolecularActivity","text":"

URI: gocam:MolecularActivity

erDiagram\nMolecularActivity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/MolecularActivity/#inheritance","title":"Inheritance","text":""},{"location":"ibd/MolecularActivity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/MolecularActivity/#usages","title":"Usages","text":"used by used in type used IBDAnnotations activities range MolecularActivity GeneMolecularActivityRelationship molecular_activity range MolecularActivity GeneMolecularActivityRelationship2 molecular_activity range MolecularActivity"},{"location":"ibd/MolecularActivity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/MolecularActivity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/MolecularActivity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"ibd/MolecularActivity/#schema-source","title":"Schema Source","text":""},{"location":"ibd/MolecularActivity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:MolecularActivity native gocam:MolecularActivity"},{"location":"ibd/MolecularActivity/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/MolecularActivity/#direct","title":"Direct","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/MolecularActivity/#induced","title":"Induced","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MolecularActivity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: MolecularActivity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/Molecule/","title":"Class: Molecule","text":"

URI: gocam:Molecule

erDiagram\nMolecule {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/Molecule/#inheritance","title":"Inheritance","text":""},{"location":"ibd/Molecule/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/Molecule/#usages","title":"Usages","text":"used by used in type used GeneMolecularActivityRelationship2 target range Molecule"},{"location":"ibd/Molecule/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Molecule/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/Molecule/#annotations","title":"Annotations","text":"property value annotators gilda:, sqlite:obo:chebi"},{"location":"ibd/Molecule/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Molecule/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Molecule native gocam:Molecule"},{"location":"ibd/Molecule/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Molecule/#direct","title":"Direct","text":"
name: Molecule\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/Molecule/#induced","title":"Induced","text":"
name: Molecule\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Molecule\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Molecule\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/NamedEntity/","title":"Class: NamedEntity","text":"

URI: gocam:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"ibd/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"ibd/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"ibd/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"ibd/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:NamedEntity native gocam:NamedEntity"},{"location":"ibd/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"ibd/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"ibd/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"ibd/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"ibd/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"ibd/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"ibd/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"ibd/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"ibd/Objectidentifier/#comments","title":"Comments","text":""},{"location":"ibd/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Organism/","title":"Class: Organism","text":"

URI: gocam:Organism

erDiagram\nOrganism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/Organism/#inheritance","title":"Inheritance","text":""},{"location":"ibd/Organism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/Organism/#usages","title":"Usages","text":"used by used in type used IBDAnnotations organisms range Organism GeneOrganismRelationship organism range Organism"},{"location":"ibd/Organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Organism/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/Organism/#annotations","title":"Annotations","text":"property value annotators gilda:, sqlite:obo:ncbitaxon"},{"location":"ibd/Organism/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Organism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Organism native gocam:Organism"},{"location":"ibd/Organism/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Organism/#direct","title":"Direct","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/Organism/#induced","title":"Induced","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/Pathway/","title":"Class: Pathway","text":"

URI: gocam:Pathway

erDiagram\nPathway {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/Pathway/#inheritance","title":"Inheritance","text":""},{"location":"ibd/Pathway/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/Pathway/#usages","title":"Usages","text":"used by used in type used IBDAnnotations pathways range Pathway"},{"location":"ibd/Pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Pathway/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/Pathway/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:pw"},{"location":"ibd/Pathway/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Pathway/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Pathway native gocam:Pathway"},{"location":"ibd/Pathway/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Pathway/#direct","title":"Direct","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/Pathway/#induced","title":"Induced","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Pathway\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Pathway\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/Publication/","title":"Class: Publication","text":"

URI: gocam:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"ibd/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"ibd/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"ibd/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Publication/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Publication native gocam:Publication"},{"location":"ibd/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/gocam\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n\n
"},{"location":"ibd/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"ibd/RelationshipType/","title":"Class: RelationshipType","text":"

URI: gocam:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"ibd/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"ibd/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"ibd/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:RelationshipType native gocam:RelationshipType"},{"location":"ibd/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"ibd/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/String/#schema-source","title":"Schema Source","text":""},{"location":"ibd/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: gocam:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"ibd/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"ibd/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:TextWithTriples native gocam:TextWithTriples"},{"location":"ibd/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"ibd/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Time/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: gocam:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd/Triple/#inheritance","title":"Inheritance","text":""},{"location":"ibd/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"ibd/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"ibd/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Triple/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Triple native gocam:Triple"},{"location":"ibd/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"ibd/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ibd/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"ibd/Uri/#comments","title":"Comments","text":""},{"location":"ibd/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Uri/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"ibd/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"ibd/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: gocam:abstract

"},{"location":"ibd/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd/abstract/#properties","title":"Properties","text":""},{"location":"ibd/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/abstract/#schema-source","title":"Schema Source","text":""},{"location":"ibd/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd/activities/","title":"Slot: activities","text":"

semicolon-separated list of molecular activities

URI: gocam:activities

"},{"location":"ibd/activities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/activities/#properties","title":"Properties","text":""},{"location":"ibd/activities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/activities/#schema-source","title":"Schema Source","text":""},{"location":"ibd/activities/#linkml-source","title":"LinkML Source","text":"
name: activities\ndescription: semicolon-separated list of molecular activities\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: activities\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: MolecularActivity\n\n
"},{"location":"ibd/cellular_processes/","title":"Slot: cellular_processes","text":"

semicolon-separated list of cellular processes

URI: gocam:cellular_processes

"},{"location":"ibd/cellular_processes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/cellular_processes/#properties","title":"Properties","text":""},{"location":"ibd/cellular_processes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/cellular_processes/#schema-source","title":"Schema Source","text":""},{"location":"ibd/cellular_processes/#linkml-source","title":"LinkML Source","text":"
name: cellular_processes\ndescription: semicolon-separated list of cellular processes\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: cellular_processes\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: CellularProcess\n\n
"},{"location":"ibd/combined_text/","title":"Slot: combined_text","text":"

URI: gocam:combined_text

"},{"location":"ibd/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd/combined_text/#properties","title":"Properties","text":""},{"location":"ibd/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: gocam:extracted_object

"},{"location":"ibd/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/extracted_object/#properties","title":"Properties","text":""},{"location":"ibd/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"ibd/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"ibd/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: gocam:full_text

"},{"location":"ibd/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd/full_text/#properties","title":"Properties","text":""},{"location":"ibd/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/full_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd/gene/","title":"Slot: gene","text":"

URI: gocam:gene

"},{"location":"ibd/gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneOrganismRelationship no GeneMolecularActivityRelationship no GeneMolecularActivityRelationship2 no GeneSubcellularLocalizationRelationship no"},{"location":"ibd/gene/#properties","title":"Properties","text":""},{"location":"ibd/gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene/#linkml-source","title":"LinkML Source","text":"
name: gene\nalias: gene\ndomain_of:\n- GeneOrganismRelationship\n- GeneMolecularActivityRelationship\n- GeneMolecularActivityRelationship2\n- GeneSubcellularLocalizationRelationship\nrange: string\n\n
"},{"location":"ibd/gene1/","title":"Slot: gene1","text":"

URI: gocam:gene1

"},{"location":"ibd/gene1/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneGeneInteraction no"},{"location":"ibd/gene1/#properties","title":"Properties","text":""},{"location":"ibd/gene1/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene1/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene1/#linkml-source","title":"LinkML Source","text":"
name: gene1\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: gene1\nowner: GeneGeneInteraction\ndomain_of:\n- GeneGeneInteraction\nrange: Gene\n\n
"},{"location":"ibd/gene2/","title":"Slot: gene2","text":"

URI: gocam:gene2

"},{"location":"ibd/gene2/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneGeneInteraction no"},{"location":"ibd/gene2/#properties","title":"Properties","text":""},{"location":"ibd/gene2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene2/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene2/#linkml-source","title":"LinkML Source","text":"
name: gene2\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: gene2\nowner: GeneGeneInteraction\ndomain_of:\n- GeneGeneInteraction\nrange: Gene\n\n
"},{"location":"ibd/gene_functions/","title":"Slot: gene_functions","text":"

semicolon-separated list of gene to molecular activity relationships

URI: gocam:gene_functions

"},{"location":"ibd/gene_functions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/gene_functions/#properties","title":"Properties","text":""},{"location":"ibd/gene_functions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene_functions/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene_functions/#linkml-source","title":"LinkML Source","text":"
name: gene_functions\ndescription: semicolon-separated list of gene to molecular activity relationships\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_functions\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: GeneMolecularActivityRelationship\n\n
"},{"location":"ibd/gene_gene_interactions/","title":"Slot: gene_gene_interactions","text":"

semicolon-separated list of gene to gene interactions

URI: gocam:gene_gene_interactions

"},{"location":"ibd/gene_gene_interactions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/gene_gene_interactions/#properties","title":"Properties","text":""},{"location":"ibd/gene_gene_interactions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene_gene_interactions/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene_gene_interactions/#linkml-source","title":"LinkML Source","text":"
name: gene_gene_interactions\ndescription: semicolon-separated list of gene to gene interactions\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_gene_interactions\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: GeneGeneInteraction\n\n
"},{"location":"ibd/gene_localizations/","title":"Slot: gene_localizations","text":"

semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"

URI: gocam:gene_localizations

"},{"location":"ibd/gene_localizations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/gene_localizations/#properties","title":"Properties","text":""},{"location":"ibd/gene_localizations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene_localizations/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene_localizations/#linkml-source","title":"LinkML Source","text":"
name: gene_localizations\ndescription: semicolon-separated list of genes plus their location in the cell; for\n  example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_localizations\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: GeneSubcellularLocalizationRelationship\n\n
"},{"location":"ibd/gene_organisms/","title":"Slot: gene_organisms","text":"

URI: gocam:gene_organisms

"},{"location":"ibd/gene_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/gene_organisms/#properties","title":"Properties","text":""},{"location":"ibd/gene_organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene_organisms/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of asterisk separated gene to organism relationships"},{"location":"ibd/gene_organisms/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene_organisms/#linkml-source","title":"LinkML Source","text":"
name: gene_organisms\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of asterisk separated gene to organism relationships\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_organisms\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: GeneOrganismRelationship\n\n
"},{"location":"ibd/genes/","title":"Slot: genes","text":"

semicolon-separated list of genes

URI: gocam:genes

"},{"location":"ibd/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/genes/#properties","title":"Properties","text":""},{"location":"ibd/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/genes/#schema-source","title":"Schema Source","text":""},{"location":"ibd/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\ndescription: semicolon-separated list of genes\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: genes\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: Gene\n\n
"},{"location":"ibd/gocam-template/","title":"gocam-template","text":"

A template for GO-CAMs

URI: http://w3id.org/ontogpt/gocam

"},{"location":"ibd/id/","title":"Slot: id","text":"

URI: gocam:id

"},{"location":"ibd/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Pathway no CellularProcess no MolecularActivity no GeneLocation yes Organism no Molecule no NamedEntity no RelationshipType no Publication no"},{"location":"ibd/id/#properties","title":"Properties","text":""},{"location":"ibd/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"ibd/input_id/","title":"Slot: input_id","text":"

URI: gocam:input_id

"},{"location":"ibd/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/input_id/#properties","title":"Properties","text":""},{"location":"ibd/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/input_id/#schema-source","title":"Schema Source","text":""},{"location":"ibd/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd/input_text/","title":"Slot: input_text","text":"

URI: gocam:input_text

"},{"location":"ibd/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/input_text/#properties","title":"Properties","text":""},{"location":"ibd/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/input_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd/input_title/","title":"Slot: input_title","text":"

URI: gocam:input_title

"},{"location":"ibd/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/input_title/#properties","title":"Properties","text":""},{"location":"ibd/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/input_title/#schema-source","title":"Schema Source","text":""},{"location":"ibd/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"ibd/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Pathway no CellularProcess no MolecularActivity no GeneLocation no Organism no Molecule no NamedEntity no RelationshipType no"},{"location":"ibd/label/#properties","title":"Properties","text":""},{"location":"ibd/label/#aliases","title":"Aliases","text":""},{"location":"ibd/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"ibd/label/#schema-source","title":"Schema Source","text":""},{"location":"ibd/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/gocam\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"ibd/location/","title":"Slot: location","text":"

URI: gocam:location

"},{"location":"ibd/location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneSubcellularLocalizationRelationship no"},{"location":"ibd/location/#properties","title":"Properties","text":""},{"location":"ibd/location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/location/#schema-source","title":"Schema Source","text":""},{"location":"ibd/location/#linkml-source","title":"LinkML Source","text":"
name: location\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: location\nowner: GeneSubcellularLocalizationRelationship\ndomain_of:\n- GeneSubcellularLocalizationRelationship\nrange: GeneLocation\n\n
"},{"location":"ibd/molecular_activity/","title":"Slot: molecular_activity","text":"

URI: gocam:molecular_activity

"},{"location":"ibd/molecular_activity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship no GeneMolecularActivityRelationship2 no"},{"location":"ibd/molecular_activity/#properties","title":"Properties","text":""},{"location":"ibd/molecular_activity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/molecular_activity/#linkml-source","title":"LinkML Source","text":"
name: molecular_activity\nalias: molecular_activity\ndomain_of:\n- GeneMolecularActivityRelationship\n- GeneMolecularActivityRelationship2\nrange: string\n\n
"},{"location":"ibd/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: gocam:named_entities

"},{"location":"ibd/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/named_entities/#properties","title":"Properties","text":""},{"location":"ibd/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"ibd/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ibd/object/","title":"Slot: object","text":"

URI: gocam:object

"},{"location":"ibd/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/object/#properties","title":"Properties","text":""},{"location":"ibd/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/object/#schema-source","title":"Schema Source","text":""},{"location":"ibd/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ibd/object_id/","title":"Slot: object_id","text":"

URI: gocam:object_id

"},{"location":"ibd/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd/object_id/#properties","title":"Properties","text":""},{"location":"ibd/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/object_id/#schema-source","title":"Schema Source","text":""},{"location":"ibd/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: gocam:object_qualifier

"},{"location":"ibd/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/object_qualifier/#properties","title":"Properties","text":""},{"location":"ibd/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ibd/object_text/","title":"Slot: object_text","text":"

URI: gocam:object_text

"},{"location":"ibd/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd/object_text/#properties","title":"Properties","text":""},{"location":"ibd/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/object_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd/organism/","title":"Slot: organism","text":"

URI: gocam:organism

"},{"location":"ibd/organism/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneOrganismRelationship no"},{"location":"ibd/organism/#properties","title":"Properties","text":""},{"location":"ibd/organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/organism/#schema-source","title":"Schema Source","text":""},{"location":"ibd/organism/#linkml-source","title":"LinkML Source","text":"
name: organism\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: organism\nowner: GeneOrganismRelationship\ndomain_of:\n- GeneOrganismRelationship\nrange: Organism\n\n
"},{"location":"ibd/organisms/","title":"Slot: organisms","text":"

semicolon-separated list of organism taxons

URI: gocam:organisms

"},{"location":"ibd/organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/organisms/#properties","title":"Properties","text":""},{"location":"ibd/organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/organisms/#schema-source","title":"Schema Source","text":""},{"location":"ibd/organisms/#linkml-source","title":"LinkML Source","text":"
name: organisms\ndescription: semicolon-separated list of organism taxons\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: organisms\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: Organism\n\n
"},{"location":"ibd/pathways/","title":"Slot: pathways","text":"

semicolon-separated list of pathways

URI: gocam:pathways

"},{"location":"ibd/pathways/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/pathways/#properties","title":"Properties","text":""},{"location":"ibd/pathways/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/pathways/#schema-source","title":"Schema Source","text":""},{"location":"ibd/pathways/#linkml-source","title":"LinkML Source","text":"
name: pathways\ndescription: semicolon-separated list of pathways\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: pathways\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: Pathway\n\n
"},{"location":"ibd/predicate/","title":"Slot: predicate","text":"

URI: gocam:predicate

"},{"location":"ibd/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/predicate/#properties","title":"Properties","text":""},{"location":"ibd/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/predicate/#schema-source","title":"Schema Source","text":""},{"location":"ibd/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"ibd/prompt/","title":"Slot: prompt","text":"

URI: gocam:prompt

"},{"location":"ibd/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/prompt/#properties","title":"Properties","text":""},{"location":"ibd/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/prompt/#schema-source","title":"Schema Source","text":""},{"location":"ibd/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd/publication/","title":"Slot: publication","text":"

URI: gocam:publication

"},{"location":"ibd/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ibd/publication/#properties","title":"Properties","text":""},{"location":"ibd/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"ibd/publication/#schema-source","title":"Schema Source","text":""},{"location":"ibd/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"ibd/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: gocam:qualifier

"},{"location":"ibd/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/qualifier/#properties","title":"Properties","text":""},{"location":"ibd/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"ibd/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: gocam:raw_completion_output

"},{"location":"ibd/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/raw_completion_output/#properties","title":"Properties","text":""},{"location":"ibd/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"ibd/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd/subject/","title":"Slot: subject","text":"

URI: gocam:subject

"},{"location":"ibd/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/subject/#properties","title":"Properties","text":""},{"location":"ibd/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/subject/#schema-source","title":"Schema Source","text":""},{"location":"ibd/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ibd/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: gocam:subject_qualifier

"},{"location":"ibd/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/subject_qualifier/#properties","title":"Properties","text":""},{"location":"ibd/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ibd/subject_text/","title":"Slot: subject_text","text":"

URI: gocam:subject_text

"},{"location":"ibd/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd/subject_text/#properties","title":"Properties","text":""},{"location":"ibd/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd/target/","title":"Slot: target","text":"

URI: gocam:target

"},{"location":"ibd/target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship2 no"},{"location":"ibd/target/#properties","title":"Properties","text":""},{"location":"ibd/target/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/target/#annotations","title":"Annotations","text":"property value prompt the name of the molecular entity that is the target of the molecular activity."},{"location":"ibd/target/#schema-source","title":"Schema Source","text":""},{"location":"ibd/target/#linkml-source","title":"LinkML Source","text":"
name: target\nannotations:\n  prompt:\n    tag: prompt\n    value: the name of the molecular entity that is the target of the molecular activity.\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: target\nowner: GeneMolecularActivityRelationship2\ndomain_of:\n- GeneMolecularActivityRelationship2\nrange: Molecule\n\n
"},{"location":"ibd/title/","title":"Slot: title","text":"

The title of the publication

URI: gocam:title

"},{"location":"ibd/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd/title/#properties","title":"Properties","text":""},{"location":"ibd/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/title/#schema-source","title":"Schema Source","text":""},{"location":"ibd/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd/triples/","title":"Slot: triples","text":"

URI: gocam:triples

"},{"location":"ibd/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ibd/triples/#properties","title":"Properties","text":""},{"location":"ibd/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/triples/#schema-source","title":"Schema Source","text":""},{"location":"ibd/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ibd_literature/","title":"IBD Literature Template","text":"

A template for extracting information from IBD literature

URI: http://w3id.org/ontogpt/ibd_literature

Name: ibd-literature-template

"},{"location":"ibd_literature/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nIBDAnnotations {\n\n}\nDiseaseCellularProcessRelationship {\n\n}\nNamedEntity {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nDiseaseToCellularProcessPredicate {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGeneExposureRelationship {\n\n}\nGene {\n    string id  \n    string label  \n}\nChemicalExposureToGenePredicate {\n    string id  \n    string label  \n}\nChemicalExposure {\n    string id  \n    string label  \n}\n\nIBDAnnotations ||--}o Gene : \"genes\"\nIBDAnnotations ||--}o ChemicalExposure : \"exposures\"\nIBDAnnotations ||--}o GeneExposureRelationship : \"gene_exposures_relationships\"\nIBDAnnotations ||--}o Disease : \"diseases\"\nIBDAnnotations ||--}o CellularProcess : \"cellular_process\"\nIBDAnnotations ||--}o DiseaseCellularProcessRelationship : \"disease_cellular_process_relationships\"\nDiseaseCellularProcessRelationship ||--|o Disease : \"subject\"\nDiseaseCellularProcessRelationship ||--|o DiseaseToCellularProcessPredicate : \"predicate\"\nDiseaseCellularProcessRelationship ||--|o CellularProcess : \"object\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"subject_qualifier\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"object_qualifier\"\nGeneExposureRelationship ||--|o ChemicalExposure : \"subject\"\nGeneExposureRelationship ||--|o ChemicalExposureToGenePredicate : \"predicate\"\nGeneExposureRelationship ||--|o Gene : \"object\"\nGeneExposureRelationship ||--|o NamedEntity : \"subject_qualifier\"\nGeneExposureRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None DiseaseCellularProcessRelationship None GeneExposureRelationship None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text IBDAnnotations None NamedEntity None CellularProcess None ChemicalExposure None ChemicalExposureToGenePredicate None Disease None DiseaseToCellularProcessPredicate None Gene None RelationshipType None Publication None TextWithTriples None"},{"location":"ibd_literature/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication cellular_process semicolon-separated list of cellular processes combined_text disease_cellular_process_relationships semicolon-separated list of disease to cellular process relationships diseases semicolon-separated list of diseases exposures semicolon-separated list of exposures extracted_object The complex objects extracted from the text full_text The full text of the publication gene_exposures_relationships semicolon-separated list of gene to molecular activity relationships genes semicolon-separated list of genes id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object The name of the gene in the pair object_id object_qualifier An optional qualifier or modifier for the gene object_text predicate The name of the type of relationship between a chemical exposure and a gene prompt publication qualifier A qualifier for the statements, e raw_completion_output subject The name of the exposure, such as a exposure to a chemical toxin subject_qualifier An optional qualifier or modifier for the chemical exposure subject_text title The title of the publication triples"},{"location":"ibd_literature/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"ibd_literature/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"ibd_literature/#subsets","title":"Subsets","text":"Subset Description"},{"location":"ibd_literature/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: ibdlit:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"ibd_literature/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"ibd_literature/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:AnnotatorResult native ibdlit:AnnotatorResult"},{"location":"ibd_literature/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n\n
"},{"location":"ibd_literature/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"ibd_literature/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"ibd_literature/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ibd_literature/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"ibd_literature/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Any/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native ibdlit:Any"},{"location":"ibd_literature/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nclass_uri: linkml:Any\n\n
"},{"location":"ibd_literature/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nclass_uri: linkml:Any\n\n
"},{"location":"ibd_literature/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"ibd_literature/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/CellularProcess/","title":"Class: CellularProcess","text":"

URI: ibdlit:CellularProcess

erDiagram\nCellularProcess {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/CellularProcess/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/CellularProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/CellularProcess/#usages","title":"Usages","text":"used by used in type used IBDAnnotations cellular_process range CellularProcess DiseaseCellularProcessRelationship object range CellularProcess"},{"location":"ibd_literature/CellularProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/CellularProcess/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/CellularProcess/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"ibd_literature/CellularProcess/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/CellularProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:CellularProcess native ibdlit:CellularProcess"},{"location":"ibd_literature/CellularProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/CellularProcess/#direct","title":"Direct","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\n  prompt:\n    tag: prompt\n    value: the name of the cellular process\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/CellularProcess/#induced","title":"Induced","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\n  prompt:\n    tag: prompt\n    value: the name of the cellular process\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/ChemicalExposure/","title":"Class: ChemicalExposure","text":"

URI: ibdlit:ChemicalExposure

erDiagram\nChemicalExposure {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/ChemicalExposure/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/ChemicalExposure/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/ChemicalExposure/#usages","title":"Usages","text":"used by used in type used IBDAnnotations exposures range ChemicalExposure GeneExposureRelationship subject range ChemicalExposure"},{"location":"ibd_literature/ChemicalExposure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/ChemicalExposure/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/ChemicalExposure/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ecto, sqlite:obo:chebi"},{"location":"ibd_literature/ChemicalExposure/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/ChemicalExposure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:ChemicalExposure native ibdlit:ChemicalExposure"},{"location":"ibd_literature/ChemicalExposure/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/ChemicalExposure/#direct","title":"Direct","text":"
name: ChemicalExposure\nid_prefixes:\n- CHEBI\n- ECTO\n- ExO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ecto, sqlite:obo:chebi\n  prompt:\n    tag: prompt\n    value: the name of the exposure, such as a exposure to a chemical toxin. For example,\n      CHEBI:17968 butyrate.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/ChemicalExposure/#induced","title":"Induced","text":"
name: ChemicalExposure\nid_prefixes:\n- CHEBI\n- ECTO\n- ExO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ecto, sqlite:obo:chebi\n  prompt:\n    tag: prompt\n    value: the name of the exposure, such as a exposure to a chemical toxin. For example,\n      CHEBI:17968 butyrate.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalExposure\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalExposure\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/","title":"Class: ChemicalExposureToGenePredicate","text":"

URI: ibdlit:ChemicalExposureToGenePredicate

erDiagram\nChemicalExposureToGenePredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#usages","title":"Usages","text":"used by used in type used GeneExposureRelationship predicate range ChemicalExposureToGenePredicate"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ro"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:ChemicalExposureToGenePredicate native ibdlit:ChemicalExposureToGenePredicate"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#direct","title":"Direct","text":"
name: ChemicalExposureToGenePredicate\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\n  prompt:\n    tag: prompt\n    value: the name of the type of relationship between a chemical exposure and a\n      gene.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#induced","title":"Induced","text":"
name: ChemicalExposureToGenePredicate\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\n  prompt:\n    tag: prompt\n    value: the name of the type of relationship between a chemical exposure and a\n      gene.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalExposureToGenePredicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalExposureToGenePredicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: ibdlit:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"ibd_literature/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ibd_literature/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:CompoundExpression native ibdlit:CompoundExpression"},{"location":"ibd_literature/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nabstract: true\n\n
"},{"location":"ibd_literature/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nabstract: true\n\n
"},{"location":"ibd_literature/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"ibd_literature/Curie/#comments","title":"Comments","text":""},{"location":"ibd_literature/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Curie/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"ibd_literature/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Date/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"ibd_literature/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"ibd_literature/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"ibd_literature/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Disease/","title":"Class: Disease","text":"

URI: ibdlit:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/Disease/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/Disease/#usages","title":"Usages","text":"used by used in type used IBDAnnotations diseases range Disease DiseaseCellularProcessRelationship subject range Disease"},{"location":"ibd_literature/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Disease/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo"},{"location":"ibd_literature/Disease/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:Disease native ibdlit:Disease"},{"location":"ibd_literature/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/Disease/#direct","title":"Direct","text":"
name: Disease\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\n  prompt:\n    tag: prompt\n    value: the name of the disease\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/Disease/#induced","title":"Induced","text":"
name: Disease\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\n  prompt:\n    tag: prompt\n    value: the name of the disease\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/","title":"Class: DiseaseCellularProcessRelationship","text":"

URI: ibdlit:DiseaseCellularProcessRelationship

erDiagram\nDiseaseCellularProcessRelationship {\n\n}\nNamedEntity {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nDiseaseToCellularProcessPredicate {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nDiseaseCellularProcessRelationship ||--|o Disease : \"subject\"\nDiseaseCellularProcessRelationship ||--|o DiseaseToCellularProcessPredicate : \"predicate\"\nDiseaseCellularProcessRelationship ||--|o CellularProcess : \"object\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"subject_qualifier\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 Disease The name of the disease direct predicate 0..1 DiseaseToCellularProcessPredicate The name of the type of relationship between a disease and a cellular process direct object 0..1 CellularProcess The name of the cellular process direct subject_qualifier 0..1 NamedEntity direct object_qualifier 0..1 NamedEntity direct"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#usages","title":"Usages","text":"used by used in type used IBDAnnotations disease_cellular_process_relationships range DiseaseCellularProcessRelationship"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:DiseaseCellularProcessRelationship native ibdlit:DiseaseCellularProcessRelationship"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#direct","title":"Direct","text":"
name: DiseaseCellularProcessRelationship\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    description: The name of the disease.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: Disease\n  predicate:\n    name: predicate\n    description: The name of the type of relationship between a disease and a cellular\n      process.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: DiseaseToCellularProcessPredicate\n  object:\n    name: object\n    description: The name of the cellular process.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: CellularProcess\n  subject_qualifier:\n    name: subject_qualifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#induced","title":"Induced","text":"
name: DiseaseCellularProcessRelationship\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    description: The name of the disease.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: subject\n    owner: DiseaseCellularProcessRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: Disease\n  predicate:\n    name: predicate\n    description: The name of the type of relationship between a disease and a cellular\n      process.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: predicate\n    owner: DiseaseCellularProcessRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: DiseaseToCellularProcessPredicate\n  object:\n    name: object\n    description: The name of the cellular process.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: object\n    owner: DiseaseCellularProcessRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: CellularProcess\n  subject_qualifier:\n    name: subject_qualifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: subject_qualifier\n    owner: DiseaseCellularProcessRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: object_qualifier\n    owner: DiseaseCellularProcessRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/","title":"Class: DiseaseToCellularProcessPredicate","text":"

URI: ibdlit:DiseaseToCellularProcessPredicate

erDiagram\nDiseaseToCellularProcessPredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#usages","title":"Usages","text":"used by used in type used DiseaseCellularProcessRelationship predicate range DiseaseToCellularProcessPredicate"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ro"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:DiseaseToCellularProcessPredicate native ibdlit:DiseaseToCellularProcessPredicate"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#direct","title":"Direct","text":"
name: DiseaseToCellularProcessPredicate\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\n  prompt:\n    tag: prompt\n    value: the name of the type of relationship between a disease and a cellular process.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#induced","title":"Induced","text":"
name: DiseaseToCellularProcessPredicate\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\n  prompt:\n    tag: prompt\n    value: the name of the type of relationship between a disease and a cellular process.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DiseaseToCellularProcessPredicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: DiseaseToCellularProcessPredicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"ibd_literature/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Double/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: ibdlit:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"ibd_literature/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"ibd_literature/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:ExtractionResult native ibdlit:ExtractionResult"},{"location":"ibd_literature/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd_literature/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd_literature/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"ibd_literature/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Float/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Gene/","title":"Class: Gene","text":"

URI: ibdlit:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/Gene/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/Gene/#usages","title":"Usages","text":"used by used in type used IBDAnnotations genes range Gene GeneExposureRelationship object range Gene"},{"location":"ibd_literature/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/Gene/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hgnc, sqlite:obo:pr"},{"location":"ibd_literature/Gene/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:Gene native ibdlit:Gene"},{"location":"ibd_literature/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, sqlite:obo:pr\n  prompt:\n    tag: prompt\n    value: the name of the gene in the pair. This comes second in the pair.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, sqlite:obo:pr\n  prompt:\n    tag: prompt\n    value: the name of the gene in the pair. This comes second in the pair.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/GeneExposureRelationship/","title":"Class: GeneExposureRelationship","text":"

URI: ibdlit:GeneExposureRelationship

erDiagram\nGeneExposureRelationship {\n\n}\nNamedEntity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nChemicalExposureToGenePredicate {\n    string id  \n    string label  \n}\nChemicalExposure {\n    string id  \n    string label  \n}\n\nGeneExposureRelationship ||--|o ChemicalExposure : \"subject\"\nGeneExposureRelationship ||--|o ChemicalExposureToGenePredicate : \"predicate\"\nGeneExposureRelationship ||--|o Gene : \"object\"\nGeneExposureRelationship ||--|o NamedEntity : \"subject_qualifier\"\nGeneExposureRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/GeneExposureRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/GeneExposureRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 ChemicalExposure The name of the exposure, such as a exposure to a chemical toxin direct predicate 0..1 ChemicalExposureToGenePredicate The name of the type of relationship between a chemical exposure and a gene direct object 0..1 Gene The name of the gene in the pair direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the chemical exposure direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the gene direct"},{"location":"ibd_literature/GeneExposureRelationship/#usages","title":"Usages","text":"used by used in type used IBDAnnotations gene_exposures_relationships range GeneExposureRelationship"},{"location":"ibd_literature/GeneExposureRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/GeneExposureRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/GeneExposureRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:GeneExposureRelationship native ibdlit:GeneExposureRelationship"},{"location":"ibd_literature/GeneExposureRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/GeneExposureRelationship/#direct","title":"Direct","text":"
name: GeneExposureRelationship\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    description: The name of the exposure, such as a exposure to a chemical toxin.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: ChemicalExposure\n  predicate:\n    name: predicate\n    description: The name of the type of relationship between a chemical exposure\n      and a gene.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: ChemicalExposureToGenePredicate\n  object:\n    name: object\n    description: The name of the gene in the pair. This comes second in the pair.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: Gene\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the chemical exposure.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the gene.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/GeneExposureRelationship/#induced","title":"Induced","text":"
name: GeneExposureRelationship\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    description: The name of the exposure, such as a exposure to a chemical toxin.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: subject\n    owner: GeneExposureRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: ChemicalExposure\n  predicate:\n    name: predicate\n    description: The name of the type of relationship between a chemical exposure\n      and a gene.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: predicate\n    owner: GeneExposureRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: ChemicalExposureToGenePredicate\n  object:\n    name: object\n    description: The name of the gene in the pair. This comes second in the pair.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: object\n    owner: GeneExposureRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: Gene\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the chemical exposure.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: subject_qualifier\n    owner: GeneExposureRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the gene.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: object_qualifier\n    owner: GeneExposureRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/IBDAnnotations/","title":"Class: IBDAnnotations","text":"

URI: ibdlit:IBDAnnotations

erDiagram\nIBDAnnotations {\n\n}\nDiseaseCellularProcessRelationship {\n\n}\nNamedEntity {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nDiseaseToCellularProcessPredicate {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGeneExposureRelationship {\n\n}\nGene {\n    string id  \n    string label  \n}\nChemicalExposureToGenePredicate {\n    string id  \n    string label  \n}\nChemicalExposure {\n    string id  \n    string label  \n}\n\nIBDAnnotations ||--}o Gene : \"genes\"\nIBDAnnotations ||--}o ChemicalExposure : \"exposures\"\nIBDAnnotations ||--}o GeneExposureRelationship : \"gene_exposures_relationships\"\nIBDAnnotations ||--}o Disease : \"diseases\"\nIBDAnnotations ||--}o CellularProcess : \"cellular_process\"\nIBDAnnotations ||--}o DiseaseCellularProcessRelationship : \"disease_cellular_process_relationships\"\nDiseaseCellularProcessRelationship ||--|o Disease : \"subject\"\nDiseaseCellularProcessRelationship ||--|o DiseaseToCellularProcessPredicate : \"predicate\"\nDiseaseCellularProcessRelationship ||--|o CellularProcess : \"object\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"subject_qualifier\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"object_qualifier\"\nGeneExposureRelationship ||--|o ChemicalExposure : \"subject\"\nGeneExposureRelationship ||--|o ChemicalExposureToGenePredicate : \"predicate\"\nGeneExposureRelationship ||--|o Gene : \"object\"\nGeneExposureRelationship ||--|o NamedEntity : \"subject_qualifier\"\nGeneExposureRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/IBDAnnotations/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance genes 0..* Gene semicolon-separated list of genes direct exposures 0..* ChemicalExposure semicolon-separated list of exposures direct gene_exposures_relationships 0..* GeneExposureRelationship semicolon-separated list of gene to molecular activity relationships direct diseases 0..* Disease semicolon-separated list of diseases direct cellular_process 0..* CellularProcess semicolon-separated list of cellular processes direct disease_cellular_process_relationships 0..* DiseaseCellularProcessRelationship semicolon-separated list of disease to cellular process relationships direct"},{"location":"ibd_literature/IBDAnnotations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/IBDAnnotations/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/IBDAnnotations/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:IBDAnnotations native ibdlit:IBDAnnotations"},{"location":"ibd_literature/IBDAnnotations/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/IBDAnnotations/#direct","title":"Direct","text":"
name: IBDAnnotations\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: Gene\n  exposures:\n    name: exposures\n    annotations:\n      prompt:\n        tag: prompt\n        value: a chemical or molecule whose direct or indirect effects cause one or\n          more entities to experience biological change\n    description: semicolon-separated list of exposures\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: ChemicalExposure\n  gene_exposures_relationships:\n    name: gene_exposures_relationships\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: GeneExposureRelationship\n  diseases:\n    name: diseases\n    description: semicolon-separated list of diseases\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: Disease\n  cellular_process:\n    name: cellular_process\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: CellularProcess\n  disease_cellular_process_relationships:\n    name: disease_cellular_process_relationships\n    description: semicolon-separated list of disease to cellular process relationships\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: DiseaseCellularProcessRelationship\ntree_root: true\n\n
"},{"location":"ibd_literature/IBDAnnotations/#induced","title":"Induced","text":"
name: IBDAnnotations\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: Gene\n  exposures:\n    name: exposures\n    annotations:\n      prompt:\n        tag: prompt\n        value: a chemical or molecule whose direct or indirect effects cause one or\n          more entities to experience biological change\n    description: semicolon-separated list of exposures\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: exposures\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: ChemicalExposure\n  gene_exposures_relationships:\n    name: gene_exposures_relationships\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: gene_exposures_relationships\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: GeneExposureRelationship\n  diseases:\n    name: diseases\n    description: semicolon-separated list of diseases\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: diseases\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: Disease\n  cellular_process:\n    name: cellular_process\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: cellular_process\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: CellularProcess\n  disease_cellular_process_relationships:\n    name: disease_cellular_process_relationships\n    description: semicolon-separated list of disease to cellular process relationships\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: disease_cellular_process_relationships\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: DiseaseCellularProcessRelationship\ntree_root: true\n\n
"},{"location":"ibd_literature/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"ibd_literature/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Integer/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/NamedEntity/","title":"Class: NamedEntity","text":"

URI: ibdlit:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"ibd_literature/NamedEntity/#usages","title":"Usages","text":"used by used in type used GeneExposureRelationship subject_qualifier range NamedEntity GeneExposureRelationship object_qualifier range NamedEntity DiseaseCellularProcessRelationship subject_qualifier range NamedEntity DiseaseCellularProcessRelationship object_qualifier range NamedEntity Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"ibd_literature/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:NamedEntity native ibdlit:NamedEntity"},{"location":"ibd_literature/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"ibd_literature/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"ibd_literature/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"ibd_literature/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"ibd_literature/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"ibd_literature/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"ibd_literature/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"ibd_literature/Objectidentifier/#comments","title":"Comments","text":""},{"location":"ibd_literature/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Publication/","title":"Class: Publication","text":"

URI: ibdlit:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"ibd_literature/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"ibd_literature/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"ibd_literature/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Publication/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:Publication native ibdlit:Publication"},{"location":"ibd_literature/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n\n
"},{"location":"ibd_literature/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"ibd_literature/RelationshipType/","title":"Class: RelationshipType","text":"

URI: ibdlit:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"ibd_literature/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:RelationshipType native ibdlit:RelationshipType"},{"location":"ibd_literature/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"ibd_literature/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/String/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: ibdlit:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"ibd_literature/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:TextWithTriples native ibdlit:TextWithTriples"},{"location":"ibd_literature/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd_literature/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd_literature/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"ibd_literature/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Time/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: ibdlit:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/Triple/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"ibd_literature/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"ibd_literature/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Triple/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:Triple native ibdlit:Triple"},{"location":"ibd_literature/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: subject\n    owner: Triple\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: object\n    owner: Triple\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"ibd_literature/Uri/#comments","title":"Comments","text":""},{"location":"ibd_literature/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Uri/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"ibd_literature/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: ibdlit:abstract

"},{"location":"ibd_literature/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd_literature/abstract/#properties","title":"Properties","text":""},{"location":"ibd_literature/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/abstract/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd_literature/cellular_process/","title":"Slot: cellular_process","text":"

semicolon-separated list of cellular processes

URI: ibdlit:cellular_process

"},{"location":"ibd_literature/cellular_process/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/cellular_process/#properties","title":"Properties","text":""},{"location":"ibd_literature/cellular_process/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/cellular_process/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/cellular_process/#linkml-source","title":"LinkML Source","text":"
name: cellular_process\ndescription: semicolon-separated list of cellular processes\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: cellular_process\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: CellularProcess\n\n
"},{"location":"ibd_literature/combined_text/","title":"Slot: combined_text","text":"

URI: ibdlit:combined_text

"},{"location":"ibd_literature/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd_literature/combined_text/#properties","title":"Properties","text":""},{"location":"ibd_literature/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd_literature/disease_cellular_process_relationships/","title":"Slot: disease_cellular_process_relationships","text":"

semicolon-separated list of disease to cellular process relationships

URI: ibdlit:disease_cellular_process_relationships

"},{"location":"ibd_literature/disease_cellular_process_relationships/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/disease_cellular_process_relationships/#properties","title":"Properties","text":""},{"location":"ibd_literature/disease_cellular_process_relationships/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/disease_cellular_process_relationships/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/disease_cellular_process_relationships/#linkml-source","title":"LinkML Source","text":"
name: disease_cellular_process_relationships\ndescription: semicolon-separated list of disease to cellular process relationships\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: disease_cellular_process_relationships\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: DiseaseCellularProcessRelationship\n\n
"},{"location":"ibd_literature/diseases/","title":"Slot: diseases","text":"

semicolon-separated list of diseases

URI: ibdlit:diseases

"},{"location":"ibd_literature/diseases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/diseases/#properties","title":"Properties","text":""},{"location":"ibd_literature/diseases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/diseases/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/diseases/#linkml-source","title":"LinkML Source","text":"
name: diseases\ndescription: semicolon-separated list of diseases\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: diseases\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: Disease\n\n
"},{"location":"ibd_literature/exposures/","title":"Slot: exposures","text":"

semicolon-separated list of exposures

URI: ibdlit:exposures

"},{"location":"ibd_literature/exposures/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/exposures/#properties","title":"Properties","text":""},{"location":"ibd_literature/exposures/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/exposures/#annotations","title":"Annotations","text":"property value prompt a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change"},{"location":"ibd_literature/exposures/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/exposures/#linkml-source","title":"LinkML Source","text":"
name: exposures\nannotations:\n  prompt:\n    tag: prompt\n    value: a chemical or molecule whose direct or indirect effects cause one or more\n      entities to experience biological change\ndescription: semicolon-separated list of exposures\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: exposures\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: ChemicalExposure\n\n
"},{"location":"ibd_literature/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: ibdlit:extracted_object

"},{"location":"ibd_literature/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/extracted_object/#properties","title":"Properties","text":""},{"location":"ibd_literature/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"ibd_literature/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: ibdlit:full_text

"},{"location":"ibd_literature/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd_literature/full_text/#properties","title":"Properties","text":""},{"location":"ibd_literature/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/full_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd_literature/gene_exposures_relationships/","title":"Slot: gene_exposures_relationships","text":"

semicolon-separated list of gene to molecular activity relationships

URI: ibdlit:gene_exposures_relationships

"},{"location":"ibd_literature/gene_exposures_relationships/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/gene_exposures_relationships/#properties","title":"Properties","text":""},{"location":"ibd_literature/gene_exposures_relationships/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/gene_exposures_relationships/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/gene_exposures_relationships/#linkml-source","title":"LinkML Source","text":"
name: gene_exposures_relationships\ndescription: semicolon-separated list of gene to molecular activity relationships\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: gene_exposures_relationships\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: GeneExposureRelationship\n\n
"},{"location":"ibd_literature/genes/","title":"Slot: genes","text":"

semicolon-separated list of genes

URI: ibdlit:genes

"},{"location":"ibd_literature/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/genes/#properties","title":"Properties","text":""},{"location":"ibd_literature/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/genes/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\ndescription: semicolon-separated list of genes\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: genes\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: Gene\n\n
"},{"location":"ibd_literature/ibd-literature-template/","title":"ibd-literature-template","text":"

A template for extracting information from IBD literature

URI: http://w3id.org/ontogpt/ibd_literature

"},{"location":"ibd_literature/id/","title":"Slot: id","text":"

URI: ibdlit:id

"},{"location":"ibd_literature/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no ChemicalExposure no ChemicalExposureToGenePredicate no Disease no CellularProcess no DiseaseToCellularProcessPredicate no NamedEntity no RelationshipType no Publication no"},{"location":"ibd_literature/id/#properties","title":"Properties","text":""},{"location":"ibd_literature/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"ibd_literature/input_id/","title":"Slot: input_id","text":"

URI: ibdlit:input_id

"},{"location":"ibd_literature/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/input_id/#properties","title":"Properties","text":""},{"location":"ibd_literature/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/input_id/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd_literature/input_text/","title":"Slot: input_text","text":"

URI: ibdlit:input_text

"},{"location":"ibd_literature/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/input_text/#properties","title":"Properties","text":""},{"location":"ibd_literature/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/input_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd_literature/input_title/","title":"Slot: input_title","text":"

URI: ibdlit:input_title

"},{"location":"ibd_literature/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/input_title/#properties","title":"Properties","text":""},{"location":"ibd_literature/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/input_title/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd_literature/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"ibd_literature/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no ChemicalExposure no ChemicalExposureToGenePredicate no Disease no CellularProcess no DiseaseToCellularProcessPredicate no NamedEntity no RelationshipType no"},{"location":"ibd_literature/label/#properties","title":"Properties","text":""},{"location":"ibd_literature/label/#aliases","title":"Aliases","text":""},{"location":"ibd_literature/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"ibd_literature/label/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"ibd_literature/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: ibdlit:named_entities

"},{"location":"ibd_literature/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/named_entities/#properties","title":"Properties","text":""},{"location":"ibd_literature/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ibd_literature/object/","title":"Slot: object","text":"

URI: ibdlit:object

"},{"location":"ibd_literature/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneExposureRelationship no DiseaseCellularProcessRelationship no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/object/#properties","title":"Properties","text":""},{"location":"ibd_literature/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/object/#linkml-source","title":"LinkML Source","text":"
name: object\nalias: object\ndomain_of:\n- GeneExposureRelationship\n- DiseaseCellularProcessRelationship\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/object_id/","title":"Slot: object_id","text":"

URI: ibdlit:object_id

"},{"location":"ibd_literature/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd_literature/object_id/#properties","title":"Properties","text":""},{"location":"ibd_literature/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/object_id/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd_literature/object_qualifier/","title":"Slot: object_qualifier","text":"

URI: ibdlit:object_qualifier

"},{"location":"ibd_literature/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneExposureRelationship no DiseaseCellularProcessRelationship no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/object_qualifier/#properties","title":"Properties","text":""},{"location":"ibd_literature/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\nalias: object_qualifier\ndomain_of:\n- GeneExposureRelationship\n- DiseaseCellularProcessRelationship\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/object_text/","title":"Slot: object_text","text":"

URI: ibdlit:object_text

"},{"location":"ibd_literature/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd_literature/object_text/#properties","title":"Properties","text":""},{"location":"ibd_literature/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/object_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd_literature/predicate/","title":"Slot: predicate","text":"

URI: ibdlit:predicate

"},{"location":"ibd_literature/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneExposureRelationship no DiseaseCellularProcessRelationship no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/predicate/#properties","title":"Properties","text":""},{"location":"ibd_literature/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nalias: predicate\ndomain_of:\n- GeneExposureRelationship\n- DiseaseCellularProcessRelationship\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/prompt/","title":"Slot: prompt","text":"

URI: ibdlit:prompt

"},{"location":"ibd_literature/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/prompt/#properties","title":"Properties","text":""},{"location":"ibd_literature/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/prompt/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd_literature/publication/","title":"Slot: publication","text":"

URI: ibdlit:publication

"},{"location":"ibd_literature/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ibd_literature/publication/#properties","title":"Properties","text":""},{"location":"ibd_literature/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"ibd_literature/publication/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"ibd_literature/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: ibdlit:qualifier

"},{"location":"ibd_literature/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/qualifier/#properties","title":"Properties","text":""},{"location":"ibd_literature/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: ibdlit:raw_completion_output

"},{"location":"ibd_literature/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/raw_completion_output/#properties","title":"Properties","text":""},{"location":"ibd_literature/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd_literature/subject/","title":"Slot: subject","text":"

URI: ibdlit:subject

"},{"location":"ibd_literature/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneExposureRelationship no DiseaseCellularProcessRelationship no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/subject/#properties","title":"Properties","text":""},{"location":"ibd_literature/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nalias: subject\ndomain_of:\n- GeneExposureRelationship\n- DiseaseCellularProcessRelationship\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/subject_qualifier/","title":"Slot: subject_qualifier","text":"

URI: ibdlit:subject_qualifier

"},{"location":"ibd_literature/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneExposureRelationship no DiseaseCellularProcessRelationship no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/subject_qualifier/#properties","title":"Properties","text":""},{"location":"ibd_literature/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\nalias: subject_qualifier\ndomain_of:\n- GeneExposureRelationship\n- DiseaseCellularProcessRelationship\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/subject_text/","title":"Slot: subject_text","text":"

URI: ibdlit:subject_text

"},{"location":"ibd_literature/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd_literature/subject_text/#properties","title":"Properties","text":""},{"location":"ibd_literature/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd_literature/title/","title":"Slot: title","text":"

The title of the publication

URI: ibdlit:title

"},{"location":"ibd_literature/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd_literature/title/#properties","title":"Properties","text":""},{"location":"ibd_literature/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/title/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd_literature/triples/","title":"Slot: triples","text":"

URI: ibdlit:triples

"},{"location":"ibd_literature/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ibd_literature/triples/#properties","title":"Properties","text":""},{"location":"ibd_literature/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/triples/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"maxo/","title":"Template for Medical Action Extraction","text":"

A template for extracting relationships relevant to the MAXO medical action ontology.

URI: http://w3id.org/ontogpt/maxo

Name: maxo

"},{"location":"maxo/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nMaxoAnnotations {\n\n}\nActionToSymptomRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nSymptom {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\nActionToDiseaseRelationship {\n    string qualifier  \n}\nDisease {\n    string id  \n    string label  \n}\n\nMaxoAnnotations ||--}o Action : \"action\"\nMaxoAnnotations ||--}o Disease : \"disease\"\nMaxoAnnotations ||--}o Symptom : \"symptom\"\nMaxoAnnotations ||--}o ActionToDiseaseRelationship : \"action_to_disease\"\nMaxoAnnotations ||--}o ActionToSymptomRelationship : \"action_to_symptom\"\nActionToSymptomRelationship ||--|o Action : \"subject\"\nActionToSymptomRelationship ||--|o NamedEntity : \"predicate\"\nActionToSymptomRelationship ||--}o Symptom : \"object\"\nActionToSymptomRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToSymptomRelationship ||--|o NamedEntity : \"object_qualifier\"\nActionToDiseaseRelationship ||--|o Action : \"subject\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"predicate\"\nActionToDiseaseRelationship ||--}o Disease : \"object\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a disease, for example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis. ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a symptom, for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion. ExtractionResult A result of extracting knowledge on text MaxoAnnotations None NamedEntity None Action A clinically prescribed procedure, therapy, intervention, or recommendation. Disease A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. RelationshipType None Symptom A condition or phenotype resulting from an abnormal health state. Publication None TextWithTriples None"},{"location":"maxo/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication action Semicolon-separated list of medical actions action_to_disease action_to_symptom combined_text disease Semicolon-separated list of diseases extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text symptom Semicolon-separated list of symptoms title The title of the publication triples"},{"location":"maxo/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"maxo/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"maxo/#subsets","title":"Subsets","text":"Subset Description"},{"location":"maxo/Action/","title":"Class: Action","text":"

A clinically prescribed procedure, therapy, intervention, or recommendation.

URI: maxo_extract:Action

erDiagram\nAction {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"maxo/Action/#inheritance","title":"Inheritance","text":""},{"location":"maxo/Action/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"maxo/Action/#usages","title":"Usages","text":"used by used in type used MaxoAnnotations action range Action ActionToDiseaseRelationship subject range Action ActionToSymptomRelationship subject range Action"},{"location":"maxo/Action/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Action/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"maxo/Action/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:maxo, sqlite:obo:ogms, sqlite:obo:ncit"},{"location":"maxo/Action/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Action/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:Action native maxo_extract:Action"},{"location":"maxo/Action/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Action/#direct","title":"Direct","text":"
name: Action\nid_prefixes:\n- MAXO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ogms, sqlite:obo:ncit\ndescription: A clinically prescribed procedure, therapy, intervention, or recommendation.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\n\n
"},{"location":"maxo/Action/#induced","title":"Induced","text":"
name: Action\nid_prefixes:\n- MAXO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ogms, sqlite:obo:ncit\ndescription: A clinically prescribed procedure, therapy, intervention, or recommendation.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Action\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Action\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"maxo/ActionToDiseaseRelationship/","title":"Class: ActionToDiseaseRelationship","text":"

A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a disease, for example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis.

URI: maxo_extract:ActionToDiseaseRelationship

erDiagram\nActionToDiseaseRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\n\nActionToDiseaseRelationship ||--|o Action : \"subject\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"predicate\"\nActionToDiseaseRelationship ||--}o Disease : \"object\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/ActionToDiseaseRelationship/#inheritance","title":"Inheritance","text":""},{"location":"maxo/ActionToDiseaseRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 Action Triple predicate 0..1 NamedEntity The relationship type, usually TREATS or IS USED TO DIAGNOSE Triple object 0..* Disease Triple qualifier 0..1 String A qualifier for the statements, e Triple subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the medical action Triple object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the disease Triple"},{"location":"maxo/ActionToDiseaseRelationship/#usages","title":"Usages","text":"used by used in type used MaxoAnnotations action_to_disease range ActionToDiseaseRelationship"},{"location":"maxo/ActionToDiseaseRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/ActionToDiseaseRelationship/#schema-source","title":"Schema Source","text":""},{"location":"maxo/ActionToDiseaseRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:ActionToDiseaseRelationship native maxo_extract:ActionToDiseaseRelationship"},{"location":"maxo/ActionToDiseaseRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/ActionToDiseaseRelationship/#direct","title":"Direct","text":"
name: ActionToDiseaseRelationship\ndescription: A triple representing a relationship between a medical action  (A clinically\n  prescribed procedure, therapy, intervention, or recommendation) and a disease, for\n  example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    domain_of:\n    - Triple\n    range: Action\n  object:\n    name: object\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Disease\n  predicate:\n    name: predicate\n    description: The relationship type, usually TREATS or IS USED TO DIAGNOSE\n    domain_of:\n    - Triple\n    range: NamedEntity\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease.\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"maxo/ActionToDiseaseRelationship/#induced","title":"Induced","text":"
name: ActionToDiseaseRelationship\ndescription: A triple representing a relationship between a medical action  (A clinically\n  prescribed procedure, therapy, intervention, or recommendation) and a disease, for\n  example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    domain_of:\n    - Triple\n    range: Action\n  object:\n    name: object\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Disease\n  predicate:\n    name: predicate\n    description: The relationship type, usually TREATS or IS USED TO DIAGNOSE\n    domain_of:\n    - Triple\n    range: NamedEntity\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease.\n    domain_of:\n    - Triple\n    range: NamedEntity\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: Action\n  predicate:\n    name: predicate\n    description: The relationship type, usually TREATS or IS USED TO DIAGNOSE\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: predicate\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: object\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: Disease\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: qualifier\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject_qualifier\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object_qualifier\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"maxo/ActionToSymptomRelationship/","title":"Class: ActionToSymptomRelationship","text":"

A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a symptom, for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.

URI: maxo_extract:ActionToSymptomRelationship

erDiagram\nActionToSymptomRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nSymptom {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\n\nActionToSymptomRelationship ||--|o Action : \"subject\"\nActionToSymptomRelationship ||--|o NamedEntity : \"predicate\"\nActionToSymptomRelationship ||--}o Symptom : \"object\"\nActionToSymptomRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToSymptomRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/ActionToSymptomRelationship/#inheritance","title":"Inheritance","text":""},{"location":"maxo/ActionToSymptomRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 Action Triple predicate 0..1 NamedEntity The relationship type, usually IS USED TO DIAGNOSE Triple object 0..* Symptom Triple qualifier 0..1 String A qualifier for the statements, e Triple subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the medical action Triple object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the symptom Triple"},{"location":"maxo/ActionToSymptomRelationship/#usages","title":"Usages","text":"used by used in type used MaxoAnnotations action_to_symptom range ActionToSymptomRelationship"},{"location":"maxo/ActionToSymptomRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/ActionToSymptomRelationship/#schema-source","title":"Schema Source","text":""},{"location":"maxo/ActionToSymptomRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:ActionToSymptomRelationship native maxo_extract:ActionToSymptomRelationship"},{"location":"maxo/ActionToSymptomRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/ActionToSymptomRelationship/#direct","title":"Direct","text":"
name: ActionToSymptomRelationship\ndescription: A triple representing a relationship between a medical action  (A clinically\n  prescribed procedure, therapy, intervention, or recommendation) and a symptom, for\n  example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    domain_of:\n    - Triple\n    range: Action\n  object:\n    name: object\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Symptom\n  predicate:\n    name: predicate\n    description: The relationship type, usually IS USED TO DIAGNOSE\n    domain_of:\n    - Triple\n    range: NamedEntity\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the symptom.\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"maxo/ActionToSymptomRelationship/#induced","title":"Induced","text":"
name: ActionToSymptomRelationship\ndescription: A triple representing a relationship between a medical action  (A clinically\n  prescribed procedure, therapy, intervention, or recommendation) and a symptom, for\n  example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    domain_of:\n    - Triple\n    range: Action\n  object:\n    name: object\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Symptom\n  predicate:\n    name: predicate\n    description: The relationship type, usually IS USED TO DIAGNOSE\n    domain_of:\n    - Triple\n    range: NamedEntity\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the symptom.\n    domain_of:\n    - Triple\n    range: NamedEntity\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: Action\n  predicate:\n    name: predicate\n    description: The relationship type, usually IS USED TO DIAGNOSE\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: predicate\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: object\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: Symptom\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: qualifier\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject_qualifier\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the symptom.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object_qualifier\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"maxo/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: maxo_extract:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"maxo/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"maxo/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"maxo/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:AnnotatorResult native maxo_extract:AnnotatorResult"},{"location":"maxo/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n\n
"},{"location":"maxo/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"maxo/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"maxo/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"maxo/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"maxo/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Any/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native maxo_extract:Any"},{"location":"maxo/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/maxo\nclass_uri: linkml:Any\n\n
"},{"location":"maxo/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/maxo\nclass_uri: linkml:Any\n\n
"},{"location":"maxo/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"maxo/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"maxo/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: maxo_extract:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"maxo/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"maxo/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"maxo/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"maxo/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:CompoundExpression native maxo_extract:CompoundExpression"},{"location":"maxo/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/maxo\nabstract: true\n\n
"},{"location":"maxo/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/maxo\nabstract: true\n\n
"},{"location":"maxo/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"maxo/Curie/#comments","title":"Comments","text":""},{"location":"maxo/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Curie/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"maxo/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Date/#schema-source","title":"Schema Source","text":""},{"location":"maxo/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"maxo/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"maxo/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"maxo/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Disease/","title":"Class: Disease","text":"

A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.

URI: maxo_extract:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"maxo/Disease/#inheritance","title":"Inheritance","text":""},{"location":"maxo/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"maxo/Disease/#usages","title":"Usages","text":"used by used in type used MaxoAnnotations disease range Disease ActionToDiseaseRelationship object range Disease"},{"location":"maxo/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Disease/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"maxo/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo"},{"location":"maxo/Disease/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:Disease native maxo_extract:Disease"},{"location":"maxo/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Disease/#direct","title":"Direct","text":"
name: Disease\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\ndescription: A disposition to undergo pathological processes that exists in an organism\n  because of one or more disorders in that organism.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\n\n
"},{"location":"maxo/Disease/#induced","title":"Induced","text":"
name: Disease\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\ndescription: A disposition to undergo pathological processes that exists in an organism\n  because of one or more disorders in that organism.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"maxo/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"maxo/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Double/#schema-source","title":"Schema Source","text":""},{"location":"maxo/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: maxo_extract:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"maxo/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"maxo/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"maxo/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:ExtractionResult native maxo_extract:ExtractionResult"},{"location":"maxo/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"maxo/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"maxo/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"maxo/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Float/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"maxo/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Integer/#schema-source","title":"Schema Source","text":""},{"location":"maxo/MaxoAnnotations/","title":"Class: MaxoAnnotations","text":"

URI: maxo_extract:MaxoAnnotations

erDiagram\nMaxoAnnotations {\n\n}\nActionToSymptomRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nSymptom {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\nActionToDiseaseRelationship {\n    string qualifier  \n}\nDisease {\n    string id  \n    string label  \n}\n\nMaxoAnnotations ||--}o Action : \"action\"\nMaxoAnnotations ||--}o Disease : \"disease\"\nMaxoAnnotations ||--}o Symptom : \"symptom\"\nMaxoAnnotations ||--}o ActionToDiseaseRelationship : \"action_to_disease\"\nMaxoAnnotations ||--}o ActionToSymptomRelationship : \"action_to_symptom\"\nActionToSymptomRelationship ||--|o Action : \"subject\"\nActionToSymptomRelationship ||--|o NamedEntity : \"predicate\"\nActionToSymptomRelationship ||--}o Symptom : \"object\"\nActionToSymptomRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToSymptomRelationship ||--|o NamedEntity : \"object_qualifier\"\nActionToDiseaseRelationship ||--|o Action : \"subject\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"predicate\"\nActionToDiseaseRelationship ||--}o Disease : \"object\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/MaxoAnnotations/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance action 0..* Action Semicolon-separated list of medical actions direct disease 0..* Disease Semicolon-separated list of diseases direct symptom 0..* Symptom Semicolon-separated list of symptoms direct action_to_disease 0..* ActionToDiseaseRelationship direct action_to_symptom 0..* ActionToSymptomRelationship direct"},{"location":"maxo/MaxoAnnotations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/MaxoAnnotations/#schema-source","title":"Schema Source","text":""},{"location":"maxo/MaxoAnnotations/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:MaxoAnnotations native maxo_extract:MaxoAnnotations"},{"location":"maxo/MaxoAnnotations/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/MaxoAnnotations/#direct","title":"Direct","text":"
name: MaxoAnnotations\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  action:\n    name: action\n    annotations:\n      prompt:\n        tag: prompt\n        value: Semicolon-separated list of medical actions, where each is a clinically\n          prescribed procedure, therapy, intervention, or recommendation.\n    description: Semicolon-separated list of medical actions.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: Action\n  disease:\n    name: disease\n    description: Semicolon-separated list of diseases.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: Disease\n  symptom:\n    name: symptom\n    description: Semicolon-separated list of symptoms.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: Symptom\n  action_to_disease:\n    name: action_to_disease\n    annotations:\n      prompt:\n        tag: prompt\n        value: Semicolon-separated list of medical action to disease relationships,\n          where each is a triple representing a relationship between a medical action  and\n          a disease, for example, radiation therapy TREATS cancer, or PET scan IS\n          USED TO DIAGNOSE myocarditis.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: ActionToDiseaseRelationship\n  action_to_symptom:\n    name: action_to_symptom\n    annotations:\n      prompt:\n        tag: prompt\n        value: A triple representing a relationship between a medical action  (A clinically\n          prescribed procedure, therapy, intervention, or recommendation) and a symptom,\n          for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: ActionToSymptomRelationship\ntree_root: true\n\n
"},{"location":"maxo/MaxoAnnotations/#induced","title":"Induced","text":"
name: MaxoAnnotations\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  action:\n    name: action\n    annotations:\n      prompt:\n        tag: prompt\n        value: Semicolon-separated list of medical actions, where each is a clinically\n          prescribed procedure, therapy, intervention, or recommendation.\n    description: Semicolon-separated list of medical actions.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: action\n    owner: MaxoAnnotations\n    domain_of:\n    - MaxoAnnotations\n    range: Action\n  disease:\n    name: disease\n    description: Semicolon-separated list of diseases.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: disease\n    owner: MaxoAnnotations\n    domain_of:\n    - MaxoAnnotations\n    range: Disease\n  symptom:\n    name: symptom\n    description: Semicolon-separated list of symptoms.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: symptom\n    owner: MaxoAnnotations\n    domain_of:\n    - MaxoAnnotations\n    range: Symptom\n  action_to_disease:\n    name: action_to_disease\n    annotations:\n      prompt:\n        tag: prompt\n        value: Semicolon-separated list of medical action to disease relationships,\n          where each is a triple representing a relationship between a medical action  and\n          a disease, for example, radiation therapy TREATS cancer, or PET scan IS\n          USED TO DIAGNOSE myocarditis.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: action_to_disease\n    owner: MaxoAnnotations\n    domain_of:\n    - MaxoAnnotations\n    range: ActionToDiseaseRelationship\n  action_to_symptom:\n    name: action_to_symptom\n    annotations:\n      prompt:\n        tag: prompt\n        value: A triple representing a relationship between a medical action  (A clinically\n          prescribed procedure, therapy, intervention, or recommendation) and a symptom,\n          for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: action_to_symptom\n    owner: MaxoAnnotations\n    domain_of:\n    - MaxoAnnotations\n    range: ActionToSymptomRelationship\ntree_root: true\n\n
"},{"location":"maxo/NamedEntity/","title":"Class: NamedEntity","text":"

URI: maxo_extract:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"maxo/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"maxo/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"maxo/NamedEntity/#usages","title":"Usages","text":"used by used in type used ActionToDiseaseRelationship predicate range NamedEntity ActionToDiseaseRelationship subject_qualifier range NamedEntity ActionToDiseaseRelationship object_qualifier range NamedEntity ActionToSymptomRelationship predicate range NamedEntity ActionToSymptomRelationship subject_qualifier range NamedEntity ActionToSymptomRelationship object_qualifier range NamedEntity Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"maxo/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"maxo/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:NamedEntity native maxo_extract:NamedEntity"},{"location":"maxo/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/maxo\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"maxo/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/maxo\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"maxo/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"maxo/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"maxo/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"maxo/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"maxo/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"maxo/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"maxo/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"maxo/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"maxo/Objectidentifier/#comments","title":"Comments","text":""},{"location":"maxo/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Publication/","title":"Class: Publication","text":"

URI: maxo_extract:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"maxo/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"maxo/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"maxo/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Publication/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:Publication native maxo_extract:Publication"},{"location":"maxo/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/maxo\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n\n
"},{"location":"maxo/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/maxo\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"maxo/RelationshipType/","title":"Class: RelationshipType","text":"

URI: maxo_extract:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"maxo/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"maxo/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"maxo/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"maxo/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"maxo/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"maxo/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:RelationshipType native maxo_extract:RelationshipType"},{"location":"maxo/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\n\n
"},{"location":"maxo/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"maxo/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"maxo/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/String/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Symptom/","title":"Class: Symptom","text":"

A condition or phenotype resulting from an abnormal health state.

URI: maxo_extract:Symptom

erDiagram\nSymptom {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"maxo/Symptom/#inheritance","title":"Inheritance","text":""},{"location":"maxo/Symptom/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"maxo/Symptom/#usages","title":"Usages","text":"used by used in type used MaxoAnnotations symptom range Symptom ActionToSymptomRelationship object range Symptom"},{"location":"maxo/Symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Symptom/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"maxo/Symptom/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp"},{"location":"maxo/Symptom/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Symptom/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:Symptom native maxo_extract:Symptom"},{"location":"maxo/Symptom/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Symptom/#direct","title":"Direct","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\ndescription: A condition or phenotype resulting from an abnormal health state.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\n\n
"},{"location":"maxo/Symptom/#induced","title":"Induced","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\ndescription: A condition or phenotype resulting from an abnormal health state.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"maxo/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: maxo_extract:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"maxo/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"maxo/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:TextWithTriples native maxo_extract:TextWithTriples"},{"location":"maxo/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"maxo/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"maxo/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"maxo/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Time/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: maxo_extract:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/Triple/#inheritance","title":"Inheritance","text":""},{"location":"maxo/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"maxo/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"maxo/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Triple/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:Triple native maxo_extract:Triple"},{"location":"maxo/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"maxo/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"maxo/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"maxo/Uri/#comments","title":"Comments","text":""},{"location":"maxo/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Uri/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"maxo/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"maxo/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: maxo_extract:abstract

"},{"location":"maxo/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"maxo/abstract/#properties","title":"Properties","text":""},{"location":"maxo/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/abstract/#schema-source","title":"Schema Source","text":""},{"location":"maxo/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"maxo/action/","title":"Slot: action","text":"

Semicolon-separated list of medical actions.

URI: maxo_extract:action

"},{"location":"maxo/action/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaxoAnnotations no"},{"location":"maxo/action/#properties","title":"Properties","text":""},{"location":"maxo/action/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/action/#annotations","title":"Annotations","text":"property value prompt Semicolon-separated list of medical actions, where each is a clinically prescribed procedure, therapy, intervention, or recommendation."},{"location":"maxo/action/#schema-source","title":"Schema Source","text":""},{"location":"maxo/action/#linkml-source","title":"LinkML Source","text":"
name: action\nannotations:\n  prompt:\n    tag: prompt\n    value: Semicolon-separated list of medical actions, where each is a clinically\n      prescribed procedure, therapy, intervention, or recommendation.\ndescription: Semicolon-separated list of medical actions.\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: action\nowner: MaxoAnnotations\ndomain_of:\n- MaxoAnnotations\nrange: Action\n\n
"},{"location":"maxo/action_to_disease/","title":"Slot: action_to_disease","text":"

URI: maxo_extract:action_to_disease

"},{"location":"maxo/action_to_disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaxoAnnotations no"},{"location":"maxo/action_to_disease/#properties","title":"Properties","text":""},{"location":"maxo/action_to_disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/action_to_disease/#annotations","title":"Annotations","text":"property value prompt Semicolon-separated list of medical action to disease relationships, where each is a triple representing a relationship between a medical action and a disease, for example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis."},{"location":"maxo/action_to_disease/#schema-source","title":"Schema Source","text":""},{"location":"maxo/action_to_disease/#linkml-source","title":"LinkML Source","text":"
name: action_to_disease\nannotations:\n  prompt:\n    tag: prompt\n    value: Semicolon-separated list of medical action to disease relationships, where\n      each is a triple representing a relationship between a medical action  and a\n      disease, for example, radiation therapy TREATS cancer, or PET scan IS USED TO\n      DIAGNOSE myocarditis.\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: action_to_disease\nowner: MaxoAnnotations\ndomain_of:\n- MaxoAnnotations\nrange: ActionToDiseaseRelationship\n\n
"},{"location":"maxo/action_to_symptom/","title":"Slot: action_to_symptom","text":"

URI: maxo_extract:action_to_symptom

"},{"location":"maxo/action_to_symptom/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaxoAnnotations no"},{"location":"maxo/action_to_symptom/#properties","title":"Properties","text":""},{"location":"maxo/action_to_symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/action_to_symptom/#annotations","title":"Annotations","text":"property value prompt A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a symptom, for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion."},{"location":"maxo/action_to_symptom/#schema-source","title":"Schema Source","text":""},{"location":"maxo/action_to_symptom/#linkml-source","title":"LinkML Source","text":"
name: action_to_symptom\nannotations:\n  prompt:\n    tag: prompt\n    value: A triple representing a relationship between a medical action  (A clinically\n      prescribed procedure, therapy, intervention, or recommendation) and a symptom,\n      for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: action_to_symptom\nowner: MaxoAnnotations\ndomain_of:\n- MaxoAnnotations\nrange: ActionToSymptomRelationship\n\n
"},{"location":"maxo/combined_text/","title":"Slot: combined_text","text":"

URI: maxo_extract:combined_text

"},{"location":"maxo/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"maxo/combined_text/#properties","title":"Properties","text":""},{"location":"maxo/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"maxo/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"maxo/disease/","title":"Slot: disease","text":"

Semicolon-separated list of diseases.

URI: maxo_extract:disease

"},{"location":"maxo/disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaxoAnnotations no"},{"location":"maxo/disease/#properties","title":"Properties","text":""},{"location":"maxo/disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/disease/#schema-source","title":"Schema Source","text":""},{"location":"maxo/disease/#linkml-source","title":"LinkML Source","text":"
name: disease\ndescription: Semicolon-separated list of diseases.\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: disease\nowner: MaxoAnnotations\ndomain_of:\n- MaxoAnnotations\nrange: Disease\n\n
"},{"location":"maxo/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: maxo_extract:extracted_object

"},{"location":"maxo/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/extracted_object/#properties","title":"Properties","text":""},{"location":"maxo/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"maxo/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"maxo/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: maxo_extract:full_text

"},{"location":"maxo/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"maxo/full_text/#properties","title":"Properties","text":""},{"location":"maxo/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/full_text/#schema-source","title":"Schema Source","text":""},{"location":"maxo/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"maxo/id/","title":"Slot: id","text":"

URI: maxo_extract:id

"},{"location":"maxo/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Action A clinically prescribed procedure, therapy, intervention, or recommendation no Disease A disposition to undergo pathological processes that exists in an organism be... no Symptom A condition or phenotype resulting from an abnormal health state no NamedEntity no RelationshipType no Publication no"},{"location":"maxo/id/#properties","title":"Properties","text":""},{"location":"maxo/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"maxo/input_id/","title":"Slot: input_id","text":"

URI: maxo_extract:input_id

"},{"location":"maxo/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/input_id/#properties","title":"Properties","text":""},{"location":"maxo/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/input_id/#schema-source","title":"Schema Source","text":""},{"location":"maxo/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"maxo/input_text/","title":"Slot: input_text","text":"

URI: maxo_extract:input_text

"},{"location":"maxo/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/input_text/#properties","title":"Properties","text":""},{"location":"maxo/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/input_text/#schema-source","title":"Schema Source","text":""},{"location":"maxo/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"maxo/input_title/","title":"Slot: input_title","text":"

URI: maxo_extract:input_title

"},{"location":"maxo/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/input_title/#properties","title":"Properties","text":""},{"location":"maxo/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/input_title/#schema-source","title":"Schema Source","text":""},{"location":"maxo/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"maxo/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"maxo/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Action A clinically prescribed procedure, therapy, intervention, or recommendation no Disease A disposition to undergo pathological processes that exists in an organism be... no Symptom A condition or phenotype resulting from an abnormal health state no NamedEntity no RelationshipType no"},{"location":"maxo/label/#properties","title":"Properties","text":""},{"location":"maxo/label/#aliases","title":"Aliases","text":""},{"location":"maxo/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"maxo/label/#schema-source","title":"Schema Source","text":""},{"location":"maxo/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/maxo\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"maxo/maxo/","title":"maxo","text":"

A template for extracting relationships relevant to the MAXO medical action ontology.

URI: http://w3id.org/ontogpt/maxo

"},{"location":"maxo/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: maxo_extract:named_entities

"},{"location":"maxo/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/named_entities/#properties","title":"Properties","text":""},{"location":"maxo/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"maxo/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"maxo/object/","title":"Slot: object","text":"

URI: maxo_extract:object

"},{"location":"maxo/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... yes ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/object/#properties","title":"Properties","text":""},{"location":"maxo/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/object/#schema-source","title":"Schema Source","text":""},{"location":"maxo/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"maxo/object_id/","title":"Slot: object_id","text":"

URI: maxo_extract:object_id

"},{"location":"maxo/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"maxo/object_id/#properties","title":"Properties","text":""},{"location":"maxo/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/object_id/#schema-source","title":"Schema Source","text":""},{"location":"maxo/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"maxo/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: maxo_extract:object_qualifier

"},{"location":"maxo/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... yes ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/object_qualifier/#properties","title":"Properties","text":""},{"location":"maxo/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"maxo/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"maxo/object_text/","title":"Slot: object_text","text":"

URI: maxo_extract:object_text

"},{"location":"maxo/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"maxo/object_text/#properties","title":"Properties","text":""},{"location":"maxo/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/object_text/#schema-source","title":"Schema Source","text":""},{"location":"maxo/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"maxo/predicate/","title":"Slot: predicate","text":"

URI: maxo_extract:predicate

"},{"location":"maxo/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... yes ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/predicate/#properties","title":"Properties","text":""},{"location":"maxo/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/predicate/#schema-source","title":"Schema Source","text":""},{"location":"maxo/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"maxo/prompt/","title":"Slot: prompt","text":"

URI: maxo_extract:prompt

"},{"location":"maxo/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/prompt/#properties","title":"Properties","text":""},{"location":"maxo/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/prompt/#schema-source","title":"Schema Source","text":""},{"location":"maxo/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"maxo/publication/","title":"Slot: publication","text":"

URI: maxo_extract:publication

"},{"location":"maxo/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"maxo/publication/#properties","title":"Properties","text":""},{"location":"maxo/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"maxo/publication/#schema-source","title":"Schema Source","text":""},{"location":"maxo/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"maxo/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: maxo_extract:qualifier

"},{"location":"maxo/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... no ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... no Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/qualifier/#properties","title":"Properties","text":""},{"location":"maxo/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"maxo/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"maxo/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: maxo_extract:raw_completion_output

"},{"location":"maxo/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/raw_completion_output/#properties","title":"Properties","text":""},{"location":"maxo/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"maxo/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"maxo/subject/","title":"Slot: subject","text":"

URI: maxo_extract:subject

"},{"location":"maxo/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... yes ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/subject/#properties","title":"Properties","text":""},{"location":"maxo/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/subject/#schema-source","title":"Schema Source","text":""},{"location":"maxo/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"maxo/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: maxo_extract:subject_qualifier

"},{"location":"maxo/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... yes ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/subject_qualifier/#properties","title":"Properties","text":""},{"location":"maxo/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"maxo/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"maxo/subject_text/","title":"Slot: subject_text","text":"

URI: maxo_extract:subject_text

"},{"location":"maxo/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"maxo/subject_text/#properties","title":"Properties","text":""},{"location":"maxo/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"maxo/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"maxo/symptom/","title":"Slot: symptom","text":"

Semicolon-separated list of symptoms.

URI: maxo_extract:symptom

"},{"location":"maxo/symptom/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaxoAnnotations no"},{"location":"maxo/symptom/#properties","title":"Properties","text":""},{"location":"maxo/symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/symptom/#schema-source","title":"Schema Source","text":""},{"location":"maxo/symptom/#linkml-source","title":"LinkML Source","text":"
name: symptom\ndescription: Semicolon-separated list of symptoms.\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: symptom\nowner: MaxoAnnotations\ndomain_of:\n- MaxoAnnotations\nrange: Symptom\n\n
"},{"location":"maxo/title/","title":"Slot: title","text":"

The title of the publication

URI: maxo_extract:title

"},{"location":"maxo/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"maxo/title/#properties","title":"Properties","text":""},{"location":"maxo/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/title/#schema-source","title":"Schema Source","text":""},{"location":"maxo/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"maxo/triples/","title":"Slot: triples","text":"

URI: maxo_extract:triples

"},{"location":"maxo/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"maxo/triples/#properties","title":"Properties","text":""},{"location":"maxo/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/triples/#schema-source","title":"Schema Source","text":""},{"location":"maxo/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"mendelian_disease/","title":"GO-CAM Template","text":"

A template for GO-CAMs

URI: http://w3id.org/ontogpt/mendelian_disease

Name: mendelian_disease-template

"},{"location":"mendelian_disease/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nMendelianDisease {\n    string name  \n    string description  \n    stringList synonyms  \n    string id  \n    string label  \n}\nDiseaseCategory {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nSymptom {\n    string characteristic  \n    string affects  \n    string severity  \n    string id  \n    string label  \n}\nOnset {\n    string years_old  \n    stringList decades  \n    string juvenile_or_adult  \n    string id  \n    string label  \n}\nInheritance {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nMendelianDisease ||--}o DiseaseCategory : \"subclass_of\"\nMendelianDisease ||--}o Symptom : \"symptoms\"\nMendelianDisease ||--|o Inheritance : \"inheritance\"\nMendelianDisease ||--}o Gene : \"genes\"\nMendelianDisease ||--}o Onset : \"disease_onsets\"\nMendelianDisease ||--}o Publication : \"publications\"\nSymptom ||--|o Onset : \"onset_of_symptom\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"mendelian_disease/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None DiseaseCategory None Gene None Inheritance None MendelianDisease None Onset None RelationshipType None Symptom None Publication None TextWithTriples None"},{"location":"mendelian_disease/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication affects characteristic combined_text decades description a description of the disease disease_onsets extracted_object The complex objects extracted from the text full_text The full text of the publication genes id A unique identifier for the named entity inheritance input_id input_text input_title juvenile_or_adult label The label (name) of the named thing name the name of the disease named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text onset_of_symptom predicate prompt publication publications qualifier A qualifier for the statements, e raw_completion_output severity subclass_of subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text symptoms synonyms title The title of the publication triples years_old"},{"location":"mendelian_disease/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"mendelian_disease/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"mendelian_disease/#subsets","title":"Subsets","text":"Subset Description"},{"location":"mendelian_disease/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: mendelian_disease:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"mendelian_disease/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"mendelian_disease/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:AnnotatorResult native mendelian_disease:AnnotatorResult"},{"location":"mendelian_disease/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n\n
"},{"location":"mendelian_disease/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"mendelian_disease/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"mendelian_disease/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"mendelian_disease/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"mendelian_disease/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Any/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native mendelian_disease:Any"},{"location":"mendelian_disease/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nclass_uri: linkml:Any\n\n
"},{"location":"mendelian_disease/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nclass_uri: linkml:Any\n\n
"},{"location":"mendelian_disease/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"mendelian_disease/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: mendelian_disease:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"mendelian_disease/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"mendelian_disease/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:CompoundExpression native mendelian_disease:CompoundExpression"},{"location":"mendelian_disease/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nabstract: true\n\n
"},{"location":"mendelian_disease/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nabstract: true\n\n
"},{"location":"mendelian_disease/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"mendelian_disease/Curie/#comments","title":"Comments","text":""},{"location":"mendelian_disease/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Curie/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"mendelian_disease/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Date/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"mendelian_disease/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"mendelian_disease/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"mendelian_disease/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/DiseaseCategory/","title":"Class: DiseaseCategory","text":"

URI: mendelian_disease:DiseaseCategory

erDiagram\nDiseaseCategory {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/DiseaseCategory/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/DiseaseCategory/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/DiseaseCategory/#usages","title":"Usages","text":"used by used in type used MendelianDisease subclass_of range DiseaseCategory"},{"location":"mendelian_disease/DiseaseCategory/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/DiseaseCategory/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"mendelian_disease/DiseaseCategory/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo"},{"location":"mendelian_disease/DiseaseCategory/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/DiseaseCategory/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:DiseaseCategory native mendelian_disease:DiseaseCategory"},{"location":"mendelian_disease/DiseaseCategory/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/DiseaseCategory/#direct","title":"Direct","text":"
name: DiseaseCategory\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\n\n
"},{"location":"mendelian_disease/DiseaseCategory/#induced","title":"Induced","text":"
name: DiseaseCategory\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DiseaseCategory\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: DiseaseCategory\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"mendelian_disease/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Double/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: mendelian_disease:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"mendelian_disease/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"mendelian_disease/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:ExtractionResult native mendelian_disease:ExtractionResult"},{"location":"mendelian_disease/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"mendelian_disease/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"mendelian_disease/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"mendelian_disease/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Float/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Gene/","title":"Class: Gene","text":"

URI: mendelian_disease:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/Gene/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/Gene/#usages","title":"Usages","text":"used by used in type used MendelianDisease genes range Gene"},{"location":"mendelian_disease/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"mendelian_disease/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, bioportal:hgnc-nr, sqlite:obo:pr"},{"location":"mendelian_disease/Gene/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Gene native mendelian_disease:Gene"},{"location":"mendelian_disease/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr, sqlite:obo:pr\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\n\n
"},{"location":"mendelian_disease/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr, sqlite:obo:pr\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/Inheritance/","title":"Class: Inheritance","text":"

URI: mendelian_disease:Inheritance

erDiagram\nInheritance {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/Inheritance/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/Inheritance/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/Inheritance/#usages","title":"Usages","text":"used by used in type used MendelianDisease inheritance range Inheritance"},{"location":"mendelian_disease/Inheritance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Inheritance/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:geno"},{"location":"mendelian_disease/Inheritance/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Inheritance/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Inheritance native mendelian_disease:Inheritance"},{"location":"mendelian_disease/Inheritance/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Inheritance/#direct","title":"Direct","text":"
name: Inheritance\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:geno\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\n\n
"},{"location":"mendelian_disease/Inheritance/#induced","title":"Induced","text":"
name: Inheritance\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:geno\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Inheritance\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Inheritance\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"mendelian_disease/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Integer/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/MendelianDisease/","title":"Class: MendelianDisease","text":"

URI: mendelian_disease:MendelianDisease

erDiagram\nMendelianDisease {\n    string name  \n    string description  \n    stringList synonyms  \n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nOnset {\n    string years_old  \n    stringList decades  \n    string juvenile_or_adult  \n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nInheritance {\n    string id  \n    string label  \n}\nSymptom {\n    string characteristic  \n    string affects  \n    string severity  \n    string id  \n    string label  \n}\nDiseaseCategory {\n    string id  \n    string label  \n}\n\nMendelianDisease ||--}o DiseaseCategory : \"subclass_of\"\nMendelianDisease ||--}o Symptom : \"symptoms\"\nMendelianDisease ||--|o Inheritance : \"inheritance\"\nMendelianDisease ||--}o Gene : \"genes\"\nMendelianDisease ||--}o Onset : \"disease_onsets\"\nMendelianDisease ||--}o Publication : \"publications\"\nSymptom ||--|o Onset : \"onset_of_symptom\"\n\n
"},{"location":"mendelian_disease/MendelianDisease/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/MendelianDisease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance name 0..1 String the name of the disease direct description 0..1 String a description of the disease direct synonyms 0..* String direct subclass_of 0..* DiseaseCategory direct symptoms 0..* Symptom direct inheritance 0..1 Inheritance direct genes 0..* Gene direct disease_onsets 0..* Onset direct publications 0..* Publication direct id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/MendelianDisease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/MendelianDisease/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/MendelianDisease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:MendelianDisease native mendelian_disease:MendelianDisease"},{"location":"mendelian_disease/MendelianDisease/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/MendelianDisease/#direct","title":"Direct","text":"
name: MendelianDisease\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  name:\n    name: name\n    description: the name of the disease\n    examples:\n    - value: peroxisome biogenesis disorder\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  description:\n    name: description\n    description: a description of the disease\n    examples:\n    - value: Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS)\n        is a group of autosomal recessive disorders affecting the formation of functional\n        peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal\n        degeneration, multiple organ dysfunction and psychomotor impairment\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  synonyms:\n    name: synonyms\n    examples:\n    - value: Zellweger syndrome spectrum\n    - value: PBD-ZSS\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n  subclass_of:\n    name: subclass_of\n    examples:\n    - value: lysosomal disease\n    - value: autosomal recessive disorder\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: DiseaseCategory\n  symptoms:\n    name: symptoms\n    examples:\n    - value: sensorineural hearing loss\n    - value: pigmentary retinal degeneration\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Symptom\n  inheritance:\n    name: inheritance\n    examples:\n    - value: autosomal recessive\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: Inheritance\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'semicolon separated list of gene symbols; for example: PEX1; PEX2;\n          PEX3'\n    examples:\n    - value: PEX1\n    - value: PEX2\n    - value: PEX3\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Gene\n  disease_onsets:\n    name: disease_onsets\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'semi-colon separated list of onsets at which the disease occurs, for\n          example: adult; juvenile; first decade'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Onset\n  publications:\n    name: publications\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Publication\n\n
"},{"location":"mendelian_disease/MendelianDisease/#induced","title":"Induced","text":"
name: MendelianDisease\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  name:\n    name: name\n    description: the name of the disease\n    examples:\n    - value: peroxisome biogenesis disorder\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: name\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: string\n  description:\n    name: description\n    description: a description of the disease\n    examples:\n    - value: Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS)\n        is a group of autosomal recessive disorders affecting the formation of functional\n        peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal\n        degeneration, multiple organ dysfunction and psychomotor impairment\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: description\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: string\n  synonyms:\n    name: synonyms\n    examples:\n    - value: Zellweger syndrome spectrum\n    - value: PBD-ZSS\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: string\n  subclass_of:\n    name: subclass_of\n    examples:\n    - value: lysosomal disease\n    - value: autosomal recessive disorder\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: subclass_of\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: DiseaseCategory\n  symptoms:\n    name: symptoms\n    examples:\n    - value: sensorineural hearing loss\n    - value: pigmentary retinal degeneration\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: symptoms\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: Symptom\n  inheritance:\n    name: inheritance\n    examples:\n    - value: autosomal recessive\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: inheritance\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: Inheritance\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'semicolon separated list of gene symbols; for example: PEX1; PEX2;\n          PEX3'\n    examples:\n    - value: PEX1\n    - value: PEX2\n    - value: PEX3\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: Gene\n  disease_onsets:\n    name: disease_onsets\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'semi-colon separated list of onsets at which the disease occurs, for\n          example: adult; juvenile; first decade'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: disease_onsets\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: Onset\n  publications:\n    name: publications\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: publications\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: Publication\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MendelianDisease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: MendelianDisease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/NamedEntity/","title":"Class: NamedEntity","text":"

URI: mendelian_disease:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"mendelian_disease/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"mendelian_disease/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:NamedEntity native mendelian_disease:NamedEntity"},{"location":"mendelian_disease/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"mendelian_disease/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"mendelian_disease/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"mendelian_disease/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"mendelian_disease/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"mendelian_disease/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"mendelian_disease/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"mendelian_disease/Objectidentifier/#comments","title":"Comments","text":""},{"location":"mendelian_disease/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Onset/","title":"Class: Onset","text":"

URI: mendelian_disease:Onset

erDiagram\nOnset {\n    string years_old  \n    stringList decades  \n    string juvenile_or_adult  \n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/Onset/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/Onset/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance years_old 0..1 String direct decades 0..* String direct juvenile_or_adult 0..1 String direct id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/Onset/#usages","title":"Usages","text":"used by used in type used MendelianDisease disease_onsets range Onset Symptom onset_of_symptom range Onset"},{"location":"mendelian_disease/Onset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Onset/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"mendelian_disease/Onset/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:hsapdv"},{"location":"mendelian_disease/Onset/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Onset/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Onset native mendelian_disease:Onset"},{"location":"mendelian_disease/Onset/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Onset/#direct","title":"Direct","text":"
name: Onset\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:hsapdv\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  years_old:\n    name: years_old\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  decades:\n    name: decades\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n  juvenile_or_adult:\n    name: juvenile_or_adult\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n\n
"},{"location":"mendelian_disease/Onset/#induced","title":"Induced","text":"
name: Onset\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:hsapdv\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  years_old:\n    name: years_old\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: years_old\n    owner: Onset\n    domain_of:\n    - Onset\n    range: string\n  decades:\n    name: decades\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: decades\n    owner: Onset\n    domain_of:\n    - Onset\n    range: string\n  juvenile_or_adult:\n    name: juvenile_or_adult\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: juvenile_or_adult\n    owner: Onset\n    domain_of:\n    - Onset\n    range: string\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Onset\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Onset\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/Publication/","title":"Class: Publication","text":"

URI: mendelian_disease:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"mendelian_disease/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"mendelian_disease/Publication/#usages","title":"Usages","text":"used by used in type used MendelianDisease publications range Publication TextWithTriples publication range Publication"},{"location":"mendelian_disease/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Publication/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Publication native mendelian_disease:Publication"},{"location":"mendelian_disease/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n\n
"},{"location":"mendelian_disease/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"mendelian_disease/RelationshipType/","title":"Class: RelationshipType","text":"

URI: mendelian_disease:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"mendelian_disease/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"mendelian_disease/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:RelationshipType native mendelian_disease:RelationshipType"},{"location":"mendelian_disease/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\n\n
"},{"location":"mendelian_disease/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"mendelian_disease/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/String/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Symptom/","title":"Class: Symptom","text":"

URI: mendelian_disease:Symptom

erDiagram\nSymptom {\n    string characteristic  \n    string affects  \n    string severity  \n    string id  \n    string label  \n}\nOnset {\n    string years_old  \n    stringList decades  \n    string juvenile_or_adult  \n    string id  \n    string label  \n}\n\nSymptom ||--|o Onset : \"onset_of_symptom\"\n\n
"},{"location":"mendelian_disease/Symptom/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/Symptom/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance characteristic 0..1 String direct affects 0..1 String direct severity 0..1 String direct onset_of_symptom 0..1 Onset direct id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/Symptom/#usages","title":"Usages","text":"used by used in type used MendelianDisease symptoms range Symptom"},{"location":"mendelian_disease/Symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Symptom/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"mendelian_disease/Symptom/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:mondo"},{"location":"mendelian_disease/Symptom/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Symptom/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Symptom native mendelian_disease:Symptom"},{"location":"mendelian_disease/Symptom/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Symptom/#direct","title":"Direct","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  characteristic:\n    name: characteristic\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  affects:\n    name: affects\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  severity:\n    name: severity\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  onset_of_symptom:\n    name: onset_of_symptom\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: Onset\n\n
"},{"location":"mendelian_disease/Symptom/#induced","title":"Induced","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  characteristic:\n    name: characteristic\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: characteristic\n    owner: Symptom\n    domain_of:\n    - Symptom\n    range: string\n  affects:\n    name: affects\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: affects\n    owner: Symptom\n    domain_of:\n    - Symptom\n    range: string\n  severity:\n    name: severity\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: severity\n    owner: Symptom\n    domain_of:\n    - Symptom\n    range: string\n  onset_of_symptom:\n    name: onset_of_symptom\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: onset_of_symptom\n    owner: Symptom\n    domain_of:\n    - Symptom\n    range: Onset\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: mendelian_disease:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"mendelian_disease/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"mendelian_disease/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:TextWithTriples native mendelian_disease:TextWithTriples"},{"location":"mendelian_disease/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"mendelian_disease/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"mendelian_disease/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"mendelian_disease/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Time/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: mendelian_disease:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"mendelian_disease/Triple/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"mendelian_disease/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"mendelian_disease/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Triple/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Triple native mendelian_disease:Triple"},{"location":"mendelian_disease/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"mendelian_disease/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"mendelian_disease/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"mendelian_disease/Uri/#comments","title":"Comments","text":""},{"location":"mendelian_disease/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Uri/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"mendelian_disease/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: mendelian_disease:abstract

"},{"location":"mendelian_disease/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"mendelian_disease/abstract/#properties","title":"Properties","text":""},{"location":"mendelian_disease/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/abstract/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"mendelian_disease/affects/","title":"Slot: affects","text":"

URI: mendelian_disease:affects

"},{"location":"mendelian_disease/affects/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Symptom no"},{"location":"mendelian_disease/affects/#properties","title":"Properties","text":""},{"location":"mendelian_disease/affects/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/affects/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/affects/#linkml-source","title":"LinkML Source","text":"
name: affects\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: affects\nowner: Symptom\ndomain_of:\n- Symptom\nrange: string\n\n
"},{"location":"mendelian_disease/characteristic/","title":"Slot: characteristic","text":"

URI: mendelian_disease:characteristic

"},{"location":"mendelian_disease/characteristic/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Symptom no"},{"location":"mendelian_disease/characteristic/#properties","title":"Properties","text":""},{"location":"mendelian_disease/characteristic/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/characteristic/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/characteristic/#linkml-source","title":"LinkML Source","text":"
name: characteristic\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: characteristic\nowner: Symptom\ndomain_of:\n- Symptom\nrange: string\n\n
"},{"location":"mendelian_disease/combined_text/","title":"Slot: combined_text","text":"

URI: mendelian_disease:combined_text

"},{"location":"mendelian_disease/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"mendelian_disease/combined_text/#properties","title":"Properties","text":""},{"location":"mendelian_disease/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"mendelian_disease/decades/","title":"Slot: decades","text":"

URI: mendelian_disease:decades

"},{"location":"mendelian_disease/decades/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Onset no"},{"location":"mendelian_disease/decades/#properties","title":"Properties","text":""},{"location":"mendelian_disease/decades/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/decades/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/decades/#linkml-source","title":"LinkML Source","text":"
name: decades\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: decades\nowner: Onset\ndomain_of:\n- Onset\nrange: string\n\n
"},{"location":"mendelian_disease/description/","title":"Slot: description","text":"

a description of the disease

URI: mendelian_disease:description

"},{"location":"mendelian_disease/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/description/#properties","title":"Properties","text":""},{"location":"mendelian_disease/description/#examples","title":"Examples","text":"Value Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment"},{"location":"mendelian_disease/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/description/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a description of the disease\nexamples:\n- value: Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is\n    a group of autosomal recessive disorders affecting the formation of functional\n    peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration,\n    multiple organ dysfunction and psychomotor impairment\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: description\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: string\n\n
"},{"location":"mendelian_disease/disease_onsets/","title":"Slot: disease_onsets","text":"

URI: mendelian_disease:disease_onsets

"},{"location":"mendelian_disease/disease_onsets/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/disease_onsets/#properties","title":"Properties","text":""},{"location":"mendelian_disease/disease_onsets/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/disease_onsets/#annotations","title":"Annotations","text":"property value prompt semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade"},{"location":"mendelian_disease/disease_onsets/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/disease_onsets/#linkml-source","title":"LinkML Source","text":"
name: disease_onsets\nannotations:\n  prompt:\n    tag: prompt\n    value: 'semi-colon separated list of onsets at which the disease occurs, for example:\n      adult; juvenile; first decade'\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: disease_onsets\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: Onset\n\n
"},{"location":"mendelian_disease/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: mendelian_disease:extracted_object

"},{"location":"mendelian_disease/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"mendelian_disease/extracted_object/#properties","title":"Properties","text":""},{"location":"mendelian_disease/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"mendelian_disease/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: mendelian_disease:full_text

"},{"location":"mendelian_disease/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"mendelian_disease/full_text/#properties","title":"Properties","text":""},{"location":"mendelian_disease/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/full_text/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"mendelian_disease/genes/","title":"Slot: genes","text":"

URI: mendelian_disease:genes

"},{"location":"mendelian_disease/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/genes/#properties","title":"Properties","text":""},{"location":"mendelian_disease/genes/#examples","title":"Examples","text":"Value PEX1 PEX2 PEX3"},{"location":"mendelian_disease/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/genes/#annotations","title":"Annotations","text":"property value prompt semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3"},{"location":"mendelian_disease/genes/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\nannotations:\n  prompt:\n    tag: prompt\n    value: 'semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3'\nexamples:\n- value: PEX1\n- value: PEX2\n- value: PEX3\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: genes\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: Gene\n\n
"},{"location":"mendelian_disease/id/","title":"Slot: id","text":"

URI: mendelian_disease:id

"},{"location":"mendelian_disease/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no DiseaseCategory no Gene no Symptom no Onset no Inheritance no NamedEntity no RelationshipType no Publication no"},{"location":"mendelian_disease/id/#properties","title":"Properties","text":""},{"location":"mendelian_disease/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"mendelian_disease/inheritance/","title":"Slot: inheritance","text":"

URI: mendelian_disease:inheritance

"},{"location":"mendelian_disease/inheritance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/inheritance/#properties","title":"Properties","text":""},{"location":"mendelian_disease/inheritance/#examples","title":"Examples","text":"Value autosomal recessive"},{"location":"mendelian_disease/inheritance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/inheritance/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/inheritance/#linkml-source","title":"LinkML Source","text":"
name: inheritance\nexamples:\n- value: autosomal recessive\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: inheritance\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: Inheritance\n\n
"},{"location":"mendelian_disease/input_id/","title":"Slot: input_id","text":"

URI: mendelian_disease:input_id

"},{"location":"mendelian_disease/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"mendelian_disease/input_id/#properties","title":"Properties","text":""},{"location":"mendelian_disease/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/input_id/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"mendelian_disease/input_text/","title":"Slot: input_text","text":"

URI: mendelian_disease:input_text

"},{"location":"mendelian_disease/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"mendelian_disease/input_text/#properties","title":"Properties","text":""},{"location":"mendelian_disease/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/input_text/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
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URI: mendelian_disease:input_title

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name: input_title\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"mendelian_disease/juvenile_or_adult/","title":"Slot: juvenile_or_adult","text":"

URI: mendelian_disease:juvenile_or_adult

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name: juvenile_or_adult\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: juvenile_or_adult\nowner: Onset\ndomain_of:\n- Onset\nrange: string\n\n
"},{"location":"mendelian_disease/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

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"},{"location":"mendelian_disease/mendelian_disease-template/","title":"mendelian_disease-template","text":"

A template for GO-CAMs

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the name of the disease

URI: mendelian_disease:name

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name: name\ndescription: the name of the disease\nexamples:\n- value: peroxisome biogenesis disorder\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: name\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: string\n\n
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Named entities extracted from the text

URI: mendelian_disease:named_entities

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name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"mendelian_disease/object/","title":"Slot: object","text":"

URI: mendelian_disease:object

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name: object\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
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URI: mendelian_disease:object_id

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name: object_id\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"mendelian_disease/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: mendelian_disease:object_qualifier

"},{"location":"mendelian_disease/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"mendelian_disease/object_qualifier/#properties","title":"Properties","text":""},{"location":"mendelian_disease/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"mendelian_disease/object_text/","title":"Slot: object_text","text":"

URI: mendelian_disease:object_text

"},{"location":"mendelian_disease/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"mendelian_disease/object_text/#properties","title":"Properties","text":""},{"location":"mendelian_disease/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/object_text/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"mendelian_disease/onset_of_symptom/","title":"Slot: onset_of_symptom","text":"

URI: mendelian_disease:onset_of_symptom

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name: onset_of_symptom\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: onset_of_symptom\nowner: Symptom\ndomain_of:\n- Symptom\nrange: Onset\n\n
"},{"location":"mendelian_disease/predicate/","title":"Slot: predicate","text":"

URI: mendelian_disease:predicate

"},{"location":"mendelian_disease/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"mendelian_disease/predicate/#properties","title":"Properties","text":""},{"location":"mendelian_disease/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/predicate/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"mendelian_disease/prompt/","title":"Slot: prompt","text":"

URI: mendelian_disease:prompt

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name: prompt\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"mendelian_disease/publication/","title":"Slot: publication","text":"

URI: mendelian_disease:publication

"},{"location":"mendelian_disease/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"mendelian_disease/publication/#properties","title":"Properties","text":""},{"location":"mendelian_disease/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"mendelian_disease/publication/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"mendelian_disease/publications/","title":"Slot: publications","text":"

URI: mendelian_disease:publications

"},{"location":"mendelian_disease/publications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/publications/#properties","title":"Properties","text":""},{"location":"mendelian_disease/publications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/publications/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"mendelian_disease/publications/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/publications/#linkml-source","title":"LinkML Source","text":"
name: publications\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: publications\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: Publication\n\n
"},{"location":"mendelian_disease/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: mendelian_disease:qualifier

"},{"location":"mendelian_disease/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"mendelian_disease/qualifier/#properties","title":"Properties","text":""},{"location":"mendelian_disease/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"mendelian_disease/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: mendelian_disease:raw_completion_output

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name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"mendelian_disease/severity/","title":"Slot: severity","text":"

URI: mendelian_disease:severity

"},{"location":"mendelian_disease/severity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Symptom no"},{"location":"mendelian_disease/severity/#properties","title":"Properties","text":""},{"location":"mendelian_disease/severity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/severity/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/severity/#linkml-source","title":"LinkML Source","text":"
name: severity\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: severity\nowner: Symptom\ndomain_of:\n- Symptom\nrange: string\n\n
"},{"location":"mendelian_disease/subclass_of/","title":"Slot: subclass_of","text":"

URI: mendelian_disease:subclass_of

"},{"location":"mendelian_disease/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/subclass_of/#properties","title":"Properties","text":""},{"location":"mendelian_disease/subclass_of/#examples","title":"Examples","text":"Value lysosomal disease autosomal recessive disorder"},{"location":"mendelian_disease/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\nexamples:\n- value: lysosomal disease\n- value: autosomal recessive disorder\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: subclass_of\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: DiseaseCategory\n\n
"},{"location":"mendelian_disease/subject/","title":"Slot: subject","text":"

URI: mendelian_disease:subject

"},{"location":"mendelian_disease/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"mendelian_disease/subject/#properties","title":"Properties","text":""},{"location":"mendelian_disease/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/subject/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"mendelian_disease/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: mendelian_disease:subject_qualifier

"},{"location":"mendelian_disease/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"mendelian_disease/subject_qualifier/#properties","title":"Properties","text":""},{"location":"mendelian_disease/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"mendelian_disease/subject_text/","title":"Slot: subject_text","text":"

URI: mendelian_disease:subject_text

"},{"location":"mendelian_disease/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"mendelian_disease/subject_text/#properties","title":"Properties","text":""},{"location":"mendelian_disease/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"mendelian_disease/symptoms/","title":"Slot: symptoms","text":"

URI: mendelian_disease:symptoms

"},{"location":"mendelian_disease/symptoms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/symptoms/#properties","title":"Properties","text":""},{"location":"mendelian_disease/symptoms/#examples","title":"Examples","text":"Value sensorineural hearing loss pigmentary retinal degeneration"},{"location":"mendelian_disease/symptoms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/symptoms/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/symptoms/#linkml-source","title":"LinkML Source","text":"
name: symptoms\nexamples:\n- value: sensorineural hearing loss\n- value: pigmentary retinal degeneration\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: symptoms\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: Symptom\n\n
"},{"location":"mendelian_disease/synonyms/","title":"Slot: synonyms","text":"

URI: mendelian_disease:synonyms

"},{"location":"mendelian_disease/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/synonyms/#properties","title":"Properties","text":""},{"location":"mendelian_disease/synonyms/#examples","title":"Examples","text":"Value Zellweger syndrome spectrum PBD-ZSS"},{"location":"mendelian_disease/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\nexamples:\n- value: Zellweger syndrome spectrum\n- value: PBD-ZSS\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: string\n\n
"},{"location":"mendelian_disease/title/","title":"Slot: title","text":"

The title of the publication

URI: mendelian_disease:title

"},{"location":"mendelian_disease/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"mendelian_disease/title/#properties","title":"Properties","text":""},{"location":"mendelian_disease/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/title/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"mendelian_disease/triples/","title":"Slot: triples","text":"

URI: mendelian_disease:triples

"},{"location":"mendelian_disease/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"mendelian_disease/triples/#properties","title":"Properties","text":""},{"location":"mendelian_disease/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/triples/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"mendelian_disease/years_old/","title":"Slot: years_old","text":"

URI: mendelian_disease:years_old

"},{"location":"mendelian_disease/years_old/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Onset no"},{"location":"mendelian_disease/years_old/#properties","title":"Properties","text":""},{"location":"mendelian_disease/years_old/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/years_old/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/years_old/#linkml-source","title":"LinkML Source","text":"
name: years_old\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: years_old\nowner: Onset\ndomain_of:\n- Onset\nrange: string\n\n
"},{"location":"metabolic_process/","title":"metabolic Process Template","text":"

A template for GO-CAMs

URI: https://w3id.org/ontogpt/metabolic_process

Name: metabolic-process-template

"},{"location":"metabolic_process/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nMetabolicProcess {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nMetabolicProcessCategory {\n    string id  \n    string label  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nMetabolicProcess ||--}o MetabolicProcessCategory : \"subclass_of\"\nMetabolicProcess ||--|o MetabolicProcessCategory : \"category\"\nMetabolicProcess ||--}o ChemicalEntity : \"inputs\"\nMetabolicProcess ||--}o ChemicalEntity : \"outputs\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"metabolic_process/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None ChemicalEntity None MetabolicProcess None MetabolicProcessCategory None RelationshipType None Publication None TextWithTriples None"},{"location":"metabolic_process/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication category the category of metabolic process, e combined_text description a textual description of the metabolic process extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title inputs the inputs of the metabolic process label the name of the metabolic process named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text outputs the outputs of the metabolic process predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subclass_of a semicolon separated list of broader metabolic processes which this is a sub... subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text synonyms alternative names of the metabolic process title The title of the publication triples"},{"location":"metabolic_process/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"metabolic_process/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"metabolic_process/#subsets","title":"Subsets","text":"Subset Description"},{"location":"metabolic_process/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: bp:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"metabolic_process/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"metabolic_process/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:AnnotatorResult native bp:AnnotatorResult"},{"location":"metabolic_process/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n\n
"},{"location":"metabolic_process/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"metabolic_process/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"metabolic_process/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"metabolic_process/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"metabolic_process/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Any/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native bp:Any"},{"location":"metabolic_process/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nclass_uri: linkml:Any\n\n
"},{"location":"metabolic_process/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nclass_uri: linkml:Any\n\n
"},{"location":"metabolic_process/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"metabolic_process/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/ChemicalEntity/","title":"Class: ChemicalEntity","text":"

URI: bp:ChemicalEntity

erDiagram\nChemicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metabolic_process/ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metabolic_process/ChemicalEntity/#usages","title":"Usages","text":"used by used in type used MetabolicProcess inputs range ChemicalEntity MetabolicProcess outputs range ChemicalEntity"},{"location":"metabolic_process/ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metabolic_process/ChemicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"metabolic_process/ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ChemicalEntity native bp:ChemicalEntity"},{"location":"metabolic_process/ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\n\n
"},{"location":"metabolic_process/ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalEntity\n    domain_of:\n    - MetabolicProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"metabolic_process/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: bp:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"metabolic_process/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"metabolic_process/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:CompoundExpression native bp:CompoundExpression"},{"location":"metabolic_process/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nabstract: true\n\n
"},{"location":"metabolic_process/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nabstract: true\n\n
"},{"location":"metabolic_process/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"metabolic_process/Curie/#comments","title":"Comments","text":""},{"location":"metabolic_process/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Curie/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"metabolic_process/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Date/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"metabolic_process/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"metabolic_process/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"metabolic_process/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"metabolic_process/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Double/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: bp:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"metabolic_process/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"metabolic_process/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ExtractionResult native bp:ExtractionResult"},{"location":"metabolic_process/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metabolic_process/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metabolic_process/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"metabolic_process/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Float/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"metabolic_process/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Integer/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/MetabolicProcess/","title":"Class: MetabolicProcess","text":"

URI: bp:MetabolicProcess

erDiagram\nMetabolicProcess {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nMetabolicProcessCategory {\n    string id  \n    string label  \n}\n\nMetabolicProcess ||--}o MetabolicProcessCategory : \"subclass_of\"\nMetabolicProcess ||--|o MetabolicProcessCategory : \"category\"\nMetabolicProcess ||--}o ChemicalEntity : \"inputs\"\nMetabolicProcess ||--}o ChemicalEntity : \"outputs\"\n\n
"},{"location":"metabolic_process/MetabolicProcess/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/MetabolicProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 0..1 String the name of the metabolic process direct description 0..1 String a textual description of the metabolic process direct synonyms 0..* String alternative names of the metabolic process direct subclass_of 0..* MetabolicProcessCategory a semicolon separated list of broader metabolic processes which this is a sub... direct category 0..1 MetabolicProcessCategory the category of metabolic process, e direct inputs 0..* ChemicalEntity the inputs of the metabolic process direct outputs 0..* ChemicalEntity the outputs of the metabolic process direct id 1..1 String A unique identifier for the named entity NamedEntity"},{"location":"metabolic_process/MetabolicProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/MetabolicProcess/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/MetabolicProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:MetabolicProcess native bp:MetabolicProcess"},{"location":"metabolic_process/MetabolicProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/MetabolicProcess/#direct","title":"Direct","text":"
name: MetabolicProcess\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  description:\n    name: description\n    description: a textual description of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  synonyms:\n    name: synonyms\n    description: alternative names of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n  subclass_of:\n    name: subclass_of\n    description: a semicolon separated list of broader metabolic processes which this\n      is a subclass of\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    range: MetabolicProcessCategory\n  category:\n    name: category\n    description: the category of metabolic process, e.g metabolic process, catabolic\n      process, biosynthetic process, small molecule sensor activity\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: MetabolicProcessCategory\n  inputs:\n    name: inputs\n    description: the inputs of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n  outputs:\n    name: outputs\n    description: the outputs of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n\n
"},{"location":"metabolic_process/MetabolicProcess/#induced","title":"Induced","text":"
name: MetabolicProcess\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: label\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    - NamedEntity\n    range: string\n  description:\n    name: description\n    description: a textual description of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: description\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: string\n  synonyms:\n    name: synonyms\n    description: alternative names of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: string\n  subclass_of:\n    name: subclass_of\n    description: a semicolon separated list of broader metabolic processes which this\n      is a subclass of\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: subclass_of\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: MetabolicProcessCategory\n  category:\n    name: category\n    description: the category of metabolic process, e.g metabolic process, catabolic\n      process, biosynthetic process, small molecule sensor activity\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: category\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: MetabolicProcessCategory\n  inputs:\n    name: inputs\n    description: the inputs of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: inputs\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: ChemicalEntity\n  outputs:\n    name: outputs\n    description: the outputs of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: outputs\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: ChemicalEntity\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetabolicProcess\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n\n
"},{"location":"metabolic_process/MetabolicProcessCategory/","title":"Class: MetabolicProcessCategory","text":"

URI: bp:MetabolicProcessCategory

erDiagram\nMetabolicProcessCategory {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metabolic_process/MetabolicProcessCategory/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/MetabolicProcessCategory/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metabolic_process/MetabolicProcessCategory/#usages","title":"Usages","text":"used by used in type used MetabolicProcess subclass_of range MetabolicProcessCategory MetabolicProcess category range MetabolicProcessCategory"},{"location":"metabolic_process/MetabolicProcessCategory/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/MetabolicProcessCategory/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metabolic_process/MetabolicProcessCategory/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"metabolic_process/MetabolicProcessCategory/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/MetabolicProcessCategory/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:MetabolicProcessCategory native bp:MetabolicProcessCategory"},{"location":"metabolic_process/MetabolicProcessCategory/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/MetabolicProcessCategory/#direct","title":"Direct","text":"
name: MetabolicProcessCategory\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\n\n
"},{"location":"metabolic_process/MetabolicProcessCategory/#induced","title":"Induced","text":"
name: MetabolicProcessCategory\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetabolicProcessCategory\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: MetabolicProcessCategory\n    domain_of:\n    - MetabolicProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"metabolic_process/NamedEntity/","title":"Class: NamedEntity","text":"

URI: bp:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metabolic_process/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"metabolic_process/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"metabolic_process/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:NamedEntity native bp:NamedEntity"},{"location":"metabolic_process/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"metabolic_process/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - MetabolicProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"metabolic_process/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"metabolic_process/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"metabolic_process/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"metabolic_process/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"metabolic_process/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"metabolic_process/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"metabolic_process/Objectidentifier/#comments","title":"Comments","text":""},{"location":"metabolic_process/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Publication/","title":"Class: Publication","text":"

URI: bp:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"metabolic_process/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"metabolic_process/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"metabolic_process/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Publication/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Publication native bp:Publication"},{"location":"metabolic_process/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n\n
"},{"location":"metabolic_process/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"metabolic_process/RelationshipType/","title":"Class: RelationshipType","text":"

URI: bp:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metabolic_process/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metabolic_process/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"metabolic_process/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metabolic_process/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:RelationshipType native bp:RelationshipType"},{"location":"metabolic_process/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\n\n
"},{"location":"metabolic_process/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - MetabolicProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"metabolic_process/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"metabolic_process/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/String/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: bp:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"metabolic_process/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"metabolic_process/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:TextWithTriples native bp:TextWithTriples"},{"location":"metabolic_process/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metabolic_process/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metabolic_process/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"metabolic_process/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Time/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: bp:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"metabolic_process/Triple/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"metabolic_process/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"metabolic_process/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Triple/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Triple native bp:Triple"},{"location":"metabolic_process/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"metabolic_process/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"metabolic_process/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"metabolic_process/Uri/#comments","title":"Comments","text":""},{"location":"metabolic_process/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Uri/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"metabolic_process/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: bp:abstract

"},{"location":"metabolic_process/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metabolic_process/abstract/#properties","title":"Properties","text":""},{"location":"metabolic_process/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/abstract/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metabolic_process/category/","title":"Slot: category","text":"

the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity

URI: bp:category

"},{"location":"metabolic_process/category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/category/#properties","title":"Properties","text":""},{"location":"metabolic_process/category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/category/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/category/#linkml-source","title":"LinkML Source","text":"
name: category\ndescription: the category of metabolic process, e.g metabolic process, catabolic process,\n  biosynthetic process, small molecule sensor activity\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: category\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: MetabolicProcessCategory\n\n
"},{"location":"metabolic_process/combined_text/","title":"Slot: combined_text","text":"

URI: bp:combined_text

"},{"location":"metabolic_process/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metabolic_process/combined_text/#properties","title":"Properties","text":""},{"location":"metabolic_process/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metabolic_process/description/","title":"Slot: description","text":"

a textual description of the metabolic process

URI: bp:description

"},{"location":"metabolic_process/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/description/#properties","title":"Properties","text":""},{"location":"metabolic_process/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/description/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a textual description of the metabolic process\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: description\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: string\n\n
"},{"location":"metabolic_process/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: bp:extracted_object

"},{"location":"metabolic_process/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/extracted_object/#properties","title":"Properties","text":""},{"location":"metabolic_process/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"metabolic_process/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: bp:full_text

"},{"location":"metabolic_process/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metabolic_process/full_text/#properties","title":"Properties","text":""},{"location":"metabolic_process/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/full_text/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metabolic_process/id/","title":"Slot: id","text":"

URI: bp:id

"},{"location":"metabolic_process/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no MetabolicProcessCategory no ChemicalEntity no NamedEntity no RelationshipType no Publication no"},{"location":"metabolic_process/id/#properties","title":"Properties","text":""},{"location":"metabolic_process/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"metabolic_process/input_id/","title":"Slot: input_id","text":"

URI: bp:input_id

"},{"location":"metabolic_process/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/input_id/#properties","title":"Properties","text":""},{"location":"metabolic_process/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/input_id/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metabolic_process/input_text/","title":"Slot: input_text","text":"

URI: bp:input_text

"},{"location":"metabolic_process/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/input_text/#properties","title":"Properties","text":""},{"location":"metabolic_process/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/input_text/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metabolic_process/input_title/","title":"Slot: input_title","text":"

URI: bp:input_title

"},{"location":"metabolic_process/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/input_title/#properties","title":"Properties","text":""},{"location":"metabolic_process/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/input_title/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metabolic_process/inputs/","title":"Slot: inputs","text":"

the inputs of the metabolic process

URI: bp:inputs

"},{"location":"metabolic_process/inputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/inputs/#properties","title":"Properties","text":""},{"location":"metabolic_process/inputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/inputs/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/inputs/#linkml-source","title":"LinkML Source","text":"
name: inputs\ndescription: the inputs of the metabolic process\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: inputs\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: ChemicalEntity\n\n
"},{"location":"metabolic_process/label/","title":"Slot: label","text":"

URI: bp:label

"},{"location":"metabolic_process/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no MetabolicProcessCategory no ChemicalEntity no NamedEntity no RelationshipType no"},{"location":"metabolic_process/label/#properties","title":"Properties","text":""},{"location":"metabolic_process/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- MetabolicProcess\n- NamedEntity\nrange: string\n\n
"},{"location":"metabolic_process/metabolic-process-template/","title":"metabolic-process-template","text":"

A template for GO-CAMs

URI: https://w3id.org/ontogpt/metabolic_process

"},{"location":"metabolic_process/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: bp:named_entities

"},{"location":"metabolic_process/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/named_entities/#properties","title":"Properties","text":""},{"location":"metabolic_process/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"metabolic_process/object/","title":"Slot: object","text":"

URI: bp:object

"},{"location":"metabolic_process/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/object/#properties","title":"Properties","text":""},{"location":"metabolic_process/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/object/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metabolic_process/object_id/","title":"Slot: object_id","text":"

URI: bp:object_id

"},{"location":"metabolic_process/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metabolic_process/object_id/#properties","title":"Properties","text":""},{"location":"metabolic_process/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/object_id/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metabolic_process/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: bp:object_qualifier

"},{"location":"metabolic_process/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/object_qualifier/#properties","title":"Properties","text":""},{"location":"metabolic_process/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metabolic_process/object_text/","title":"Slot: object_text","text":"

URI: bp:object_text

"},{"location":"metabolic_process/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metabolic_process/object_text/#properties","title":"Properties","text":""},{"location":"metabolic_process/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/object_text/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metabolic_process/outputs/","title":"Slot: outputs","text":"

the outputs of the metabolic process

URI: bp:outputs

"},{"location":"metabolic_process/outputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/outputs/#properties","title":"Properties","text":""},{"location":"metabolic_process/outputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/outputs/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/outputs/#linkml-source","title":"LinkML Source","text":"
name: outputs\ndescription: the outputs of the metabolic process\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: outputs\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: ChemicalEntity\n\n
"},{"location":"metabolic_process/predicate/","title":"Slot: predicate","text":"

URI: bp:predicate

"},{"location":"metabolic_process/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/predicate/#properties","title":"Properties","text":""},{"location":"metabolic_process/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/predicate/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"metabolic_process/prompt/","title":"Slot: prompt","text":"

URI: bp:prompt

"},{"location":"metabolic_process/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/prompt/#properties","title":"Properties","text":""},{"location":"metabolic_process/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/prompt/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metabolic_process/publication/","title":"Slot: publication","text":"

URI: bp:publication

"},{"location":"metabolic_process/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"metabolic_process/publication/#properties","title":"Properties","text":""},{"location":"metabolic_process/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"metabolic_process/publication/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"metabolic_process/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: bp:qualifier

"},{"location":"metabolic_process/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/qualifier/#properties","title":"Properties","text":""},{"location":"metabolic_process/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"metabolic_process/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: bp:raw_completion_output

"},{"location":"metabolic_process/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/raw_completion_output/#properties","title":"Properties","text":""},{"location":"metabolic_process/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metabolic_process/subclass_of/","title":"Slot: subclass_of","text":"

a semicolon separated list of broader metabolic processes which this is a subclass of

URI: bp:subclass_of

"},{"location":"metabolic_process/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/subclass_of/#properties","title":"Properties","text":""},{"location":"metabolic_process/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\ndescription: a semicolon separated list of broader metabolic processes which this\n  is a subclass of\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: subclass_of\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: MetabolicProcessCategory\n\n
"},{"location":"metabolic_process/subject/","title":"Slot: subject","text":"

URI: bp:subject

"},{"location":"metabolic_process/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/subject/#properties","title":"Properties","text":""},{"location":"metabolic_process/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/subject/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metabolic_process/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: bp:subject_qualifier

"},{"location":"metabolic_process/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/subject_qualifier/#properties","title":"Properties","text":""},{"location":"metabolic_process/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metabolic_process/subject_text/","title":"Slot: subject_text","text":"

URI: bp:subject_text

"},{"location":"metabolic_process/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metabolic_process/subject_text/#properties","title":"Properties","text":""},{"location":"metabolic_process/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metabolic_process/synonyms/","title":"Slot: synonyms","text":"

alternative names of the metabolic process

URI: bp:synonyms

"},{"location":"metabolic_process/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/synonyms/#properties","title":"Properties","text":""},{"location":"metabolic_process/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\ndescription: alternative names of the metabolic process\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: string\n\n
"},{"location":"metabolic_process/title/","title":"Slot: title","text":"

The title of the publication

URI: bp:title

"},{"location":"metabolic_process/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metabolic_process/title/#properties","title":"Properties","text":""},{"location":"metabolic_process/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/title/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metabolic_process/triples/","title":"Slot: triples","text":"

URI: bp:triples

"},{"location":"metabolic_process/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"metabolic_process/triples/#properties","title":"Properties","text":""},{"location":"metabolic_process/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/triples/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"metagenome_study/","title":"Environmental Metagenome Template","text":"

A template for Environmental Metagenome Studies

URI: http://w3id.org/ontogpt/metagenome

Name: environmental-metagenome

"},{"location":"metagenome_study/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nStudy {\n\n}\nLocation {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nEnvironment {\n    string id  \n    string label  \n}\nVariable {\n    string id  \n    string label  \n}\nUnit {\n    string id  \n    string label  \n}\nMeasurement {\n    string value  \n}\nCausalRelationship {\n\n}\nSequencingTechnology {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nOrganism {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nStudy ||--}o Environment : \"environments\"\nStudy ||--}o CausalRelationship : \"causal_relationships\"\nStudy ||--}o Variable : \"variables\"\nStudy ||--}o Treatment : \"treatments\"\nStudy ||--}o Measurement : \"measurements\"\nStudy ||--}o Location : \"location\"\nStudy ||--}o EnvironmentalMaterial : \"environmental_material\"\nStudy ||--|o SequencingTechnology : \"sequencing_technologies\"\nStudy ||--}o Organism : \"organisms\"\nMeasurement ||--|o Unit : \"unit\"\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"metagenome_study/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None CausalRelationship None Measurement None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None Environment None EnvironmentalMaterial None Location None Organism None RelationshipType None SequencingTechnology None Treatment None Unit None Variable None Publication None Study None TextWithTriples None"},{"location":"metagenome_study/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication causal_relationships cause the variable that is the cause of the effect combined_text effect the things that is affected environmental_material the environmental material that was sampled environments extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing location the sites at which the study was conducted measurements named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text organisms semicolon-separated list of all studied organism taxons predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output sequencing_technologies subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication treatments triples unit the unit of the measurement value the value of the measurement variables"},{"location":"metagenome_study/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"metagenome_study/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"metagenome_study/#subsets","title":"Subsets","text":"Subset Description"},{"location":"metagenome_study/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: eg:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"metagenome_study/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"metagenome_study/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:AnnotatorResult native eg:AnnotatorResult"},{"location":"metagenome_study/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n\n
"},{"location":"metagenome_study/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"metagenome_study/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"metagenome_study/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"metagenome_study/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"metagenome_study/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Any/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native eg:Any"},{"location":"metagenome_study/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/metagenome\nclass_uri: linkml:Any\n\n
"},{"location":"metagenome_study/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/metagenome\nclass_uri: linkml:Any\n\n
"},{"location":"metagenome_study/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"metagenome_study/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/CausalRelationship/","title":"Class: CausalRelationship","text":"

URI: eg:CausalRelationship

erDiagram\nCausalRelationship {\n\n}\nVariable {\n    string id  \n    string label  \n}\n\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\n\n
"},{"location":"metagenome_study/CausalRelationship/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/CausalRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance cause 0..1 Variable the variable that is the cause of the effect direct effect 0..1 Variable the things that is affected direct"},{"location":"metagenome_study/CausalRelationship/#usages","title":"Usages","text":"used by used in type used Study causal_relationships range CausalRelationship"},{"location":"metagenome_study/CausalRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/CausalRelationship/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/CausalRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:CausalRelationship native eg:CausalRelationship"},{"location":"metagenome_study/CausalRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/CausalRelationship/#direct","title":"Direct","text":"
name: CausalRelationship\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nattributes:\n  cause:\n    name: cause\n    description: the variable that is the cause of the effect\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: Variable\n  effect:\n    name: effect\n    description: the things that is affected\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: Variable\n\n
"},{"location":"metagenome_study/CausalRelationship/#induced","title":"Induced","text":"
name: CausalRelationship\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nattributes:\n  cause:\n    name: cause\n    description: the variable that is the cause of the effect\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: cause\n    owner: CausalRelationship\n    domain_of:\n    - CausalRelationship\n    range: Variable\n  effect:\n    name: effect\n    description: the things that is affected\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: effect\n    owner: CausalRelationship\n    domain_of:\n    - CausalRelationship\n    range: Variable\n\n
"},{"location":"metagenome_study/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: eg:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"metagenome_study/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"metagenome_study/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:CompoundExpression native eg:CompoundExpression"},{"location":"metagenome_study/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/metagenome\nabstract: true\n\n
"},{"location":"metagenome_study/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/metagenome\nabstract: true\n\n
"},{"location":"metagenome_study/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"metagenome_study/Curie/#comments","title":"Comments","text":""},{"location":"metagenome_study/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Curie/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"metagenome_study/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Date/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"metagenome_study/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"metagenome_study/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"metagenome_study/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"metagenome_study/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Double/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Environment/","title":"Class: Environment","text":"

URI: eg:Environment

erDiagram\nEnvironment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Environment/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Environment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Environment/#usages","title":"Usages","text":"used by used in type used Study environments range Environment"},{"location":"metagenome_study/Environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Environment/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Environment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo"},{"location":"metagenome_study/Environment/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Environment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Environment native eg:Environment"},{"location":"metagenome_study/Environment/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Environment/#direct","title":"Direct","text":"
name: Environment\nid_prefixes:\n- ENVO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Environment/#induced","title":"Induced","text":"
name: Environment\nid_prefixes:\n- ENVO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/EnvironmentalMaterial/","title":"Class: EnvironmentalMaterial","text":"

URI: eg:EnvironmentalMaterial

erDiagram\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/EnvironmentalMaterial/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/EnvironmentalMaterial/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/EnvironmentalMaterial/#usages","title":"Usages","text":"used by used in type used Study environmental_material range EnvironmentalMaterial"},{"location":"metagenome_study/EnvironmentalMaterial/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/EnvironmentalMaterial/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/EnvironmentalMaterial/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo"},{"location":"metagenome_study/EnvironmentalMaterial/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/EnvironmentalMaterial/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:EnvironmentalMaterial native eg:EnvironmentalMaterial"},{"location":"metagenome_study/EnvironmentalMaterial/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/EnvironmentalMaterial/#direct","title":"Direct","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/EnvironmentalMaterial/#induced","title":"Induced","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: eg:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"metagenome_study/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"metagenome_study/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:ExtractionResult native eg:ExtractionResult"},{"location":"metagenome_study/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metagenome_study/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metagenome_study/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"metagenome_study/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Float/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"metagenome_study/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Integer/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Location/","title":"Class: Location","text":"

URI: eg:Location

erDiagram\nLocation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Location/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Location/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Location/#usages","title":"Usages","text":"used by used in type used Study location range Location"},{"location":"metagenome_study/Location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Location/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Location/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:gaz"},{"location":"metagenome_study/Location/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Location/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Location native eg:Location"},{"location":"metagenome_study/Location/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Location/#direct","title":"Direct","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:gaz\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Location/#induced","title":"Induced","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:gaz\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Location\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Location\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/Measurement/","title":"Class: Measurement","text":"

URI: eg:Measurement

erDiagram\nMeasurement {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\n\nMeasurement ||--|o Unit : \"unit\"\n\n
"},{"location":"metagenome_study/Measurement/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Measurement/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance value 0..1 String the value of the measurement direct unit 0..1 Unit the unit of the measurement direct"},{"location":"metagenome_study/Measurement/#usages","title":"Usages","text":"used by used in type used Study measurements range Measurement"},{"location":"metagenome_study/Measurement/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Measurement/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Measurement/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Measurement native eg:Measurement"},{"location":"metagenome_study/Measurement/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Measurement/#direct","title":"Direct","text":"
name: Measurement\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    description: the value of the measurement\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  unit:\n    name: unit\n    description: the unit of the measurement\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: Unit\n\n
"},{"location":"metagenome_study/Measurement/#induced","title":"Induced","text":"
name: Measurement\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    description: the value of the measurement\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: value\n    owner: Measurement\n    domain_of:\n    - Measurement\n    range: string\n  unit:\n    name: unit\n    description: the unit of the measurement\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: unit\n    owner: Measurement\n    domain_of:\n    - Measurement\n    range: Unit\n\n
"},{"location":"metagenome_study/NamedEntity/","title":"Class: NamedEntity","text":"

URI: eg:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"metagenome_study/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"metagenome_study/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:NamedEntity native eg:NamedEntity"},{"location":"metagenome_study/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/metagenome\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"metagenome_study/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/metagenome\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"metagenome_study/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"metagenome_study/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"metagenome_study/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"metagenome_study/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"metagenome_study/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"metagenome_study/Objectidentifier/#comments","title":"Comments","text":""},{"location":"metagenome_study/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Organism/","title":"Class: Organism","text":"

URI: eg:Organism

erDiagram\nOrganism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Organism/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Organism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Organism/#usages","title":"Usages","text":"used by used in type used Study organisms range Organism"},{"location":"metagenome_study/Organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Organism/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Organism/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ncbitaxon, gilda:"},{"location":"metagenome_study/Organism/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Organism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Organism native eg:Organism"},{"location":"metagenome_study/Organism/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Organism/#direct","title":"Direct","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\nannotations:\n  annotators:\n    tag: annotators\n    value: 'sqlite:obo:ncbitaxon, gilda:'\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Organism/#induced","title":"Induced","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\nannotations:\n  annotators:\n    tag: annotators\n    value: 'sqlite:obo:ncbitaxon, gilda:'\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/Publication/","title":"Class: Publication","text":"

URI: eg:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"metagenome_study/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"metagenome_study/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"metagenome_study/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Publication/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Publication native eg:Publication"},{"location":"metagenome_study/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/metagenome\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n\n
"},{"location":"metagenome_study/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/metagenome\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"metagenome_study/RelationshipType/","title":"Class: RelationshipType","text":"

URI: eg:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"metagenome_study/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:RelationshipType native eg:RelationshipType"},{"location":"metagenome_study/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/SequencingTechnology/","title":"Class: SequencingTechnology","text":"

URI: eg:SequencingTechnology

erDiagram\nSequencingTechnology {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/SequencingTechnology/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/SequencingTechnology/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/SequencingTechnology/#usages","title":"Usages","text":"used by used in type used Study sequencing_technologies range SequencingTechnology"},{"location":"metagenome_study/SequencingTechnology/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/SequencingTechnology/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/SequencingTechnology/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:obi, sqlite:obo:efo, bioportal:bero"},{"location":"metagenome_study/SequencingTechnology/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/SequencingTechnology/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:SequencingTechnology native eg:SequencingTechnology"},{"location":"metagenome_study/SequencingTechnology/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/SequencingTechnology/#direct","title":"Direct","text":"
name: SequencingTechnology\nid_prefixes:\n- IDO\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:obi, sqlite:obo:efo, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/SequencingTechnology/#induced","title":"Induced","text":"
name: SequencingTechnology\nid_prefixes:\n- IDO\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:obi, sqlite:obo:efo, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: SequencingTechnology\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: SequencingTechnology\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"metagenome_study/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/String/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Study/","title":"Class: Study","text":"

URI: eg:Study

erDiagram\nStudy {\n\n}\nOrganism {\n    string id  \n    string label  \n}\nSequencingTechnology {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nLocation {\n    string id  \n    string label  \n}\nMeasurement {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nVariable {\n    string id  \n    string label  \n}\nCausalRelationship {\n\n}\nEnvironment {\n    string id  \n    string label  \n}\n\nStudy ||--}o Environment : \"environments\"\nStudy ||--}o CausalRelationship : \"causal_relationships\"\nStudy ||--}o Variable : \"variables\"\nStudy ||--}o Treatment : \"treatments\"\nStudy ||--}o Measurement : \"measurements\"\nStudy ||--}o Location : \"location\"\nStudy ||--}o EnvironmentalMaterial : \"environmental_material\"\nStudy ||--|o SequencingTechnology : \"sequencing_technologies\"\nStudy ||--}o Organism : \"organisms\"\nMeasurement ||--|o Unit : \"unit\"\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\n\n
"},{"location":"metagenome_study/Study/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance environments 0..* Environment direct causal_relationships 0..* CausalRelationship direct variables 0..* Variable direct treatments 0..* Treatment direct measurements 0..* Measurement direct location 0..* Location the sites at which the study was conducted direct environmental_material 0..* EnvironmentalMaterial the environmental material that was sampled direct sequencing_technologies 0..1 SequencingTechnology direct organisms 0..* Organism semicolon-separated list of all studied organism taxons direct"},{"location":"metagenome_study/Study/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Study/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Study/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Study native eg:Study"},{"location":"metagenome_study/Study/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Study/#direct","title":"Direct","text":"
name: Study\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental systems or biomes in which\n          the study was conducted\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Environment\n  causal_relationships:\n    name: causal_relationships\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of cause-effect pairs, for example, effect\n          of temperature on growth\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: CausalRelationship\n  variables:\n    name: variables\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental variables which are studies.\n          E.g. temperature, pH, salinity\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Variable\n  treatments:\n    name: treatments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of treatments that are applied\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Treatment\n  measurements:\n    name: measurements\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of value-measurement pairs\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Measurement\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of sites at which the study was conducted\n    description: the sites at which the study was conducted\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: EnvironmentalMaterial\n  sequencing_technologies:\n    name: sequencing_technologies\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of  sequencing technologies used in the project\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: SequencingTechnology\n  organisms:\n    name: organisms\n    description: semicolon-separated list of all studied organism taxons\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Organism\n\n
"},{"location":"metagenome_study/Study/#induced","title":"Induced","text":"
name: Study\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental systems or biomes in which\n          the study was conducted\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: environments\n    owner: Study\n    domain_of:\n    - Study\n    range: Environment\n  causal_relationships:\n    name: causal_relationships\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of cause-effect pairs, for example, effect\n          of temperature on growth\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: causal_relationships\n    owner: Study\n    domain_of:\n    - Study\n    range: CausalRelationship\n  variables:\n    name: variables\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental variables which are studies.\n          E.g. temperature, pH, salinity\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: variables\n    owner: Study\n    domain_of:\n    - Study\n    range: Variable\n  treatments:\n    name: treatments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of treatments that are applied\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: treatments\n    owner: Study\n    domain_of:\n    - Study\n    range: Treatment\n  measurements:\n    name: measurements\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of value-measurement pairs\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: measurements\n    owner: Study\n    domain_of:\n    - Study\n    range: Measurement\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of sites at which the study was conducted\n    description: the sites at which the study was conducted\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: location\n    owner: Study\n    domain_of:\n    - Study\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: environmental_material\n    owner: Study\n    domain_of:\n    - Study\n    range: EnvironmentalMaterial\n  sequencing_technologies:\n    name: sequencing_technologies\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of  sequencing technologies used in the project\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: sequencing_technologies\n    owner: Study\n    domain_of:\n    - Study\n    range: SequencingTechnology\n  organisms:\n    name: organisms\n    description: semicolon-separated list of all studied organism taxons\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: organisms\n    owner: Study\n    domain_of:\n    - Study\n    range: Organism\n\n
"},{"location":"metagenome_study/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: eg:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"metagenome_study/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"metagenome_study/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:TextWithTriples native eg:TextWithTriples"},{"location":"metagenome_study/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metagenome_study/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metagenome_study/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"metagenome_study/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Time/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Treatment/","title":"Class: Treatment","text":"

URI: eg:Treatment

erDiagram\nTreatment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Treatment/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Treatment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Treatment/#usages","title":"Usages","text":"used by used in type used Study treatments range Treatment"},{"location":"metagenome_study/Treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Treatment/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Treatment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:peco, sqlite:obo:obi, bioportal:bero"},{"location":"metagenome_study/Treatment/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Treatment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Treatment native eg:Treatment"},{"location":"metagenome_study/Treatment/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Treatment/#direct","title":"Direct","text":"
name: Treatment\nid_prefixes:\n- PECO\n- OBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:peco, sqlite:obo:obi, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Treatment/#induced","title":"Induced","text":"
name: Treatment\nid_prefixes:\n- PECO\n- OBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:peco, sqlite:obo:obi, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: eg:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"metagenome_study/Triple/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"metagenome_study/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"metagenome_study/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Triple/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Triple native eg:Triple"},{"location":"metagenome_study/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"metagenome_study/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"metagenome_study/Unit/","title":"Class: Unit","text":"

URI: eg:Unit

erDiagram\nUnit {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Unit/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Unit/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Unit/#usages","title":"Usages","text":"used by used in type used Measurement unit range Unit"},{"location":"metagenome_study/Unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Unit/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Unit/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uo, bioportal:ncit"},{"location":"metagenome_study/Unit/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Unit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Unit native eg:Unit"},{"location":"metagenome_study/Unit/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Unit/#direct","title":"Direct","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, bioportal:ncit\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Unit/#induced","title":"Induced","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, bioportal:ncit\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"metagenome_study/Uri/#comments","title":"Comments","text":""},{"location":"metagenome_study/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Uri/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"metagenome_study/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Variable/","title":"Class: Variable","text":"

URI: eg:Variable

erDiagram\nVariable {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Variable/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Variable/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Variable/#usages","title":"Usages","text":"used by used in type used Study variables range Variable CausalRelationship cause range Variable CausalRelationship effect range Variable"},{"location":"metagenome_study/Variable/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Variable/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Variable/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:bero"},{"location":"metagenome_study/Variable/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Variable/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Variable native eg:Variable"},{"location":"metagenome_study/Variable/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Variable/#direct","title":"Direct","text":"
name: Variable\nid_prefixes:\n- ENVO\n- MIXS\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Variable/#induced","title":"Induced","text":"
name: Variable\nid_prefixes:\n- ENVO\n- MIXS\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Variable\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Variable\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: eg:abstract

"},{"location":"metagenome_study/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metagenome_study/abstract/#properties","title":"Properties","text":""},{"location":"metagenome_study/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/abstract/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metagenome_study/causal_relationships/","title":"Slot: causal_relationships","text":"

URI: eg:causal_relationships

"},{"location":"metagenome_study/causal_relationships/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/causal_relationships/#properties","title":"Properties","text":""},{"location":"metagenome_study/causal_relationships/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/causal_relationships/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth"},{"location":"metagenome_study/causal_relationships/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/causal_relationships/#linkml-source","title":"LinkML Source","text":"
name: causal_relationships\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of cause-effect pairs, for example, effect of\n      temperature on growth\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: causal_relationships\nowner: Study\ndomain_of:\n- Study\nrange: CausalRelationship\n\n
"},{"location":"metagenome_study/cause/","title":"Slot: cause","text":"

the variable that is the cause of the effect

URI: eg:cause

"},{"location":"metagenome_study/cause/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CausalRelationship no"},{"location":"metagenome_study/cause/#properties","title":"Properties","text":""},{"location":"metagenome_study/cause/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/cause/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/cause/#linkml-source","title":"LinkML Source","text":"
name: cause\ndescription: the variable that is the cause of the effect\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: cause\nowner: CausalRelationship\ndomain_of:\n- CausalRelationship\nrange: Variable\n\n
"},{"location":"metagenome_study/combined_text/","title":"Slot: combined_text","text":"

URI: eg:combined_text

"},{"location":"metagenome_study/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metagenome_study/combined_text/#properties","title":"Properties","text":""},{"location":"metagenome_study/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metagenome_study/effect/","title":"Slot: effect","text":"

the things that is affected

URI: eg:effect

"},{"location":"metagenome_study/effect/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CausalRelationship no"},{"location":"metagenome_study/effect/#properties","title":"Properties","text":""},{"location":"metagenome_study/effect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/effect/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/effect/#linkml-source","title":"LinkML Source","text":"
name: effect\ndescription: the things that is affected\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: effect\nowner: CausalRelationship\ndomain_of:\n- CausalRelationship\nrange: Variable\n\n
"},{"location":"metagenome_study/environmental-metagenome/","title":"environmental-metagenome","text":"

A template for Environmental Metagenome Studies

URI: http://w3id.org/ontogpt/metagenome

"},{"location":"metagenome_study/environmental_material/","title":"Slot: environmental_material","text":"

the environmental material that was sampled

URI: eg:environmental_material

"},{"location":"metagenome_study/environmental_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/environmental_material/#properties","title":"Properties","text":""},{"location":"metagenome_study/environmental_material/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/environmental_material/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental materials"},{"location":"metagenome_study/environmental_material/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/environmental_material/#linkml-source","title":"LinkML Source","text":"
name: environmental_material\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental materials\ndescription: the environmental material that was sampled\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: environmental_material\nowner: Study\ndomain_of:\n- Study\nrange: EnvironmentalMaterial\n\n
"},{"location":"metagenome_study/environments/","title":"Slot: environments","text":"

URI: eg:environments

"},{"location":"metagenome_study/environments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/environments/#properties","title":"Properties","text":""},{"location":"metagenome_study/environments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/environments/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental systems or biomes in which the study was conducted"},{"location":"metagenome_study/environments/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/environments/#linkml-source","title":"LinkML Source","text":"
name: environments\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental systems or biomes in which the\n      study was conducted\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: environments\nowner: Study\ndomain_of:\n- Study\nrange: Environment\n\n
"},{"location":"metagenome_study/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: eg:extracted_object

"},{"location":"metagenome_study/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/extracted_object/#properties","title":"Properties","text":""},{"location":"metagenome_study/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"metagenome_study/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: eg:full_text

"},{"location":"metagenome_study/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metagenome_study/full_text/#properties","title":"Properties","text":""},{"location":"metagenome_study/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/full_text/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metagenome_study/id/","title":"Slot: id","text":"

URI: eg:id

"},{"location":"metagenome_study/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Location no EnvironmentalMaterial no Environment no Variable no Unit no SequencingTechnology no Treatment no Organism no NamedEntity no RelationshipType no Publication no"},{"location":"metagenome_study/id/#properties","title":"Properties","text":""},{"location":"metagenome_study/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"metagenome_study/input_id/","title":"Slot: input_id","text":"

URI: eg:input_id

"},{"location":"metagenome_study/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/input_id/#properties","title":"Properties","text":""},{"location":"metagenome_study/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/input_id/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metagenome_study/input_text/","title":"Slot: input_text","text":"

URI: eg:input_text

"},{"location":"metagenome_study/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/input_text/#properties","title":"Properties","text":""},{"location":"metagenome_study/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/input_text/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metagenome_study/input_title/","title":"Slot: input_title","text":"

URI: eg:input_title

"},{"location":"metagenome_study/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/input_title/#properties","title":"Properties","text":""},{"location":"metagenome_study/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/input_title/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metagenome_study/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"metagenome_study/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Location no EnvironmentalMaterial no Environment no Variable no Unit no SequencingTechnology no Treatment no Organism no NamedEntity no RelationshipType no"},{"location":"metagenome_study/label/#properties","title":"Properties","text":""},{"location":"metagenome_study/label/#aliases","title":"Aliases","text":""},{"location":"metagenome_study/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"metagenome_study/label/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/metagenome\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"metagenome_study/location/","title":"Slot: location","text":"

the sites at which the study was conducted

URI: eg:location

"},{"location":"metagenome_study/location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/location/#properties","title":"Properties","text":""},{"location":"metagenome_study/location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/location/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of sites at which the study was conducted"},{"location":"metagenome_study/location/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/location/#linkml-source","title":"LinkML Source","text":"
name: location\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of sites at which the study was conducted\ndescription: the sites at which the study was conducted\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: location\nowner: Study\ndomain_of:\n- Study\nrange: Location\n\n
"},{"location":"metagenome_study/measurements/","title":"Slot: measurements","text":"

URI: eg:measurements

"},{"location":"metagenome_study/measurements/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/measurements/#properties","title":"Properties","text":""},{"location":"metagenome_study/measurements/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/measurements/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of value-measurement pairs"},{"location":"metagenome_study/measurements/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/measurements/#linkml-source","title":"LinkML Source","text":"
name: measurements\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of value-measurement pairs\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: measurements\nowner: Study\ndomain_of:\n- Study\nrange: Measurement\n\n
"},{"location":"metagenome_study/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: eg:named_entities

"},{"location":"metagenome_study/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/named_entities/#properties","title":"Properties","text":""},{"location":"metagenome_study/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"metagenome_study/object/","title":"Slot: object","text":"

URI: eg:object

"},{"location":"metagenome_study/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/object/#properties","title":"Properties","text":""},{"location":"metagenome_study/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/object/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metagenome_study/object_id/","title":"Slot: object_id","text":"

URI: eg:object_id

"},{"location":"metagenome_study/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metagenome_study/object_id/#properties","title":"Properties","text":""},{"location":"metagenome_study/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/object_id/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metagenome_study/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: eg:object_qualifier

"},{"location":"metagenome_study/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/object_qualifier/#properties","title":"Properties","text":""},{"location":"metagenome_study/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metagenome_study/object_text/","title":"Slot: object_text","text":"

URI: eg:object_text

"},{"location":"metagenome_study/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metagenome_study/object_text/#properties","title":"Properties","text":""},{"location":"metagenome_study/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/object_text/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metagenome_study/organisms/","title":"Slot: organisms","text":"

semicolon-separated list of all studied organism taxons

URI: eg:organisms

"},{"location":"metagenome_study/organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/organisms/#properties","title":"Properties","text":""},{"location":"metagenome_study/organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/organisms/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/organisms/#linkml-source","title":"LinkML Source","text":"
name: organisms\ndescription: semicolon-separated list of all studied organism taxons\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: organisms\nowner: Study\ndomain_of:\n- Study\nrange: Organism\n\n
"},{"location":"metagenome_study/predicate/","title":"Slot: predicate","text":"

URI: eg:predicate

"},{"location":"metagenome_study/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/predicate/#properties","title":"Properties","text":""},{"location":"metagenome_study/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/predicate/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"metagenome_study/prompt/","title":"Slot: prompt","text":"

URI: eg:prompt

"},{"location":"metagenome_study/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/prompt/#properties","title":"Properties","text":""},{"location":"metagenome_study/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/prompt/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metagenome_study/publication/","title":"Slot: publication","text":"

URI: eg:publication

"},{"location":"metagenome_study/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"metagenome_study/publication/#properties","title":"Properties","text":""},{"location":"metagenome_study/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"metagenome_study/publication/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"metagenome_study/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: eg:qualifier

"},{"location":"metagenome_study/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/qualifier/#properties","title":"Properties","text":""},{"location":"metagenome_study/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"metagenome_study/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: eg:raw_completion_output

"},{"location":"metagenome_study/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/raw_completion_output/#properties","title":"Properties","text":""},{"location":"metagenome_study/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metagenome_study/sequencing_technologies/","title":"Slot: sequencing_technologies","text":"

URI: eg:sequencing_technologies

"},{"location":"metagenome_study/sequencing_technologies/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/sequencing_technologies/#properties","title":"Properties","text":""},{"location":"metagenome_study/sequencing_technologies/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/sequencing_technologies/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of sequencing technologies used in the project"},{"location":"metagenome_study/sequencing_technologies/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/sequencing_technologies/#linkml-source","title":"LinkML Source","text":"
name: sequencing_technologies\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of  sequencing technologies used in the project\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: sequencing_technologies\nowner: Study\ndomain_of:\n- Study\nrange: SequencingTechnology\n\n
"},{"location":"metagenome_study/subject/","title":"Slot: subject","text":"

URI: eg:subject

"},{"location":"metagenome_study/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/subject/#properties","title":"Properties","text":""},{"location":"metagenome_study/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/subject/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metagenome_study/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: eg:subject_qualifier

"},{"location":"metagenome_study/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/subject_qualifier/#properties","title":"Properties","text":""},{"location":"metagenome_study/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metagenome_study/subject_text/","title":"Slot: subject_text","text":"

URI: eg:subject_text

"},{"location":"metagenome_study/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metagenome_study/subject_text/#properties","title":"Properties","text":""},{"location":"metagenome_study/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metagenome_study/title/","title":"Slot: title","text":"

The title of the publication

URI: eg:title

"},{"location":"metagenome_study/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metagenome_study/title/#properties","title":"Properties","text":""},{"location":"metagenome_study/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/title/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metagenome_study/treatments/","title":"Slot: treatments","text":"

URI: eg:treatments

"},{"location":"metagenome_study/treatments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/treatments/#properties","title":"Properties","text":""},{"location":"metagenome_study/treatments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/treatments/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of treatments that are applied"},{"location":"metagenome_study/treatments/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/treatments/#linkml-source","title":"LinkML Source","text":"
name: treatments\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of treatments that are applied\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: treatments\nowner: Study\ndomain_of:\n- Study\nrange: Treatment\n\n
"},{"location":"metagenome_study/triples/","title":"Slot: triples","text":"

URI: eg:triples

"},{"location":"metagenome_study/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"metagenome_study/triples/#properties","title":"Properties","text":""},{"location":"metagenome_study/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/triples/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"metagenome_study/unit/","title":"Slot: unit","text":"

the unit of the measurement

URI: eg:unit

"},{"location":"metagenome_study/unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Measurement no"},{"location":"metagenome_study/unit/#properties","title":"Properties","text":""},{"location":"metagenome_study/unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/unit/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/unit/#linkml-source","title":"LinkML Source","text":"
name: unit\ndescription: the unit of the measurement\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: unit\nowner: Measurement\ndomain_of:\n- Measurement\nrange: Unit\n\n
"},{"location":"metagenome_study/value/","title":"Slot: value","text":"

the value of the measurement

URI: eg:value

"},{"location":"metagenome_study/value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Measurement no"},{"location":"metagenome_study/value/#properties","title":"Properties","text":""},{"location":"metagenome_study/value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/value/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/value/#linkml-source","title":"LinkML Source","text":"
name: value\ndescription: the value of the measurement\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: value\nowner: Measurement\ndomain_of:\n- Measurement\nrange: string\n\n
"},{"location":"metagenome_study/variables/","title":"Slot: variables","text":"

URI: eg:variables

"},{"location":"metagenome_study/variables/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/variables/#properties","title":"Properties","text":""},{"location":"metagenome_study/variables/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/variables/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity"},{"location":"metagenome_study/variables/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/variables/#linkml-source","title":"LinkML Source","text":"
name: variables\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental variables which are studies.\n      E.g. temperature, pH, salinity\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: variables\nowner: Study\ndomain_of:\n- Study\nrange: Variable\n\n
"},{"location":"ontology_class/","title":"Ontology Class Template","text":"

A template for Ontology Classes

URI: https://w3id.org/ontogpt/ontology_class

Name: ontology-class

"},{"location":"ontology_class/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nOntologyClass {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nLogicalDefinition {\n\n}\nRelation {\n    string id  \n    string label  \n}\n\nOntologyClass ||--}o OntologyClass : \"categories\"\nOntologyClass ||--}o OntologyClass : \"subclass_of\"\nOntologyClass ||--|o LogicalDefinition : \"logical_definition\"\nLogicalDefinition ||--}o OntologyClass : \"genus\"\nLogicalDefinition ||--|o Relation : \"differentiating_characteristic_relationship\"\nLogicalDefinition ||--}o OntologyClass : \"differentiating_characteristic_parents\"\n\n
"},{"location":"ontology_class/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text LogicalDefinition None NamedEntity None OntologyClass None Relation None RelationshipType None Publication None TextWithTriples None"},{"location":"ontology_class/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication categories the categories to which this entity belongs combined_text description a textual description of the entity differentiating_characteristic_parents differentiating_characteristic_relationship extracted_object The complex objects extracted from the text full_text The full text of the publication genus id A unique identifier for the named entity input_id input_text input_title label the name of the main entity being defined logical_definition the necessary and sufficient conditions for this entity to be an instance of ... named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subclass_of subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text synonyms alternative names of the entity title The title of the publication triples"},{"location":"ontology_class/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"ontology_class/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"ontology_class/#subsets","title":"Subsets","text":"Subset Description"},{"location":"ontology_class/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: oc:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"ontology_class/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"ontology_class/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:AnnotatorResult native oc:AnnotatorResult"},{"location":"ontology_class/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n\n
"},{"location":"ontology_class/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"ontology_class/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"ontology_class/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ontology_class/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"ontology_class/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Any/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native oc:Any"},{"location":"ontology_class/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nclass_uri: linkml:Any\n\n
"},{"location":"ontology_class/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nclass_uri: linkml:Any\n\n
"},{"location":"ontology_class/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"ontology_class/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: oc:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"ontology_class/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ontology_class/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:CompoundExpression native oc:CompoundExpression"},{"location":"ontology_class/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nabstract: true\n\n
"},{"location":"ontology_class/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nabstract: true\n\n
"},{"location":"ontology_class/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"ontology_class/Curie/#comments","title":"Comments","text":""},{"location":"ontology_class/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Curie/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"ontology_class/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Date/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"ontology_class/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"ontology_class/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"ontology_class/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"ontology_class/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Double/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: oc:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"ontology_class/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"ontology_class/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:ExtractionResult native oc:ExtractionResult"},{"location":"ontology_class/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_class/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_class/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"ontology_class/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Float/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"ontology_class/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Integer/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/LogicalDefinition/","title":"Class: LogicalDefinition","text":"

URI: oc:LogicalDefinition

erDiagram\nLogicalDefinition {\n\n}\nOntologyClass {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nRelation {\n    string id  \n    string label  \n}\n\nLogicalDefinition ||--}o OntologyClass : \"genus\"\nLogicalDefinition ||--|o Relation : \"differentiating_characteristic_relationship\"\nLogicalDefinition ||--}o OntologyClass : \"differentiating_characteristic_parents\"\nOntologyClass ||--}o OntologyClass : \"categories\"\nOntologyClass ||--}o OntologyClass : \"subclass_of\"\nOntologyClass ||--|o LogicalDefinition : \"logical_definition\"\n\n
"},{"location":"ontology_class/LogicalDefinition/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance genus 0..* OntologyClass direct differentiating_characteristic_relationship 0..1 Relation direct differentiating_characteristic_parents 0..* OntologyClass direct"},{"location":"ontology_class/LogicalDefinition/#usages","title":"Usages","text":"used by used in type used OntologyClass logical_definition range LogicalDefinition"},{"location":"ontology_class/LogicalDefinition/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/LogicalDefinition/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/LogicalDefinition/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:LogicalDefinition native oc:LogicalDefinition"},{"location":"ontology_class/LogicalDefinition/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/LogicalDefinition/#direct","title":"Direct","text":"
name: LogicalDefinition\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  genus:\n    name: genus\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this is the parent (genus) class,\n          e.g. bone\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n  differentiating_characteristic_relationship:\n    name: differentiating_characteristic_relationship\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this is the parent (differentiating\n          characteristic) relationship type, e.g. part of\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: Relation\n  differentiating_characteristic_parents:\n    name: differentiating_characteristic_parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this the parent (differentiating\n          characteristic) class, e.g. hand\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n\n
"},{"location":"ontology_class/LogicalDefinition/#induced","title":"Induced","text":"
name: LogicalDefinition\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  genus:\n    name: genus\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this is the parent (genus) class,\n          e.g. bone\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: genus\n    owner: LogicalDefinition\n    domain_of:\n    - LogicalDefinition\n    range: OntologyClass\n  differentiating_characteristic_relationship:\n    name: differentiating_characteristic_relationship\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this is the parent (differentiating\n          characteristic) relationship type, e.g. part of\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: differentiating_characteristic_relationship\n    owner: LogicalDefinition\n    domain_of:\n    - LogicalDefinition\n    range: Relation\n  differentiating_characteristic_parents:\n    name: differentiating_characteristic_parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this the parent (differentiating\n          characteristic) class, e.g. hand\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: differentiating_characteristic_parents\n    owner: LogicalDefinition\n    domain_of:\n    - LogicalDefinition\n    range: OntologyClass\n\n
"},{"location":"ontology_class/NamedEntity/","title":"Class: NamedEntity","text":"

URI: oc:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_class/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"ontology_class/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"ontology_class/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:NamedEntity native oc:NamedEntity"},{"location":"ontology_class/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"ontology_class/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - OntologyClass\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_class/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"ontology_class/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"ontology_class/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"ontology_class/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"ontology_class/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"ontology_class/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"ontology_class/Objectidentifier/#comments","title":"Comments","text":""},{"location":"ontology_class/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/OntologyClass/","title":"Class: OntologyClass","text":"

URI: oc:OntologyClass

erDiagram\nOntologyClass {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nLogicalDefinition {\n\n}\nRelation {\n    string id  \n    string label  \n}\n\nOntologyClass ||--}o OntologyClass : \"categories\"\nOntologyClass ||--}o OntologyClass : \"subclass_of\"\nOntologyClass ||--|o LogicalDefinition : \"logical_definition\"\nLogicalDefinition ||--}o OntologyClass : \"genus\"\nLogicalDefinition ||--|o Relation : \"differentiating_characteristic_relationship\"\nLogicalDefinition ||--}o OntologyClass : \"differentiating_characteristic_parents\"\n\n
"},{"location":"ontology_class/OntologyClass/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/OntologyClass/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 0..1 String the name of the main entity being defined direct description 0..1 String a textual description of the entity direct synonyms 0..* String alternative names of the entity direct categories 0..* OntologyClass the categories to which this entity belongs direct subclass_of 0..* OntologyClass direct logical_definition 0..1 LogicalDefinition the necessary and sufficient conditions for this entity to be an instance of ... direct id 1..1 String A unique identifier for the named entity NamedEntity"},{"location":"ontology_class/OntologyClass/#usages","title":"Usages","text":"used by used in type used OntologyClass categories range OntologyClass OntologyClass subclass_of range OntologyClass LogicalDefinition genus range OntologyClass LogicalDefinition differentiating_characteristic_parents range OntologyClass"},{"location":"ontology_class/OntologyClass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/OntologyClass/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/OntologyClass/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyClass native oc:OntologyClass"},{"location":"ontology_class/OntologyClass/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/OntologyClass/#direct","title":"Direct","text":"
name: OntologyClass\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the main entity being defined\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  description:\n    name: description\n    description: a textual description of the entity\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  synonyms:\n    name: synonyms\n    description: alternative names of the entity\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n  categories:\n    name: categories\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of categories to which the entity belongs.\n          These may be taken from an upper level ontology such as COB, BioLink, or\n          UMLS semantic types.\n    description: the categories to which this entity belongs.\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n  subclass_of:\n    name: subclass_of\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent classes, indicating broader concepts.\n          E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n  logical_definition:\n    name: logical_definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: the necessary and sufficient conditions for this entity to be an instance\n          of this class, written in OWL manchester syntax, e.g. bone and (part_of\n          some 'hand')\n    description: the necessary and sufficient conditions for this entity to be an\n      instance of this class\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: LogicalDefinition\ntree_root: true\n\n
"},{"location":"ontology_class/OntologyClass/#induced","title":"Induced","text":"
name: OntologyClass\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the main entity being defined\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: label\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    - NamedEntity\n    range: string\n  description:\n    name: description\n    description: a textual description of the entity\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: description\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    range: string\n  synonyms:\n    name: synonyms\n    description: alternative names of the entity\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    range: string\n  categories:\n    name: categories\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of categories to which the entity belongs.\n          These may be taken from an upper level ontology such as COB, BioLink, or\n          UMLS semantic types.\n    description: the categories to which this entity belongs.\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: categories\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    range: OntologyClass\n  subclass_of:\n    name: subclass_of\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent classes, indicating broader concepts.\n          E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: subclass_of\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    range: OntologyClass\n  logical_definition:\n    name: logical_definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: the necessary and sufficient conditions for this entity to be an instance\n          of this class, written in OWL manchester syntax, e.g. bone and (part_of\n          some 'hand')\n    description: the necessary and sufficient conditions for this entity to be an\n      instance of this class\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: logical_definition\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    range: LogicalDefinition\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: OntologyClass\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\ntree_root: true\n\n
"},{"location":"ontology_class/Publication/","title":"Class: Publication","text":"

URI: oc:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"ontology_class/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"ontology_class/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"ontology_class/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Publication/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Publication native oc:Publication"},{"location":"ontology_class/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/ontology_class\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n\n
"},{"location":"ontology_class/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"ontology_class/Relation/","title":"Class: Relation","text":"

URI: oc:Relation

erDiagram\nRelation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_class/Relation/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/Relation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ontology_class/Relation/#usages","title":"Usages","text":"used by used in type used LogicalDefinition differentiating_characteristic_relationship range Relation"},{"location":"ontology_class/Relation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Relation/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ontology_class/Relation/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ro"},{"location":"ontology_class/Relation/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Relation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Relation native oc:Relation"},{"location":"ontology_class/Relation/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/Relation/#direct","title":"Direct","text":"
name: Relation\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\n\n
"},{"location":"ontology_class/Relation/#induced","title":"Induced","text":"
name: Relation\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Relation\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Relation\n    domain_of:\n    - OntologyClass\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_class/RelationshipType/","title":"Class: RelationshipType","text":"

URI: oc:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_class/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ontology_class/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"ontology_class/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ontology_class/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:RelationshipType native oc:RelationshipType"},{"location":"ontology_class/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\n\n
"},{"location":"ontology_class/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - OntologyClass\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_class/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"ontology_class/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/String/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: oc:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ontology_class/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"ontology_class/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:TextWithTriples native oc:TextWithTriples"},{"location":"ontology_class/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_class/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_class/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"ontology_class/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Time/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: oc:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ontology_class/Triple/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"ontology_class/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"ontology_class/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Triple/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Triple native oc:Triple"},{"location":"ontology_class/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"ontology_class/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ontology_class/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"ontology_class/Uri/#comments","title":"Comments","text":""},{"location":"ontology_class/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Uri/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"ontology_class/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: oc:abstract

"},{"location":"ontology_class/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_class/abstract/#properties","title":"Properties","text":""},{"location":"ontology_class/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/abstract/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_class/categories/","title":"Slot: categories","text":"

the categories to which this entity belongs.

URI: oc:categories

"},{"location":"ontology_class/categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no"},{"location":"ontology_class/categories/#properties","title":"Properties","text":""},{"location":"ontology_class/categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/categories/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types."},{"location":"ontology_class/categories/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/categories/#linkml-source","title":"LinkML Source","text":"
name: categories\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of categories to which the entity belongs. These\n      may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic\n      types.\ndescription: the categories to which this entity belongs.\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: categories\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: OntologyClass\n\n
"},{"location":"ontology_class/combined_text/","title":"Slot: combined_text","text":"

URI: oc:combined_text

"},{"location":"ontology_class/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_class/combined_text/#properties","title":"Properties","text":""},{"location":"ontology_class/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_class/description/","title":"Slot: description","text":"

a textual description of the entity

URI: oc:description

"},{"location":"ontology_class/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no"},{"location":"ontology_class/description/#properties","title":"Properties","text":""},{"location":"ontology_class/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/description/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a textual description of the entity\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: description\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: string\n\n
"},{"location":"ontology_class/differentiating_characteristic_parents/","title":"Slot: differentiating_characteristic_parents","text":"

URI: oc:differentiating_characteristic_parents

"},{"location":"ontology_class/differentiating_characteristic_parents/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LogicalDefinition no"},{"location":"ontology_class/differentiating_characteristic_parents/#properties","title":"Properties","text":""},{"location":"ontology_class/differentiating_characteristic_parents/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/differentiating_characteristic_parents/#annotations","title":"Annotations","text":"property value prompt in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand"},{"location":"ontology_class/differentiating_characteristic_parents/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/differentiating_characteristic_parents/#linkml-source","title":"LinkML Source","text":"
name: differentiating_characteristic_parents\nannotations:\n  prompt:\n    tag: prompt\n    value: in a logical definition expression, this the parent (differentiating characteristic)\n      class, e.g. hand\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: differentiating_characteristic_parents\nowner: LogicalDefinition\ndomain_of:\n- LogicalDefinition\nrange: OntologyClass\n\n
"},{"location":"ontology_class/differentiating_characteristic_relationship/","title":"Slot: differentiating_characteristic_relationship","text":"

URI: oc:differentiating_characteristic_relationship

"},{"location":"ontology_class/differentiating_characteristic_relationship/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LogicalDefinition no"},{"location":"ontology_class/differentiating_characteristic_relationship/#properties","title":"Properties","text":""},{"location":"ontology_class/differentiating_characteristic_relationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/differentiating_characteristic_relationship/#annotations","title":"Annotations","text":"property value prompt in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of"},{"location":"ontology_class/differentiating_characteristic_relationship/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/differentiating_characteristic_relationship/#linkml-source","title":"LinkML Source","text":"
name: differentiating_characteristic_relationship\nannotations:\n  prompt:\n    tag: prompt\n    value: in a logical definition expression, this is the parent (differentiating\n      characteristic) relationship type, e.g. part of\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: differentiating_characteristic_relationship\nowner: LogicalDefinition\ndomain_of:\n- LogicalDefinition\nrange: Relation\n\n
"},{"location":"ontology_class/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: oc:extracted_object

"},{"location":"ontology_class/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/extracted_object/#properties","title":"Properties","text":""},{"location":"ontology_class/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"ontology_class/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: oc:full_text

"},{"location":"ontology_class/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_class/full_text/#properties","title":"Properties","text":""},{"location":"ontology_class/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/full_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_class/genus/","title":"Slot: genus","text":"

URI: oc:genus

"},{"location":"ontology_class/genus/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LogicalDefinition no"},{"location":"ontology_class/genus/#properties","title":"Properties","text":""},{"location":"ontology_class/genus/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/genus/#annotations","title":"Annotations","text":"property value prompt in a logical definition expression, this is the parent (genus) class, e.g. bone"},{"location":"ontology_class/genus/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/genus/#linkml-source","title":"LinkML Source","text":"
name: genus\nannotations:\n  prompt:\n    tag: prompt\n    value: in a logical definition expression, this is the parent (genus) class, e.g.\n      bone\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: genus\nowner: LogicalDefinition\ndomain_of:\n- LogicalDefinition\nrange: OntologyClass\n\n
"},{"location":"ontology_class/id/","title":"Slot: id","text":"

URI: oc:id

"},{"location":"ontology_class/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no Relation no NamedEntity no RelationshipType no Publication no"},{"location":"ontology_class/id/#properties","title":"Properties","text":""},{"location":"ontology_class/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"ontology_class/input_id/","title":"Slot: input_id","text":"

URI: oc:input_id

"},{"location":"ontology_class/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/input_id/#properties","title":"Properties","text":""},{"location":"ontology_class/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/input_id/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_class/input_text/","title":"Slot: input_text","text":"

URI: oc:input_text

"},{"location":"ontology_class/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/input_text/#properties","title":"Properties","text":""},{"location":"ontology_class/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/input_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_class/input_title/","title":"Slot: input_title","text":"

URI: oc:input_title

"},{"location":"ontology_class/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/input_title/#properties","title":"Properties","text":""},{"location":"ontology_class/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/input_title/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_class/label/","title":"Slot: label","text":"

URI: oc:label

"},{"location":"ontology_class/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no Relation no NamedEntity no RelationshipType no"},{"location":"ontology_class/label/#properties","title":"Properties","text":""},{"location":"ontology_class/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- OntologyClass\n- NamedEntity\nrange: string\n\n
"},{"location":"ontology_class/logical_definition/","title":"Slot: logical_definition","text":"

the necessary and sufficient conditions for this entity to be an instance of this class

URI: oc:logical_definition

"},{"location":"ontology_class/logical_definition/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no"},{"location":"ontology_class/logical_definition/#properties","title":"Properties","text":""},{"location":"ontology_class/logical_definition/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/logical_definition/#annotations","title":"Annotations","text":"property value prompt the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')"},{"location":"ontology_class/logical_definition/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/logical_definition/#linkml-source","title":"LinkML Source","text":"
name: logical_definition\nannotations:\n  prompt:\n    tag: prompt\n    value: the necessary and sufficient conditions for this entity to be an instance\n      of this class, written in OWL manchester syntax, e.g. bone and (part_of some\n      'hand')\ndescription: the necessary and sufficient conditions for this entity to be an instance\n  of this class\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: logical_definition\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: LogicalDefinition\n\n
"},{"location":"ontology_class/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: oc:named_entities

"},{"location":"ontology_class/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/named_entities/#properties","title":"Properties","text":""},{"location":"ontology_class/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ontology_class/object/","title":"Slot: object","text":"

URI: oc:object

"},{"location":"ontology_class/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/object/#properties","title":"Properties","text":""},{"location":"ontology_class/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/object/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_class/object_id/","title":"Slot: object_id","text":"

URI: oc:object_id

"},{"location":"ontology_class/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_class/object_id/#properties","title":"Properties","text":""},{"location":"ontology_class/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/object_id/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_class/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: oc:object_qualifier

"},{"location":"ontology_class/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/object_qualifier/#properties","title":"Properties","text":""},{"location":"ontology_class/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_class/object_text/","title":"Slot: object_text","text":"

URI: oc:object_text

"},{"location":"ontology_class/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_class/object_text/#properties","title":"Properties","text":""},{"location":"ontology_class/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/object_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_class/ontology-class/","title":"ontology-class","text":"

A template for Ontology Classes

URI: https://w3id.org/ontogpt/ontology_class

"},{"location":"ontology_class/predicate/","title":"Slot: predicate","text":"

URI: oc:predicate

"},{"location":"ontology_class/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/predicate/#properties","title":"Properties","text":""},{"location":"ontology_class/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/predicate/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"ontology_class/prompt/","title":"Slot: prompt","text":"

URI: oc:prompt

"},{"location":"ontology_class/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/prompt/#properties","title":"Properties","text":""},{"location":"ontology_class/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/prompt/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_class/publication/","title":"Slot: publication","text":"

URI: oc:publication

"},{"location":"ontology_class/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ontology_class/publication/#properties","title":"Properties","text":""},{"location":"ontology_class/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"ontology_class/publication/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"ontology_class/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: oc:qualifier

"},{"location":"ontology_class/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/qualifier/#properties","title":"Properties","text":""},{"location":"ontology_class/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"ontology_class/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: oc:raw_completion_output

"},{"location":"ontology_class/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/raw_completion_output/#properties","title":"Properties","text":""},{"location":"ontology_class/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_class/subclass_of/","title":"Slot: subclass_of","text":"

URI: oc:subclass_of

"},{"location":"ontology_class/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no"},{"location":"ontology_class/subclass_of/#properties","title":"Properties","text":""},{"location":"ontology_class/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/subclass_of/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\""},{"location":"ontology_class/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of parent classes, indicating broader concepts.\n      E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: subclass_of\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: OntologyClass\n\n
"},{"location":"ontology_class/subject/","title":"Slot: subject","text":"

URI: oc:subject

"},{"location":"ontology_class/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/subject/#properties","title":"Properties","text":""},{"location":"ontology_class/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/subject/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_class/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: oc:subject_qualifier

"},{"location":"ontology_class/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/subject_qualifier/#properties","title":"Properties","text":""},{"location":"ontology_class/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_class/subject_text/","title":"Slot: subject_text","text":"

URI: oc:subject_text

"},{"location":"ontology_class/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_class/subject_text/#properties","title":"Properties","text":""},{"location":"ontology_class/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_class/synonyms/","title":"Slot: synonyms","text":"

alternative names of the entity

URI: oc:synonyms

"},{"location":"ontology_class/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no"},{"location":"ontology_class/synonyms/#properties","title":"Properties","text":""},{"location":"ontology_class/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\ndescription: alternative names of the entity\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: string\n\n
"},{"location":"ontology_class/title/","title":"Slot: title","text":"

The title of the publication

URI: oc:title

"},{"location":"ontology_class/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_class/title/#properties","title":"Properties","text":""},{"location":"ontology_class/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/title/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_class/triples/","title":"Slot: triples","text":"

URI: oc:triples

"},{"location":"ontology_class/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ontology_class/triples/#properties","title":"Properties","text":""},{"location":"ontology_class/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/triples/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ontology_issue/","title":"Ontology Issue Data Model","text":"

A data model for representing the contents of a GitHub issue on an ontology tracker

URI: https://w3id.org/ontogpt/ontology_issue

Name: ontology-issue

"},{"location":"ontology_issue/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nOntologyIssue {\n    string title  \n    string summary  \n    string status  \n}\nOntologyChange {\n    string description  \n    ChangeType category  \n}\nOntologyClass {\n    string id  \n    string label  \n}\nOntologyProblem {\n    string description  \n    string severity  \n    ProblemType category  \n}\n\nOntologyIssue ||--}o OntologyClass : \"domains\"\nOntologyIssue ||--}o OntologyProblem : \"problem_list\"\nOntologyIssue ||--}o OntologyChange : \"proposed_changes\"\nOntologyChange ||--}o OntologyClass : \"about\"\nOntologyProblem ||--}o OntologyClass : \"about\"\n\n
"},{"location":"ontology_issue/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None OntologyChange None OntologyProblem None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None OntologyClass None RelationshipType None OntologyIssue None Publication None TextWithTriples None"},{"location":"ontology_issue/#slots","title":"Slots","text":"Slot Description about What terms in the ontology is this problem about? abstract The abstract of the publication category What category does this problem fall into? combined_text description A succinct description of the problem domains What part of the ontology does this pertain to extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate problem_list A list of problems stated at a high level prompt proposed_changes What part of the ontology does this pertain to publication qualifier A qualifier for the statements, e raw_completion_output severity How severe is this problem? status subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text summary a high level summary title the title of the issue triples"},{"location":"ontology_issue/#enumerations","title":"Enumerations","text":"Enumeration Description ChangeType NullDataOptions ProblemType"},{"location":"ontology_issue/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"ontology_issue/#subsets","title":"Subsets","text":"Subset Description"},{"location":"ontology_issue/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: oc:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"ontology_issue/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"ontology_issue/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:AnnotatorResult native oc:AnnotatorResult"},{"location":"ontology_issue/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n\n
"},{"location":"ontology_issue/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"ontology_issue/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"ontology_issue/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ontology_issue/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"ontology_issue/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Any/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native oc:Any"},{"location":"ontology_issue/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nclass_uri: linkml:Any\n\n
"},{"location":"ontology_issue/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nclass_uri: linkml:Any\n\n
"},{"location":"ontology_issue/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"ontology_issue/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/ChangeType/","title":"Enum: ChangeType","text":"

URI: ChangeType

"},{"location":"ontology_issue/ChangeType/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNKNOWN None CHANGE_DEFINITION None CHANGE_LABEL None CHANGE_XREF None MOVE_TERM None"},{"location":"ontology_issue/ChangeType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/ChangeType/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/ChangeType/#linkml-source","title":"LinkML Source","text":"
name: ChangeType\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\npermissible_values:\n  UNKNOWN:\n    text: UNKNOWN\n  CHANGE_DEFINITION:\n    text: CHANGE_DEFINITION\n  CHANGE_LABEL:\n    text: CHANGE_LABEL\n  CHANGE_XREF:\n    text: CHANGE_XREF\n  MOVE_TERM:\n    text: MOVE_TERM\n\n
"},{"location":"ontology_issue/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: oc:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"ontology_issue/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ontology_issue/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:CompoundExpression native oc:CompoundExpression"},{"location":"ontology_issue/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nabstract: true\n\n
"},{"location":"ontology_issue/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nabstract: true\n\n
"},{"location":"ontology_issue/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"ontology_issue/Curie/#comments","title":"Comments","text":""},{"location":"ontology_issue/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Curie/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"ontology_issue/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Date/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"ontology_issue/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"ontology_issue/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"ontology_issue/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"ontology_issue/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Double/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: oc:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"ontology_issue/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"ontology_issue/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:ExtractionResult native oc:ExtractionResult"},{"location":"ontology_issue/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_issue/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_issue/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"ontology_issue/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Float/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"ontology_issue/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Integer/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/NamedEntity/","title":"Class: NamedEntity","text":"

URI: oc:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_issue/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"ontology_issue/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"ontology_issue/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:NamedEntity native oc:NamedEntity"},{"location":"ontology_issue/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"ontology_issue/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_issue/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"ontology_issue/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"ontology_issue/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"ontology_issue/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"ontology_issue/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"ontology_issue/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"ontology_issue/Objectidentifier/#comments","title":"Comments","text":""},{"location":"ontology_issue/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/OntologyChange/","title":"Class: OntologyChange","text":"

URI: oc:OntologyChange

erDiagram\nOntologyChange {\n    string description  \n    ChangeType category  \n}\nOntologyClass {\n    string id  \n    string label  \n}\n\nOntologyChange ||--}o OntologyClass : \"about\"\n\n
"},{"location":"ontology_issue/OntologyChange/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/OntologyChange/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance description 0..1 String A succinct description of the proposed change direct category 0..1 ChangeType What kind of change? direct about 0..* OntologyClass What terms in the ontology will this change affect? direct"},{"location":"ontology_issue/OntologyChange/#usages","title":"Usages","text":"used by used in type used OntologyIssue proposed_changes range OntologyChange"},{"location":"ontology_issue/OntologyChange/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/OntologyChange/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/OntologyChange/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyChange native oc:OntologyChange"},{"location":"ontology_issue/OntologyChange/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/OntologyChange/#direct","title":"Direct","text":"
name: OntologyChange\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nattributes:\n  description:\n    name: description\n    description: A succinct description of the proposed change\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n  category:\n    name: category\n    description: What kind of change?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    range: ChangeType\n  about:\n    name: about\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of specific terms in the ontology which will\n          be affected by the change.\n    description: What terms in the ontology will this change affect?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    multivalued: true\n    range: OntologyClass\n\n
"},{"location":"ontology_issue/OntologyChange/#induced","title":"Induced","text":"
name: OntologyChange\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nattributes:\n  description:\n    name: description\n    description: A succinct description of the proposed change\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    alias: description\n    owner: OntologyChange\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: string\n  category:\n    name: category\n    description: What kind of change?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    alias: category\n    owner: OntologyChange\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: ChangeType\n  about:\n    name: about\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of specific terms in the ontology which will\n          be affected by the change.\n    description: What terms in the ontology will this change affect?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    multivalued: true\n    alias: about\n    owner: OntologyChange\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: OntologyClass\n\n
"},{"location":"ontology_issue/OntologyClass/","title":"Class: OntologyClass","text":"

URI: oc:OntologyClass

erDiagram\nOntologyClass {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_issue/OntologyClass/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/OntologyClass/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ontology_issue/OntologyClass/#usages","title":"Usages","text":"used by used in type used OntologyIssue domains range OntologyClass OntologyProblem about range OntologyClass OntologyChange about range OntologyClass"},{"location":"ontology_issue/OntologyClass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/OntologyClass/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"ontology_issue/OntologyClass/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/OntologyClass/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyClass native oc:OntologyClass"},{"location":"ontology_issue/OntologyClass/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/OntologyClass/#direct","title":"Direct","text":"
name: OntologyClass\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: NamedEntity\n\n
"},{"location":"ontology_issue/OntologyClass/#induced","title":"Induced","text":"
name: OntologyClass\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: OntologyClass\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: OntologyClass\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_issue/OntologyIssue/","title":"Class: OntologyIssue","text":"

URI: oc:OntologyIssue

erDiagram\nOntologyIssue {\n    string title  \n    string summary  \n    string status  \n}\nOntologyChange {\n    string description  \n    ChangeType category  \n}\nOntologyClass {\n    string id  \n    string label  \n}\nOntologyProblem {\n    string description  \n    string severity  \n    ProblemType category  \n}\n\nOntologyIssue ||--}o OntologyClass : \"domains\"\nOntologyIssue ||--}o OntologyProblem : \"problem_list\"\nOntologyIssue ||--}o OntologyChange : \"proposed_changes\"\nOntologyChange ||--}o OntologyClass : \"about\"\nOntologyProblem ||--}o OntologyClass : \"about\"\n\n
"},{"location":"ontology_issue/OntologyIssue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance title 0..1 String the title of the issue direct summary 0..1 String a high level summary direct status 0..1 String direct domains 0..* OntologyClass What part of the ontology does this pertain to direct problem_list 0..* OntologyProblem A list of problems stated at a high level direct proposed_changes 0..* OntologyChange What part of the ontology does this pertain to direct"},{"location":"ontology_issue/OntologyIssue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/OntologyIssue/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/OntologyIssue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyIssue native oc:OntologyIssue"},{"location":"ontology_issue/OntologyIssue/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/OntologyIssue/#direct","title":"Direct","text":"
name: OntologyIssue\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  title:\n    name: title\n    description: the title of the issue\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  summary:\n    name: summary\n    annotations:\n      prompt:\n        tag: prompt\n        value: a high level one or two line summary of the issue, e.g. \"the definition\n          of the class 'bone' is too vague\"\n    description: a high level summary\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  status:\n    name: status\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  domains:\n    name: domains\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of grouping terms in the ontology.\n    description: What part of the ontology does this pertain to.\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n  problem_list:\n    name: problem_list\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of problems each written as a simple statement.\n          For example \"T cell is classified in the wrong place\"\n    description: A list of problems stated at a high level\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: OntologyProblem\n  proposed_changes:\n    name: proposed_changes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of grouping terms in the ontology. Example\n          terms will be high level terms in the relevant ontology, e.g. \"skeletal\n          system\" for an anatomy ontology.\n    description: What part of the ontology does this pertain to.\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: OntologyChange\ntree_root: true\n\n
"},{"location":"ontology_issue/OntologyIssue/#induced","title":"Induced","text":"
name: OntologyIssue\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  title:\n    name: title\n    description: the title of the issue\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: title\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    - Publication\n    range: string\n  summary:\n    name: summary\n    annotations:\n      prompt:\n        tag: prompt\n        value: a high level one or two line summary of the issue, e.g. \"the definition\n          of the class 'bone' is too vague\"\n    description: a high level summary\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: summary\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    range: string\n  status:\n    name: status\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: status\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    range: string\n  domains:\n    name: domains\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of grouping terms in the ontology.\n    description: What part of the ontology does this pertain to.\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: domains\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    range: OntologyClass\n  problem_list:\n    name: problem_list\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of problems each written as a simple statement.\n          For example \"T cell is classified in the wrong place\"\n    description: A list of problems stated at a high level\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: problem_list\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    range: OntologyProblem\n  proposed_changes:\n    name: proposed_changes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of grouping terms in the ontology. Example\n          terms will be high level terms in the relevant ontology, e.g. \"skeletal\n          system\" for an anatomy ontology.\n    description: What part of the ontology does this pertain to.\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: proposed_changes\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    range: OntologyChange\ntree_root: true\n\n
"},{"location":"ontology_issue/OntologyProblem/","title":"Class: OntologyProblem","text":"

URI: oc:OntologyProblem

erDiagram\nOntologyProblem {\n    string description  \n    string severity  \n    ProblemType category  \n}\nOntologyClass {\n    string id  \n    string label  \n}\n\nOntologyProblem ||--}o OntologyClass : \"about\"\n\n
"},{"location":"ontology_issue/OntologyProblem/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/OntologyProblem/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance description 0..1 String A succinct description of the problem direct severity 0..1 String How severe is this problem? direct category 0..1 ProblemType What category does this problem fall into? direct about 0..* OntologyClass What terms in the ontology is this problem about? direct"},{"location":"ontology_issue/OntologyProblem/#usages","title":"Usages","text":"used by used in type used OntologyIssue problem_list range OntologyProblem"},{"location":"ontology_issue/OntologyProblem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/OntologyProblem/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/OntologyProblem/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyProblem native oc:OntologyProblem"},{"location":"ontology_issue/OntologyProblem/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/OntologyProblem/#direct","title":"Direct","text":"
name: OntologyProblem\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nattributes:\n  description:\n    name: description\n    description: A succinct description of the problem\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  severity:\n    name: severity\n    description: How severe is this problem?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  category:\n    name: category\n    description: What category does this problem fall into?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: ProblemType\n  about:\n    name: about\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of terms in the ontology that are problematic.\n    description: What terms in the ontology is this problem about?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n\n
"},{"location":"ontology_issue/OntologyProblem/#induced","title":"Induced","text":"
name: OntologyProblem\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nattributes:\n  description:\n    name: description\n    description: A succinct description of the problem\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: description\n    owner: OntologyProblem\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: string\n  severity:\n    name: severity\n    description: How severe is this problem?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: severity\n    owner: OntologyProblem\n    domain_of:\n    - OntologyProblem\n    range: string\n  category:\n    name: category\n    description: What category does this problem fall into?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: category\n    owner: OntologyProblem\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: ProblemType\n  about:\n    name: about\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of terms in the ontology that are problematic.\n    description: What terms in the ontology is this problem about?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: about\n    owner: OntologyProblem\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: OntologyClass\n\n
"},{"location":"ontology_issue/ProblemType/","title":"Enum: ProblemType","text":"

URI: ProblemType

"},{"location":"ontology_issue/ProblemType/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNKNOWN None TYPO None BAD_XREF None MISSING_DEFINITION None MISSING_PARENT None BAD_RELATIONSHIP None OTHER None"},{"location":"ontology_issue/ProblemType/#slots","title":"Slots","text":"Name Description category What category does this problem fall into?"},{"location":"ontology_issue/ProblemType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/ProblemType/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/ProblemType/#linkml-source","title":"LinkML Source","text":"
name: ProblemType\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\npermissible_values:\n  UNKNOWN:\n    text: UNKNOWN\n  TYPO:\n    text: TYPO\n  BAD_XREF:\n    text: BAD_XREF\n  MISSING_DEFINITION:\n    text: MISSING_DEFINITION\n  MISSING_PARENT:\n    text: MISSING_PARENT\n  BAD_RELATIONSHIP:\n    text: BAD_RELATIONSHIP\n  OTHER:\n    text: OTHER\n\n
"},{"location":"ontology_issue/Publication/","title":"Class: Publication","text":"

URI: oc:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"ontology_issue/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"ontology_issue/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"ontology_issue/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Publication/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Publication native oc:Publication"},{"location":"ontology_issue/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n\n
"},{"location":"ontology_issue/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    alias: title\n    owner: Publication\n    domain_of:\n    - OntologyIssue\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"ontology_issue/RelationshipType/","title":"Class: RelationshipType","text":"

URI: oc:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_issue/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ontology_issue/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"ontology_issue/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ontology_issue/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:RelationshipType native oc:RelationshipType"},{"location":"ontology_issue/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: NamedEntity\n\n
"},{"location":"ontology_issue/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_issue/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"ontology_issue/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/String/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: oc:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ontology_issue/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"ontology_issue/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:TextWithTriples native oc:TextWithTriples"},{"location":"ontology_issue/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_issue/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_issue/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"ontology_issue/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Time/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: oc:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ontology_issue/Triple/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"ontology_issue/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"ontology_issue/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Triple/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Triple native oc:Triple"},{"location":"ontology_issue/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"ontology_issue/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ontology_issue/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"ontology_issue/Uri/#comments","title":"Comments","text":""},{"location":"ontology_issue/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Uri/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"ontology_issue/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/about/","title":"Slot: about","text":"

URI: oc:about

"},{"location":"ontology_issue/about/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyProblem no OntologyChange no"},{"location":"ontology_issue/about/#properties","title":"Properties","text":""},{"location":"ontology_issue/about/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/about/#linkml-source","title":"LinkML Source","text":"
name: about\nalias: about\ndomain_of:\n- OntologyProblem\n- OntologyChange\nrange: string\n\n
"},{"location":"ontology_issue/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: oc:abstract

"},{"location":"ontology_issue/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_issue/abstract/#properties","title":"Properties","text":""},{"location":"ontology_issue/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/abstract/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_issue/category/","title":"Slot: category","text":"

URI: oc:category

"},{"location":"ontology_issue/category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyProblem no OntologyChange no"},{"location":"ontology_issue/category/#properties","title":"Properties","text":""},{"location":"ontology_issue/category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/category/#linkml-source","title":"LinkML Source","text":"
name: category\nalias: category\ndomain_of:\n- OntologyProblem\n- OntologyChange\nrange: string\n\n
"},{"location":"ontology_issue/combined_text/","title":"Slot: combined_text","text":"

URI: oc:combined_text

"},{"location":"ontology_issue/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_issue/combined_text/#properties","title":"Properties","text":""},{"location":"ontology_issue/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_issue/description/","title":"Slot: description","text":"

URI: oc:description

"},{"location":"ontology_issue/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyProblem no OntologyChange no"},{"location":"ontology_issue/description/#properties","title":"Properties","text":""},{"location":"ontology_issue/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/description/#linkml-source","title":"LinkML Source","text":"
name: description\nalias: description\ndomain_of:\n- OntologyProblem\n- OntologyChange\nrange: string\n\n
"},{"location":"ontology_issue/domains/","title":"Slot: domains","text":"

What part of the ontology does this pertain to.

URI: oc:domains

"},{"location":"ontology_issue/domains/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no"},{"location":"ontology_issue/domains/#properties","title":"Properties","text":""},{"location":"ontology_issue/domains/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/domains/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of grouping terms in the ontology."},{"location":"ontology_issue/domains/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/domains/#linkml-source","title":"LinkML Source","text":"
name: domains\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of grouping terms in the ontology.\ndescription: What part of the ontology does this pertain to.\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nmultivalued: true\nalias: domains\nowner: OntologyIssue\ndomain_of:\n- OntologyIssue\nrange: OntologyClass\n\n
"},{"location":"ontology_issue/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: oc:extracted_object

"},{"location":"ontology_issue/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/extracted_object/#properties","title":"Properties","text":""},{"location":"ontology_issue/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"ontology_issue/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: oc:full_text

"},{"location":"ontology_issue/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_issue/full_text/#properties","title":"Properties","text":""},{"location":"ontology_issue/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/full_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_issue/id/","title":"Slot: id","text":"

URI: oc:id

"},{"location":"ontology_issue/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no NamedEntity no RelationshipType no Publication no"},{"location":"ontology_issue/id/#properties","title":"Properties","text":""},{"location":"ontology_issue/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"ontology_issue/input_id/","title":"Slot: input_id","text":"

URI: oc:input_id

"},{"location":"ontology_issue/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/input_id/#properties","title":"Properties","text":""},{"location":"ontology_issue/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/input_id/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_issue/input_text/","title":"Slot: input_text","text":"

URI: oc:input_text

"},{"location":"ontology_issue/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/input_text/#properties","title":"Properties","text":""},{"location":"ontology_issue/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/input_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_issue/input_title/","title":"Slot: input_title","text":"

URI: oc:input_title

"},{"location":"ontology_issue/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/input_title/#properties","title":"Properties","text":""},{"location":"ontology_issue/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/input_title/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_issue/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"ontology_issue/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no NamedEntity no RelationshipType no"},{"location":"ontology_issue/label/#properties","title":"Properties","text":""},{"location":"ontology_issue/label/#aliases","title":"Aliases","text":""},{"location":"ontology_issue/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"ontology_issue/label/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"ontology_issue/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: oc:named_entities

"},{"location":"ontology_issue/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/named_entities/#properties","title":"Properties","text":""},{"location":"ontology_issue/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ontology_issue/object/","title":"Slot: object","text":"

URI: oc:object

"},{"location":"ontology_issue/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/object/#properties","title":"Properties","text":""},{"location":"ontology_issue/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/object/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_issue/object_id/","title":"Slot: object_id","text":"

URI: oc:object_id

"},{"location":"ontology_issue/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_issue/object_id/#properties","title":"Properties","text":""},{"location":"ontology_issue/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/object_id/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_issue/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: oc:object_qualifier

"},{"location":"ontology_issue/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/object_qualifier/#properties","title":"Properties","text":""},{"location":"ontology_issue/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_issue/object_text/","title":"Slot: object_text","text":"

URI: oc:object_text

"},{"location":"ontology_issue/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_issue/object_text/#properties","title":"Properties","text":""},{"location":"ontology_issue/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/object_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_issue/ontology-issue/","title":"ontology-issue","text":"

A data model for representing the contents of a GitHub issue on an ontology tracker

URI: https://w3id.org/ontogpt/ontology_issue

"},{"location":"ontology_issue/predicate/","title":"Slot: predicate","text":"

URI: oc:predicate

"},{"location":"ontology_issue/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/predicate/#properties","title":"Properties","text":""},{"location":"ontology_issue/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/predicate/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"ontology_issue/problem_list/","title":"Slot: problem_list","text":"

A list of problems stated at a high level

URI: oc:problem_list

"},{"location":"ontology_issue/problem_list/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no"},{"location":"ontology_issue/problem_list/#properties","title":"Properties","text":""},{"location":"ontology_issue/problem_list/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/problem_list/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\""},{"location":"ontology_issue/problem_list/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/problem_list/#linkml-source","title":"LinkML Source","text":"
name: problem_list\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of problems each written as a simple statement.\n      For example \"T cell is classified in the wrong place\"\ndescription: A list of problems stated at a high level\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nmultivalued: true\nalias: problem_list\nowner: OntologyIssue\ndomain_of:\n- OntologyIssue\nrange: OntologyProblem\n\n
"},{"location":"ontology_issue/prompt/","title":"Slot: prompt","text":"

URI: oc:prompt

"},{"location":"ontology_issue/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/prompt/#properties","title":"Properties","text":""},{"location":"ontology_issue/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/prompt/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_issue/proposed_changes/","title":"Slot: proposed_changes","text":"

What part of the ontology does this pertain to.

URI: oc:proposed_changes

"},{"location":"ontology_issue/proposed_changes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no"},{"location":"ontology_issue/proposed_changes/#properties","title":"Properties","text":""},{"location":"ontology_issue/proposed_changes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/proposed_changes/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology."},{"location":"ontology_issue/proposed_changes/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/proposed_changes/#linkml-source","title":"LinkML Source","text":"
name: proposed_changes\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of grouping terms in the ontology. Example terms\n      will be high level terms in the relevant ontology, e.g. \"skeletal system\" for\n      an anatomy ontology.\ndescription: What part of the ontology does this pertain to.\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nmultivalued: true\nalias: proposed_changes\nowner: OntologyIssue\ndomain_of:\n- OntologyIssue\nrange: OntologyChange\n\n
"},{"location":"ontology_issue/publication/","title":"Slot: publication","text":"

URI: oc:publication

"},{"location":"ontology_issue/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ontology_issue/publication/#properties","title":"Properties","text":""},{"location":"ontology_issue/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"ontology_issue/publication/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"ontology_issue/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: oc:qualifier

"},{"location":"ontology_issue/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/qualifier/#properties","title":"Properties","text":""},{"location":"ontology_issue/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"ontology_issue/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: oc:raw_completion_output

"},{"location":"ontology_issue/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/raw_completion_output/#properties","title":"Properties","text":""},{"location":"ontology_issue/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_issue/severity/","title":"Slot: severity","text":"

How severe is this problem?

URI: oc:severity

"},{"location":"ontology_issue/severity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyProblem no"},{"location":"ontology_issue/severity/#properties","title":"Properties","text":""},{"location":"ontology_issue/severity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/severity/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/severity/#linkml-source","title":"LinkML Source","text":"
name: severity\ndescription: How severe is this problem?\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: severity\nowner: OntologyProblem\ndomain_of:\n- OntologyProblem\nrange: string\n\n
"},{"location":"ontology_issue/status/","title":"Slot: status","text":"

URI: oc:status

"},{"location":"ontology_issue/status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no"},{"location":"ontology_issue/status/#properties","title":"Properties","text":""},{"location":"ontology_issue/status/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/status/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/status/#linkml-source","title":"LinkML Source","text":"
name: status\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: status\nowner: OntologyIssue\ndomain_of:\n- OntologyIssue\nrange: string\n\n
"},{"location":"ontology_issue/subject/","title":"Slot: subject","text":"

URI: oc:subject

"},{"location":"ontology_issue/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/subject/#properties","title":"Properties","text":""},{"location":"ontology_issue/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/subject/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_issue/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: oc:subject_qualifier

"},{"location":"ontology_issue/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/subject_qualifier/#properties","title":"Properties","text":""},{"location":"ontology_issue/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_issue/subject_text/","title":"Slot: subject_text","text":"

URI: oc:subject_text

"},{"location":"ontology_issue/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_issue/subject_text/#properties","title":"Properties","text":""},{"location":"ontology_issue/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_issue/summary/","title":"Slot: summary","text":"

a high level summary

URI: oc:summary

"},{"location":"ontology_issue/summary/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no"},{"location":"ontology_issue/summary/#properties","title":"Properties","text":""},{"location":"ontology_issue/summary/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/summary/#annotations","title":"Annotations","text":"property value prompt a high level one or two line summary of the issue, e.g. \"the definition of the class 'bone' is too vague\""},{"location":"ontology_issue/summary/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/summary/#linkml-source","title":"LinkML Source","text":"
name: summary\nannotations:\n  prompt:\n    tag: prompt\n    value: a high level one or two line summary of the issue, e.g. \"the definition\n      of the class 'bone' is too vague\"\ndescription: a high level summary\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: summary\nowner: OntologyIssue\ndomain_of:\n- OntologyIssue\nrange: string\n\n
"},{"location":"ontology_issue/title/","title":"Slot: title","text":"

URI: oc:title

"},{"location":"ontology_issue/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no Publication no"},{"location":"ontology_issue/title/#properties","title":"Properties","text":""},{"location":"ontology_issue/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/title/#linkml-source","title":"LinkML Source","text":"
name: title\nalias: title\ndomain_of:\n- OntologyIssue\n- Publication\nrange: string\n\n
"},{"location":"ontology_issue/triples/","title":"Slot: triples","text":"

URI: oc:triples

"},{"location":"ontology_issue/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ontology_issue/triples/#properties","title":"Properties","text":""},{"location":"ontology_issue/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/triples/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"phenotype/","title":"EQ Template","text":"

A template for Computational Phenotypes

URI: http://w3id.org/ontogpt/eq

Name: eq-template

"},{"location":"phenotype/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nTrait {\n\n}\nChemicalEntity {\n    string id  \n    string label  \n}\nAnatomicalEntity {\n    string id  \n    string label  \n}\nQuality {\n    string id  \n    string label  \n}\n\nTrait ||--|o Quality : \"quality\"\nTrait ||--|o AnatomicalEntity : \"anatomical_entity\"\nTrait ||--|o ChemicalEntity : \"chemical_entity\"\n\n
"},{"location":"phenotype/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None AnatomicalEntity None ChemicalEntity None Quality None RelationshipType None Publication None TextWithTriples None Trait None"},{"location":"phenotype/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication anatomical_entity The anatomical location that the chemical entity is measured in chemical_entity The chemical entity that is being measured combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e quality The property being measured, or changes in this property, for example, amount... raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"phenotype/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"phenotype/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"phenotype/#subsets","title":"Subsets","text":"Subset Description"},{"location":"phenotype/AnatomicalEntity/","title":"Class: AnatomicalEntity","text":"

URI: phenotype:AnatomicalEntity

erDiagram\nAnatomicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"phenotype/AnatomicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/AnatomicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"phenotype/AnatomicalEntity/#usages","title":"Usages","text":"used by used in type used Trait anatomical_entity range AnatomicalEntity"},{"location":"phenotype/AnatomicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/AnatomicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"phenotype/AnatomicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uberon"},{"location":"phenotype/AnatomicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/AnatomicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:AnatomicalEntity native phenotype:AnatomicalEntity"},{"location":"phenotype/AnatomicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/AnatomicalEntity/#direct","title":"Direct","text":"
name: AnatomicalEntity\nid_prefixes:\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\n\n
"},{"location":"phenotype/AnatomicalEntity/#induced","title":"Induced","text":"
name: AnatomicalEntity\nid_prefixes:\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: AnatomicalEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: AnatomicalEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"phenotype/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: phenotype:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"phenotype/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"phenotype/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:AnnotatorResult native phenotype:AnnotatorResult"},{"location":"phenotype/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n\n
"},{"location":"phenotype/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"phenotype/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"phenotype/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"phenotype/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"phenotype/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Any/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native phenotype:Any"},{"location":"phenotype/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/eq\nclass_uri: linkml:Any\n\n
"},{"location":"phenotype/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/eq\nclass_uri: linkml:Any\n\n
"},{"location":"phenotype/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"phenotype/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/ChemicalEntity/","title":"Class: ChemicalEntity","text":"

URI: phenotype:ChemicalEntity

erDiagram\nChemicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"phenotype/ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"phenotype/ChemicalEntity/#usages","title":"Usages","text":"used by used in type used Trait chemical_entity range ChemicalEntity"},{"location":"phenotype/ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"phenotype/ChemicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"phenotype/ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:ChemicalEntity native phenotype:ChemicalEntity"},{"location":"phenotype/ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\n\n
"},{"location":"phenotype/ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"phenotype/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: phenotype:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"phenotype/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"phenotype/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:CompoundExpression native phenotype:CompoundExpression"},{"location":"phenotype/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/eq\nabstract: true\n\n
"},{"location":"phenotype/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/eq\nabstract: true\n\n
"},{"location":"phenotype/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"phenotype/Curie/#comments","title":"Comments","text":""},{"location":"phenotype/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Curie/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"phenotype/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Date/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"phenotype/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"phenotype/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"phenotype/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"phenotype/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Double/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: phenotype:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"phenotype/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"phenotype/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:ExtractionResult native phenotype:ExtractionResult"},{"location":"phenotype/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"phenotype/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"phenotype/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"phenotype/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Float/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"phenotype/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Integer/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/NamedEntity/","title":"Class: NamedEntity","text":"

URI: phenotype:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"phenotype/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"phenotype/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"phenotype/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:NamedEntity native phenotype:NamedEntity"},{"location":"phenotype/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/eq\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"phenotype/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/eq\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"phenotype/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"phenotype/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"phenotype/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"phenotype/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"phenotype/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"phenotype/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"phenotype/Objectidentifier/#comments","title":"Comments","text":""},{"location":"phenotype/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Publication/","title":"Class: Publication","text":"

URI: phenotype:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"phenotype/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"phenotype/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"phenotype/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Publication/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:Publication native phenotype:Publication"},{"location":"phenotype/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/eq\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n\n
"},{"location":"phenotype/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/eq\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"phenotype/Quality/","title":"Class: Quality","text":"

URI: phenotype:Quality

erDiagram\nQuality {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"phenotype/Quality/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/Quality/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"phenotype/Quality/#usages","title":"Usages","text":"used by used in type used Trait quality range Quality"},{"location":"phenotype/Quality/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Quality/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"phenotype/Quality/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:pato"},{"location":"phenotype/Quality/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Quality/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:Quality native phenotype:Quality"},{"location":"phenotype/Quality/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/Quality/#direct","title":"Direct","text":"
name: Quality\nid_prefixes:\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:pato\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\n\n
"},{"location":"phenotype/Quality/#induced","title":"Induced","text":"
name: Quality\nid_prefixes:\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:pato\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Quality\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Quality\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"phenotype/RelationshipType/","title":"Class: RelationshipType","text":"

URI: phenotype:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"phenotype/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"phenotype/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"phenotype/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"phenotype/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:RelationshipType native phenotype:RelationshipType"},{"location":"phenotype/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\n\n
"},{"location":"phenotype/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"phenotype/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"phenotype/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/String/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: phenotype:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"phenotype/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"phenotype/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:TextWithTriples native phenotype:TextWithTriples"},{"location":"phenotype/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"phenotype/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"phenotype/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"phenotype/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Time/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Trait/","title":"Class: Trait","text":"

URI: phenotype:Trait

erDiagram\nTrait {\n\n}\nChemicalEntity {\n    string id  \n    string label  \n}\nAnatomicalEntity {\n    string id  \n    string label  \n}\nQuality {\n    string id  \n    string label  \n}\n\nTrait ||--|o Quality : \"quality\"\nTrait ||--|o AnatomicalEntity : \"anatomical_entity\"\nTrait ||--|o ChemicalEntity : \"chemical_entity\"\n\n
"},{"location":"phenotype/Trait/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance quality 0..1 Quality The property being measured, or changes in this property, for example, amount... direct anatomical_entity 0..1 AnatomicalEntity The anatomical location that the chemical entity is measured in direct chemical_entity 0..1 ChemicalEntity The chemical entity that is being measured direct"},{"location":"phenotype/Trait/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Trait/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Trait/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:Trait native phenotype:Trait"},{"location":"phenotype/Trait/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/Trait/#direct","title":"Direct","text":"
name: Trait\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  quality:\n    name: quality\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: amount, level, increased amount, decreased concentration\n    description: The property being measured, or changes in this property, for example,\n      amount, level, increased amount, decreased concentration\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: Quality\n  anatomical_entity:\n    name: anatomical_entity\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: liver, heart, brain, finger\n    description: The anatomical location that the chemical entity is measured in\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: AnatomicalEntity\n  chemical_entity:\n    name: chemical_entity\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: lysine, metabolite\n    description: The chemical entity that is being measured\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: ChemicalEntity\ntree_root: true\n\n
"},{"location":"phenotype/Trait/#induced","title":"Induced","text":"
name: Trait\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  quality:\n    name: quality\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: amount, level, increased amount, decreased concentration\n    description: The property being measured, or changes in this property, for example,\n      amount, level, increased amount, decreased concentration\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: quality\n    owner: Trait\n    domain_of:\n    - Trait\n    range: Quality\n  anatomical_entity:\n    name: anatomical_entity\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: liver, heart, brain, finger\n    description: The anatomical location that the chemical entity is measured in\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: anatomical_entity\n    owner: Trait\n    domain_of:\n    - Trait\n    range: AnatomicalEntity\n  chemical_entity:\n    name: chemical_entity\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: lysine, metabolite\n    description: The chemical entity that is being measured\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: chemical_entity\n    owner: Trait\n    domain_of:\n    - Trait\n    range: ChemicalEntity\ntree_root: true\n\n
"},{"location":"phenotype/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: phenotype:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"phenotype/Triple/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"phenotype/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"phenotype/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Triple/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:Triple native phenotype:Triple"},{"location":"phenotype/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"phenotype/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"phenotype/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"phenotype/Uri/#comments","title":"Comments","text":""},{"location":"phenotype/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Uri/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"phenotype/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: phenotype:abstract

"},{"location":"phenotype/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"phenotype/abstract/#properties","title":"Properties","text":""},{"location":"phenotype/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/abstract/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"phenotype/anatomical_entity/","title":"Slot: anatomical_entity","text":"

The anatomical location that the chemical entity is measured in

URI: phenotype:anatomical_entity

"},{"location":"phenotype/anatomical_entity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Trait no"},{"location":"phenotype/anatomical_entity/#properties","title":"Properties","text":""},{"location":"phenotype/anatomical_entity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/anatomical_entity/#annotations","title":"Annotations","text":"property value prompt.example liver, heart, brain, finger"},{"location":"phenotype/anatomical_entity/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/anatomical_entity/#linkml-source","title":"LinkML Source","text":"
name: anatomical_entity\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: liver, heart, brain, finger\ndescription: The anatomical location that the chemical entity is measured in\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: anatomical_entity\nowner: Trait\ndomain_of:\n- Trait\nrange: AnatomicalEntity\n\n
"},{"location":"phenotype/chemical_entity/","title":"Slot: chemical_entity","text":"

The chemical entity that is being measured

URI: phenotype:chemical_entity

"},{"location":"phenotype/chemical_entity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Trait no"},{"location":"phenotype/chemical_entity/#properties","title":"Properties","text":""},{"location":"phenotype/chemical_entity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/chemical_entity/#annotations","title":"Annotations","text":"property value prompt.example lysine, metabolite"},{"location":"phenotype/chemical_entity/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/chemical_entity/#linkml-source","title":"LinkML Source","text":"
name: chemical_entity\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: lysine, metabolite\ndescription: The chemical entity that is being measured\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: chemical_entity\nowner: Trait\ndomain_of:\n- Trait\nrange: ChemicalEntity\n\n
"},{"location":"phenotype/combined_text/","title":"Slot: combined_text","text":"

URI: phenotype:combined_text

"},{"location":"phenotype/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"phenotype/combined_text/#properties","title":"Properties","text":""},{"location":"phenotype/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"phenotype/eq-template/","title":"eq-template","text":"

A template for Computational Phenotypes

URI: http://w3id.org/ontogpt/eq

"},{"location":"phenotype/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: phenotype:extracted_object

"},{"location":"phenotype/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/extracted_object/#properties","title":"Properties","text":""},{"location":"phenotype/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"phenotype/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: phenotype:full_text

"},{"location":"phenotype/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"phenotype/full_text/#properties","title":"Properties","text":""},{"location":"phenotype/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/full_text/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"phenotype/id/","title":"Slot: id","text":"

URI: phenotype:id

"},{"location":"phenotype/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Quality no ChemicalEntity no AnatomicalEntity no NamedEntity no RelationshipType no Publication no"},{"location":"phenotype/id/#properties","title":"Properties","text":""},{"location":"phenotype/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"phenotype/input_id/","title":"Slot: input_id","text":"

URI: phenotype:input_id

"},{"location":"phenotype/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/input_id/#properties","title":"Properties","text":""},{"location":"phenotype/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/input_id/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"phenotype/input_text/","title":"Slot: input_text","text":"

URI: phenotype:input_text

"},{"location":"phenotype/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/input_text/#properties","title":"Properties","text":""},{"location":"phenotype/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/input_text/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"phenotype/input_title/","title":"Slot: input_title","text":"

URI: phenotype:input_title

"},{"location":"phenotype/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/input_title/#properties","title":"Properties","text":""},{"location":"phenotype/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/input_title/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"phenotype/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"phenotype/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Quality no ChemicalEntity no AnatomicalEntity no NamedEntity no RelationshipType no"},{"location":"phenotype/label/#properties","title":"Properties","text":""},{"location":"phenotype/label/#aliases","title":"Aliases","text":""},{"location":"phenotype/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"phenotype/label/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/eq\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"phenotype/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: phenotype:named_entities

"},{"location":"phenotype/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/named_entities/#properties","title":"Properties","text":""},{"location":"phenotype/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"phenotype/object/","title":"Slot: object","text":"

URI: phenotype:object

"},{"location":"phenotype/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/object/#properties","title":"Properties","text":""},{"location":"phenotype/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/object/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"phenotype/object_id/","title":"Slot: object_id","text":"

URI: phenotype:object_id

"},{"location":"phenotype/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"phenotype/object_id/#properties","title":"Properties","text":""},{"location":"phenotype/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/object_id/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"phenotype/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: phenotype:object_qualifier

"},{"location":"phenotype/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/object_qualifier/#properties","title":"Properties","text":""},{"location":"phenotype/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"phenotype/object_text/","title":"Slot: object_text","text":"

URI: phenotype:object_text

"},{"location":"phenotype/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"phenotype/object_text/#properties","title":"Properties","text":""},{"location":"phenotype/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/object_text/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"phenotype/predicate/","title":"Slot: predicate","text":"

URI: phenotype:predicate

"},{"location":"phenotype/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/predicate/#properties","title":"Properties","text":""},{"location":"phenotype/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/predicate/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"phenotype/prompt/","title":"Slot: prompt","text":"

URI: phenotype:prompt

"},{"location":"phenotype/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/prompt/#properties","title":"Properties","text":""},{"location":"phenotype/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/prompt/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"phenotype/publication/","title":"Slot: publication","text":"

URI: phenotype:publication

"},{"location":"phenotype/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"phenotype/publication/#properties","title":"Properties","text":""},{"location":"phenotype/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"phenotype/publication/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"phenotype/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: phenotype:qualifier

"},{"location":"phenotype/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/qualifier/#properties","title":"Properties","text":""},{"location":"phenotype/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"phenotype/quality/","title":"Slot: quality","text":"

The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration

URI: phenotype:quality

"},{"location":"phenotype/quality/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Trait no"},{"location":"phenotype/quality/#properties","title":"Properties","text":""},{"location":"phenotype/quality/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/quality/#annotations","title":"Annotations","text":"property value prompt.example amount, level, increased amount, decreased concentration"},{"location":"phenotype/quality/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/quality/#linkml-source","title":"LinkML Source","text":"
name: quality\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: amount, level, increased amount, decreased concentration\ndescription: The property being measured, or changes in this property, for example,\n  amount, level, increased amount, decreased concentration\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: quality\nowner: Trait\ndomain_of:\n- Trait\nrange: Quality\n\n
"},{"location":"phenotype/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: phenotype:raw_completion_output

"},{"location":"phenotype/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/raw_completion_output/#properties","title":"Properties","text":""},{"location":"phenotype/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"phenotype/subject/","title":"Slot: subject","text":"

URI: phenotype:subject

"},{"location":"phenotype/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/subject/#properties","title":"Properties","text":""},{"location":"phenotype/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/subject/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"phenotype/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: phenotype:subject_qualifier

"},{"location":"phenotype/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/subject_qualifier/#properties","title":"Properties","text":""},{"location":"phenotype/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"phenotype/subject_text/","title":"Slot: subject_text","text":"

URI: phenotype:subject_text

"},{"location":"phenotype/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"phenotype/subject_text/#properties","title":"Properties","text":""},{"location":"phenotype/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"phenotype/title/","title":"Slot: title","text":"

The title of the publication

URI: phenotype:title

"},{"location":"phenotype/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"phenotype/title/#properties","title":"Properties","text":""},{"location":"phenotype/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/title/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"phenotype/triples/","title":"Slot: triples","text":"

URI: phenotype:triples

"},{"location":"phenotype/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"phenotype/triples/#properties","title":"Properties","text":""},{"location":"phenotype/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/triples/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"reaction/","title":"reaction Template","text":"

A template for reactions

URI: https://w3id.org/ontogpt/reaction

Name: reaction-template

"},{"location":"reaction/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nReaction {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nGeneToReaction {\n\n}\nReactionDocument {\n\n}\nGeneReactionPairing {\n\n}\nReactionGrouping {\n    string id  \n    string label  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nEvidence {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nOrganism {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nReaction ||--|o ReactionGrouping : \"subclass_of\"\nReaction ||--}o ChemicalEntity : \"left_side\"\nReaction ||--}o ChemicalEntity : \"right_side\"\nGeneToReaction ||--|o Gene : \"gene\"\nGeneToReaction ||--}o Reaction : \"reactions\"\nGeneToReaction ||--|o Organism : \"organism\"\nReactionDocument ||--}o Gene : \"genes\"\nReactionDocument ||--}o Reaction : \"reactions\"\nReactionDocument ||--}o GeneReactionPairing : \"gene_reaction_pairings\"\nReactionDocument ||--|o Organism : \"organism\"\nReactionDocument ||--}o Evidence : \"has_evidence\"\nGeneReactionPairing ||--|o Gene : \"gene\"\nGeneReactionPairing ||--|o Reaction : \"reaction\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"reaction/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None GeneReactionPairing None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text GeneToReaction None NamedEntity None ChemicalEntity None Evidence None Gene None Organism None Reaction None ReactionGrouping None RelationshipType None Publication None ReactionDocument None TextWithTriples None"},{"location":"reaction/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text description a textual description of the reaction extracted_object The complex objects extracted from the text full_text The full text of the publication gene name of the gene that catalyzes the reaction gene_reaction_pairings semicolon separated list of gene to reaction pairings genes semicolon separated list of genes that catalyzes the mentioned reactions has_evidence evidence for the reaction id A unique identifier for the named entity input_id input_text input_title label the name of the reaction left_side semicolon separated list of chemical entities on the left side named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text organism predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output reaction equation describing the reaction (e reactions semicolon separated list of reaction equations (e right_side semicolon separated list of chemical entities on the right side subclass_of the category to which this biological process belongs subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text synonyms alternative names of the reaction title The title of the publication triples"},{"location":"reaction/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"reaction/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"reaction/#subsets","title":"Subsets","text":"Subset Description"},{"location":"reaction/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: reaction:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"reaction/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"reaction/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"reaction/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:AnnotatorResult native reaction:AnnotatorResult"},{"location":"reaction/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n\n
"},{"location":"reaction/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"reaction/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"reaction/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"reaction/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"reaction/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Any/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native reaction:Any"},{"location":"reaction/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/reaction\nclass_uri: linkml:Any\n\n
"},{"location":"reaction/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/reaction\nclass_uri: linkml:Any\n\n
"},{"location":"reaction/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"reaction/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"reaction/ChemicalEntity/","title":"Class: ChemicalEntity","text":"

URI: reaction:ChemicalEntity

erDiagram\nChemicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"reaction/ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/ChemicalEntity/#usages","title":"Usages","text":"used by used in type used Reaction left_side range ChemicalEntity Reaction right_side range ChemicalEntity"},{"location":"reaction/ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/ChemicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"reaction/ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"reaction/ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:ChemicalEntity native reaction:ChemicalEntity"},{"location":"reaction/ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalEntity\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: reaction:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"reaction/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"reaction/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"reaction/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"reaction/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:CompoundExpression native reaction:CompoundExpression"},{"location":"reaction/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/reaction\nabstract: true\n\n
"},{"location":"reaction/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/reaction\nabstract: true\n\n
"},{"location":"reaction/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"reaction/Curie/#comments","title":"Comments","text":""},{"location":"reaction/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Curie/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"reaction/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Date/#schema-source","title":"Schema Source","text":""},{"location":"reaction/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"reaction/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"reaction/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"reaction/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"reaction/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Double/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Evidence/","title":"Class: Evidence","text":"

URI: reaction:Evidence

erDiagram\nEvidence {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/Evidence/#inheritance","title":"Inheritance","text":""},{"location":"reaction/Evidence/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/Evidence/#usages","title":"Usages","text":"used by used in type used ReactionDocument has_evidence range Evidence"},{"location":"reaction/Evidence/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Evidence/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/Evidence/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms"},{"location":"reaction/Evidence/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Evidence/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Evidence native reaction:Evidence"},{"location":"reaction/Evidence/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Evidence/#direct","title":"Direct","text":"
name: Evidence\nid_prefixes:\n- OBI\n- ECO\n- MS\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/Evidence/#induced","title":"Induced","text":"
name: Evidence\nid_prefixes:\n- OBI\n- ECO\n- MS\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Evidence\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Evidence\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: reaction:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"reaction/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"reaction/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"reaction/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:ExtractionResult native reaction:ExtractionResult"},{"location":"reaction/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"reaction/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"reaction/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"reaction/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Float/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Gene/","title":"Class: Gene","text":"

URI: reaction:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/Gene/#inheritance","title":"Inheritance","text":""},{"location":"reaction/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/Gene/#usages","title":"Usages","text":"used by used in type used GeneToReaction gene range Gene ReactionDocument genes range Gene GeneReactionPairing gene range Gene"},{"location":"reaction/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, bioportal:hgnc-nr, bioportal:pr"},{"location":"reaction/Gene/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Gene native reaction:Gene"},{"location":"reaction/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr, bioportal:pr\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr, bioportal:pr\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/GeneReactionPairing/","title":"Class: GeneReactionPairing","text":"

URI: reaction:GeneReactionPairing

erDiagram\nGeneReactionPairing {\n\n}\nReaction {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nReactionGrouping {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneReactionPairing ||--|o Gene : \"gene\"\nGeneReactionPairing ||--|o Reaction : \"reaction\"\nReaction ||--|o ReactionGrouping : \"subclass_of\"\nReaction ||--}o ChemicalEntity : \"left_side\"\nReaction ||--}o ChemicalEntity : \"right_side\"\n\n
"},{"location":"reaction/GeneReactionPairing/#inheritance","title":"Inheritance","text":""},{"location":"reaction/GeneReactionPairing/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene name of the gene that catalyzes the reaction direct reaction 0..1 Reaction equation describing the reaction (e direct"},{"location":"reaction/GeneReactionPairing/#usages","title":"Usages","text":"used by used in type used ReactionDocument gene_reaction_pairings range GeneReactionPairing"},{"location":"reaction/GeneReactionPairing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/GeneReactionPairing/#schema-source","title":"Schema Source","text":""},{"location":"reaction/GeneReactionPairing/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:GeneReactionPairing native reaction:GeneReactionPairing"},{"location":"reaction/GeneReactionPairing/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/GeneReactionPairing/#direct","title":"Direct","text":"
name: GeneReactionPairing\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    description: name of the gene that catalyzes the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    range: Gene\n  reaction:\n    name: reaction\n    description: equation describing the reaction (e.g. A+B = C+D) catalyzed by the\n      gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: Reaction\n\n
"},{"location":"reaction/GeneReactionPairing/#induced","title":"Induced","text":"
name: GeneReactionPairing\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    description: name of the gene that catalyzes the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    alias: gene\n    owner: GeneReactionPairing\n    domain_of:\n    - GeneToReaction\n    - GeneReactionPairing\n    range: Gene\n  reaction:\n    name: reaction\n    description: equation describing the reaction (e.g. A+B = C+D) catalyzed by the\n      gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: reaction\n    owner: GeneReactionPairing\n    domain_of:\n    - GeneReactionPairing\n    range: Reaction\n\n
"},{"location":"reaction/GeneToReaction/","title":"Class: GeneToReaction","text":"

URI: reaction:GeneToReaction

erDiagram\nGeneToReaction {\n\n}\nOrganism {\n    string id  \n    string label  \n}\nReaction {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nReactionGrouping {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneToReaction ||--|o Gene : \"gene\"\nGeneToReaction ||--}o Reaction : \"reactions\"\nGeneToReaction ||--|o Organism : \"organism\"\nReaction ||--|o ReactionGrouping : \"subclass_of\"\nReaction ||--}o ChemicalEntity : \"left_side\"\nReaction ||--}o ChemicalEntity : \"right_side\"\n\n
"},{"location":"reaction/GeneToReaction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene name of the gene that catalyzes the reaction direct reactions 0..* Reaction semicolon separated list of reaction equations (e direct organism 0..1 Organism direct"},{"location":"reaction/GeneToReaction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/GeneToReaction/#schema-source","title":"Schema Source","text":""},{"location":"reaction/GeneToReaction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:GeneToReaction native reaction:GeneToReaction"},{"location":"reaction/GeneToReaction/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/GeneToReaction/#direct","title":"Direct","text":"
name: GeneToReaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  gene:\n    name: gene\n    description: name of the gene that catalyzes the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: Gene\n  reactions:\n    name: reactions\n    description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed\n      by the gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: Reaction\n    inlined: true\n  organism:\n    name: organism\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: Organism\n\n
"},{"location":"reaction/GeneToReaction/#induced","title":"Induced","text":"
name: GeneToReaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  gene:\n    name: gene\n    description: name of the gene that catalyzes the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: gene\n    owner: GeneToReaction\n    domain_of:\n    - GeneToReaction\n    - GeneReactionPairing\n    range: Gene\n  reactions:\n    name: reactions\n    description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed\n      by the gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: reactions\n    owner: GeneToReaction\n    domain_of:\n    - GeneToReaction\n    - ReactionDocument\n    range: Reaction\n    inlined: true\n  organism:\n    name: organism\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: organism\n    owner: GeneToReaction\n    domain_of:\n    - GeneToReaction\n    - ReactionDocument\n    range: Organism\n\n
"},{"location":"reaction/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"reaction/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Integer/#schema-source","title":"Schema Source","text":""},{"location":"reaction/NamedEntity/","title":"Class: NamedEntity","text":"

URI: reaction:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"reaction/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"reaction/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"reaction/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"reaction/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:NamedEntity native reaction:NamedEntity"},{"location":"reaction/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/reaction\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"reaction/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/reaction\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"reaction/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"reaction/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"reaction/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"reaction/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"reaction/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"reaction/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"reaction/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"reaction/Objectidentifier/#comments","title":"Comments","text":""},{"location":"reaction/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Organism/","title":"Class: Organism","text":"

URI: reaction:Organism

erDiagram\nOrganism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/Organism/#inheritance","title":"Inheritance","text":""},{"location":"reaction/Organism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/Organism/#usages","title":"Usages","text":"used by used in type used GeneToReaction organism range Organism ReactionDocument organism range Organism"},{"location":"reaction/Organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Organism/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/Organism/#annotations","title":"Annotations","text":"property value annotators gilda:, sqlite:obo:ncbitaxon"},{"location":"reaction/Organism/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Organism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Organism native reaction:Organism"},{"location":"reaction/Organism/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Organism/#direct","title":"Direct","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/Organism/#induced","title":"Induced","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Organism\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/Publication/","title":"Class: Publication","text":"

URI: reaction:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"reaction/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"reaction/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"reaction/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Publication/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Publication native reaction:Publication"},{"location":"reaction/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/reaction\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n\n
"},{"location":"reaction/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/reaction\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"reaction/Reaction/","title":"Class: Reaction","text":"

URI: reaction:Reaction

erDiagram\nReaction {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nReactionGrouping {\n    string id  \n    string label  \n}\n\nReaction ||--|o ReactionGrouping : \"subclass_of\"\nReaction ||--}o ChemicalEntity : \"left_side\"\nReaction ||--}o ChemicalEntity : \"right_side\"\n\n
"},{"location":"reaction/Reaction/#inheritance","title":"Inheritance","text":""},{"location":"reaction/Reaction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 0..1 String the name of the reaction direct description 0..1 String a textual description of the reaction direct synonyms 0..* String alternative names of the reaction direct subclass_of 0..1 ReactionGrouping the category to which this biological process belongs direct left_side 0..* ChemicalEntity semicolon separated list of chemical entities on the left side direct right_side 0..* ChemicalEntity semicolon separated list of chemical entities on the right side direct id 1..1 String A unique identifier for the named entity NamedEntity"},{"location":"reaction/Reaction/#usages","title":"Usages","text":"used by used in type used GeneToReaction reactions range Reaction ReactionDocument reactions range Reaction GeneReactionPairing reaction range Reaction"},{"location":"reaction/Reaction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Reaction/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Reaction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Reaction native reaction:Reaction"},{"location":"reaction/Reaction/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Reaction/#direct","title":"Direct","text":"
name: Reaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  description:\n    name: description\n    description: a textual description of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  synonyms:\n    name: synonyms\n    description: alternative names of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n  subclass_of:\n    name: subclass_of\n    description: the category to which this biological process belongs\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: ReactionGrouping\n  left_side:\n    name: left_side\n    description: semicolon separated list of chemical entities on the left side\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n  right_side:\n    name: right_side\n    description: semicolon separated list of chemical entities on the right side\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n\n
"},{"location":"reaction/Reaction/#induced","title":"Induced","text":"
name: Reaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: label\n    owner: Reaction\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n  description:\n    name: description\n    description: a textual description of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: description\n    owner: Reaction\n    domain_of:\n    - Reaction\n    range: string\n  synonyms:\n    name: synonyms\n    description: alternative names of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: Reaction\n    domain_of:\n    - Reaction\n    range: string\n  subclass_of:\n    name: subclass_of\n    description: the category to which this biological process belongs\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: subclass_of\n    owner: Reaction\n    domain_of:\n    - Reaction\n    range: ReactionGrouping\n  left_side:\n    name: left_side\n    description: semicolon separated list of chemical entities on the left side\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: left_side\n    owner: Reaction\n    domain_of:\n    - Reaction\n    range: ChemicalEntity\n  right_side:\n    name: right_side\n    description: semicolon separated list of chemical entities on the right side\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: right_side\n    owner: Reaction\n    domain_of:\n    - Reaction\n    range: ChemicalEntity\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Reaction\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n\n
"},{"location":"reaction/ReactionDocument/","title":"Class: ReactionDocument","text":"

URI: reaction:ReactionDocument

erDiagram\nReactionDocument {\n\n}\nEvidence {\n    string id  \n    string label  \n}\nOrganism {\n    string id  \n    string label  \n}\nGeneReactionPairing {\n\n}\nReaction {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nGene {\n    string id  \n    string label  \n}\n\nReactionDocument ||--}o Gene : \"genes\"\nReactionDocument ||--}o Reaction : \"reactions\"\nReactionDocument ||--}o GeneReactionPairing : \"gene_reaction_pairings\"\nReactionDocument ||--|o Organism : \"organism\"\nReactionDocument ||--}o Evidence : \"has_evidence\"\nGeneReactionPairing ||--|o Gene : \"gene\"\nGeneReactionPairing ||--|o Reaction : \"reaction\"\nReaction ||--|o ReactionGrouping : \"subclass_of\"\nReaction ||--}o ChemicalEntity : \"left_side\"\nReaction ||--}o ChemicalEntity : \"right_side\"\n\n
"},{"location":"reaction/ReactionDocument/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance genes 0..* Gene semicolon separated list of genes that catalyzes the mentioned reactions direct reactions 0..* Reaction semicolon separated list of reaction equations (e direct gene_reaction_pairings 0..* GeneReactionPairing semicolon separated list of gene to reaction pairings direct organism 0..1 Organism direct has_evidence 0..* Evidence evidence for the reaction direct"},{"location":"reaction/ReactionDocument/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/ReactionDocument/#schema-source","title":"Schema Source","text":""},{"location":"reaction/ReactionDocument/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:ReactionDocument native reaction:ReactionDocument"},{"location":"reaction/ReactionDocument/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/ReactionDocument/#direct","title":"Direct","text":"
name: ReactionDocument\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  genes:\n    name: genes\n    description: semicolon separated list of genes that catalyzes the mentioned reactions\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: Gene\n  reactions:\n    name: reactions\n    description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed\n      by the gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    multivalued: true\n    range: Reaction\n    inlined: true\n  gene_reaction_pairings:\n    name: gene_reaction_pairings\n    description: semicolon separated list of gene to reaction pairings\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: GeneReactionPairing\n    inlined: true\n  organism:\n    name: organism\n    from_schema: https://w3id.org/ontogpt/reaction\n    range: Organism\n  has_evidence:\n    name: has_evidence\n    description: evidence for the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: Evidence\n\n
"},{"location":"reaction/ReactionDocument/#induced","title":"Induced","text":"
name: ReactionDocument\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  genes:\n    name: genes\n    description: semicolon separated list of genes that catalyzes the mentioned reactions\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: ReactionDocument\n    domain_of:\n    - ReactionDocument\n    range: Gene\n  reactions:\n    name: reactions\n    description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed\n      by the gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    multivalued: true\n    alias: reactions\n    owner: ReactionDocument\n    domain_of:\n    - GeneToReaction\n    - ReactionDocument\n    range: Reaction\n    inlined: true\n  gene_reaction_pairings:\n    name: gene_reaction_pairings\n    description: semicolon separated list of gene to reaction pairings\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: gene_reaction_pairings\n    owner: ReactionDocument\n    domain_of:\n    - ReactionDocument\n    range: GeneReactionPairing\n    inlined: true\n  organism:\n    name: organism\n    from_schema: https://w3id.org/ontogpt/reaction\n    alias: organism\n    owner: ReactionDocument\n    domain_of:\n    - GeneToReaction\n    - ReactionDocument\n    range: Organism\n  has_evidence:\n    name: has_evidence\n    description: evidence for the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: has_evidence\n    owner: ReactionDocument\n    domain_of:\n    - ReactionDocument\n    range: Evidence\n\n
"},{"location":"reaction/ReactionGrouping/","title":"Class: ReactionGrouping","text":"

URI: reaction:ReactionGrouping

erDiagram\nReactionGrouping {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/ReactionGrouping/#inheritance","title":"Inheritance","text":""},{"location":"reaction/ReactionGrouping/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/ReactionGrouping/#usages","title":"Usages","text":"used by used in type used Reaction subclass_of range ReactionGrouping"},{"location":"reaction/ReactionGrouping/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/ReactionGrouping/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/ReactionGrouping/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"reaction/ReactionGrouping/#schema-source","title":"Schema Source","text":""},{"location":"reaction/ReactionGrouping/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:ReactionGrouping native reaction:ReactionGrouping"},{"location":"reaction/ReactionGrouping/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/ReactionGrouping/#direct","title":"Direct","text":"
name: ReactionGrouping\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/ReactionGrouping/#induced","title":"Induced","text":"
name: ReactionGrouping\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ReactionGrouping\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ReactionGrouping\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/RelationshipType/","title":"Class: RelationshipType","text":"

URI: reaction:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"reaction/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"reaction/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"reaction/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:RelationshipType native reaction:RelationshipType"},{"location":"reaction/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"reaction/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/String/#schema-source","title":"Schema Source","text":""},{"location":"reaction/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: reaction:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"reaction/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"reaction/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"reaction/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:TextWithTriples native reaction:TextWithTriples"},{"location":"reaction/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"reaction/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"reaction/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"reaction/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Time/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: reaction:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"reaction/Triple/#inheritance","title":"Inheritance","text":""},{"location":"reaction/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"reaction/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"reaction/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Triple/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Triple native reaction:Triple"},{"location":"reaction/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"reaction/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"reaction/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"reaction/Uri/#comments","title":"Comments","text":""},{"location":"reaction/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Uri/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"reaction/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"reaction/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: reaction:abstract

"},{"location":"reaction/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"reaction/abstract/#properties","title":"Properties","text":""},{"location":"reaction/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/abstract/#schema-source","title":"Schema Source","text":""},{"location":"reaction/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"reaction/combined_text/","title":"Slot: combined_text","text":"

URI: reaction:combined_text

"},{"location":"reaction/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"reaction/combined_text/#properties","title":"Properties","text":""},{"location":"reaction/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"reaction/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"reaction/description/","title":"Slot: description","text":"

a textual description of the reaction

URI: reaction:description

"},{"location":"reaction/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no"},{"location":"reaction/description/#properties","title":"Properties","text":""},{"location":"reaction/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/description/#schema-source","title":"Schema Source","text":""},{"location":"reaction/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a textual description of the reaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: description\nowner: Reaction\ndomain_of:\n- Reaction\nrange: string\n\n
"},{"location":"reaction/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: reaction:extracted_object

"},{"location":"reaction/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/extracted_object/#properties","title":"Properties","text":""},{"location":"reaction/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"reaction/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"reaction/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: reaction:full_text

"},{"location":"reaction/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"reaction/full_text/#properties","title":"Properties","text":""},{"location":"reaction/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/full_text/#schema-source","title":"Schema Source","text":""},{"location":"reaction/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"reaction/gene/","title":"Slot: gene","text":"

URI: reaction:gene

"},{"location":"reaction/gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneToReaction no GeneReactionPairing no"},{"location":"reaction/gene/#properties","title":"Properties","text":""},{"location":"reaction/gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/gene/#linkml-source","title":"LinkML Source","text":"
name: gene\nalias: gene\ndomain_of:\n- GeneToReaction\n- GeneReactionPairing\nrange: string\n\n
"},{"location":"reaction/gene_reaction_pairings/","title":"Slot: gene_reaction_pairings","text":"

semicolon separated list of gene to reaction pairings

URI: reaction:gene_reaction_pairings

"},{"location":"reaction/gene_reaction_pairings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionDocument no"},{"location":"reaction/gene_reaction_pairings/#properties","title":"Properties","text":""},{"location":"reaction/gene_reaction_pairings/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/gene_reaction_pairings/#schema-source","title":"Schema Source","text":""},{"location":"reaction/gene_reaction_pairings/#linkml-source","title":"LinkML Source","text":"
name: gene_reaction_pairings\ndescription: semicolon separated list of gene to reaction pairings\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: gene_reaction_pairings\nowner: ReactionDocument\ndomain_of:\n- ReactionDocument\nrange: GeneReactionPairing\ninlined: true\n\n
"},{"location":"reaction/genes/","title":"Slot: genes","text":"

semicolon separated list of genes that catalyzes the mentioned reactions

URI: reaction:genes

"},{"location":"reaction/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionDocument no"},{"location":"reaction/genes/#properties","title":"Properties","text":""},{"location":"reaction/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/genes/#schema-source","title":"Schema Source","text":""},{"location":"reaction/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\ndescription: semicolon separated list of genes that catalyzes the mentioned reactions\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: genes\nowner: ReactionDocument\ndomain_of:\n- ReactionDocument\nrange: Gene\n\n
"},{"location":"reaction/has_evidence/","title":"Slot: has_evidence","text":"

evidence for the reaction

URI: reaction:has_evidence

"},{"location":"reaction/has_evidence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionDocument no"},{"location":"reaction/has_evidence/#properties","title":"Properties","text":""},{"location":"reaction/has_evidence/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/has_evidence/#schema-source","title":"Schema Source","text":""},{"location":"reaction/has_evidence/#linkml-source","title":"LinkML Source","text":"
name: has_evidence\ndescription: evidence for the reaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: has_evidence\nowner: ReactionDocument\ndomain_of:\n- ReactionDocument\nrange: Evidence\n\n
"},{"location":"reaction/id/","title":"Slot: id","text":"

URI: reaction:id

"},{"location":"reaction/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no ReactionGrouping no ChemicalEntity no Evidence no Gene no Organism no NamedEntity no RelationshipType no Publication no"},{"location":"reaction/id/#properties","title":"Properties","text":""},{"location":"reaction/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"reaction/input_id/","title":"Slot: input_id","text":"

URI: reaction:input_id

"},{"location":"reaction/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/input_id/#properties","title":"Properties","text":""},{"location":"reaction/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/input_id/#schema-source","title":"Schema Source","text":""},{"location":"reaction/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"reaction/input_text/","title":"Slot: input_text","text":"

URI: reaction:input_text

"},{"location":"reaction/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/input_text/#properties","title":"Properties","text":""},{"location":"reaction/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/input_text/#schema-source","title":"Schema Source","text":""},{"location":"reaction/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"reaction/input_title/","title":"Slot: input_title","text":"

URI: reaction:input_title

"},{"location":"reaction/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/input_title/#properties","title":"Properties","text":""},{"location":"reaction/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/input_title/#schema-source","title":"Schema Source","text":""},{"location":"reaction/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"reaction/label/","title":"Slot: label","text":"

URI: reaction:label

"},{"location":"reaction/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no ReactionGrouping no ChemicalEntity no Evidence no Gene no Organism no NamedEntity no RelationshipType no"},{"location":"reaction/label/#properties","title":"Properties","text":""},{"location":"reaction/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- Reaction\n- NamedEntity\nrange: string\n\n
"},{"location":"reaction/left_side/","title":"Slot: left_side","text":"

semicolon separated list of chemical entities on the left side

URI: reaction:left_side

"},{"location":"reaction/left_side/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no"},{"location":"reaction/left_side/#properties","title":"Properties","text":""},{"location":"reaction/left_side/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/left_side/#schema-source","title":"Schema Source","text":""},{"location":"reaction/left_side/#linkml-source","title":"LinkML Source","text":"
name: left_side\ndescription: semicolon separated list of chemical entities on the left side\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: left_side\nowner: Reaction\ndomain_of:\n- Reaction\nrange: ChemicalEntity\n\n
"},{"location":"reaction/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: reaction:named_entities

"},{"location":"reaction/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/named_entities/#properties","title":"Properties","text":""},{"location":"reaction/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"reaction/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"reaction/object/","title":"Slot: object","text":"

URI: reaction:object

"},{"location":"reaction/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/object/#properties","title":"Properties","text":""},{"location":"reaction/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/object/#schema-source","title":"Schema Source","text":""},{"location":"reaction/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"reaction/object_id/","title":"Slot: object_id","text":"

URI: reaction:object_id

"},{"location":"reaction/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"reaction/object_id/#properties","title":"Properties","text":""},{"location":"reaction/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/object_id/#schema-source","title":"Schema Source","text":""},{"location":"reaction/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"reaction/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: reaction:object_qualifier

"},{"location":"reaction/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/object_qualifier/#properties","title":"Properties","text":""},{"location":"reaction/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"reaction/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"reaction/object_text/","title":"Slot: object_text","text":"

URI: reaction:object_text

"},{"location":"reaction/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"reaction/object_text/#properties","title":"Properties","text":""},{"location":"reaction/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/object_text/#schema-source","title":"Schema Source","text":""},{"location":"reaction/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"reaction/organism/","title":"Slot: organism","text":"

URI: reaction:organism

"},{"location":"reaction/organism/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneToReaction no ReactionDocument no"},{"location":"reaction/organism/#properties","title":"Properties","text":""},{"location":"reaction/organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/organism/#linkml-source","title":"LinkML Source","text":"
name: organism\nalias: organism\ndomain_of:\n- GeneToReaction\n- ReactionDocument\nrange: string\n\n
"},{"location":"reaction/predicate/","title":"Slot: predicate","text":"

URI: reaction:predicate

"},{"location":"reaction/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/predicate/#properties","title":"Properties","text":""},{"location":"reaction/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/predicate/#schema-source","title":"Schema Source","text":""},{"location":"reaction/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"reaction/prompt/","title":"Slot: prompt","text":"

URI: reaction:prompt

"},{"location":"reaction/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/prompt/#properties","title":"Properties","text":""},{"location":"reaction/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/prompt/#schema-source","title":"Schema Source","text":""},{"location":"reaction/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"reaction/publication/","title":"Slot: publication","text":"

URI: reaction:publication

"},{"location":"reaction/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"reaction/publication/#properties","title":"Properties","text":""},{"location":"reaction/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"reaction/publication/#schema-source","title":"Schema Source","text":""},{"location":"reaction/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"reaction/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: reaction:qualifier

"},{"location":"reaction/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/qualifier/#properties","title":"Properties","text":""},{"location":"reaction/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"reaction/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"reaction/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: reaction:raw_completion_output

"},{"location":"reaction/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/raw_completion_output/#properties","title":"Properties","text":""},{"location":"reaction/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"reaction/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"reaction/reaction-template/","title":"reaction-template","text":"

A template for reactions

URI: https://w3id.org/ontogpt/reaction

"},{"location":"reaction/reaction/","title":"Slot: reaction","text":"

equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene

URI: reaction:reaction

"},{"location":"reaction/reaction/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneReactionPairing no"},{"location":"reaction/reaction/#properties","title":"Properties","text":""},{"location":"reaction/reaction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/reaction/#schema-source","title":"Schema Source","text":""},{"location":"reaction/reaction/#linkml-source","title":"LinkML Source","text":"
name: reaction\ndescription: equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: reaction\nowner: GeneReactionPairing\ndomain_of:\n- GeneReactionPairing\nrange: Reaction\n\n
"},{"location":"reaction/reactions/","title":"Slot: reactions","text":"

URI: reaction:reactions

"},{"location":"reaction/reactions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneToReaction no ReactionDocument no"},{"location":"reaction/reactions/#properties","title":"Properties","text":""},{"location":"reaction/reactions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/reactions/#linkml-source","title":"LinkML Source","text":"
name: reactions\nalias: reactions\ndomain_of:\n- GeneToReaction\n- ReactionDocument\nrange: string\n\n
"},{"location":"reaction/right_side/","title":"Slot: right_side","text":"

semicolon separated list of chemical entities on the right side

URI: reaction:right_side

"},{"location":"reaction/right_side/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no"},{"location":"reaction/right_side/#properties","title":"Properties","text":""},{"location":"reaction/right_side/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/right_side/#schema-source","title":"Schema Source","text":""},{"location":"reaction/right_side/#linkml-source","title":"LinkML Source","text":"
name: right_side\ndescription: semicolon separated list of chemical entities on the right side\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: right_side\nowner: Reaction\ndomain_of:\n- Reaction\nrange: ChemicalEntity\n\n
"},{"location":"reaction/subclass_of/","title":"Slot: subclass_of","text":"

the category to which this biological process belongs

URI: reaction:subclass_of

"},{"location":"reaction/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no"},{"location":"reaction/subclass_of/#properties","title":"Properties","text":""},{"location":"reaction/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"reaction/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\ndescription: the category to which this biological process belongs\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: subclass_of\nowner: Reaction\ndomain_of:\n- Reaction\nrange: ReactionGrouping\n\n
"},{"location":"reaction/subject/","title":"Slot: subject","text":"

URI: reaction:subject

"},{"location":"reaction/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/subject/#properties","title":"Properties","text":""},{"location":"reaction/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/subject/#schema-source","title":"Schema Source","text":""},{"location":"reaction/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"reaction/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: reaction:subject_qualifier

"},{"location":"reaction/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/subject_qualifier/#properties","title":"Properties","text":""},{"location":"reaction/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"reaction/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"reaction/subject_text/","title":"Slot: subject_text","text":"

URI: reaction:subject_text

"},{"location":"reaction/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"reaction/subject_text/#properties","title":"Properties","text":""},{"location":"reaction/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"reaction/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"reaction/synonyms/","title":"Slot: synonyms","text":"

alternative names of the reaction

URI: reaction:synonyms

"},{"location":"reaction/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no"},{"location":"reaction/synonyms/#properties","title":"Properties","text":""},{"location":"reaction/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"reaction/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\ndescription: alternative names of the reaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: Reaction\ndomain_of:\n- Reaction\nrange: string\n\n
"},{"location":"reaction/title/","title":"Slot: title","text":"

The title of the publication

URI: reaction:title

"},{"location":"reaction/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"reaction/title/#properties","title":"Properties","text":""},{"location":"reaction/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/title/#schema-source","title":"Schema Source","text":""},{"location":"reaction/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"reaction/triples/","title":"Slot: triples","text":"

URI: reaction:triples

"},{"location":"reaction/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"reaction/triples/#properties","title":"Properties","text":""},{"location":"reaction/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/triples/#schema-source","title":"Schema Source","text":""},{"location":"reaction/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"recipe/","title":"Food Recipe Template","text":"

A template for food recipes

URI: https://w3id.org/ontogpt/recipe

Name: recipe-template

"},{"location":"recipe/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nRecipe {\n    uriorcurie url  \n    string label  \n    string description  \n}\nStep {\n\n}\nUtensilType {\n    string id  \n    string label  \n}\nFoodItem {\n    string state  \n}\nFoodType {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\nIngredient {\n\n}\nQuantity {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\nRecipeCategory {\n    string id  \n    string label  \n}\n\nRecipe ||--}o RecipeCategory : \"categories\"\nRecipe ||--}o Ingredient : \"ingredients\"\nRecipe ||--}o Step : \"steps\"\nStep ||--|o Action : \"action\"\nStep ||--}o FoodItem : \"inputs\"\nStep ||--}o FoodItem : \"outputs\"\nStep ||--}o UtensilType : \"utensils\"\nFoodItem ||--|o FoodType : \"food\"\nIngredient ||--|o FoodItem : \"food_item\"\nIngredient ||--|o Quantity : \"amount\"\nQuantity ||--|o Unit : \"unit\"\n\n
"},{"location":"recipe/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None FoodItem None Ingredient None Quantity None Step None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None Action None FoodType None RecipeCategory None RelationshipType None Unit None UtensilType None Publication None Recipe None TextWithTriples None"},{"location":"recipe/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication action the action taken in this step (e amount the quantity of the ingredient, e categories a semicolon separated list of the categories to which this recipe belongs combined_text description a brief textual description of the recipe extracted_object The complex objects extracted from the text food the food item food_item the food item full_text The full text of the publication id A unique identifier for the named entity ingredients a semicolon separated list of the ingredients plus quantities of the recipe input_id input_text input_title inputs a semicolon separated list of the inputs of this step label the name of the recipe named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text outputs a semicolon separated list of the outputs of this step predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output state the state of the food item (e steps a semicolon separated list of the individual steps involved in this recipe subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples unit the unit of the quantity, e url utensils the kitchen utensil used in this step (e value the value of the quantity"},{"location":"recipe/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"recipe/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"recipe/#subsets","title":"Subsets","text":"Subset Description"},{"location":"recipe/Action/","title":"Class: Action","text":"

URI: recipe:Action

erDiagram\nAction {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/Action/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Action/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/Action/#usages","title":"Usages","text":"used by used in type used Step action range Action"},{"location":"recipe/Action/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Action/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/Action/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:dbpediaont, sqlite:obo:foodon"},{"location":"recipe/Action/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Action/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Action native recipe:Action"},{"location":"recipe/Action/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Action/#direct","title":"Direct","text":"
name: Action\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/Action/#induced","title":"Induced","text":"
name: Action\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Action\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Action\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: recipe:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"recipe/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"recipe/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"recipe/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:AnnotatorResult native recipe:AnnotatorResult"},{"location":"recipe/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n\n
"},{"location":"recipe/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"recipe/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"recipe/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"recipe/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"recipe/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Any/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native recipe:Any"},{"location":"recipe/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/recipe\nclass_uri: linkml:Any\n\n
"},{"location":"recipe/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/recipe\nclass_uri: linkml:Any\n\n
"},{"location":"recipe/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"recipe/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"recipe/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: recipe:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"recipe/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"recipe/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"recipe/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"recipe/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:CompoundExpression native recipe:CompoundExpression"},{"location":"recipe/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/recipe\nabstract: true\n\n
"},{"location":"recipe/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/recipe\nabstract: true\n\n
"},{"location":"recipe/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"recipe/Curie/#comments","title":"Comments","text":""},{"location":"recipe/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Curie/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"recipe/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Date/#schema-source","title":"Schema Source","text":""},{"location":"recipe/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"recipe/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"recipe/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"recipe/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"recipe/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Double/#schema-source","title":"Schema Source","text":""},{"location":"recipe/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: recipe:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"recipe/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"recipe/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"recipe/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:ExtractionResult native recipe:ExtractionResult"},{"location":"recipe/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"recipe/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"recipe/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"recipe/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Float/#schema-source","title":"Schema Source","text":""},{"location":"recipe/FoodItem/","title":"Class: FoodItem","text":"

URI: recipe:FoodItem

erDiagram\nFoodItem {\n    string state  \n}\nFoodType {\n    string id  \n    string label  \n}\n\nFoodItem ||--|o FoodType : \"food\"\n\n
"},{"location":"recipe/FoodItem/#inheritance","title":"Inheritance","text":""},{"location":"recipe/FoodItem/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance food 0..1 FoodType the food item direct state 0..1 String the state of the food item (e direct"},{"location":"recipe/FoodItem/#usages","title":"Usages","text":"used by used in type used Ingredient food_item range FoodItem Step inputs range FoodItem Step outputs range FoodItem"},{"location":"recipe/FoodItem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/FoodItem/#annotations","title":"Annotations","text":"property value owl IntersectionOf"},{"location":"recipe/FoodItem/#schema-source","title":"Schema Source","text":""},{"location":"recipe/FoodItem/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:FoodItem native recipe:FoodItem"},{"location":"recipe/FoodItem/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/FoodItem/#direct","title":"Direct","text":"
name: FoodItem\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  food:\n    name: food\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the food item\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: BFO:0000051\n    range: FoodType\n  state:\n    name: state\n    annotations:\n      owl:\n        tag: owl\n        value: DataProperty, DataHasValue\n    description: the state of the food item (e.g. chopped, diced)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n\n
"},{"location":"recipe/FoodItem/#induced","title":"Induced","text":"
name: FoodItem\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  food:\n    name: food\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the food item\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: BFO:0000051\n    alias: food\n    owner: FoodItem\n    domain_of:\n    - FoodItem\n    range: FoodType\n  state:\n    name: state\n    annotations:\n      owl:\n        tag: owl\n        value: DataProperty, DataHasValue\n    description: the state of the food item (e.g. chopped, diced)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: state\n    owner: FoodItem\n    domain_of:\n    - FoodItem\n    range: string\n\n
"},{"location":"recipe/FoodType/","title":"Class: FoodType","text":"

URI: recipe:FoodType

erDiagram\nFoodType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/FoodType/#inheritance","title":"Inheritance","text":""},{"location":"recipe/FoodType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/FoodType/#usages","title":"Usages","text":"used by used in type used FoodItem food range FoodType"},{"location":"recipe/FoodType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/FoodType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/FoodType/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:foodon, sqlite:obo:dbpediaont"},{"location":"recipe/FoodType/#schema-source","title":"Schema Source","text":""},{"location":"recipe/FoodType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:FoodType native recipe:FoodType"},{"location":"recipe/FoodType/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/FoodType/#direct","title":"Direct","text":"
name: FoodType\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon, sqlite:obo:dbpediaont\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/FoodType/#induced","title":"Induced","text":"
name: FoodType\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon, sqlite:obo:dbpediaont\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: FoodType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: FoodType\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/Ingredient/","title":"Class: Ingredient","text":"

URI: FOODON:00004085

erDiagram\nIngredient {\n\n}\nQuantity {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\nFoodItem {\n    string state  \n}\nFoodType {\n    string id  \n    string label  \n}\n\nIngredient ||--|o FoodItem : \"food_item\"\nIngredient ||--|o Quantity : \"amount\"\nQuantity ||--|o Unit : \"unit\"\nFoodItem ||--|o FoodType : \"food\"\n\n
"},{"location":"recipe/Ingredient/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Ingredient/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance food_item 0..1 FoodItem the food item direct amount 0..1 Quantity the quantity of the ingredient, e direct"},{"location":"recipe/Ingredient/#usages","title":"Usages","text":"used by used in type used Recipe ingredients range Ingredient"},{"location":"recipe/Ingredient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Ingredient/#annotations","title":"Annotations","text":"property value owl IntersectionOf"},{"location":"recipe/Ingredient/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Ingredient/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self FOODON:00004085 native recipe:Ingredient"},{"location":"recipe/Ingredient/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Ingredient/#direct","title":"Direct","text":"
name: Ingredient\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  food_item:\n    name: food_item\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the food item\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: FoodItem\n  amount:\n    name: amount\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the quantity of the ingredient, e.g. 2 lbs\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: Quantity\nclass_uri: FOODON:00004085\n\n
"},{"location":"recipe/Ingredient/#induced","title":"Induced","text":"
name: Ingredient\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  food_item:\n    name: food_item\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the food item\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: food_item\n    owner: Ingredient\n    domain_of:\n    - Ingredient\n    range: FoodItem\n  amount:\n    name: amount\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the quantity of the ingredient, e.g. 2 lbs\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: amount\n    owner: Ingredient\n    domain_of:\n    - Ingredient\n    range: Quantity\nclass_uri: FOODON:00004085\n\n
"},{"location":"recipe/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"recipe/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Integer/#schema-source","title":"Schema Source","text":""},{"location":"recipe/NamedEntity/","title":"Class: NamedEntity","text":"

URI: recipe:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"recipe/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"recipe/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"recipe/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"recipe/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:NamedEntity native recipe:NamedEntity"},{"location":"recipe/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/recipe\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"recipe/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/recipe\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"recipe/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"recipe/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"recipe/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"recipe/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"recipe/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"recipe/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"recipe/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"recipe/Objectidentifier/#comments","title":"Comments","text":""},{"location":"recipe/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Publication/","title":"Class: Publication","text":"

URI: recipe:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"recipe/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"recipe/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"recipe/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Publication/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Publication native recipe:Publication"},{"location":"recipe/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/recipe\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n\n
"},{"location":"recipe/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/recipe\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"recipe/Quantity/","title":"Class: Quantity","text":"

URI: recipe:Quantity

erDiagram\nQuantity {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\n\nQuantity ||--|o Unit : \"unit\"\n\n
"},{"location":"recipe/Quantity/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Quantity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance value 0..1 String the value of the quantity direct unit 0..1 Unit the unit of the quantity, e direct"},{"location":"recipe/Quantity/#usages","title":"Usages","text":"used by used in type used Ingredient amount range Quantity"},{"location":"recipe/Quantity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Quantity/#annotations","title":"Annotations","text":"property value owl IntersectionOf"},{"location":"recipe/Quantity/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Quantity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Quantity native recipe:Quantity"},{"location":"recipe/Quantity/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Quantity/#direct","title":"Direct","text":"
name: Quantity\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    annotations:\n      owl:\n        tag: owl\n        value: DataProperty, DataHasValue\n    description: the value of the quantity\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  unit:\n    name: unit\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the unit of the quantity, e.g. grams, cups, etc.\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: qudt:unit\n    range: Unit\n\n
"},{"location":"recipe/Quantity/#induced","title":"Induced","text":"
name: Quantity\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    annotations:\n      owl:\n        tag: owl\n        value: DataProperty, DataHasValue\n    description: the value of the quantity\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: value\n    owner: Quantity\n    domain_of:\n    - Quantity\n    range: string\n  unit:\n    name: unit\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the unit of the quantity, e.g. grams, cups, etc.\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: qudt:unit\n    alias: unit\n    owner: Quantity\n    domain_of:\n    - Quantity\n    range: Unit\n\n
"},{"location":"recipe/Recipe/","title":"Class: Recipe","text":"

URI: recipe:Recipe

erDiagram\nRecipe {\n    uriorcurie url  \n    string label  \n    string description  \n}\nStep {\n\n}\nUtensilType {\n    string id  \n    string label  \n}\nFoodItem {\n    string state  \n}\nAction {\n    string id  \n    string label  \n}\nIngredient {\n\n}\nQuantity {\n    string value  \n}\nRecipeCategory {\n    string id  \n    string label  \n}\n\nRecipe ||--}o RecipeCategory : \"categories\"\nRecipe ||--}o Ingredient : \"ingredients\"\nRecipe ||--}o Step : \"steps\"\nStep ||--|o Action : \"action\"\nStep ||--}o FoodItem : \"inputs\"\nStep ||--}o FoodItem : \"outputs\"\nStep ||--}o UtensilType : \"utensils\"\nFoodItem ||--|o FoodType : \"food\"\nIngredient ||--|o FoodItem : \"food_item\"\nIngredient ||--|o Quantity : \"amount\"\nQuantity ||--|o Unit : \"unit\"\n\n
"},{"location":"recipe/Recipe/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance url 1..1 Uriorcurie direct label 0..1 String the name of the recipe direct description 0..1 String a brief textual description of the recipe direct categories 0..* RecipeCategory a semicolon separated list of the categories to which this recipe belongs direct ingredients 0..* Ingredient a semicolon separated list of the ingredients plus quantities of the recipe direct steps 0..* Step a semicolon separated list of the individual steps involved in this recipe direct"},{"location":"recipe/Recipe/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Recipe/#annotations","title":"Annotations","text":"property value owl Class {{url}} ObjectIntersectionOf( recipe:Recipe 
{% for step in steps %}\nObjectSomeValuesFrom(\n  recipe:steps\n  {{tr(step)}}\n)\n{% endfor %}\n{% for ingredient in ingredients %}\nObjectSomeValuesFrom(\n  FOODON:00002420\n  {{tr(ingredient)}}\n)\n{% endfor %}\n

) ) |

"},{"location":"recipe/Recipe/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Recipe/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Recipe native recipe:Recipe close FOODON:00004081"},{"location":"recipe/Recipe/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Recipe/#direct","title":"Direct","text":"
name: Recipe\nannotations:\n  owl:\n    tag: owl\n    value: Class\n  owl.template:\n    tag: owl.template\n    value: \"EquivalentClasses(\\n  {{url}}\\n  ObjectIntersectionOf(\\n    recipe:Recipe\\n\\\n      \\    \\n    {% for step in steps %}\\n    ObjectSomeValuesFrom(\\n      recipe:steps\\n\\\n      \\      {{tr(step)}}\\n    )\\n    {% endfor %}\\n    {% for ingredient in ingredients\\\n      \\ %}\\n    ObjectSomeValuesFrom(\\n      FOODON:00002420\\n      {{tr(ingredient)}}\\n\\\n      \\    )\\n    {% endfor %}\\n  )\\n)\\n\"\nfrom_schema: https://w3id.org/ontogpt/recipe\nclose_mappings:\n- FOODON:00004081\nattributes:\n  url:\n    name: url\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: the name of the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: rdfs:label\n  description:\n    name: description\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: a brief textual description of the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: dcterms:description\n  categories:\n    name: categories\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: a semicolon separated list of the categories to which this recipe\n      belongs\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: dcterms:subject\n    multivalued: true\n    range: RecipeCategory\n  ingredients:\n    name: ingredients\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the ingredients plus quantities of\n      the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: FOODON:00002420\n    multivalued: true\n    range: Ingredient\n  steps:\n    name: steps\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the individual steps involved in this\n      recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    range: Step\ntree_root: true\n\n
"},{"location":"recipe/Recipe/#induced","title":"Induced","text":"
name: Recipe\nannotations:\n  owl:\n    tag: owl\n    value: Class\n  owl.template:\n    tag: owl.template\n    value: \"EquivalentClasses(\\n  {{url}}\\n  ObjectIntersectionOf(\\n    recipe:Recipe\\n\\\n      \\    \\n    {% for step in steps %}\\n    ObjectSomeValuesFrom(\\n      recipe:steps\\n\\\n      \\      {{tr(step)}}\\n    )\\n    {% endfor %}\\n    {% for ingredient in ingredients\\\n      \\ %}\\n    ObjectSomeValuesFrom(\\n      FOODON:00002420\\n      {{tr(ingredient)}}\\n\\\n      \\    )\\n    {% endfor %}\\n  )\\n)\\n\"\nfrom_schema: https://w3id.org/ontogpt/recipe\nclose_mappings:\n- FOODON:00004081\nattributes:\n  url:\n    name: url\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    alias: url\n    owner: Recipe\n    domain_of:\n    - Recipe\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: the name of the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Recipe\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n  description:\n    name: description\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: a brief textual description of the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Recipe\n    domain_of:\n    - Recipe\n    range: string\n  categories:\n    name: categories\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: a semicolon separated list of the categories to which this recipe\n      belongs\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: dcterms:subject\n    multivalued: true\n    alias: categories\n    owner: Recipe\n    domain_of:\n    - Recipe\n    range: RecipeCategory\n  ingredients:\n    name: ingredients\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the ingredients plus quantities of\n      the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: FOODON:00002420\n    multivalued: true\n    alias: ingredients\n    owner: Recipe\n    domain_of:\n    - Recipe\n    range: Ingredient\n  steps:\n    name: steps\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the individual steps involved in this\n      recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    alias: steps\n    owner: Recipe\n    domain_of:\n    - Recipe\n    range: Step\ntree_root: true\n\n
"},{"location":"recipe/RecipeCategory/","title":"Class: RecipeCategory","text":"

URI: recipe:RecipeCategory

erDiagram\nRecipeCategory {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/RecipeCategory/#inheritance","title":"Inheritance","text":""},{"location":"recipe/RecipeCategory/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/RecipeCategory/#usages","title":"Usages","text":"used by used in type used Recipe categories range RecipeCategory"},{"location":"recipe/RecipeCategory/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/RecipeCategory/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/RecipeCategory/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:foodon, sqlite:obo:dbpediaont"},{"location":"recipe/RecipeCategory/#schema-source","title":"Schema Source","text":""},{"location":"recipe/RecipeCategory/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:RecipeCategory native recipe:RecipeCategory"},{"location":"recipe/RecipeCategory/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/RecipeCategory/#direct","title":"Direct","text":"
name: RecipeCategory\nid_prefixes:\n- dbpediaont\n- FOODON\n- HANCESTRO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon, sqlite:obo:dbpediaont\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/RecipeCategory/#induced","title":"Induced","text":"
name: RecipeCategory\nid_prefixes:\n- dbpediaont\n- FOODON\n- HANCESTRO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon, sqlite:obo:dbpediaont\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RecipeCategory\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RecipeCategory\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/RelationshipType/","title":"Class: RelationshipType","text":"

URI: recipe:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"recipe/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"recipe/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"recipe/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:RelationshipType native recipe:RelationshipType"},{"location":"recipe/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/Step/","title":"Class: Step","text":"

URI: FOODON:00004087

erDiagram\nStep {\n\n}\nUtensilType {\n    string id  \n    string label  \n}\nFoodItem {\n    string state  \n}\nFoodType {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\n\nStep ||--|o Action : \"action\"\nStep ||--}o FoodItem : \"inputs\"\nStep ||--}o FoodItem : \"outputs\"\nStep ||--}o UtensilType : \"utensils\"\nFoodItem ||--|o FoodType : \"food\"\n\n
"},{"location":"recipe/Step/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Step/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance action 0..1 Action the action taken in this step (e direct inputs 0..* FoodItem a semicolon separated list of the inputs of this step direct outputs 0..* FoodItem a semicolon separated list of the outputs of this step direct utensils 0..* UtensilType the kitchen utensil used in this step (e direct"},{"location":"recipe/Step/#usages","title":"Usages","text":"used by used in type used Recipe steps range Step"},{"location":"recipe/Step/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Step/#annotations","title":"Annotations","text":"property value owl IntersectionOf"},{"location":"recipe/Step/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Step/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self FOODON:00004087 native recipe:Step"},{"location":"recipe/Step/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Step/#direct","title":"Direct","text":"
name: Step\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  action:\n    name: action\n    description: the action taken in this step (e.g. mix, add)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: Action\n  inputs:\n    name: inputs\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the inputs of this step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002233\n    multivalued: true\n    range: FoodItem\n  outputs:\n    name: outputs\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the outputs of this step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002234\n    multivalued: true\n    range: FoodItem\n  utensils:\n    name: utensils\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the kitchen utensil used in this step (e.g. pan, bowl)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002500\n    multivalued: true\n    range: UtensilType\nclass_uri: FOODON:00004087\n\n
"},{"location":"recipe/Step/#induced","title":"Induced","text":"
name: Step\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  action:\n    name: action\n    description: the action taken in this step (e.g. mix, add)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: action\n    owner: Step\n    domain_of:\n    - Step\n    range: Action\n  inputs:\n    name: inputs\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the inputs of this step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002233\n    multivalued: true\n    alias: inputs\n    owner: Step\n    domain_of:\n    - Step\n    range: FoodItem\n  outputs:\n    name: outputs\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the outputs of this step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002234\n    multivalued: true\n    alias: outputs\n    owner: Step\n    domain_of:\n    - Step\n    range: FoodItem\n  utensils:\n    name: utensils\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the kitchen utensil used in this step (e.g. pan, bowl)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002500\n    multivalued: true\n    alias: utensils\n    owner: Step\n    domain_of:\n    - Step\n    range: UtensilType\nclass_uri: FOODON:00004087\n\n
"},{"location":"recipe/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"recipe/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/String/#schema-source","title":"Schema Source","text":""},{"location":"recipe/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: recipe:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"recipe/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"recipe/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"recipe/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:TextWithTriples native recipe:TextWithTriples"},{"location":"recipe/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"recipe/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"recipe/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"recipe/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Time/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: recipe:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"recipe/Triple/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"recipe/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"recipe/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Triple/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Triple native recipe:Triple"},{"location":"recipe/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"recipe/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"recipe/Unit/","title":"Class: Unit","text":"

URI: recipe:Unit

erDiagram\nUnit {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/Unit/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Unit/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/Unit/#usages","title":"Usages","text":"used by used in type used Quantity unit range Unit"},{"location":"recipe/Unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Unit/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/Unit/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon"},{"location":"recipe/Unit/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Unit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Unit native recipe:Unit"},{"location":"recipe/Unit/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Unit/#direct","title":"Direct","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\n- dbpediaont\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/Unit/#induced","title":"Induced","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\n- dbpediaont\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Unit\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"recipe/Uri/#comments","title":"Comments","text":""},{"location":"recipe/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Uri/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"recipe/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"recipe/UtensilType/","title":"Class: UtensilType","text":"

URI: recipe:UtensilType

erDiagram\nUtensilType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/UtensilType/#inheritance","title":"Inheritance","text":""},{"location":"recipe/UtensilType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/UtensilType/#usages","title":"Usages","text":"used by used in type used Step utensils range UtensilType"},{"location":"recipe/UtensilType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/UtensilType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/UtensilType/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:dbpediaont, sqlite:obo:foodon"},{"location":"recipe/UtensilType/#schema-source","title":"Schema Source","text":""},{"location":"recipe/UtensilType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:UtensilType native recipe:UtensilType"},{"location":"recipe/UtensilType/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/UtensilType/#direct","title":"Direct","text":"
name: UtensilType\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/UtensilType/#induced","title":"Induced","text":"
name: UtensilType\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: UtensilType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: UtensilType\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: recipe:abstract

"},{"location":"recipe/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"recipe/abstract/#properties","title":"Properties","text":""},{"location":"recipe/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/abstract/#schema-source","title":"Schema Source","text":""},{"location":"recipe/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"recipe/action/","title":"Slot: action","text":"

the action taken in this step (e.g. mix, add)

URI: recipe:action

"},{"location":"recipe/action/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Step no"},{"location":"recipe/action/#properties","title":"Properties","text":""},{"location":"recipe/action/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/action/#schema-source","title":"Schema Source","text":""},{"location":"recipe/action/#linkml-source","title":"LinkML Source","text":"
name: action\ndescription: the action taken in this step (e.g. mix, add)\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: action\nowner: Step\ndomain_of:\n- Step\nrange: Action\n\n
"},{"location":"recipe/amount/","title":"Slot: amount","text":"

the quantity of the ingredient, e.g. 2 lbs

URI: recipe:amount

"},{"location":"recipe/amount/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Ingredient no"},{"location":"recipe/amount/#properties","title":"Properties","text":""},{"location":"recipe/amount/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/amount/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/amount/#schema-source","title":"Schema Source","text":""},{"location":"recipe/amount/#linkml-source","title":"LinkML Source","text":"
name: amount\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: the quantity of the ingredient, e.g. 2 lbs\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: amount\nowner: Ingredient\ndomain_of:\n- Ingredient\nrange: Quantity\n\n
"},{"location":"recipe/categories/","title":"Slot: categories","text":"

a semicolon separated list of the categories to which this recipe belongs

URI: dcterms:subject

"},{"location":"recipe/categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no"},{"location":"recipe/categories/#properties","title":"Properties","text":""},{"location":"recipe/categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/categories/#annotations","title":"Annotations","text":"property value owl AnnotationAssertion"},{"location":"recipe/categories/#schema-source","title":"Schema Source","text":""},{"location":"recipe/categories/#linkml-source","title":"LinkML Source","text":"
name: categories\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationAssertion\ndescription: a semicolon separated list of the categories to which this recipe belongs\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: dcterms:subject\nmultivalued: true\nalias: categories\nowner: Recipe\ndomain_of:\n- Recipe\nrange: RecipeCategory\n\n
"},{"location":"recipe/combined_text/","title":"Slot: combined_text","text":"

URI: recipe:combined_text

"},{"location":"recipe/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"recipe/combined_text/#properties","title":"Properties","text":""},{"location":"recipe/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"recipe/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"recipe/description/","title":"Slot: description","text":"

a brief textual description of the recipe

URI: dcterms:description

"},{"location":"recipe/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no"},{"location":"recipe/description/#properties","title":"Properties","text":""},{"location":"recipe/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/description/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"recipe/description/#schema-source","title":"Schema Source","text":""},{"location":"recipe/description/#linkml-source","title":"LinkML Source","text":"
name: description\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: a brief textual description of the recipe\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: dcterms:description\nalias: description\nowner: Recipe\ndomain_of:\n- Recipe\nrange: string\n\n
"},{"location":"recipe/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: recipe:extracted_object

"},{"location":"recipe/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/extracted_object/#properties","title":"Properties","text":""},{"location":"recipe/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"recipe/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"recipe/food/","title":"Slot: food","text":"

the food item

URI: BFO:0000051

"},{"location":"recipe/food/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FoodItem no"},{"location":"recipe/food/#properties","title":"Properties","text":""},{"location":"recipe/food/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/food/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/food/#schema-source","title":"Schema Source","text":""},{"location":"recipe/food/#linkml-source","title":"LinkML Source","text":"
name: food\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: the food item\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: BFO:0000051\nalias: food\nowner: FoodItem\ndomain_of:\n- FoodItem\nrange: FoodType\n\n
"},{"location":"recipe/food_item/","title":"Slot: food_item","text":"

the food item

URI: recipe:food_item

"},{"location":"recipe/food_item/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Ingredient no"},{"location":"recipe/food_item/#properties","title":"Properties","text":""},{"location":"recipe/food_item/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/food_item/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/food_item/#schema-source","title":"Schema Source","text":""},{"location":"recipe/food_item/#linkml-source","title":"LinkML Source","text":"
name: food_item\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: the food item\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: food_item\nowner: Ingredient\ndomain_of:\n- Ingredient\nrange: FoodItem\n\n
"},{"location":"recipe/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: recipe:full_text

"},{"location":"recipe/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"recipe/full_text/#properties","title":"Properties","text":""},{"location":"recipe/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/full_text/#schema-source","title":"Schema Source","text":""},{"location":"recipe/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"recipe/id/","title":"Slot: id","text":"

URI: recipe:id

"},{"location":"recipe/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FoodType no RecipeCategory no Action no UtensilType no Unit no NamedEntity no RelationshipType no Publication no"},{"location":"recipe/id/#properties","title":"Properties","text":""},{"location":"recipe/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"recipe/ingredients/","title":"Slot: ingredients","text":"

a semicolon separated list of the ingredients plus quantities of the recipe

URI: FOODON:00002420

"},{"location":"recipe/ingredients/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no"},{"location":"recipe/ingredients/#properties","title":"Properties","text":""},{"location":"recipe/ingredients/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/ingredients/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/ingredients/#schema-source","title":"Schema Source","text":""},{"location":"recipe/ingredients/#linkml-source","title":"LinkML Source","text":"
name: ingredients\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: a semicolon separated list of the ingredients plus quantities of the\n  recipe\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: FOODON:00002420\nmultivalued: true\nalias: ingredients\nowner: Recipe\ndomain_of:\n- Recipe\nrange: Ingredient\n\n
"},{"location":"recipe/input_id/","title":"Slot: input_id","text":"

URI: recipe:input_id

"},{"location":"recipe/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/input_id/#properties","title":"Properties","text":""},{"location":"recipe/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/input_id/#schema-source","title":"Schema Source","text":""},{"location":"recipe/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"recipe/input_text/","title":"Slot: input_text","text":"

URI: recipe:input_text

"},{"location":"recipe/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/input_text/#properties","title":"Properties","text":""},{"location":"recipe/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/input_text/#schema-source","title":"Schema Source","text":""},{"location":"recipe/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"recipe/input_title/","title":"Slot: input_title","text":"

URI: recipe:input_title

"},{"location":"recipe/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/input_title/#properties","title":"Properties","text":""},{"location":"recipe/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/input_title/#schema-source","title":"Schema Source","text":""},{"location":"recipe/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"recipe/inputs/","title":"Slot: inputs","text":"

a semicolon separated list of the inputs of this step

URI: RO:0002233

"},{"location":"recipe/inputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Step no"},{"location":"recipe/inputs/#properties","title":"Properties","text":""},{"location":"recipe/inputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/inputs/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/inputs/#schema-source","title":"Schema Source","text":""},{"location":"recipe/inputs/#linkml-source","title":"LinkML Source","text":"
name: inputs\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: a semicolon separated list of the inputs of this step\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: RO:0002233\nmultivalued: true\nalias: inputs\nowner: Step\ndomain_of:\n- Step\nrange: FoodItem\n\n
"},{"location":"recipe/label/","title":"Slot: label","text":"

URI: recipe:label

"},{"location":"recipe/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no FoodType no RecipeCategory no Action no UtensilType no Unit no NamedEntity no RelationshipType no"},{"location":"recipe/label/#properties","title":"Properties","text":""},{"location":"recipe/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- Recipe\n- NamedEntity\nrange: string\n\n
"},{"location":"recipe/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: recipe:named_entities

"},{"location":"recipe/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/named_entities/#properties","title":"Properties","text":""},{"location":"recipe/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"recipe/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"recipe/object/","title":"Slot: object","text":"

URI: recipe:object

"},{"location":"recipe/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/object/#properties","title":"Properties","text":""},{"location":"recipe/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/object/#schema-source","title":"Schema Source","text":""},{"location":"recipe/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"recipe/object_id/","title":"Slot: object_id","text":"

URI: recipe:object_id

"},{"location":"recipe/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"recipe/object_id/#properties","title":"Properties","text":""},{"location":"recipe/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/object_id/#schema-source","title":"Schema Source","text":""},{"location":"recipe/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"recipe/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: recipe:object_qualifier

"},{"location":"recipe/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/object_qualifier/#properties","title":"Properties","text":""},{"location":"recipe/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"recipe/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"recipe/object_text/","title":"Slot: object_text","text":"

URI: recipe:object_text

"},{"location":"recipe/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"recipe/object_text/#properties","title":"Properties","text":""},{"location":"recipe/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/object_text/#schema-source","title":"Schema Source","text":""},{"location":"recipe/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"recipe/outputs/","title":"Slot: outputs","text":"

a semicolon separated list of the outputs of this step

URI: RO:0002234

"},{"location":"recipe/outputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Step no"},{"location":"recipe/outputs/#properties","title":"Properties","text":""},{"location":"recipe/outputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/outputs/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/outputs/#schema-source","title":"Schema Source","text":""},{"location":"recipe/outputs/#linkml-source","title":"LinkML Source","text":"
name: outputs\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: a semicolon separated list of the outputs of this step\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: RO:0002234\nmultivalued: true\nalias: outputs\nowner: Step\ndomain_of:\n- Step\nrange: FoodItem\n\n
"},{"location":"recipe/predicate/","title":"Slot: predicate","text":"

URI: recipe:predicate

"},{"location":"recipe/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/predicate/#properties","title":"Properties","text":""},{"location":"recipe/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/predicate/#schema-source","title":"Schema Source","text":""},{"location":"recipe/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"recipe/prompt/","title":"Slot: prompt","text":"

URI: recipe:prompt

"},{"location":"recipe/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/prompt/#properties","title":"Properties","text":""},{"location":"recipe/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/prompt/#schema-source","title":"Schema Source","text":""},{"location":"recipe/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"recipe/publication/","title":"Slot: publication","text":"

URI: recipe:publication

"},{"location":"recipe/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"recipe/publication/#properties","title":"Properties","text":""},{"location":"recipe/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"recipe/publication/#schema-source","title":"Schema Source","text":""},{"location":"recipe/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"recipe/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: recipe:qualifier

"},{"location":"recipe/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/qualifier/#properties","title":"Properties","text":""},{"location":"recipe/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"recipe/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"recipe/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: recipe:raw_completion_output

"},{"location":"recipe/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/raw_completion_output/#properties","title":"Properties","text":""},{"location":"recipe/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"recipe/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"recipe/recipe-template/","title":"recipe-template","text":"

A template for food recipes

URI: https://w3id.org/ontogpt/recipe

"},{"location":"recipe/state/","title":"Slot: state","text":"

the state of the food item (e.g. chopped, diced)

URI: recipe:state

"},{"location":"recipe/state/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FoodItem no"},{"location":"recipe/state/#properties","title":"Properties","text":""},{"location":"recipe/state/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/state/#annotations","title":"Annotations","text":"property value owl DataProperty, DataHasValue"},{"location":"recipe/state/#schema-source","title":"Schema Source","text":""},{"location":"recipe/state/#linkml-source","title":"LinkML Source","text":"
name: state\nannotations:\n  owl:\n    tag: owl\n    value: DataProperty, DataHasValue\ndescription: the state of the food item (e.g. chopped, diced)\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: state\nowner: FoodItem\ndomain_of:\n- FoodItem\nrange: string\n\n
"},{"location":"recipe/steps/","title":"Slot: steps","text":"

a semicolon separated list of the individual steps involved in this recipe

URI: recipe:steps

"},{"location":"recipe/steps/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no"},{"location":"recipe/steps/#properties","title":"Properties","text":""},{"location":"recipe/steps/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/steps/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/steps/#schema-source","title":"Schema Source","text":""},{"location":"recipe/steps/#linkml-source","title":"LinkML Source","text":"
name: steps\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: a semicolon separated list of the individual steps involved in this recipe\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nmultivalued: true\nalias: steps\nowner: Recipe\ndomain_of:\n- Recipe\nrange: Step\n\n
"},{"location":"recipe/subject/","title":"Slot: subject","text":"

URI: recipe:subject

"},{"location":"recipe/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/subject/#properties","title":"Properties","text":""},{"location":"recipe/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/subject/#schema-source","title":"Schema Source","text":""},{"location":"recipe/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"recipe/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: recipe:subject_qualifier

"},{"location":"recipe/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/subject_qualifier/#properties","title":"Properties","text":""},{"location":"recipe/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"recipe/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"recipe/subject_text/","title":"Slot: subject_text","text":"

URI: recipe:subject_text

"},{"location":"recipe/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"recipe/subject_text/#properties","title":"Properties","text":""},{"location":"recipe/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"recipe/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"recipe/title/","title":"Slot: title","text":"

The title of the publication

URI: recipe:title

"},{"location":"recipe/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"recipe/title/#properties","title":"Properties","text":""},{"location":"recipe/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/title/#schema-source","title":"Schema Source","text":""},{"location":"recipe/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"recipe/triples/","title":"Slot: triples","text":"

URI: recipe:triples

"},{"location":"recipe/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"recipe/triples/#properties","title":"Properties","text":""},{"location":"recipe/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/triples/#schema-source","title":"Schema Source","text":""},{"location":"recipe/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"recipe/unit/","title":"Slot: unit","text":"

the unit of the quantity, e.g. grams, cups, etc.

URI: qudt:unit

"},{"location":"recipe/unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Quantity no"},{"location":"recipe/unit/#properties","title":"Properties","text":""},{"location":"recipe/unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/unit/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/unit/#schema-source","title":"Schema Source","text":""},{"location":"recipe/unit/#linkml-source","title":"LinkML Source","text":"
name: unit\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: the unit of the quantity, e.g. grams, cups, etc.\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: qudt:unit\nalias: unit\nowner: Quantity\ndomain_of:\n- Quantity\nrange: Unit\n\n
"},{"location":"recipe/url/","title":"Slot: url","text":"

URI: rdf:Resource

"},{"location":"recipe/url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no"},{"location":"recipe/url/#properties","title":"Properties","text":""},{"location":"recipe/url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/url/#annotations","title":"Annotations","text":"property value prompt.skip True"},{"location":"recipe/url/#schema-source","title":"Schema Source","text":""},{"location":"recipe/url/#linkml-source","title":"LinkML Source","text":"
name: url\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'True'\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: rdf:Resource\nidentifier: true\nalias: url\nowner: Recipe\ndomain_of:\n- Recipe\nrange: uriorcurie\nrequired: true\n\n
"},{"location":"recipe/utensils/","title":"Slot: utensils","text":"

the kitchen utensil used in this step (e.g. pan, bowl)

URI: RO:0002500

"},{"location":"recipe/utensils/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Step no"},{"location":"recipe/utensils/#properties","title":"Properties","text":""},{"location":"recipe/utensils/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/utensils/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/utensils/#schema-source","title":"Schema Source","text":""},{"location":"recipe/utensils/#linkml-source","title":"LinkML Source","text":"
name: utensils\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: the kitchen utensil used in this step (e.g. pan, bowl)\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: RO:0002500\nmultivalued: true\nalias: utensils\nowner: Step\ndomain_of:\n- Step\nrange: UtensilType\n\n
"},{"location":"recipe/value/","title":"Slot: value","text":"

the value of the quantity

URI: recipe:value

"},{"location":"recipe/value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Quantity no"},{"location":"recipe/value/#properties","title":"Properties","text":""},{"location":"recipe/value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/value/#annotations","title":"Annotations","text":"property value owl DataProperty, DataHasValue"},{"location":"recipe/value/#schema-source","title":"Schema Source","text":""},{"location":"recipe/value/#linkml-source","title":"LinkML Source","text":"
name: value\nannotations:\n  owl:\n    tag: owl\n    value: DataProperty, DataHasValue\ndescription: the value of the quantity\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: value\nowner: Quantity\ndomain_of:\n- Quantity\nrange: string\n\n
"},{"location":"traits/","title":"Traits Template","text":"

A template for Traits

URI: http://w3id.org/ontogpt/traits

Name: traits

"},{"location":"traits/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nTaxon {\n\n}\nTrait {\n    string id  \n    string label  \n}\n\nTaxon ||--}o Trait : \"metabolic_traits\"\nTaxon ||--}o Trait : \"morphological_traits\"\nTaxon ||--}o Trait : \"genetic_traits\"\nTaxon ||--}o Trait : \"cellular_traits\"\nTaxon ||--}o Trait : \"ecological_traits\"\nTaxon ||--}o Trait : \"reproductive_traits\"\nTaxon ||--}o Trait : \"survival_traits\"\nTaxon ||--}o Trait : \"phenotypic_plasticiticy_traits\"\nTaxon ||--}o Trait : \"preferred_environments\"\n\n
"},{"location":"traits/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None RelationshipType None Trait None Publication None Taxon None TextWithTriples None"},{"location":"traits/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication cellular_traits The cellular traits for the taxon combined_text ecological_traits The ecological traits for the taxon extracted_object The complex objects extracted from the text full_text The full text of the publication genetic_traits The genetic traits for the taxon id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing metabolic_traits The metabolic traits for the taxon morphological_traits The morphological traits for the taxon named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text phenotypic_plasticiticy_traits The phenotypic plasticiticy traits for the taxon predicate preferred_environments The preferred environments for the taxon prompt publication qualifier A qualifier for the statements, e raw_completion_output reproductive_traits The reproductive traits for the taxon subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text survival_traits The survival traits for the taxon title The title of the publication triples"},{"location":"traits/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"traits/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"traits/#subsets","title":"Subsets","text":"Subset Description"},{"location":"traits/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: traits:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"traits/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"traits/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"traits/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:AnnotatorResult native traits:AnnotatorResult"},{"location":"traits/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n\n
"},{"location":"traits/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"traits/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"traits/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"traits/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"traits/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Any/#schema-source","title":"Schema Source","text":""},{"location":"traits/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native traits:Any"},{"location":"traits/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/traits\nclass_uri: linkml:Any\n\n
"},{"location":"traits/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/traits\nclass_uri: linkml:Any\n\n
"},{"location":"traits/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"traits/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"traits/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: traits:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"traits/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"traits/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"traits/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"traits/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:CompoundExpression native traits:CompoundExpression"},{"location":"traits/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/traits\nabstract: true\n\n
"},{"location":"traits/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/traits\nabstract: true\n\n
"},{"location":"traits/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"traits/Curie/#comments","title":"Comments","text":""},{"location":"traits/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Curie/#schema-source","title":"Schema Source","text":""},{"location":"traits/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"traits/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Date/#schema-source","title":"Schema Source","text":""},{"location":"traits/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"traits/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"traits/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"traits/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"traits/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"traits/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"traits/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"traits/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Double/#schema-source","title":"Schema Source","text":""},{"location":"traits/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: traits:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"traits/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"traits/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"traits/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:ExtractionResult native traits:ExtractionResult"},{"location":"traits/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"traits/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"traits/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"traits/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Float/#schema-source","title":"Schema Source","text":""},{"location":"traits/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"traits/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Integer/#schema-source","title":"Schema Source","text":""},{"location":"traits/NamedEntity/","title":"Class: NamedEntity","text":"

URI: traits:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"traits/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"traits/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"traits/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"traits/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"traits/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:NamedEntity native traits:NamedEntity"},{"location":"traits/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/traits\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/traits\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"traits/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/traits\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/traits\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"traits/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"traits/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"traits/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"traits/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"traits/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"traits/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"traits/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"traits/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"traits/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"traits/Objectidentifier/#comments","title":"Comments","text":""},{"location":"traits/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"traits/Publication/","title":"Class: Publication","text":"

URI: traits:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"traits/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"traits/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"traits/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Publication/#schema-source","title":"Schema Source","text":""},{"location":"traits/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:Publication native traits:Publication"},{"location":"traits/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/traits\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n\n
"},{"location":"traits/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/traits\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"traits/RelationshipType/","title":"Class: RelationshipType","text":"

URI: traits:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"traits/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"traits/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"traits/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"traits/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"traits/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"traits/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:RelationshipType native traits:RelationshipType"},{"location":"traits/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: NamedEntity\n\n
"},{"location":"traits/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/traits\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"traits/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"traits/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/String/#schema-source","title":"Schema Source","text":""},{"location":"traits/Taxon/","title":"Class: Taxon","text":"

URI: traits:Taxon

erDiagram\nTaxon {\n\n}\nTrait {\n    string id  \n    string label  \n}\n\nTaxon ||--}o Trait : \"metabolic_traits\"\nTaxon ||--}o Trait : \"morphological_traits\"\nTaxon ||--}o Trait : \"genetic_traits\"\nTaxon ||--}o Trait : \"cellular_traits\"\nTaxon ||--}o Trait : \"ecological_traits\"\nTaxon ||--}o Trait : \"reproductive_traits\"\nTaxon ||--}o Trait : \"survival_traits\"\nTaxon ||--}o Trait : \"phenotypic_plasticiticy_traits\"\nTaxon ||--}o Trait : \"preferred_environments\"\n\n
"},{"location":"traits/Taxon/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance metabolic_traits 0..* Trait The metabolic traits for the taxon direct morphological_traits 0..* Trait The morphological traits for the taxon direct genetic_traits 0..* Trait The genetic traits for the taxon direct cellular_traits 0..* Trait The cellular traits for the taxon direct ecological_traits 0..* Trait The ecological traits for the taxon direct reproductive_traits 0..* Trait The reproductive traits for the taxon direct survival_traits 0..* Trait The survival traits for the taxon direct phenotypic_plasticiticy_traits 0..* Trait The phenotypic plasticiticy traits for the taxon direct preferred_environments 0..* Trait The preferred environments for the taxon direct"},{"location":"traits/Taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Taxon/#schema-source","title":"Schema Source","text":""},{"location":"traits/Taxon/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:Taxon native traits:Taxon"},{"location":"traits/Taxon/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/Taxon/#direct","title":"Direct","text":"
name: Taxon\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  metabolic_traits:\n    name: metabolic_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism metabolic trait\n    description: The metabolic traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  morphological_traits:\n    name: morphological_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism morphological\n          trait\n    description: The morphological traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  genetic_traits:\n    name: genetic_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism genetic trait\n    description: The genetic traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  cellular_traits:\n    name: cellular_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism cellular trait\n    description: The cellular traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  ecological_traits:\n    name: ecological_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism ecological trait\n    description: The ecological traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  reproductive_traits:\n    name: reproductive_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism reproductive\n          trait\n    description: The reproductive traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  survival_traits:\n    name: survival_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism survival trait\n    description: The survival traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  phenotypic_plasticiticy_traits:\n    name: phenotypic_plasticiticy_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism phenotypic plasticiticy\n          trait\n    description: The phenotypic plasticiticy traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  preferred_environments:\n    name: preferred_environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of the environments the organism is typically\n          found in or isolated from\n    description: The preferred environments for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\ntree_root: true\n\n
"},{"location":"traits/Taxon/#induced","title":"Induced","text":"
name: Taxon\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  metabolic_traits:\n    name: metabolic_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism metabolic trait\n    description: The metabolic traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: metabolic_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  morphological_traits:\n    name: morphological_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism morphological\n          trait\n    description: The morphological traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: morphological_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  genetic_traits:\n    name: genetic_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism genetic trait\n    description: The genetic traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: genetic_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  cellular_traits:\n    name: cellular_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism cellular trait\n    description: The cellular traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: cellular_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  ecological_traits:\n    name: ecological_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism ecological trait\n    description: The ecological traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: ecological_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  reproductive_traits:\n    name: reproductive_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism reproductive\n          trait\n    description: The reproductive traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: reproductive_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  survival_traits:\n    name: survival_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism survival trait\n    description: The survival traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: survival_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  phenotypic_plasticiticy_traits:\n    name: phenotypic_plasticiticy_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism phenotypic plasticiticy\n          trait\n    description: The phenotypic plasticiticy traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: phenotypic_plasticiticy_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  preferred_environments:\n    name: preferred_environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of the environments the organism is typically\n          found in or isolated from\n    description: The preferred environments for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: preferred_environments\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\ntree_root: true\n\n
"},{"location":"traits/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: traits:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"traits/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"traits/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"traits/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:TextWithTriples native traits:TextWithTriples"},{"location":"traits/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"traits/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"traits/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"traits/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Time/#schema-source","title":"Schema Source","text":""},{"location":"traits/Trait/","title":"Class: Trait","text":"

URI: traits:Trait

erDiagram\nTrait {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"traits/Trait/#inheritance","title":"Inheritance","text":""},{"location":"traits/Trait/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"traits/Trait/#usages","title":"Usages","text":"used by used in type used Taxon metabolic_traits range Trait Taxon morphological_traits range Trait Taxon genetic_traits range Trait Taxon cellular_traits range Trait Taxon ecological_traits range Trait Taxon reproductive_traits range Trait Taxon survival_traits range Trait Taxon phenotypic_plasticiticy_traits range Trait Taxon preferred_environments range Trait"},{"location":"traits/Trait/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Trait/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"traits/Trait/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes"},{"location":"traits/Trait/#schema-source","title":"Schema Source","text":""},{"location":"traits/Trait/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:Trait native traits:Trait"},{"location":"traits/Trait/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/Trait/#direct","title":"Direct","text":"
name: Trait\nid_prefixes:\n- ECOCORE\n- PATO\n- GO\n- OBA\n- BIODIVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: NamedEntity\n\n
"},{"location":"traits/Trait/#induced","title":"Induced","text":"
name: Trait\nid_prefixes:\n- ECOCORE\n- PATO\n- GO\n- OBA\n- BIODIVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Trait\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/traits\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Trait\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"traits/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: traits:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"traits/Triple/#inheritance","title":"Inheritance","text":""},{"location":"traits/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"traits/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"traits/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Triple/#schema-source","title":"Schema Source","text":""},{"location":"traits/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:Triple native traits:Triple"},{"location":"traits/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"traits/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"traits/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"traits/Uri/#comments","title":"Comments","text":""},{"location":"traits/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Uri/#schema-source","title":"Schema Source","text":""},{"location":"traits/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"traits/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"traits/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: traits:abstract

"},{"location":"traits/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"traits/abstract/#properties","title":"Properties","text":""},{"location":"traits/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/abstract/#schema-source","title":"Schema Source","text":""},{"location":"traits/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"traits/cellular_traits/","title":"Slot: cellular_traits","text":"

The cellular traits for the taxon.

URI: traits:cellular_traits

"},{"location":"traits/cellular_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/cellular_traits/#properties","title":"Properties","text":""},{"location":"traits/cellular_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/cellular_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism cellular trait"},{"location":"traits/cellular_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/cellular_traits/#linkml-source","title":"LinkML Source","text":"
name: cellular_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism cellular trait\ndescription: The cellular traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: cellular_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/combined_text/","title":"Slot: combined_text","text":"

URI: traits:combined_text

"},{"location":"traits/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"traits/combined_text/#properties","title":"Properties","text":""},{"location":"traits/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"traits/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"traits/ecological_traits/","title":"Slot: ecological_traits","text":"

The ecological traits for the taxon.

URI: traits:ecological_traits

"},{"location":"traits/ecological_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/ecological_traits/#properties","title":"Properties","text":""},{"location":"traits/ecological_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/ecological_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism ecological trait"},{"location":"traits/ecological_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/ecological_traits/#linkml-source","title":"LinkML Source","text":"
name: ecological_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism ecological trait\ndescription: The ecological traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: ecological_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: traits:extracted_object

"},{"location":"traits/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/extracted_object/#properties","title":"Properties","text":""},{"location":"traits/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"traits/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"traits/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: traits:full_text

"},{"location":"traits/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"traits/full_text/#properties","title":"Properties","text":""},{"location":"traits/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/full_text/#schema-source","title":"Schema Source","text":""},{"location":"traits/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"traits/genetic_traits/","title":"Slot: genetic_traits","text":"

The genetic traits for the taxon.

URI: traits:genetic_traits

"},{"location":"traits/genetic_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/genetic_traits/#properties","title":"Properties","text":""},{"location":"traits/genetic_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/genetic_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism genetic trait"},{"location":"traits/genetic_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/genetic_traits/#linkml-source","title":"LinkML Source","text":"
name: genetic_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism genetic trait\ndescription: The genetic traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: genetic_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/id/","title":"Slot: id","text":"

URI: traits:id

"},{"location":"traits/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Trait no NamedEntity no RelationshipType no Publication no"},{"location":"traits/id/#properties","title":"Properties","text":""},{"location":"traits/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"traits/input_id/","title":"Slot: input_id","text":"

URI: traits:input_id

"},{"location":"traits/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/input_id/#properties","title":"Properties","text":""},{"location":"traits/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/input_id/#schema-source","title":"Schema Source","text":""},{"location":"traits/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"traits/input_text/","title":"Slot: input_text","text":"

URI: traits:input_text

"},{"location":"traits/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/input_text/#properties","title":"Properties","text":""},{"location":"traits/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/input_text/#schema-source","title":"Schema Source","text":""},{"location":"traits/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"traits/input_title/","title":"Slot: input_title","text":"

URI: traits:input_title

"},{"location":"traits/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/input_title/#properties","title":"Properties","text":""},{"location":"traits/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/input_title/#schema-source","title":"Schema Source","text":""},{"location":"traits/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"traits/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"traits/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Trait no NamedEntity no RelationshipType no"},{"location":"traits/label/#properties","title":"Properties","text":""},{"location":"traits/label/#aliases","title":"Aliases","text":""},{"location":"traits/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"traits/label/#schema-source","title":"Schema Source","text":""},{"location":"traits/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/traits\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"traits/metabolic_traits/","title":"Slot: metabolic_traits","text":"

The metabolic traits for the taxon.

URI: traits:metabolic_traits

"},{"location":"traits/metabolic_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/metabolic_traits/#properties","title":"Properties","text":""},{"location":"traits/metabolic_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/metabolic_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism metabolic trait"},{"location":"traits/metabolic_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/metabolic_traits/#linkml-source","title":"LinkML Source","text":"
name: metabolic_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism metabolic trait\ndescription: The metabolic traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: metabolic_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/morphological_traits/","title":"Slot: morphological_traits","text":"

The morphological traits for the taxon.

URI: traits:morphological_traits

"},{"location":"traits/morphological_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/morphological_traits/#properties","title":"Properties","text":""},{"location":"traits/morphological_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/morphological_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism morphological trait"},{"location":"traits/morphological_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/morphological_traits/#linkml-source","title":"LinkML Source","text":"
name: morphological_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism morphological trait\ndescription: The morphological traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: morphological_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: traits:named_entities

"},{"location":"traits/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/named_entities/#properties","title":"Properties","text":""},{"location":"traits/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"traits/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"traits/object/","title":"Slot: object","text":"

URI: traits:object

"},{"location":"traits/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/object/#properties","title":"Properties","text":""},{"location":"traits/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/object/#schema-source","title":"Schema Source","text":""},{"location":"traits/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"traits/object_id/","title":"Slot: object_id","text":"

URI: traits:object_id

"},{"location":"traits/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"traits/object_id/#properties","title":"Properties","text":""},{"location":"traits/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/object_id/#schema-source","title":"Schema Source","text":""},{"location":"traits/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"traits/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: traits:object_qualifier

"},{"location":"traits/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/object_qualifier/#properties","title":"Properties","text":""},{"location":"traits/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"traits/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"traits/object_text/","title":"Slot: object_text","text":"

URI: traits:object_text

"},{"location":"traits/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"traits/object_text/#properties","title":"Properties","text":""},{"location":"traits/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/object_text/#schema-source","title":"Schema Source","text":""},{"location":"traits/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"traits/phenotypic_plasticiticy_traits/","title":"Slot: phenotypic_plasticiticy_traits","text":"

The phenotypic plasticiticy traits for the taxon.

URI: traits:phenotypic_plasticiticy_traits

"},{"location":"traits/phenotypic_plasticiticy_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/phenotypic_plasticiticy_traits/#properties","title":"Properties","text":""},{"location":"traits/phenotypic_plasticiticy_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/phenotypic_plasticiticy_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism phenotypic plasticiticy trait"},{"location":"traits/phenotypic_plasticiticy_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/phenotypic_plasticiticy_traits/#linkml-source","title":"LinkML Source","text":"
name: phenotypic_plasticiticy_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism phenotypic plasticiticy\n      trait\ndescription: The phenotypic plasticiticy traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: phenotypic_plasticiticy_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/predicate/","title":"Slot: predicate","text":"

URI: traits:predicate

"},{"location":"traits/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/predicate/#properties","title":"Properties","text":""},{"location":"traits/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/predicate/#schema-source","title":"Schema Source","text":""},{"location":"traits/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"traits/preferred_environments/","title":"Slot: preferred_environments","text":"

The preferred environments for the taxon.

URI: traits:preferred_environments

"},{"location":"traits/preferred_environments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/preferred_environments/#properties","title":"Properties","text":""},{"location":"traits/preferred_environments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/preferred_environments/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of the environments the organism is typically found in or isolated from"},{"location":"traits/preferred_environments/#schema-source","title":"Schema Source","text":""},{"location":"traits/preferred_environments/#linkml-source","title":"LinkML Source","text":"
name: preferred_environments\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of the environments the organism is typically\n      found in or isolated from\ndescription: The preferred environments for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: preferred_environments\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/prompt/","title":"Slot: prompt","text":"

URI: traits:prompt

"},{"location":"traits/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/prompt/#properties","title":"Properties","text":""},{"location":"traits/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/prompt/#schema-source","title":"Schema Source","text":""},{"location":"traits/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"traits/publication/","title":"Slot: publication","text":"

URI: traits:publication

"},{"location":"traits/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"traits/publication/#properties","title":"Properties","text":""},{"location":"traits/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"traits/publication/#schema-source","title":"Schema Source","text":""},{"location":"traits/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"traits/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: traits:qualifier

"},{"location":"traits/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/qualifier/#properties","title":"Properties","text":""},{"location":"traits/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"traits/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"traits/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: traits:raw_completion_output

"},{"location":"traits/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/raw_completion_output/#properties","title":"Properties","text":""},{"location":"traits/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"traits/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"traits/reproductive_traits/","title":"Slot: reproductive_traits","text":"

The reproductive traits for the taxon.

URI: traits:reproductive_traits

"},{"location":"traits/reproductive_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/reproductive_traits/#properties","title":"Properties","text":""},{"location":"traits/reproductive_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/reproductive_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism reproductive trait"},{"location":"traits/reproductive_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/reproductive_traits/#linkml-source","title":"LinkML Source","text":"
name: reproductive_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism reproductive trait\ndescription: The reproductive traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: reproductive_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/subject/","title":"Slot: subject","text":"

URI: traits:subject

"},{"location":"traits/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/subject/#properties","title":"Properties","text":""},{"location":"traits/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/subject/#schema-source","title":"Schema Source","text":""},{"location":"traits/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"traits/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: traits:subject_qualifier

"},{"location":"traits/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/subject_qualifier/#properties","title":"Properties","text":""},{"location":"traits/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"traits/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"traits/subject_text/","title":"Slot: subject_text","text":"

URI: traits:subject_text

"},{"location":"traits/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"traits/subject_text/#properties","title":"Properties","text":""},{"location":"traits/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"traits/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"traits/survival_traits/","title":"Slot: survival_traits","text":"

The survival traits for the taxon.

URI: traits:survival_traits

"},{"location":"traits/survival_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/survival_traits/#properties","title":"Properties","text":""},{"location":"traits/survival_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/survival_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism survival trait"},{"location":"traits/survival_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/survival_traits/#linkml-source","title":"LinkML Source","text":"
name: survival_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism survival trait\ndescription: The survival traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: survival_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/title/","title":"Slot: title","text":"

The title of the publication

URI: traits:title

"},{"location":"traits/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"traits/title/#properties","title":"Properties","text":""},{"location":"traits/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/title/#schema-source","title":"Schema Source","text":""},{"location":"traits/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"traits/traits/","title":"traits","text":"

A template for Traits

URI: http://w3id.org/ontogpt/traits

"},{"location":"traits/triples/","title":"Slot: triples","text":"

URI: traits:triples

"},{"location":"traits/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"traits/triples/#properties","title":"Properties","text":""},{"location":"traits/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/triples/#schema-source","title":"Schema Source","text":""},{"location":"traits/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"treatment/","title":"MAXO treatment Template","text":"

A template for MAXO treatments

URI: http://w3id.org/ontogpt/treatment

Name: treatment-template

"},{"location":"treatment/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nDiseaseTreatmentSummary {\n\n}\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nDiseaseTreatmentSummary ||--|o Disease : \"disease\"\nDiseaseTreatmentSummary ||--}o Drug : \"drugs\"\nDiseaseTreatmentSummary ||--}o Treatment : \"treatments\"\nDiseaseTreatmentSummary ||--}o Treatment : \"contraindications\"\nDiseaseTreatmentSummary ||--}o TreatmentMechanism : \"treatment_mechanisms\"\nDiseaseTreatmentSummary ||--}o TreatmentEfficacy : \"treatment_efficacies\"\nDiseaseTreatmentSummary ||--}o TreatmentAdverseEffect : \"treatment_adverse_effects\"\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"treatment/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None TreatmentAdverseEffect None TreatmentEfficacy None TreatmentMechanism None Triple Abstract parent for Relation Extraction tasks DiseaseTreatmentSummary None ExtractionResult A result of extracting knowledge on text NamedEntity None AdverseEffect None Disease None Drug None Gene None Mechanism None RelationshipType None Symptom None Treatment None Publication None TextWithTriples None"},{"location":"treatment/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication adverse_effects combined_text contraindications semicolon-separated list of therapies and treatments that are contra-indicate... disease the name of the disease that is treated drugs semicolon-separated list of named small molecule drugs efficacy extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing mechanism named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication treatment treatment_adverse_effects semicolon-separated list of treatment to adverse effect associations, e treatment_efficacies semicolon-separated list of treatment to efficacy associations, e treatment_mechanisms semicolon-separated list of treatment to asterisk-separated mechanism associa... treatments semicolon-separated list of therapies and treatments are indicated for treati... triples"},{"location":"treatment/#enumerations","title":"Enumerations","text":"Enumeration Description CHEBIDrugType MAXOActionType MESHTherapeuticType NCITDrugType NCITTActivityType NCITTreatmentType NullDataOptions"},{"location":"treatment/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"treatment/#subsets","title":"Subsets","text":"Subset Description"},{"location":"treatment/AdverseEffect/","title":"Class: AdverseEffect","text":"

URI: treatment:AdverseEffect

erDiagram\nAdverseEffect {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/AdverseEffect/#inheritance","title":"Inheritance","text":""},{"location":"treatment/AdverseEffect/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/AdverseEffect/#usages","title":"Usages","text":"used by used in type used TreatmentAdverseEffect adverse_effects range AdverseEffect"},{"location":"treatment/AdverseEffect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/AdverseEffect/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:ncit"},{"location":"treatment/AdverseEffect/#schema-source","title":"Schema Source","text":""},{"location":"treatment/AdverseEffect/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:AdverseEffect native treatment:AdverseEffect"},{"location":"treatment/AdverseEffect/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/AdverseEffect/#direct","title":"Direct","text":"
name: AdverseEffect\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/AdverseEffect/#induced","title":"Induced","text":"
name: AdverseEffect\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: AdverseEffect\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: AdverseEffect\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: treatment:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"treatment/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"treatment/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"treatment/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:AnnotatorResult native treatment:AnnotatorResult"},{"location":"treatment/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n\n
"},{"location":"treatment/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"treatment/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"treatment/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"treatment/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"treatment/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Any/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native treatment:Any"},{"location":"treatment/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/treatment\nclass_uri: linkml:Any\n\n
"},{"location":"treatment/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/treatment\nclass_uri: linkml:Any\n\n
"},{"location":"treatment/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"treatment/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"treatment/CHEBIDrugType/","title":"Enum: CHEBIDrugType","text":"

URI: CHEBIDrugType

This is a dynamic enum

"},{"location":"treatment/CHEBIDrugType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/CHEBIDrugType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/CHEBIDrugType/#linkml-source","title":"LinkML Source","text":"
name: CHEBIDrugType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:chebi\n  source_nodes:\n  - CHEBI:23888\n  relationship_types:\n  - rdfs:subClassOf\n  - RO:0000087\n\n
"},{"location":"treatment/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: treatment:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"treatment/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"treatment/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"treatment/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"treatment/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:CompoundExpression native treatment:CompoundExpression"},{"location":"treatment/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/treatment\nabstract: true\n\n
"},{"location":"treatment/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/treatment\nabstract: true\n\n
"},{"location":"treatment/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"treatment/Curie/#comments","title":"Comments","text":""},{"location":"treatment/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Curie/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"treatment/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Date/#schema-source","title":"Schema Source","text":""},{"location":"treatment/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"treatment/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"treatment/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"treatment/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Disease/","title":"Class: Disease","text":"

URI: treatment:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Disease/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Disease/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary disease range Disease"},{"location":"treatment/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo"},{"location":"treatment/Disease/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Disease native treatment:Disease"},{"location":"treatment/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Disease/#direct","title":"Direct","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/Disease/#induced","title":"Induced","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/DiseaseTreatmentSummary/","title":"Class: DiseaseTreatmentSummary","text":"

URI: treatment:DiseaseTreatmentSummary

erDiagram\nDiseaseTreatmentSummary {\n\n}\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nDiseaseTreatmentSummary ||--|o Disease : \"disease\"\nDiseaseTreatmentSummary ||--}o Drug : \"drugs\"\nDiseaseTreatmentSummary ||--}o Treatment : \"treatments\"\nDiseaseTreatmentSummary ||--}o Treatment : \"contraindications\"\nDiseaseTreatmentSummary ||--}o TreatmentMechanism : \"treatment_mechanisms\"\nDiseaseTreatmentSummary ||--}o TreatmentEfficacy : \"treatment_efficacies\"\nDiseaseTreatmentSummary ||--}o TreatmentAdverseEffect : \"treatment_adverse_effects\"\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"treatment/DiseaseTreatmentSummary/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance disease 0..1 Disease the name of the disease that is treated direct drugs 0..* Drug semicolon-separated list of named small molecule drugs direct treatments 0..* Treatment semicolon-separated list of therapies and treatments are indicated for treati... direct contraindications 0..* Treatment semicolon-separated list of therapies and treatments that are contra-indicate... direct treatment_mechanisms 0..* TreatmentMechanism semicolon-separated list of treatment to asterisk-separated mechanism associa... direct treatment_efficacies 0..* TreatmentEfficacy semicolon-separated list of treatment to efficacy associations, e direct treatment_adverse_effects 0..* TreatmentAdverseEffect semicolon-separated list of treatment to adverse effect associations, e direct"},{"location":"treatment/DiseaseTreatmentSummary/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/DiseaseTreatmentSummary/#schema-source","title":"Schema Source","text":""},{"location":"treatment/DiseaseTreatmentSummary/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:DiseaseTreatmentSummary native treatment:DiseaseTreatmentSummary"},{"location":"treatment/DiseaseTreatmentSummary/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/DiseaseTreatmentSummary/#direct","title":"Direct","text":"
name: DiseaseTreatmentSummary\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  disease:\n    name: disease\n    description: the name of the disease that is treated.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: Disease\n  drugs:\n    name: drugs\n    description: semicolon-separated list of named small molecule drugs\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: Drug\n  treatments:\n    name: treatments\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Imatinib, exercise, surgery\n    description: semicolon-separated list of therapies and treatments are indicated\n      for treating the disease.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: Treatment\n  contraindications:\n    name: contraindications\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Beta-blockers, exercise, surgery\n    description: semicolon-separated list of therapies and treatments that are contra-indicated\n      for the disease, and should not be used, due to risk of adverse effects.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: Treatment\n  treatment_mechanisms:\n    name: treatment_mechanisms\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to asterisk-separated mechanism\n      associations\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: TreatmentMechanism\n  treatment_efficacies:\n    name: treatment_efficacies\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to efficacy associations, e.g.\n      Imatinib*effective\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: TreatmentEfficacy\n  treatment_adverse_effects:\n    name: treatment_adverse_effects\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to adverse effect associations,\n      e.g. Imatinib*nausea\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: TreatmentAdverseEffect\ntree_root: true\n\n
"},{"location":"treatment/DiseaseTreatmentSummary/#induced","title":"Induced","text":"
name: DiseaseTreatmentSummary\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  disease:\n    name: disease\n    description: the name of the disease that is treated.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: disease\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: Disease\n  drugs:\n    name: drugs\n    description: semicolon-separated list of named small molecule drugs\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: drugs\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: Drug\n  treatments:\n    name: treatments\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Imatinib, exercise, surgery\n    description: semicolon-separated list of therapies and treatments are indicated\n      for treating the disease.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: treatments\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: Treatment\n  contraindications:\n    name: contraindications\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Beta-blockers, exercise, surgery\n    description: semicolon-separated list of therapies and treatments that are contra-indicated\n      for the disease, and should not be used, due to risk of adverse effects.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: contraindications\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: Treatment\n  treatment_mechanisms:\n    name: treatment_mechanisms\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to asterisk-separated mechanism\n      associations\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: treatment_mechanisms\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: TreatmentMechanism\n  treatment_efficacies:\n    name: treatment_efficacies\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to efficacy associations, e.g.\n      Imatinib*effective\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: treatment_efficacies\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: TreatmentEfficacy\n  treatment_adverse_effects:\n    name: treatment_adverse_effects\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to adverse effect associations,\n      e.g. Imatinib*nausea\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: treatment_adverse_effects\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: TreatmentAdverseEffect\ntree_root: true\n\n
"},{"location":"treatment/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"treatment/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Double/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Drug/","title":"Class: Drug","text":"

URI: treatment:Drug

erDiagram\nDrug {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Drug/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Drug/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Drug/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary drugs range Drug"},{"location":"treatment/Drug/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Drug/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi, sqlite:obo:drugbank"},{"location":"treatment/Drug/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Drug/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Drug native treatment:Drug"},{"location":"treatment/Drug/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Drug/#direct","title":"Direct","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/Drug/#induced","title":"Induced","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: treatment:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"treatment/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"treatment/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"treatment/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:ExtractionResult native treatment:ExtractionResult"},{"location":"treatment/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"treatment/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"treatment/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"treatment/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Float/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Gene/","title":"Class: Gene","text":"

URI: treatment:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Gene/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"treatment/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, obo:sql:hgnc, bioportal:hgnc-nr"},{"location":"treatment/Gene/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Gene native treatment:Gene"},{"location":"treatment/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, obo:sql:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, obo:sql:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"treatment/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Integer/#schema-source","title":"Schema Source","text":""},{"location":"treatment/MAXOActionType/","title":"Enum: MAXOActionType","text":"

URI: MAXOActionType

This is a dynamic enum

"},{"location":"treatment/MAXOActionType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/MAXOActionType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/MAXOActionType/#linkml-source","title":"LinkML Source","text":"
name: MAXOActionType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:maxo\n  source_nodes:\n  - MAXO:0000001\n\n
"},{"location":"treatment/MESHTherapeuticType/","title":"Enum: MESHTherapeuticType","text":"

URI: MESHTherapeuticType

This is a dynamic enum

"},{"location":"treatment/MESHTherapeuticType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/MESHTherapeuticType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/MESHTherapeuticType/#linkml-source","title":"LinkML Source","text":"
name: MESHTherapeuticType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:mesh\n  source_nodes:\n  - MESH:D013812\n\n
"},{"location":"treatment/Mechanism/","title":"Class: Mechanism","text":"

URI: treatment:Mechanism

erDiagram\nMechanism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Mechanism/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Mechanism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Mechanism/#usages","title":"Usages","text":"used by used in type used TreatmentMechanism mechanism range Mechanism"},{"location":"treatment/Mechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Mechanism/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh"},{"location":"treatment/Mechanism/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Mechanism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Mechanism native treatment:Mechanism"},{"location":"treatment/Mechanism/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Mechanism/#direct","title":"Direct","text":"
name: Mechanism\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/Mechanism/#induced","title":"Induced","text":"
name: Mechanism\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Mechanism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Mechanism\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/NCITDrugType/","title":"Enum: NCITDrugType","text":"

URI: NCITDrugType

This is a dynamic enum

"},{"location":"treatment/NCITDrugType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/NCITDrugType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NCITDrugType/#linkml-source","title":"LinkML Source","text":"
name: NCITDrugType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C1908\n\n
"},{"location":"treatment/NCITTActivityType/","title":"Enum: NCITTActivityType","text":"

URI: NCITTActivityType

This is a dynamic enum

"},{"location":"treatment/NCITTActivityType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/NCITTActivityType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NCITTActivityType/#linkml-source","title":"LinkML Source","text":"
name: NCITTActivityType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C43431\n\n
"},{"location":"treatment/NCITTreatmentType/","title":"Enum: NCITTreatmentType","text":"

URI: NCITTreatmentType

This is a dynamic enum

"},{"location":"treatment/NCITTreatmentType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/NCITTreatmentType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NCITTreatmentType/#linkml-source","title":"LinkML Source","text":"
name: NCITTreatmentType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C25218\n\n
"},{"location":"treatment/NamedEntity/","title":"Class: NamedEntity","text":"

URI: treatment:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"treatment/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"treatment/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"treatment/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:NamedEntity native treatment:NamedEntity"},{"location":"treatment/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/treatment\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"treatment/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/treatment\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"treatment/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"treatment/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"treatment/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"treatment/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"treatment/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"treatment/Objectidentifier/#comments","title":"Comments","text":""},{"location":"treatment/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Publication/","title":"Class: Publication","text":"

URI: treatment:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"treatment/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"treatment/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"treatment/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Publication/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Publication native treatment:Publication"},{"location":"treatment/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/treatment\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n\n
"},{"location":"treatment/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/treatment\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"treatment/RelationshipType/","title":"Class: RelationshipType","text":"

URI: treatment:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"treatment/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"treatment/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"treatment/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:RelationshipType native treatment:RelationshipType"},{"location":"treatment/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"treatment/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/String/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Symptom/","title":"Class: Symptom","text":"

URI: treatment:Symptom

erDiagram\nSymptom {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Symptom/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Symptom/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Symptom/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"treatment/Symptom/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp"},{"location":"treatment/Symptom/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Symptom/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Symptom native treatment:Symptom"},{"location":"treatment/Symptom/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Symptom/#direct","title":"Direct","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/Symptom/#induced","title":"Induced","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: treatment:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"treatment/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"treatment/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"treatment/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:TextWithTriples native treatment:TextWithTriples"},{"location":"treatment/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"treatment/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"treatment/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"treatment/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Time/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Treatment/","title":"Class: Treatment","text":"

URI: treatment:Treatment

erDiagram\nTreatment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Treatment/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Treatment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Treatment/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary treatments range Treatment DiseaseTreatmentSummary contraindications range Treatment TreatmentMechanism treatment range Treatment TreatmentAdverseEffect treatment range Treatment TreatmentEfficacy treatment range Treatment"},{"location":"treatment/Treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Treatment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi"},{"location":"treatment/Treatment/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Treatment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Treatment native treatment:Treatment"},{"location":"treatment/Treatment/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Treatment/#direct","title":"Direct","text":"
name: Treatment\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nvalues_from:\n- NCITDrugType\n- NCITTreatmentType\n- NCITActivityType\n- MAXOTreatmentType\n- MESHTherapeuticType\n- CHEBIDrugType\n\n
"},{"location":"treatment/Treatment/#induced","title":"Induced","text":"
name: Treatment\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nvalues_from:\n- NCITDrugType\n- NCITTreatmentType\n- NCITActivityType\n- MAXOTreatmentType\n- MESHTherapeuticType\n- CHEBIDrugType\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/TreatmentAdverseEffect/","title":"Class: TreatmentAdverseEffect","text":"

URI: treatment:TreatmentAdverseEffect

erDiagram\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\n\n
"},{"location":"treatment/TreatmentAdverseEffect/#inheritance","title":"Inheritance","text":""},{"location":"treatment/TreatmentAdverseEffect/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct adverse_effects 0..* AdverseEffect direct"},{"location":"treatment/TreatmentAdverseEffect/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary treatment_adverse_effects range TreatmentAdverseEffect"},{"location":"treatment/TreatmentAdverseEffect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/TreatmentAdverseEffect/#schema-source","title":"Schema Source","text":""},{"location":"treatment/TreatmentAdverseEffect/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:TreatmentAdverseEffect native treatment:TreatmentAdverseEffect"},{"location":"treatment/TreatmentAdverseEffect/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/TreatmentAdverseEffect/#direct","title":"Direct","text":"
name: TreatmentAdverseEffect\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    range: Treatment\n  adverse_effects:\n    name: adverse_effects\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: AdverseEffect\n\n
"},{"location":"treatment/TreatmentAdverseEffect/#induced","title":"Induced","text":"
name: TreatmentAdverseEffect\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    alias: treatment\n    owner: TreatmentAdverseEffect\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  adverse_effects:\n    name: adverse_effects\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: adverse_effects\n    owner: TreatmentAdverseEffect\n    domain_of:\n    - TreatmentAdverseEffect\n    range: AdverseEffect\n\n
"},{"location":"treatment/TreatmentEfficacy/","title":"Class: TreatmentEfficacy","text":"

URI: treatment:TreatmentEfficacy

erDiagram\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\n\n
"},{"location":"treatment/TreatmentEfficacy/#inheritance","title":"Inheritance","text":""},{"location":"treatment/TreatmentEfficacy/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct efficacy 0..1 String direct"},{"location":"treatment/TreatmentEfficacy/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary treatment_efficacies range TreatmentEfficacy"},{"location":"treatment/TreatmentEfficacy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/TreatmentEfficacy/#schema-source","title":"Schema Source","text":""},{"location":"treatment/TreatmentEfficacy/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:TreatmentEfficacy native treatment:TreatmentEfficacy"},{"location":"treatment/TreatmentEfficacy/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/TreatmentEfficacy/#direct","title":"Direct","text":"
name: TreatmentEfficacy\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    range: Treatment\n  efficacy:\n    name: efficacy\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: string\n\n
"},{"location":"treatment/TreatmentEfficacy/#induced","title":"Induced","text":"
name: TreatmentEfficacy\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    alias: treatment\n    owner: TreatmentEfficacy\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  efficacy:\n    name: efficacy\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: efficacy\n    owner: TreatmentEfficacy\n    domain_of:\n    - TreatmentEfficacy\n    range: string\n\n
"},{"location":"treatment/TreatmentMechanism/","title":"Class: TreatmentMechanism","text":"

URI: treatment:TreatmentMechanism

erDiagram\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"treatment/TreatmentMechanism/#inheritance","title":"Inheritance","text":""},{"location":"treatment/TreatmentMechanism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct mechanism 0..1 Mechanism direct"},{"location":"treatment/TreatmentMechanism/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary treatment_mechanisms range TreatmentMechanism"},{"location":"treatment/TreatmentMechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/TreatmentMechanism/#schema-source","title":"Schema Source","text":""},{"location":"treatment/TreatmentMechanism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:TreatmentMechanism native treatment:TreatmentMechanism"},{"location":"treatment/TreatmentMechanism/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/TreatmentMechanism/#direct","title":"Direct","text":"
name: TreatmentMechanism\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: Treatment\n  mechanism:\n    name: mechanism\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: Mechanism\n\n
"},{"location":"treatment/TreatmentMechanism/#induced","title":"Induced","text":"
name: TreatmentMechanism\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: treatment\n    owner: TreatmentMechanism\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  mechanism:\n    name: mechanism\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: mechanism\n    owner: TreatmentMechanism\n    domain_of:\n    - TreatmentMechanism\n    range: Mechanism\n\n
"},{"location":"treatment/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: treatment:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"treatment/Triple/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"treatment/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"treatment/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Triple/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Triple native treatment:Triple"},{"location":"treatment/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"treatment/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"treatment/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"treatment/Uri/#comments","title":"Comments","text":""},{"location":"treatment/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Uri/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"treatment/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"treatment/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: treatment:abstract

"},{"location":"treatment/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"treatment/abstract/#properties","title":"Properties","text":""},{"location":"treatment/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/abstract/#schema-source","title":"Schema Source","text":""},{"location":"treatment/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"treatment/adverse_effects/","title":"Slot: adverse_effects","text":"

URI: treatment:adverse_effects

"},{"location":"treatment/adverse_effects/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentAdverseEffect no"},{"location":"treatment/adverse_effects/#properties","title":"Properties","text":""},{"location":"treatment/adverse_effects/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/adverse_effects/#schema-source","title":"Schema Source","text":""},{"location":"treatment/adverse_effects/#linkml-source","title":"LinkML Source","text":"
name: adverse_effects\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: adverse_effects\nowner: TreatmentAdverseEffect\ndomain_of:\n- TreatmentAdverseEffect\nrange: AdverseEffect\n\n
"},{"location":"treatment/combined_text/","title":"Slot: combined_text","text":"

URI: treatment:combined_text

"},{"location":"treatment/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"treatment/combined_text/#properties","title":"Properties","text":""},{"location":"treatment/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"treatment/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"treatment/contraindications/","title":"Slot: contraindications","text":"

semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.

URI: treatment:contraindications

"},{"location":"treatment/contraindications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/contraindications/#properties","title":"Properties","text":""},{"location":"treatment/contraindications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/contraindications/#annotations","title":"Annotations","text":"property value prompt.examples Beta-blockers, exercise, surgery"},{"location":"treatment/contraindications/#schema-source","title":"Schema Source","text":""},{"location":"treatment/contraindications/#linkml-source","title":"LinkML Source","text":"
name: contraindications\nannotations:\n  prompt.examples:\n    tag: prompt.examples\n    value: Beta-blockers, exercise, surgery\ndescription: semicolon-separated list of therapies and treatments that are contra-indicated\n  for the disease, and should not be used, due to risk of adverse effects.\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: contraindications\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: Treatment\n\n
"},{"location":"treatment/disease/","title":"Slot: disease","text":"

the name of the disease that is treated.

URI: treatment:disease

"},{"location":"treatment/disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/disease/#properties","title":"Properties","text":""},{"location":"treatment/disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/disease/#schema-source","title":"Schema Source","text":""},{"location":"treatment/disease/#linkml-source","title":"LinkML Source","text":"
name: disease\ndescription: the name of the disease that is treated.\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: disease\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: Disease\n\n
"},{"location":"treatment/drugs/","title":"Slot: drugs","text":"

semicolon-separated list of named small molecule drugs

URI: treatment:drugs

"},{"location":"treatment/drugs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/drugs/#properties","title":"Properties","text":""},{"location":"treatment/drugs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/drugs/#schema-source","title":"Schema Source","text":""},{"location":"treatment/drugs/#linkml-source","title":"LinkML Source","text":"
name: drugs\ndescription: semicolon-separated list of named small molecule drugs\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: drugs\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: Drug\n\n
"},{"location":"treatment/efficacy/","title":"Slot: efficacy","text":"

URI: treatment:efficacy

"},{"location":"treatment/efficacy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentEfficacy no"},{"location":"treatment/efficacy/#properties","title":"Properties","text":""},{"location":"treatment/efficacy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/efficacy/#schema-source","title":"Schema Source","text":""},{"location":"treatment/efficacy/#linkml-source","title":"LinkML Source","text":"
name: efficacy\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: efficacy\nowner: TreatmentEfficacy\ndomain_of:\n- TreatmentEfficacy\nrange: string\n\n
"},{"location":"treatment/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: treatment:extracted_object

"},{"location":"treatment/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/extracted_object/#properties","title":"Properties","text":""},{"location":"treatment/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"treatment/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"treatment/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: treatment:full_text

"},{"location":"treatment/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"treatment/full_text/#properties","title":"Properties","text":""},{"location":"treatment/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/full_text/#schema-source","title":"Schema Source","text":""},{"location":"treatment/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"treatment/id/","title":"Slot: id","text":"

URI: treatment:id

"},{"location":"treatment/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Symptom no Disease no AdverseEffect no Treatment no Mechanism no Drug no NamedEntity no RelationshipType no Publication no"},{"location":"treatment/id/#properties","title":"Properties","text":""},{"location":"treatment/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"treatment/input_id/","title":"Slot: input_id","text":"

URI: treatment:input_id

"},{"location":"treatment/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/input_id/#properties","title":"Properties","text":""},{"location":"treatment/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/input_id/#schema-source","title":"Schema Source","text":""},{"location":"treatment/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"treatment/input_text/","title":"Slot: input_text","text":"

URI: treatment:input_text

"},{"location":"treatment/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/input_text/#properties","title":"Properties","text":""},{"location":"treatment/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/input_text/#schema-source","title":"Schema Source","text":""},{"location":"treatment/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"treatment/input_title/","title":"Slot: input_title","text":"

URI: treatment:input_title

"},{"location":"treatment/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/input_title/#properties","title":"Properties","text":""},{"location":"treatment/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/input_title/#schema-source","title":"Schema Source","text":""},{"location":"treatment/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"treatment/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"treatment/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Symptom no Disease no AdverseEffect no Treatment no Mechanism no Drug no NamedEntity no RelationshipType no"},{"location":"treatment/label/#properties","title":"Properties","text":""},{"location":"treatment/label/#aliases","title":"Aliases","text":""},{"location":"treatment/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"treatment/label/#schema-source","title":"Schema Source","text":""},{"location":"treatment/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/treatment\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"treatment/mechanism/","title":"Slot: mechanism","text":"

URI: treatment:mechanism

"},{"location":"treatment/mechanism/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentMechanism no"},{"location":"treatment/mechanism/#properties","title":"Properties","text":""},{"location":"treatment/mechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/mechanism/#schema-source","title":"Schema Source","text":""},{"location":"treatment/mechanism/#linkml-source","title":"LinkML Source","text":"
name: mechanism\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: mechanism\nowner: TreatmentMechanism\ndomain_of:\n- TreatmentMechanism\nrange: Mechanism\n\n
"},{"location":"treatment/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: treatment:named_entities

"},{"location":"treatment/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/named_entities/#properties","title":"Properties","text":""},{"location":"treatment/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"treatment/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"treatment/object/","title":"Slot: object","text":"

URI: treatment:object

"},{"location":"treatment/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"treatment/object/#properties","title":"Properties","text":""},{"location":"treatment/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/object/#schema-source","title":"Schema Source","text":""},{"location":"treatment/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"treatment/object_id/","title":"Slot: object_id","text":"

URI: treatment:object_id

"},{"location":"treatment/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"treatment/object_id/#properties","title":"Properties","text":""},{"location":"treatment/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/object_id/#schema-source","title":"Schema Source","text":""},{"location":"treatment/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"treatment/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: treatment:object_qualifier

"},{"location":"treatment/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"treatment/object_qualifier/#properties","title":"Properties","text":""},{"location":"treatment/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"treatment/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"treatment/object_text/","title":"Slot: object_text","text":"

URI: treatment:object_text

"},{"location":"treatment/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"treatment/object_text/#properties","title":"Properties","text":""},{"location":"treatment/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/object_text/#schema-source","title":"Schema Source","text":""},{"location":"treatment/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"treatment/predicate/","title":"Slot: predicate","text":"

URI: treatment:predicate

"},{"location":"treatment/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"treatment/predicate/#properties","title":"Properties","text":""},{"location":"treatment/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/predicate/#schema-source","title":"Schema Source","text":""},{"location":"treatment/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"treatment/prompt/","title":"Slot: prompt","text":"

URI: treatment:prompt

"},{"location":"treatment/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/prompt/#properties","title":"Properties","text":""},{"location":"treatment/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/prompt/#schema-source","title":"Schema Source","text":""},{"location":"treatment/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"treatment/publication/","title":"Slot: publication","text":"

URI: treatment:publication

"},{"location":"treatment/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"treatment/publication/#properties","title":"Properties","text":""},{"location":"treatment/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"treatment/publication/#schema-source","title":"Schema Source","text":""},{"location":"treatment/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"treatment/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: treatment:qualifier

"},{"location":"treatment/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"treatment/qualifier/#properties","title":"Properties","text":""},{"location":"treatment/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"treatment/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"treatment/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: treatment:raw_completion_output

"},{"location":"treatment/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/raw_completion_output/#properties","title":"Properties","text":""},{"location":"treatment/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"treatment/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"treatment/subject/","title":"Slot: subject","text":"

URI: treatment:subject

"},{"location":"treatment/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"treatment/subject/#properties","title":"Properties","text":""},{"location":"treatment/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/subject/#schema-source","title":"Schema Source","text":""},{"location":"treatment/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"treatment/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: treatment:subject_qualifier

"},{"location":"treatment/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"treatment/subject_qualifier/#properties","title":"Properties","text":""},{"location":"treatment/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"treatment/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"treatment/subject_text/","title":"Slot: subject_text","text":"

URI: treatment:subject_text

"},{"location":"treatment/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"treatment/subject_text/#properties","title":"Properties","text":""},{"location":"treatment/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"treatment/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"treatment/title/","title":"Slot: title","text":"

The title of the publication

URI: treatment:title

"},{"location":"treatment/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"treatment/title/#properties","title":"Properties","text":""},{"location":"treatment/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/title/#schema-source","title":"Schema Source","text":""},{"location":"treatment/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"treatment/treatment-template/","title":"treatment-template","text":"

A template for MAXO treatments

URI: http://w3id.org/ontogpt/treatment

"},{"location":"treatment/treatment/","title":"Slot: treatment","text":"

URI: treatment:treatment

"},{"location":"treatment/treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentMechanism no TreatmentAdverseEffect no TreatmentEfficacy no"},{"location":"treatment/treatment/#properties","title":"Properties","text":""},{"location":"treatment/treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/treatment/#linkml-source","title":"LinkML Source","text":"
name: treatment\nalias: treatment\ndomain_of:\n- TreatmentMechanism\n- TreatmentAdverseEffect\n- TreatmentEfficacy\nrange: string\n\n
"},{"location":"treatment/treatment_adverse_effects/","title":"Slot: treatment_adverse_effects","text":"

semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea

URI: treatment:treatment_adverse_effects

"},{"location":"treatment/treatment_adverse_effects/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/treatment_adverse_effects/#properties","title":"Properties","text":""},{"location":"treatment/treatment_adverse_effects/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/treatment_adverse_effects/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"treatment/treatment_adverse_effects/#schema-source","title":"Schema Source","text":""},{"location":"treatment/treatment_adverse_effects/#linkml-source","title":"LinkML Source","text":"
name: treatment_adverse_effects\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to adverse effect associations,\n  e.g. Imatinib*nausea\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: treatment_adverse_effects\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: TreatmentAdverseEffect\n\n
"},{"location":"treatment/treatment_efficacies/","title":"Slot: treatment_efficacies","text":"

semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective

URI: treatment:treatment_efficacies

"},{"location":"treatment/treatment_efficacies/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/treatment_efficacies/#properties","title":"Properties","text":""},{"location":"treatment/treatment_efficacies/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/treatment_efficacies/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"treatment/treatment_efficacies/#schema-source","title":"Schema Source","text":""},{"location":"treatment/treatment_efficacies/#linkml-source","title":"LinkML Source","text":"
name: treatment_efficacies\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to efficacy associations, e.g.\n  Imatinib*effective\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: treatment_efficacies\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: TreatmentEfficacy\n\n
"},{"location":"treatment/treatment_mechanisms/","title":"Slot: treatment_mechanisms","text":"

semicolon-separated list of treatment to asterisk-separated mechanism associations

URI: treatment:treatment_mechanisms

"},{"location":"treatment/treatment_mechanisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/treatment_mechanisms/#properties","title":"Properties","text":""},{"location":"treatment/treatment_mechanisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/treatment_mechanisms/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"treatment/treatment_mechanisms/#schema-source","title":"Schema Source","text":""},{"location":"treatment/treatment_mechanisms/#linkml-source","title":"LinkML Source","text":"
name: treatment_mechanisms\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to asterisk-separated mechanism\n  associations\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: treatment_mechanisms\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: TreatmentMechanism\n\n
"},{"location":"treatment/treatments/","title":"Slot: treatments","text":"

semicolon-separated list of therapies and treatments are indicated for treating the disease.

URI: treatment:treatments

"},{"location":"treatment/treatments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/treatments/#properties","title":"Properties","text":""},{"location":"treatment/treatments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/treatments/#annotations","title":"Annotations","text":"property value prompt.examples Imatinib, exercise, surgery"},{"location":"treatment/treatments/#schema-source","title":"Schema Source","text":""},{"location":"treatment/treatments/#linkml-source","title":"LinkML Source","text":"
name: treatments\nannotations:\n  prompt.examples:\n    tag: prompt.examples\n    value: Imatinib, exercise, surgery\ndescription: semicolon-separated list of therapies and treatments are indicated for\n  treating the disease.\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: treatments\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: Treatment\n\n
"},{"location":"treatment/triples/","title":"Slot: triples","text":"

URI: treatment:triples

"},{"location":"treatment/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"treatment/triples/#properties","title":"Properties","text":""},{"location":"treatment/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/triples/#schema-source","title":"Schema Source","text":""},{"location":"treatment/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"}]} \ No newline at end of file +{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Introduction","text":"

OntoGPT is a Python package for extracting structured information from text with large language models (LLMs), instruction prompts, and ontology-based grounding. It works well with OpenAI's GPT-3.5 and GPT-4 models as well as a selection of other LLMs. OntoGPT's output can be used for general-purpose natural language tasks (e.g., named entity recognition and relation extraction), summarization, knowledge base and knowledge graph construction, and more.

"},{"location":"#methods","title":"Methods","text":"

Two different strategies for knowledge extraction are currently implemented in OntoGPT:

"},{"location":"#quick-start","title":"Quick Start","text":"

Please see the Setup page on the left for more detailed instructions.

OntoGPT runs on the command line, though there's also a minimal web app interface (see Web Application section below).

  1. Ensure you have Python 3.9 or greater installed.

  2. Install with pip:

    bash pip install ontogpt

  3. Set your OpenAI API key:

    bash runoak set-apikey -e openai <your openai api key>

  4. See the list of all OntoGPT commands:

    bash ontogpt --help

  5. Try a simple example of information extraction:

    bash echo \"One treatment for high blood pressure is carvedilol.\" > example.txt ontogpt extract -i example.txt -t drug

    OntoGPT will retrieve the necessary ontologies and output results to the command line. Your output will provide all extracted objects under the heading extracted_object.

"},{"location":"#web-applications","title":"Web Applications","text":"

There is a bare bones web application for running OntoGPT and viewing results.

First, install the required dependencies with pip by running the following command:

pip install ontogpt[web]\n

Then run this command to start the web application:

web-ontogpt\n

NOTE: We do not recommend hosting this webapp publicly without authentication.

Gene enrichment has its own webapp powered by Streamlit:

streamlit run src/ontogpt/streamlit/spindoctor.py\n
"},{"location":"#citation","title":"Citation","text":"

SPIRES is described further in: Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, Matentzoglu N, et al. Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning. arXiv publication: http://arxiv.org/abs/2304.02711

SPINDOCTOR is described further in: Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv publication: http://arxiv.org/abs/2305.13338

"},{"location":"#contributing","title":"Contributing","text":"

Contributions are welcome! One way to get started with contributing to OntoGPT is to submit an

Contributions on recipes to test welcome from anyone! Just make a PR here. See this list for accepted URLs

"},{"location":"#acknowledgements","title":"Acknowledgements","text":"

We gratefully acknowledge Bosch Research for their support of this research project.

"},{"location":"custom/","title":"Custom Schemas","text":""},{"location":"custom/#build-a-custom-schema","title":"Build a custom schema","text":"

Define a schema (using a subset of LinkML) that describes the structure in which you want to extract knowledge from your text.

There are a number of pre-defined LinkML data models already developed here - src/ontogpt/templates/ which you can use as reference when creating your own data models.

"},{"location":"custom/#the-header","title":"The header","text":"

The header of the schema defines metadata, parameters instructing LinkML to interpret prefixes in specific ways, and names of imports.

You will find these fields in the schema header:

An example:

id: http://w3id.org/ontogpt/gocam\nname: gocam-template\ntitle: GO-CAM Template\ndescription: >-\n  A template for GO-CAMs\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\nprefixes:\n  linkml: https://w3id.org/linkml/\n  gocam: http://w3id.org/ontogpt/gocam/\n  GO: http://purl.obolibrary.org/obo/GO_\n  CL: http://purl.obolibrary.org/obo/CL_\n\ndefault_prefix: gocam\ndefault_range: string\n\nimports:\n  - linkml:types\n  - core\n
"},{"location":"custom/#the-classes","title":"The classes","text":"

The classes in the schema define the \"things\" you are interested in extracting. LinkML doesn't make many assumptions about the difference between a class and a relationship, a node and an edge, or a relation and a property. It's designed to be flexibile enough to handle a variety of data models.

The start of this section is indicated by classes:.

A minimal class may look like this:

  ClassName:\n    is_a: NamedEntity\n    attributes:\n      entity:\n        range: string\n        description: >- \n          A named entity.\n

In practice, this class won't do much, as it doesn't contain much for OntoGPT to work with or many instructions to form an LLM prompt out of. And that's fine, because we can do more.

These fields may be used in classes:

An example, continuing from where the header left off:

classes:\n  GoCamAnnotations:\n    tree_root: true\n    attributes:\n      genes:\n        description: semicolon-separated list of genes\n        multivalued: true\n        range: Gene\n      organisms:\n        description: semicolon-separated list of organism taxons\n        multivalued: true\n        range: Organism\n      gene_organisms:\n        annotations:\n          prompt: semicolon-separated list of asterisk separated gene to organism relationships\n        multivalued: true\n        range: GeneOrganismRelationship\n      activities:\n        description: semicolon-separated list of molecular activities\n        multivalued: true\n        range: MolecularActivity\n      gene_functions:\n        description: semicolon-separated list of gene to molecular activity relationships\n        multivalued: true\n        range: GeneMolecularActivityRelationship\n      cellular_processes:\n        description: semicolon-separated list of cellular processes\n        multivalued: true\n        range: CellularProcess\n      pathways:\n        description: semicolon-separated list of pathways\n        multivalued: true\n        range: Pathway\n      gene_gene_interactions:\n        description: semicolon-separated list of gene to gene interactions\n        multivalued: true\n        range: GeneGeneInteraction\n      gene_localizations:\n        description: >-\n          semicolon-separated list of genes plus their location in the cell;\n          for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\n        multivalued: true\n        range: GeneSubcellularLocalizationRelationship\n\n  Gene:\n    is_a: NamedEntity\n    id_prefixes:\n      - HGNC\n      - PR\n      - UniProtKB\n    annotations:\n      annotators: gilda:, bioportal:hgnc-nr\n  Pathway:\n    is_a: NamedEntity\n    id_prefixes:\n      - GO\n      - PW\n    annotations:\n      annotators: sqlite:obo:go, sqlite:obo:pw\n  CellularProcess:\n    is_a: NamedEntity\n    id_prefixes:\n      - GO\n    annotations:\n      annotators: sqlite:obo:go\n  MolecularActivity:\n    is_a: NamedEntity\n    id_prefixes:\n      - GO\n    annotations:\n      annotators: sqlite:obo:go\n  GeneLocation:\n    is_a: NamedEntity\n    id_prefixes:\n      - GO\n      - CL\n      - UBERON\n    annotations:\n      annotators: \"sqlite:obo:go, sqlite:obo:cl\"\n    slot_usage:\n      id:\n        values_from:\n          - GOCellComponentType\n          - CellType\n  Organism:\n    is_a: NamedEntity\n    id_prefixes:\n      - NCBITaxon\n      - EFO\n    annotations:\n      annotators: gilda:, sqlite:obo:ncbitaxon\n  Molecule:\n    is_a: NamedEntity\n    id_prefixes:\n      - CHEBI\n      - PR\n    annotations:\n      annotators: gilda:, sqlite:obo:chebi\n\n  GeneOrganismRelationship:\n    is_a: CompoundExpression\n    attributes:\n      gene:\n        range: Gene\n      organism:\n        range: Organism\n\n  GeneMolecularActivityRelationship:\n    is_a:   CompoundExpression\n    attributes:\n      gene:\n        range: Gene\n        annotations:\n          prompt: the name of the gene in the pair. This comes first.\n      molecular_activity:\n        range: MolecularActivity\n        annotations:\n          prompt: the name of the molecular function in the pair. This comes second. May be a GO term.\n\n  GeneMolecularActivityRelationship2:\n    is_a:   CompoundExpression\n    attributes:\n      gene:\n        range: Gene\n        annotations:\n          prompt: the name of the gene.\n      molecular_activity:\n        range: MolecularActivity\n        annotations:\n          prompt: the name of the molecular activity, for example, ubiquitination. May be a GO term.\n      target:\n        range: Molecule\n        annotations:\n          prompt: the name of the molecular entity that is the target of the molecular activity.\n\n  GeneSubcellularLocalizationRelationship:\n    is_a:   CompoundExpression\n    attributes:\n      gene:\n        range: Gene\n      location:\n        range: GeneLocation\n\n  GeneGeneInteraction:\n    is_a:   CompoundExpression\n    attributes:\n      gene1:\n        range: Gene\n      gene2:\n        range: Gene\n
"},{"location":"custom/#enums","title":"Enums","text":"

LinkML supports defining enums, or sets of values. In OntoGPT this allows schemas to work with subsets of identifiers. Enums have their own hierarchy. In the example below, the reachable_from slot is used to define sets of values: in GOCellComponentType these are all children of the GO term with the ID GO:0005575 (cellular component), so restricting a set of identifiers based on this enum will ensure they all correspond to cellular components.

Example, starting where the classes left off above:

enums:\n\n  GeneLocationEnum:\n    inherits:\n      - GOCellComponent\n      - CellType\n\n  GOCellComponentType:\n    reachable_from:\n      source_ontology: obo:go\n      source_nodes:\n        - GO:0005575 ## cellular_component\n  CellType:\n    reachable_from:\n      source_ontology: obo:cl\n      source_nodes:\n        - CL:0000000 ## cell\n
"},{"location":"custom/#schema-design-tips","title":"Schema design tips","text":"

It helps to have an understanding of the LinkML schema language, but it should be possible to define your own schemas using the examples in src/ontogpt/templates as a guide.

We recommend following an established schema like BioLink Model, but you can define your own.

Once you have defined your own schema / data model and placed in the correct directory, you can run the extract command.

Ex.:

ontogpt extract -t mendelian_disease.MendelianDisease -i marfan-wikipedia.txt\n

OntoGPT-specific extensions are specified as annotations.

You can specify a set of annotators for a field using the annotators annotation.

Ex.:

  Gene:\n    is_a: NamedThing\n    id_prefixes:\n      - HGNC\n    annotations:\n      annotators: gilda:, bioportal:hgnc-nr, obo:pr\n

The annotators are applied in order.

Additionally, when performing grounding, the following measures can be taken to improve accuracy:

Ex.:

classes:\n  ...\n  GeneLocation:\n    is_a: NamedEntity\n    id_prefixes:\n      - GO\n      - CL\n    annotations:\n      annotators: \"sqlite:obo:go, sqlite:obo:cl\"\n    slot_usage:\n      id:\n        values_from:\n          - GOCellComponentType\n          - CellType\n\nenums:\n  GOCellComponentType:\n    reachable_from:\n      source_ontology: obo:go\n      source_nodes:\n        - GO:0005575 ## cellular_component\n  CellType:\n    reachable_from:\n      source_ontology: obo:cl\n      source_nodes:\n        - CL:0000000 ## cell\n
"},{"location":"custom/#multiple-levels-of-nesting","title":"Multiple levels of nesting","text":"

Currently no more than two levels of nesting are recommended.

If a field has a range which is itself a class and not a primitive, it will attempt to nest.

Ex. the gocam schema has an attribute:

  attributes:\n      ...\n      gene_functions:\n        description: semicolon-separated list of gene to molecular activity relationships\n        multivalued: true\n        range: GeneMolecularActivityRelationship\n

The range GeneMolecularActivityRelationship has been specified inline, so it will nest.

The generated prompt is:

gene_functions : <semicolon-separated list of gene to molecular activities relationships>\n

The output of this is then passed through further SPIRES iterations.

"},{"location":"custom/#text-length-limit","title":"Text length limit","text":"

LLMs have context sizes limiting the combined length of their inputs and outputs. The gpt-3.5-turbo model, for example, has a 4,096 token limit (prompt + completion), while the gpt-3.5-turbo-16k model has a larger context of 16,384 tokens.

"},{"location":"custom/#advanced-functionality-with-linkml-owl","title":"Advanced functionality with linkml-owl","text":"

A LinkML schema used in OntoGPT may include annotations describing how each component relates to OWL syntax.

This level of detail may be necessary if your data model includes complex logic beyond simple hierarchical relationships.

For example, if you are extracting details of chemical reactions, it may be necessary to keep track of details like stoichiometry or charge. See a relevant example here.

Incorporating OWL annotations into the custom schema (remember to export using the -O owl option) also supports importing the results into an ontology editor like Protege, at which point it may be reasoned over.

The recipe template in OntoGPT incorporates several OWL annotations:

classes:\n  Recipe:\n    tree_root: true\n    close_mappings:\n      - FOODON:00004081\n    attributes:\n      url:\n        identifier: true\n        range: uriorcurie\n        slot_uri: rdf:Resource\n        annotations:\n          prompt.skip: true\n      label:\n        description: the name of the recipe\n        slot_uri: rdfs:label\n        annotations:\n          owl: AnnotationProperty, AnnotationAssertion\n      description:\n        description: a brief textual description of the recipe\n        slot_uri: dcterms:description\n        annotations:\n          owl: AnnotationProperty, AnnotationAssertion\n      categories:\n        description: a semicolon separated list of the categories to which this recipe belongs\n        range: RecipeCategory\n        multivalued: true\n        slot_uri: dcterms:subject\n        annotations:\n          owl: AnnotationAssertion\n      ingredients:\n        description: a semicolon separated list of the ingredients plus quantities of the recipe\n        multivalued: true\n        range: Ingredient\n        slot_uri: FOODON:00002420\n        annotations:\n          owl: ObjectProperty, ObjectSomeValuesFrom\n      steps:\n        description: a semicolon separated list of the individual steps involved in this recipe\n        multivalued: true\n        range: Step\n        annotations:\n          owl: ObjectProperty, ObjectSomeValuesFrom\n    annotations:\n      owl: Class\n      owl.template: |\n        EquivalentClasses(\n          {{url}}\n          ObjectIntersectionOf(\n            recipe:Recipe\n\n            {% for step in steps %}\n            ObjectSomeValuesFrom(\n              recipe:steps\n              {{tr(step)}}\n            )\n            {% endfor %}\n            {% for ingredient in ingredients %}\n            ObjectSomeValuesFrom(\n              FOODON:00002420\n              {{tr(ingredient)}}\n            )\n            {% endfor %}\n          )\n        )\n...\n

Several of the slots above, like close_mappings and slot_uri, aren't exclusive to OWL but define the parts of this data model in terms of existing vocabularies, so the schema and any extracted results will be more compatible with other models and methods. Here, close_mappings is used to show that the Recipe class is close but not necessarily identical to FOODON:00004081, or \"food recipe\".

The owl slot under annotations for these attributes defines one or more corresponding OWL axiom types. Because the label attribute may be AnnotationProperty, AnnotationAssertion in OWL (see the OWL2 syntax on Annotations) we know it can be applied as a property for something else, like an axiom or a specific entity with an IRI. This is how the rdfs:label annotation property usually works so this isn't surprising.

The owl.template slot defines template logic relating a Recipe to its component objects: steps and ingredients. It begins with an EquivalentClasses axiom to define the identifier of the recipe, which we assume to be a URL, as identical to the class expression in subsequent lines. Specifically, that Recipe must include both a series of steps (e.g., \"fry\", \"chop\", etc.) and a series of ingredients. The ingredients relate to the recipe through the property FOODON:00002420, or \"has ingredient\".

Note that everything in {curly brackets} is a template of some kind. The Jinja template system is used in the example in lines like {% for step in steps %} where a loop is used. Template slots like {{url}} may be accessed directly with their names. So what makes {{tr(step)}} different from {{step}}? The tr() function used here translates its input into an OWL entity so it may be used to generate valid OWL axioms.

See also: the documentation page on OWL exports and the linkml-owl documentation.

"},{"location":"custom/#install-a-custom-schema","title":"Install a custom schema","text":"

If you have installed OntoGPT directly from its GitHub repository, then you may install a custom schema like this:

  1. Move the schema file to the src/ontogpt/templates directory.
  2. Run make from the root of the repository to generate Pydantic versions of the schema.

If you have installed OntoGPT from pip, or if you can't use the make command, the process is similar, though it will depend on where the package is installed.

  1. Use the LinkML gen-pydantic tool to generate Pydantic classes. If your schema is named alfred.yaml, then run the following:

    bash gen-pydantic --pydantic_version 2 alfred.yaml > alfred.py

  2. Move both the .yaml and the .py versions of your schema to the templates directory of wherever OntoGPT is installed. In a virtual environment named temp that may be something like /temp/lib/python3.9/site-packages/ontogpt/templates.

You may then use the schema like any other. For example, if your schema is named albatross.yaml, then an extract command is:

ontogpt extract -t albatross -i input.txt\n
"},{"location":"evaluations/","title":"Evaluations","text":"

OpenAI's functions have been evaluated on test data sets.

All evaluation results include OpenAI cache databases (openai_cache.db.gz) as a reference of the prompts and responses obtained during the evaluation. This may be used by extracting the cache database to the root directory of the project.

Tests may be run with the eval command followed by the test name, e.g., for the BC5CDR test below:

ontogpt eval EvalCTD \n

By default, the evaluation will only be executed over a subset of the test corpus.

The exact number of inputs to run the test over can be controlled with the --num-tests option, like this:

ontogpt eval --num-tests 1 EvalCTD\n

To run the full set of tests, set num-tests to the input count for a given evaluation, as defined below.

For each document, the evaluation process will attempt to process the full text without preprocessing.

If the --chunking option is used, then the input text will instead be chunked into segments of a few tokens each, essentially creating new queries for each segment. This alternate strategy may impact test results and will result in longer run time.

"},{"location":"evaluations/#bc5cdr","title":"BC5CDR","text":"

Test Name: EvalCTD Input Count: 500

Results for OntoGPT on the BioCreative V Chemical Disease Relation Task (BC5CDR) are available on Zenodo here: https://zenodo.org/record/7657763

Evaluation functions for BC5CDR are available in src/ontogpt/evaluation/ctd/eval_ctd.py.

Note that the project also includes test and train data (CDR_TestSet.BioC.xml.gz and CDR_TrainSet.BioC.xml.gz, respectively) as well as a set of synonyms for MeSH terms (see synonyms.yaml).

"},{"location":"evaluations/#template","title":"Template","text":"

This evaluation uses the following schema template:

id: http://w3id.org/ontogpt/ctd\nname: ctd\ntitle: Chemical to Disease Template\ndescription: >-\n  A template for Chemical to Disease associations.\n\n  This template is intended to represent associations between chemicals and diseases,\n  and for evaluating Semantic Llama against BioCreative V Chemical Disease\n  Relation (CDR) Task (BC5CDR).\nsee_also:\n  - https://biocreative.bioinformatics.udel.edu/media/store/files/2015/BC5CDR_overview.final.pdf\n  - https://academic.oup.com/database/article/doi/10.1093/database/baw068/2630414\nsource: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/track-3-cdr/\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\nprefixes:\n  linkml: https://w3id.org/linkml/\n  drug: http://w3id.org/ontogpt/drug/\n\ndefault_prefix: drug\ndefault_range: string\n\nimports:\n  - linkml:types\n  - core\n\nclasses:\n\n  ChemicalToDiseaseDocument:\n    description: A document that contains chemical to disease relations.\n    is_a: TextWithTriples\n    slot_usage:\n      triples:\n        range: ChemicalToDiseaseRelationship\n        annotations:\n          prompt: >-\n            A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES\n            or TREATS.\n            for example: Lidocaine INDUCES cardiac asystole; \n            Hydroxychloroquine NOT TREATS COVID-19;\n            Methyldopa INDUCES Hypotension;\n            Monosodium Glutamate NOT INDUCES Headache;\n            Imatinib TREATS cancer\n          exclude: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer\n\n\n  ChemicalToDiseaseRelationship:\n    is_a: Triple\n    description: A triple where the subject is a chemical and the object is a disease.\n    slot_usage:\n      subject:\n        range: Chemical\n        description: >-\n          The chemical substance, drug, or small molecule. \n          For example: Lidocaine, Monosodium Glutamate, Imatinib.\n      object:\n        range: Disease\n        description: >-\n          The disease or condition that is being treated or induced by the chemical.\n          For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache.\n      predicate:\n        range: ChemicalToDiseasePredicate\n        description: The relationship type, e.g. INDUCES, TREATS.\n      subject_qualifier:\n        range: NamedEntity\n        description: >-\n          An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"\n      object_qualifier:\n        range: NamedEntity\n        description: >-\n          An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"\n\n  Disease:\n    is_a: NamedEntity\n    annotations:\n      annotators: \"sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra\"\n      prompt.examples: cardiac asystole, COVID-19, Headache, cancer\n    id_prefixes:\n      - MESH\n    slot_usage:\n      id:\n        pattern: \"^MESH:[CD][0-9]{6}$\"\n        values_from:\n          - MeshDiseaseIdentifier\n\n  Chemical:\n    is_a: NamedEntity\n    annotations:\n      annotators: \"sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:\"\n      prompt.examples: Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib\n    id_prefixes:\n      - MESH\n    slot_usage:\n      id:\n        pattern: \"^MESH:[CD][0-9]{6}$\"\n        values_from:\n          - MeshChemicalIdentifier\n\n  ChemicalToDiseasePredicate:\n    is_a: RelationshipType\n    description: >-\n      A predicate for chemical to disease relationships\n    comments:\n      - for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored.\n\nenums:\n\n  MeshChemicalIdentifier:\n    reachable_from:\n      source_ontology: obo:mesh\n      source_nodes:\n        - MESH:D000602 ## Amino Acids, Peptides, and Proteins\n        - MESH:D001685 ## Biological Factors\n        - MESH:D002241 ## Carbohydrates\n        - MESH:D004364 ## Pharmaceutical Preparations\n        - MESH:D006571 ## Heterocyclic Compounds\n        - MESH:D007287 ## Inorganic Chemicals\n        - MESH:D008055 ## Lipids\n        - MESH:D009706 ## Nucleic Acids, Nucleotides, and Nucleosides\n        - MESH:D009930 ## Organic Chemicals\n        - MESH:D011083 ## Polycyclic Compounds\n        - MESH:D013812 ## Therapeutics\n        - MESH:D019602 ## Food and Beverages\n        - MESH:D045424 ## Complex Mixtures\n        - MESH:D045762 ## Enzymes and Coenzymes\n        - MESH:D046911 ## Macromolecular Substances\n  MeshDiseaseIdentifier:\n    reachable_from:\n      source_ontology: obo:mesh\n      source_nodes:\n        - MESH:D001423 ## Bacterial Infections and Mycoses\n        - MESH:D001523 ## Mental Disorders\n        - MESH:D002318 ## Cardiovascular Diseases\n        - MESH:D002943 ## Circulatory and Respiratory Physiological Phenomena\n        - MESH:D004066 ## Digestive System Diseases\n        - MESH:D004700 ## Endocrine System Diseases\n        - MESH:D005128 ## Eye Diseases\n        - MESH:D005261 ## Female Urogenital Diseases and Pregnancy Complications\n        - MESH:D006425 ## Hemic and Lymphatic Diseases\n        - MESH:D007154 ## Immune System Diseases\n        - MESH:D007280 ## Disorders of Environmental Origin\n        - MESH:D009057 ## Stomatognathic Diseases\n        - MESH:D009140 ## Musculoskeletal Diseases\n        - MESH:D009358 ## Congenital, Hereditary, and Neonatal Diseases and Abnormalities\n        - MESH:D009369 ## Neoplasms\n        - MESH:D009422 ## Nervous System Diseases\n        - MESH:D009750 ## Nutritional and Metabolic Diseases\n        - MESH:D009784 ## Occupational Diseases\n        - MESH:D010038 ## Otorhinolaryngologic Diseases\n        - MESH:D010272 ## Parasitic Diseases\n        - MESH:D012140 ## Respiratory Tract Diseases\n        - MESH:D013568 ## Pathological Conditions, Signs and Symptoms\n        - MESH:D014777 ## Virus Diseases\n        - MESH:D014947 ## Wounds and Injuries\n        - MESH:D017437 ## Skin and Connective Tissue Diseases\n        - MESH:D052801 ## Male Urogenital Diseases\n        - MESH:D064419 ## Chemically-Induced Disorders\n
"},{"location":"functions/","title":"OntoGPT Functions","text":"

All OntoGPT functions are run from the command line.

Precede all commands with ontogpt.

To see the full list of available commands, run this:

ontogpt --help\n
"},{"location":"functions/#basic-parameters","title":"Basic Parameters","text":"

To see verbose output, run:

ontogpt -v\n

The options -vv and -vvv will enable progressively more verbose output.

"},{"location":"functions/#cache-db","title":"cache-db","text":"

Use the option --cache-db to specify a path to a sqlite database to cache the prompt-completion results.

"},{"location":"functions/#skip-annotator","title":"skip-annotator","text":"

Use the option --skip-annotator to skip one or more annotators (e.g. --skip-annotator gilda).

"},{"location":"functions/#common-parameters","title":"Common Parameters","text":"

The following options are available for most functions unless stated otherwise.

"},{"location":"functions/#inputfile","title":"inputfile","text":"

Use the option --inputfile to specify a path to a file containing input text.

For the extract command, this may be a single file or a directory of files.

In the latter case, all .txt files will be assumed to be input, and the path will not be parsed recursively.

"},{"location":"functions/#template","title":"template","text":"

Use the option --template to specify a template to use. This is a required parameter.

Only the name is required, without any filename suffix.

To use the gocam template, for example, the parameter will be --template gocam

This may be one of the templates included with OntoGPT or a custom template, but in the latter case, the schema, generated Pydantic classes, and any imported schemas should be present in the same location.

"},{"location":"functions/#target-class","title":"target-class","text":"

Use the option --target-class to specify a class in a schema to treat as the root.

If a schema does not already specify a root class, this is required.

Alternatively, the target class can be specified as part of the --template option, like so: --template mendelian_disease.MendelianDisease

"},{"location":"functions/#model","title":"model","text":"

Use the option model to specify the name of a large language model to be used.

For example, this may be --model gpt-4.

Consult the full list of available models with:

ontogpt list-models\n
"},{"location":"functions/#recurse","title":"recurse","text":"

Use the option recurse to specify whether recursion should be used when parsing the schema.

Recursion is on by default.

Disable it with --no-recurse.

"},{"location":"functions/#use-textract","title":"use-textract","text":"

Use the option use-textract to specify whether to use the textract package to extract text from the input document. Textract supports retrieving raw text from PDFs, images, audio, and a variety of other formats.

Textract extraction is off by default.

Enable it with --use-textract.

"},{"location":"functions/#output","title":"output","text":"

Use the option output to provide a path to write an output file to.

If this path is not provided, OntoGPT will write to stdout.

"},{"location":"functions/#output-format","title":"output-format","text":"

Use the option output-format to specify the desired output file format.

This may be one of:

"},{"location":"functions/#auto-prefix","title":"auto-prefix","text":"

Use the option auto-prefix to define a prefix to use for entities without a matching namespace.

When OntoGPT's extract functions find an entity matching the input schema but cannot ground it, the entity will still be included in the output.

By default, these entities will be assigned identifiers like AUTO:tangerine. If you ground this term to the Food Ontology, however, the entity may be FOODON:00003488 instead.

"},{"location":"functions/#show-prompt","title":"show-prompt","text":"

Use the option show-prompt to show all prompts constructed and sent to the model. Otherwise, only the final prompt will be shown.

Showing the full prompt is off by default.

Enable it by using --show-prompt and setting the verbosity level to high (-vvv).

"},{"location":"functions/#functions","title":"Functions","text":""},{"location":"functions/#categorize-mappings","title":"categorize-mappings","text":"

Categorize a collection of mappings in the Simple Standard for Sharing Ontological Mappings (SSSOM) format.

Mappings in this format may not include their specific mapping types (e.g., broad or close mappings).

This function will attempt to apply more specific mappings wherever possible.

Example:

Using an example SSSOM mapping collection

ontogpt categorize-mappings -i mp-hp-exact-0.0.1.sssom.tsv\n

Note that OntoGPT will attempt to retrieve the resources specified in the mapping (in the above example, that will include HP and MP). If it cannot find a corresponding resource it will raise a HTTP 404 error.

"},{"location":"functions/#clinical-notes","title":"clinical-notes","text":"

Create mock clinical notes.

Options:

Example:

ontogpt clinical-notes -d \"middle-aged female patient with syncope and recent travel to the Amazon rainforest\"\n
"},{"location":"functions/#complete","title":"complete","text":"

Prompt completion.

Given the path to a file containing text to continue, this command will simply pass it to the model as a completion task.

Example:

The file example2.txt contains the text \"Here's a good joke about high blood pressure:\"

ontogpt complete example2.txt\n

We take no responsibility for joke quality or lack thereof.

"},{"location":"functions/#convert","title":"convert","text":"

Convert output format.

Rather than a direct format translation, this function performs a full SPIRES extraction on the input file and writes the output in the specified format.

Example:

ontogpt convert -o outputfile.md -O md inputfile.yaml\n
"},{"location":"functions/#convert-examples","title":"convert-examples","text":"

Convert training examples from YAML.

This can be necessary for performing evaluations.

Given the path to a YAML-format input file containing training examples in a format like this:

---\nexamples:\n    - prompt: <text prompt>\n      completion: <text of completion of the prompt>\n    - prompt: <another text prompt>\n      completion: <text of completion of another prompt>\n

the function will convert it to equivalent JSON.

Example:

ontogpt convert-examples inputfile.yaml\n
"},{"location":"functions/#convert-geneset","title":"convert-geneset","text":"

Convert gene set to YAML.

The gene set may be in JSON (msigdb format) or text (one gene symbol per line) format.

See also the create-gene-set command (see below).

Options:

Example:

ontogpt convert-geneset -U inputfile.json\n
"},{"location":"functions/#create-gene-set","title":"create-gene-set","text":"

Create a gene set.

This is primarily relevant to the TALISMAN method for creating gene set summaries.

It creates a gene set given a set of gene annotations in two-column TSV or GAF format.

The function also requires a single argument for the term to create the gene set with.

The output is provided in YAML format.

Options:

Example:

ontogpt create-gene-set -A inputfile.tsv \"positive regulation of mitotic cytokinesis\"\n
"},{"location":"functions/#diagnose","title":"diagnose","text":"

Diagnose a clinical case represented as one or more Phenopackets.

This function takes one or more file paths as arguments, where each must contain a phenopacket in JSON format.

Example inputs may be found at the Phenomics Exchange repository.

Example:

ontogpt diagnose case1.json case2.json \n
"},{"location":"functions/#dump-completions","title":"dump-completions","text":"

Dump cached completions.

OntoGPT saves queries and successful text completions to an sqlite database.

Caching is not currently supported for local models.

Use this function to retrieve the contents of this database.

See also: the cache-db parameter described above.

Options:

Example:

ontogpt dump-completions -m \"soup\"\n
"},{"location":"functions/#embed","title":"embed","text":"

Embed text.

This function will return an embedding vector for the input text or texts.

Embedding retrieval is not currently supported for local models.

Options:

Example:

ontogpt embed \"obstreperous muskrat\"\n

For OpenAI's \"text-embedding-ada-002\" model, the output will be a vector of length 1536, like so:

[-0.015013165771961212, -0.013102399185299873, -0.005333086010068655, ...]\n
"},{"location":"functions/#enrichment","title":"enrichment","text":"

Gene class summary enriching. This is OntoGPT's implementation of TALISMAN.

The goal of gene summary enrichment is to assemble a textual summary of the functions of a set of genes and their products.

TALISMAN can run in three different ways:

  1. Map gene symbols to IDs using the resolver (unless IDs are specified)
  2. Fetch gene descriptions using Alliance API
  3. Create a prompt using descriptions

Options:

Example:

ontogpt enrichment -r sqlite:obo:hgnc -U tests/input/genesets/EDS.yaml\n

In this case, the prompt will include gene summaries retrieved from the database.

The response text will include, among other fields, a summary like this:

Summary: The common function among these genes is their involvement in the regulation and organization of the extracellular matrix, particularly collagen fibril organization and biosynthesis.\n
"},{"location":"functions/#entity-similarity","title":"entity-similarity","text":"

Determine similarity between ontology entities by comparing their embeddings.

Options:

Example:

ontogpt entity-similarity -r sqlite:obo:hp HP:0012228 HP:0000629\n

In this case, the output will look like this:

subject_id      subject_label   object_id       object_label    embedding_cosine_similarity     object_rank_for_subject\nHP:0012228      Tension-type headache   HP:0012228      Tension-type headache   0.9999999999999999      0\nHP:0012228      Tension-type headache   HP:0000629      Periorbital fullness    0.7755551231762359      1\nHP:0000629      Periorbital fullness    HP:0000629      Periorbital fullness    1.0000000000000002      0\nHP:0000629      Periorbital fullness    HP:0012228      Tension-type headache   0.7755551231762359      1\n
"},{"location":"functions/#eval","title":"eval","text":"

Evaluate an extractor.

See the Evaluations section for more details.

Options:

Example:

ontogpt eval --num-tests 1 EvalCTD\n
"},{"location":"functions/#eval-enrichment","title":"eval-enrichment","text":"

Run enrichment (TALISMAN) using multiple methods.

This function runs a set of evaluations specific to the TALISMAN gene set summary process.

It will iterate through all relevant models to compare results.

The function assumes genes will have HGNC identifiers.

Options:

Example:

ontogpt enrichment -U tests/input/genesets/EDS.yaml\n
"},{"location":"functions/#extract","title":"extract","text":"

Extract knowledge from text guided by a schema.

This is OntoGPT's implementation of SPIRES.

Output includes the input text (or a truncated part), the raw completion output, the prompt (specifically, the last iteration of the prompts used), and an extracted object containing all parts identified in the input text, as well as a list of named entities and their labels.

Options:

Examples:

ontogpt extract -t gocam.GoCamAnnotations -i tests/input/cases/gocam-33246504.txt\n

In this case, you will an extracted object in the output like:

extracted_object:\n  genes:\n    - HGNC:5992\n    - AUTO:F4/80\n    - HGNC:16400\n    - HGNC:1499\n    - HGNC:5992\n    - HGNC:5993\n  organisms:\n    - NCBITaxon:10088\n    - AUTO:bone%20marrow-derived%20macrophages\n    - AUTO:astrocytes\n    - AUTO:bipolar%20cells\n    - AUTO:vascular%20cells\n    - AUTO:perivascular%20MPs\n  gene_organisms:\n    - gene: HGNC:5992\n      organism: AUTO:mononuclear%20phagocytes\n    - gene: HGNC:16400\n      organism: AUTO:F4/80%2B%20mononuclear%20phagocytes\n    - gene: HGNC:1499\n      organism: AUTO:F4/80%2B%20mononuclear%20phagocytes\n    - gene: HGNC:5992\n      organism: AUTO:perivascular%20macrophages\n    - gene: HGNC:5993\n      organism: AUTO:None\n  activities:\n    - GO:0006954\n    - AUTO:photoreceptor%20death\n    - AUTO:retinal%20function\n  gene_functions:\n    - gene: HGNC:5992\n      molecular_activity: GO:0006954\n    - gene: AUTO:F4/80\n      molecular_activity: AUTO:mononuclear%20phagocyte%20recruitment\n    - gene: HGNC:1499\n      molecular_activity: GO:0006954\n    - gene: HGNC:5992\n      molecular_activity: AUTO:immune-specific%20expression\n    - gene: HGNC:5993\n      molecular_activity: AUTO:IL-1%CE%B2%20receptor\n    - gene: AUTO:rytvela\n      molecular_activity: AUTO:IL-1R%20modulation\n    - gene: AUTO:Kineret\n      molecular_activity: AUTO:IL-1R%20antagonism\n  cellular_processes:\n    - AUTO:macrophage-induced%20photoreceptor%20death\n  gene_localizations:\n    - gene: HGNC:5992\n      location: AUTO:subretinal%20space\n

Or, we can extract information about a drug and specify which model to use:

ontogpt extract -t drug -i tests/input/cases/drug-DB00316-moa.txt --auto-prefix UNKNOWN -m gpt-4\n

The ontology_class schema may be used to perform more domain-agnostic entity recognition, though this is generally incompatible with grounding.

ontogpt extract -t ontology_class -i tests/input/cases/human_urban_green_space.txt\n
"},{"location":"functions/#fill","title":"fill","text":"

Fill in missing values.

Requires the path to a file containing a data object to be passed (as an argument) and a set of examples as an input file.

Options:

"},{"location":"functions/#generate-extract","title":"generate-extract","text":"

Generate text and then extract knowledge from it.

This command runs two operations:

  1. Generate a natural language description of something
  2. Parse the generated description using SPIRES

For example, given a cell type such as Acinar Cell Of Salivary Gland, generate a description using GPT describing many aspects of the cell type, from its marker genes through to its function and diseases it is implicated in.

After that, use the cell-type schema to extract this into structured form.

As an optional next step use linkml-owl to generate OWL TBox axioms.

See also: iteratively-generate-extract below.

Example:

ontogpt generate-extract -t cell_type CL:0002623\n
"},{"location":"functions/#iteratively-generate-extract","title":"iteratively-generate-extract","text":"

Iterate through generate-extract.

This runs the generate-extract command in iterative mode. It will traverse the extracted subtypes with each iteration, gradually building up an ontology that is entirely generated from the \"latent knowledge\" in the LLM.

Currently each iteration is independent so the method remains unaware as to whether it has already made a concept. Ungrounded concepts may indicate gaps in available knowledgebases.

Unlike the generate-extract command, this command requires some additional parameters to be specified.

Please specify the input ontology and the output path.

Options:

Example:

ontogpt iteratively-generate-extract -t cell_type -r sqlite:obo:cl -D cells.yaml CL:0002623 \n
"},{"location":"functions/#list-models","title":"list-models","text":"

List all available models.

Example:

ontogpt list-models\n
"},{"location":"functions/#list-templates","title":"list-templates","text":"

List the templates.

Alternatively, run make list_templates.

Example:

ontogpt list-templates\n
"},{"location":"functions/#pubmed-annotate","title":"pubmed-annotate","text":"

Retrieve a collection of PubMed IDs for a given search, then perform extraction on them with SPIRES.

The search argument will accept all parameters known to PubMed search, such as filtering by publication year.

Works for single publications, too - set the --limit parameter to 1 and specify a PubMed ID as the search argument.

Options:

Examples:

ontogpt pubmed-annotate -t phenotype \"Takotsubo Cardiomyopathy: A Brief Review\" --get-pmc --model gpt-3.5-turbo-16k --limit 3\n
ontogpt pubmed-annotate -t environmental_sample \"33126925\" --limit 1\n
ontogpt pubmed-annotate -t composite_disease \"(earplugs) AND ((\"1950\"[Date - Publication] : \"1990\"[Date - Publication]))\" --limit 4\n
"},{"location":"functions/#pubmed-extract","title":"pubmed-extract","text":"

Extract knowledge from a single PubMed ID.

DEPRECATED - use pubmed-annotate instead.

"},{"location":"functions/#recipe-extract","title":"recipe-extract","text":"

Extract from a recipe on the web.

This uses the recipe template and the recipe_scrapers package. The latter supports many different recipe web sites, so give your favorite a try.

Pass a URL as the argument, or use the -R option to specify the path to a file containing one URL per line.

Options:

Example:

ontogpt recipe-extract https://www.allrecipes.com/recipe/17445/grilled-asparagus/\n

In this case, expect an extracted object like the following:

extracted_object:\n  url: https://www.allrecipes.com/recipe/17445/grilled-asparagus/\n  label: Grilled Asparagus\n  description: Grilled asparagus with olive oil, salt, and pepper.\n  categories:\n    - AUTO:None\n  ingredients:\n    - food_item:\n        food: FOODON:03311349\n        state: fresh, spears\n      amount:\n        value: '1'\n        unit: UO:0010034\n    - food_item:\n        food: FOODON:03301826\n      amount:\n        value: '1'\n        unit: UO:0010042\n    - food_item:\n        food: AUTO:salt\n        state: and pepper\n      amount:\n        value: N/A\n        unit: AUTO:N/A\n  steps:\n    - action: AUTO:Preheat\n      inputs:\n        - food: AUTO:outdoor%20grill\n          state: None\n      outputs:\n        - food: AUTO:None\n          state: None\n      utensils:\n        - AUTO:None\n    - action: dbpediaont:season\n      inputs:\n        - food: FOODON:00003458\n          state: coated\n        - food: AUTO:salt\n          state: None\n        - food: FOODON:00003520\n      outputs:\n        - food: FOODON:00003458\n          state: seasoned\n      utensils:\n        - AUTO:None\n    - action: AUTO:cook\n      inputs:\n        - food: FOODON:03311349\n          state: None\n      outputs:\n        - food: FOODON:03311349\n          state: cooked\n      utensils:\n        - AUTO:grill\n
"},{"location":"functions/#synonyms","title":"synonyms","text":"

Extract synonyms, based on embeddings.

The context parameter is required.

Options:

Example:

ontogpt synonyms --context astronomy star\n
"},{"location":"functions/#text-distance","title":"text-distance","text":"

Embed text and calculate euclidian distance between the embeddings.

The terms must be separated by an @ character.

Options:

Example:

ontogpt text-distance pancakes @ syrup\n
"},{"location":"functions/#text-similarity","title":"text-similarity","text":"

Like text-distance, this command compares the embeddings of input terms.

This command returns the cosine similarity of the embedding vectors.

Options:

Example:

ontogpt text-similarity basketball @ basket-weaving\n
"},{"location":"functions/#web-extract","title":"web-extract","text":"

Extract knowledge from web page.

Pass a URL as an argument and OntoGPT will use the SPIRES method to extract information based on the specified template.

Because this depends upon scraping a page, results may vary depending on a site's complexity and structure.

Even relatively short pages may exceed a model's context size, so larger context models may be necessary.

Example:

ontogpt web-extract -t reaction.Reaction -m gpt-3.5-turbo-16k https://www.scienceofcooking.com/maillard_reaction.htm \n
"},{"location":"functions/#wikipedia-extract","title":"wikipedia-extract","text":"

Extract knowledge from a Wikipedia page.

Pass an article title as an argument and OntoGPT will use the SPIRES method to extract information based on the specified template.

Even relatively short pages may exceed a model's context size, so larger context models may be necessary.

Example:

ontogpt wikipedia-extract -t mendelian_disease.MendelianDisease -m gpt-3.5-turbo-16k \"Cartilage\u2013hair hypoplasia\"\n
"},{"location":"functions/#wikipedia-search","title":"wikipedia-search","text":"

Extract knowledge from Wikipedia pages based on a search.

Pass a search phrase as an argument and OntoGPT will use the SPIRES method to extract information based on the specified template.

Even relatively short pages may exceed a model's context size, so larger context models may be necessary.

Example:

ontogpt wikipedia-search -t biological_process -m gpt-3.5-turbo-16k \"digestion\"\n
"},{"location":"operation/","title":"Operation","text":""},{"location":"operation/#getting-started","title":"Getting Started","text":"

OntoGPT is run from the command line. See the full list of commands with:

ontogpt --help\n

For a simple example of text completion and testing to ensure OntoGPT is set up correctly, create a text file containing the following, saving the file as example.txt:

Why did the squid cross the coral reef?\n

Then try the following command:

ontogpt complete example.txt\n

You should get text output like the following:

Perhaps the squid crossed the coral reef for a variety of reasons:\n\n1. Food: Squids are known to feed on small fish and other marine organisms, and there could have been a rich food source on the other side of the reef.\n\n...\n

OntoGPT is intended to be used for information extraction. The following examples show how to accomplish this.

"},{"location":"operation/#strategy-1-knowledge-extraction-using-spires","title":"Strategy 1: Knowledge extraction using SPIRES","text":""},{"location":"operation/#working-mechanism","title":"Working Mechanism","text":"
  1. You provide an arbitrary data model, describing the structure you want to extract text into. This can be nested (but see limitations below). The predefined templates may be used.
  2. Provide your preferred annotations for grounding NamedEntity fields
  3. OntoGPT will:
    • Generate a prompt
    • Feed the prompt to a language model
    • Parse the results into a dictionary structure
    • Ground the results using a preferred annotator (e.g., an ontology)
"},{"location":"operation/#input","title":"Input","text":"

Consider some text from one of the input files being used in the OntoGPT test suite. You can find the text file here. You can download the raw file from the GitHub link to that input text file, or copy its contents over into another file, say, abstract.txt. An excerpt:

The cGAS/STING-mediated DNA-sensing signaling pathway is crucial for interferon (IFN) production and host antiviral responses

... [snip] ...

The underlying mechanism was the interaction of US3 with \u03b2-catenin and its hyperphosphorylation of \u03b2-catenin at Thr556 to block its nuclear translocation ... ...

We can extract knowledge from the above text this into the GO pathway datamodel by running the following command:

"},{"location":"operation/#command","title":"Command","text":"
ontogpt extract -t gocam.GoCamAnnotations -i ~/path/to/abstract.txt\n

Note: The value accepted by the -t / --template argument is the base name of one of the LinkML schema / data model which can be found in the templates folder.

"},{"location":"operation/#output","title":"Output","text":"

The output returned from the above command can be optionally redirected into an output file using the -o / --output.

The following is a small part of what the larger schema-compliant output looks like:

genes:\n- HGNC:2514\n- HGNC:21367\n- HGNC:27962\n- US3\n- FPLX:Interferon\n- ISG\ngene_gene_interactions:\n- gene1: US3\n  gene2: HGNC:2514\ngene_localizations:\n- gene: HGNC:2514\n  location: Nuclear\ngene_functions:\n- gene: HGNC:2514\n  molecular_activity: Transcription\n- gene: HGNC:21367\n  molecular_activity: Production\n...\n
"},{"location":"operation/#local-models","title":"Local Models","text":"

To use a local model, specify it with the -m or --model option.

Example:

ontogpt extract -t drug -i ~/path/to/abstract.txt -m nous-hermes-13b\n

See the list of all available models with this command:

ontogpt list-models\n

When specifying a local model for the first time, it will be downloaded to your local system.

"},{"location":"operation/#strategy-2-gene-enrichment-using-spindoctor","title":"Strategy 2: Gene Enrichment using SPINDOCTOR","text":"

Given a set of genes, OntoGPT can find similarities among them.

Ex.:

ontogpt enrichment -U tests/input/genesets/sensory-ataxia.yaml\n

The default is to use ontological gene function synopses (via the Alliance API).

This strategy does not currently support using local models.

"},{"location":"owl_exports/","title":"OWL Exports","text":"

The extract command will let you export the results as OWL axioms, utilizing linkml-owl mappings in the schema.

Ex.:

ontogpt extract -t recipe -i recipe-spaghetti.txt -o recipe-spaghetti.owl -O owl\n

src/ontogpt/templates/recipe.yaml is an example schema that uses linkml-owl mappings.

See the Makefile for a full pipeline that involves using robot to extract a subset of FOODON and merge in the extracted results. This uses recipe-scrapers.

OWL output: recipe-all-merged.owl

Classification:

"},{"location":"setup/","title":"Setup","text":""},{"location":"setup/#prerequisites","title":"Prerequisites","text":"

OntoGPT may be installed through pip or used directly from the GitHub repository. In the latter case, you will need to install the poetry dependency manager and precede commands with poetry run. See the poetry installation documentation for more details.

"},{"location":"setup/#additional-requirements-and-options","title":"Additional requirements and options","text":"

You may also set additional API keys for optional resources:

"},{"location":"setup/#installation","title":"Installation","text":"

To simply start using the package in your workspace:

pip install ontogpt\n

Note that some features require installing additional, optional dependencies. These may be installed as:

pip install ontogpt[extra_name]\n

where extra_name is one of the following:

For installation from the GitHub repository, particularly if you plan to contribute to feature development or other package code:

git clone https://github.com/monarch-initiative/ontogpt.git\ncd ontogpt/\npoetry install\n

Extras listed above may be installed as:

poetry install --extras extra_name\n

All commands should then be preceded by poetry run, or simply run poetry shell to create and enter a virtual environment for the project.

"},{"location":"setup/#setting-api-keys","title":"Setting API keys","text":"

One OntoGPT and all of its dependencies are installed, you will need to set your API keys using the Ontology Access Kit:

runoak set-apikey -e openai <your openai api key>\n

The optional keys may be set as follows:

runoak set-apikey -e bioportal <your bioportal api key>\nrunoak set-apikey -e ncbi-email <your email address>\nrunoak set-apikey -e ncbi-key <your NCBI api key>\nrunoak set-apikey -e hfhub-key <your HuggingFace Hub api key>\n
"},{"location":"setup/#running-local-models","title":"Running local models","text":"

Using local models currently depends upon using the gpt4all package and may require additional setup steps specific to your computing environment.

See the gpt4all documentation for more details.

"},{"location":"start_with_owl/","title":"Starting with OWL","text":"

OWL, or Web Ontology Language, is a popular format for ontologies, so what is the best way to start working with OntoGPT if you have an OWL ontology already?

OWL is a data model for expressing ontologies, oriented around set-theoretic logical Axioms. OWL is not strictly an ontology format, but it may be represented in the RDF language, among others. Much, much more detail here.

OWL may encode a data schema, or it may encode something else. In the latter case, think very carefully about what data you wish to extract and how it relates to what is present in your OWL.

The crucial question is this: does your OWL literally contain a set of terms you wish to ground extractions to, or does it define a set of concepts and their relationships you would like to extract?

For example, let's use this very simple example ontology:

<rdf:RDF\n    xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n    xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"\n    xmlns:owl=\"http://www.w3.org/2002/07/owl#\"\n    xmlns:fruits=\"http://example.org/fruits#\">\n\n  <!-- Classes -->\n  <owl:Class rdf:about=\"#Fruit\"/>\n  <owl:Class rdf:about=\"#CitrusFruit\">\n    <rdf:type rdf:resource=\"http://www.w3.org/2002/07/owl#Class\"/>\n    <rdfs:subClassOf rdf:resource=\"#Fruit\"/>\n  </owl:Class>\n\n  <!-- Individuals -->\n  <owl:NamedIndividual rdf:about=\"#Apple\">\n    <rdf:type rdf:resource=\"#Fruit\"/>\n    <rdfs:label>Apple</rdfs:label>\n  </owl:NamedIndividual>\n  <owl:NamedIndividual rdf:about=\"#Orange\">\n    <rdf:type rdf:resource=\"#CitrusFruit\"/>\n    <rdfs:label>Orange</rdfs:label>\n  </owl:NamedIndividual>\n\n</rdf:RDF>\n

If you want to extract entities from text (and they may be anything - foods, flavors, etc.) and then ground them to individuals in the ontology, then continue to Option 1.

If you want to extract all Fruit entities from input text while also recognizing that some of them may be CitrusFruit, then continue to Option 2.

"},{"location":"start_with_owl/#option-1-grounding-to-a-set-of-terms","title":"Option 1 - grounding to a set of terms","text":"

You may use an OWL file the same way as any other annotator.

Note that the example ontology above doesn't use prefixes, so let us imagine that each named individual has an identifier like FRUIT:12345.

If your input text contains the word \"orange\", then it will be grounded based on the provided OWL, but any terms not in the OWL, like \"snakeskin fruit\" will not be grounded unless you provide additional annotators capable of grounding the term.

If your ontology is in fruit.owl, then your schema may define a class like this:

  Fruit:\n    is_a: NamedEntity\n    id_prefixes:\n      - FRUIT   \n    annotations:\n      annotators: fruit.owl\n

The OWL file should be in the same path as where you will run ontogpt from.

If your ontology is already in the OBO Foundry, then you may also specify the annotator as something like sqlite:obo:fruit (that's just an example, but try something like the Food Ontology with sqlite:obo:foodon for an equivalent).

"},{"location":"start_with_owl/#option-2-transforming-an-owl-into-ontogpt-schema","title":"Option 2 - transforming an OWL into OntoGPT schema","text":"

This path is a bit more complicated.

If you'd rather use the OWL more like a schema to develop a corresponding extraction schema for OntoGPT, you may be able to do so with the schema-automator tool.

After installing the tool, try something like this:

$ schemauto import-owl fruit.owl\n... schema-automator attempts to transform the OWL ...\n

This process may encounter some errors along the way. One frequent issue is that the input ontology may not be in functional syntax, but may be converted using the robot tool like this:

$ robot convert -i fruit.owl -o fruit.ofn\n... a magical transformation happens ...\n$ schemauto import-owl fruit.ofn\n

The process may still go poorly if the input ontology is heavily dependent on imports.

If everything goes well, however, you should get a LinkML YAML version of the ontology. It will still require addition of description and annotation slots to each class before it will be useful for extraction operations.

Overall, you may find that it is easier to modify an existing OntoGPT schema to fit your schema.

"},{"location":"troubleshooting/","title":"Troubleshooting","text":"

Encountering an error, mystery, or other unexplained oddity? Open a ticket on the GitHub repository: https://github.com/monarch-initiative/ontogpt/issues

"},{"location":"troubleshooting/#i-get-an-error-like-typeerror-configuredbasemodel__init_subclass__-takes-no-keyword-arguments","title":"I get an error like TypeError: ConfiguredBaseModel.__init_subclass__() takes no keyword arguments","text":"

This can happen if you have installed a version of the Pydantic package older than version 2 and/or if you're using a schema generated for Pydantic v1. Versions of OntoGPT of v0.3.3 and above should prevent this from happening, but if you're still seeing the error, then running make again may fix it.

"},{"location":"troubleshooting/#i-get-an-error-like-urlliberrorhttperror-http-error-404-not-found","title":"I get an error like urllib.error.HTTPError: HTTP Error 404: Not Found","text":"

There are a variety of reasons why this may happen, but one cause is if your schema specifies an annotator which does not exist. If the stack trace of the error includes the get_adapter method from oaklib, then this is a likely cause, and you may want to verify that all annotators are accessible to OAK.

"},{"location":"troubleshooting/#i-get-a-lot-of-warnings-like-warningrootcould-not-find-any-mappings-for-and-i-dont-get-the-expected-identifiers-in-my-extracted-object","title":"I get a lot of warnings like WARNING:root:Could not find any mappings for ... and I don't get the expected identifiers in my extracted object","text":"

Verify that the id_prefixes you specify in your schema correspond to those provided by the annotator. If your annotator is sqlite:obo:hp, for example, the prefix will be HP rather than HPO.

"},{"location":"troubleshooting/#i-need-to-store-the-annotator-files-ontogpt-downloads-somewhere-other-than-dataoaklib","title":"I need to store the annotator files OntoGPT downloads somewhere other than ~/.data/oaklib","text":"

OntoGPT uses oaklib to handle the ontologies it uses as annotators, and oaklib uses the pystow package to determine where downloads should go.

To change the download location, set the PYSTOW_HOME variable in your environment to your preferred path.

For example, to save downloads to /tmp/oaklib, set the varible like this:

export PYSTOW_HOME='/tmp/'\n

You may then reset that variable with this command:

unset PYSTOW_HOME\n

Or make the change more permanent by adding it to your .bashrc file and then run

source ~/.bashrc\n
"},{"location":"biological_process/","title":"Biological Process Template","text":"

A template for GO-CAMs

URI: https://w3id.org/ontogpt/biological_process

Name: biological-process-template

"},{"location":"biological_process/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nBiologicalProcess {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\n\nBiologicalProcess ||--|o BiologicalProcess : \"subclass_of\"\nBiologicalProcess ||--}o ChemicalEntity : \"inputs\"\nBiologicalProcess ||--}o ChemicalEntity : \"outputs\"\nBiologicalProcess ||--}o MolecularActivity : \"steps\"\nBiologicalProcess ||--}o Gene : \"genes\"\nBiologicalProcess ||--}o GeneMolecularActivityRelationship : \"gene_activities\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\n\n
"},{"location":"biological_process/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text GeneMolecularActivityRelationship None NamedEntity None BiologicalProcess None ChemicalEntity None Gene None MolecularActivity None RelationshipType None Publication None TextWithTriples None"},{"location":"biological_process/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text description a textual description of the biological process extracted_object The complex objects extracted from the text full_text The full text of the publication gene gene_activities semicolon-separated list of gene to molecular activity relationships genes id A unique identifier for the named entity input_id input_text input_title inputs the inputs of the biological process label the name of the biological process molecular_activity named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text outputs the outputs of the biological process predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output steps the steps involved in this biological process subclass_of the category to which this biological process belongs subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text synonyms alternative names of the biological process title The title of the publication triples"},{"location":"biological_process/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"biological_process/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"biological_process/#subsets","title":"Subsets","text":"Subset Description"},{"location":"biological_process/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: bp:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"biological_process/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"biological_process/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:AnnotatorResult native bp:AnnotatorResult"},{"location":"biological_process/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n\n
"},{"location":"biological_process/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"biological_process/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"biological_process/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"biological_process/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"biological_process/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Any/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native bp:Any"},{"location":"biological_process/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/biological_process\nclass_uri: linkml:Any\n\n
"},{"location":"biological_process/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/biological_process\nclass_uri: linkml:Any\n\n
"},{"location":"biological_process/BiologicalProcess/","title":"Class: BiologicalProcess","text":"

URI: bp:BiologicalProcess

erDiagram\nBiologicalProcess {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\n\nBiologicalProcess ||--|o BiologicalProcess : \"subclass_of\"\nBiologicalProcess ||--}o ChemicalEntity : \"inputs\"\nBiologicalProcess ||--}o ChemicalEntity : \"outputs\"\nBiologicalProcess ||--}o MolecularActivity : \"steps\"\nBiologicalProcess ||--}o Gene : \"genes\"\nBiologicalProcess ||--}o GeneMolecularActivityRelationship : \"gene_activities\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\n\n
"},{"location":"biological_process/BiologicalProcess/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/BiologicalProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 0..1 String the name of the biological process direct description 0..1 String a textual description of the biological process direct synonyms 0..* String alternative names of the biological process direct subclass_of 0..1 BiologicalProcess the category to which this biological process belongs direct inputs 0..* ChemicalEntity the inputs of the biological process direct outputs 0..* ChemicalEntity the outputs of the biological process direct steps 0..* MolecularActivity the steps involved in this biological process direct genes 0..* Gene direct gene_activities 0..* GeneMolecularActivityRelationship semicolon-separated list of gene to molecular activity relationships direct id 1..1 String A unique identifier for the named entity NamedEntity"},{"location":"biological_process/BiologicalProcess/#usages","title":"Usages","text":"used by used in type used BiologicalProcess subclass_of range BiologicalProcess"},{"location":"biological_process/BiologicalProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/BiologicalProcess/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/BiologicalProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:BiologicalProcess native bp:BiologicalProcess"},{"location":"biological_process/BiologicalProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/BiologicalProcess/#direct","title":"Direct","text":"
name: BiologicalProcess\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  description:\n    name: description\n    description: a textual description of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  synonyms:\n    name: synonyms\n    description: alternative names of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n  subclass_of:\n    name: subclass_of\n    description: the category to which this biological process belongs\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: BiologicalProcess\n  inputs:\n    name: inputs\n    description: the inputs of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n  outputs:\n    name: outputs\n    description: the outputs of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n  steps:\n    name: steps\n    description: the steps involved in this biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: MolecularActivity\n  genes:\n    name: genes\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: Gene\n  gene_activities:\n    name: gene_activities\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: GeneMolecularActivityRelationship\ntree_root: true\n\n
"},{"location":"biological_process/BiologicalProcess/#induced","title":"Induced","text":"
name: BiologicalProcess\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: label\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n  description:\n    name: description\n    description: a textual description of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: description\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: string\n  synonyms:\n    name: synonyms\n    description: alternative names of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: string\n  subclass_of:\n    name: subclass_of\n    description: the category to which this biological process belongs\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: subclass_of\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: BiologicalProcess\n  inputs:\n    name: inputs\n    description: the inputs of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: inputs\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: ChemicalEntity\n  outputs:\n    name: outputs\n    description: the outputs of the biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: outputs\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: ChemicalEntity\n  steps:\n    name: steps\n    description: the steps involved in this biological process\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: steps\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: MolecularActivity\n  genes:\n    name: genes\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: Gene\n  gene_activities:\n    name: gene_activities\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: gene_activities\n    owner: BiologicalProcess\n    domain_of:\n    - BiologicalProcess\n    range: GeneMolecularActivityRelationship\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: BiologicalProcess\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\ntree_root: true\n\n
"},{"location":"biological_process/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"biological_process/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/ChemicalEntity/","title":"Class: ChemicalEntity","text":"

URI: bp:ChemicalEntity

erDiagram\nChemicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biological_process/ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biological_process/ChemicalEntity/#usages","title":"Usages","text":"used by used in type used BiologicalProcess inputs range ChemicalEntity BiologicalProcess outputs range ChemicalEntity"},{"location":"biological_process/ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biological_process/ChemicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"biological_process/ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ChemicalEntity native bp:ChemicalEntity"},{"location":"biological_process/ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\n\n
"},{"location":"biological_process/ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalEntity\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"biological_process/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: bp:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"biological_process/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"biological_process/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:CompoundExpression native bp:CompoundExpression"},{"location":"biological_process/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/biological_process\nabstract: true\n\n
"},{"location":"biological_process/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/biological_process\nabstract: true\n\n
"},{"location":"biological_process/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"biological_process/Curie/#comments","title":"Comments","text":""},{"location":"biological_process/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Curie/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"biological_process/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Date/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"biological_process/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"biological_process/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"biological_process/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"biological_process/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Double/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: bp:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"biological_process/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"biological_process/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ExtractionResult native bp:ExtractionResult"},{"location":"biological_process/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biological_process/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biological_process/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"biological_process/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Float/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Gene/","title":"Class: Gene","text":"

URI: bp:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biological_process/Gene/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biological_process/Gene/#usages","title":"Usages","text":"used by used in type used BiologicalProcess genes range Gene GeneMolecularActivityRelationship gene range Gene"},{"location":"biological_process/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biological_process/Gene/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hgnc"},{"location":"biological_process/Gene/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Gene native bp:Gene"},{"location":"biological_process/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\n\n
"},{"location":"biological_process/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"biological_process/GeneMolecularActivityRelationship/","title":"Class: GeneMolecularActivityRelationship","text":"

URI: bp:GeneMolecularActivityRelationship

erDiagram\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\n\n
"},{"location":"biological_process/GeneMolecularActivityRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct molecular_activity 0..1 MolecularActivity direct"},{"location":"biological_process/GeneMolecularActivityRelationship/#usages","title":"Usages","text":"used by used in type used BiologicalProcess gene_activities range GeneMolecularActivityRelationship"},{"location":"biological_process/GeneMolecularActivityRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/GeneMolecularActivityRelationship/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/GeneMolecularActivityRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:GeneMolecularActivityRelationship native bp:GeneMolecularActivityRelationship"},{"location":"biological_process/GeneMolecularActivityRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/GeneMolecularActivityRelationship/#direct","title":"Direct","text":"
name: GeneMolecularActivityRelationship\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  gene:\n    name: gene\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: MolecularActivity\n\n
"},{"location":"biological_process/GeneMolecularActivityRelationship/#induced","title":"Induced","text":"
name: GeneMolecularActivityRelationship\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  gene:\n    name: gene\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: gene\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneMolecularActivityRelationship\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: molecular_activity\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneMolecularActivityRelationship\n    range: MolecularActivity\n\n
"},{"location":"biological_process/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"biological_process/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Integer/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/MolecularActivity/","title":"Class: MolecularActivity","text":"

URI: bp:MolecularActivity

erDiagram\nMolecularActivity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biological_process/MolecularActivity/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/MolecularActivity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biological_process/MolecularActivity/#usages","title":"Usages","text":"used by used in type used BiologicalProcess steps range MolecularActivity GeneMolecularActivityRelationship molecular_activity range MolecularActivity"},{"location":"biological_process/MolecularActivity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/MolecularActivity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biological_process/MolecularActivity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"biological_process/MolecularActivity/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/MolecularActivity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:MolecularActivity native bp:MolecularActivity"},{"location":"biological_process/MolecularActivity/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/MolecularActivity/#direct","title":"Direct","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\n\n
"},{"location":"biological_process/MolecularActivity/#induced","title":"Induced","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MolecularActivity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: MolecularActivity\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"biological_process/NamedEntity/","title":"Class: NamedEntity","text":"

URI: bp:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biological_process/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"biological_process/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"biological_process/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:NamedEntity native bp:NamedEntity"},{"location":"biological_process/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/biological_process\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"biological_process/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/biological_process\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"biological_process/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"biological_process/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"biological_process/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"biological_process/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"biological_process/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"biological_process/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"biological_process/Objectidentifier/#comments","title":"Comments","text":""},{"location":"biological_process/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Publication/","title":"Class: Publication","text":"

URI: bp:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"biological_process/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"biological_process/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"biological_process/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Publication/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Publication native bp:Publication"},{"location":"biological_process/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/biological_process\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n\n
"},{"location":"biological_process/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/biological_process\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"biological_process/RelationshipType/","title":"Class: RelationshipType","text":"

URI: bp:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biological_process/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biological_process/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"biological_process/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biological_process/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:RelationshipType native bp:RelationshipType"},{"location":"biological_process/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\n\n
"},{"location":"biological_process/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biological_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - BiologicalProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"biological_process/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"biological_process/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/String/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: bp:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"biological_process/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"biological_process/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:TextWithTriples native bp:TextWithTriples"},{"location":"biological_process/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biological_process/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/biological_process\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biological_process/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"biological_process/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Time/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: bp:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"biological_process/Triple/#inheritance","title":"Inheritance","text":""},{"location":"biological_process/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"biological_process/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"biological_process/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Triple/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Triple native bp:Triple"},{"location":"biological_process/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"biological_process/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"biological_process/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/biological_process\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/biological_process\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"biological_process/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"biological_process/Uri/#comments","title":"Comments","text":""},{"location":"biological_process/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Uri/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"biological_process/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: bp:abstract

"},{"location":"biological_process/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biological_process/abstract/#properties","title":"Properties","text":""},{"location":"biological_process/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/abstract/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biological_process/biological-process-template/","title":"biological-process-template","text":"

A template for GO-CAMs

URI: https://w3id.org/ontogpt/biological_process

"},{"location":"biological_process/combined_text/","title":"Slot: combined_text","text":"

URI: bp:combined_text

"},{"location":"biological_process/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biological_process/combined_text/#properties","title":"Properties","text":""},{"location":"biological_process/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biological_process/description/","title":"Slot: description","text":"

a textual description of the biological process

URI: bp:description

"},{"location":"biological_process/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/description/#properties","title":"Properties","text":""},{"location":"biological_process/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/description/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a textual description of the biological process\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: description\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: string\n\n
"},{"location":"biological_process/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: bp:extracted_object

"},{"location":"biological_process/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/extracted_object/#properties","title":"Properties","text":""},{"location":"biological_process/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"biological_process/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: bp:full_text

"},{"location":"biological_process/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biological_process/full_text/#properties","title":"Properties","text":""},{"location":"biological_process/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/full_text/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biological_process/gene/","title":"Slot: gene","text":"

URI: bp:gene

"},{"location":"biological_process/gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship no"},{"location":"biological_process/gene/#properties","title":"Properties","text":""},{"location":"biological_process/gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/gene/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/gene/#linkml-source","title":"LinkML Source","text":"
name: gene\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: gene\nowner: GeneMolecularActivityRelationship\ndomain_of:\n- GeneMolecularActivityRelationship\nrange: Gene\n\n
"},{"location":"biological_process/gene_activities/","title":"Slot: gene_activities","text":"

semicolon-separated list of gene to molecular activity relationships

URI: bp:gene_activities

"},{"location":"biological_process/gene_activities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/gene_activities/#properties","title":"Properties","text":""},{"location":"biological_process/gene_activities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/gene_activities/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/gene_activities/#linkml-source","title":"LinkML Source","text":"
name: gene_activities\ndescription: semicolon-separated list of gene to molecular activity relationships\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: gene_activities\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: GeneMolecularActivityRelationship\n\n
"},{"location":"biological_process/genes/","title":"Slot: genes","text":"

URI: bp:genes

"},{"location":"biological_process/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/genes/#properties","title":"Properties","text":""},{"location":"biological_process/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/genes/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: genes\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: Gene\n\n
"},{"location":"biological_process/id/","title":"Slot: id","text":"

URI: bp:id

"},{"location":"biological_process/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no Gene no MolecularActivity no ChemicalEntity no NamedEntity no RelationshipType no Publication no"},{"location":"biological_process/id/#properties","title":"Properties","text":""},{"location":"biological_process/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"biological_process/input_id/","title":"Slot: input_id","text":"

URI: bp:input_id

"},{"location":"biological_process/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/input_id/#properties","title":"Properties","text":""},{"location":"biological_process/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/input_id/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biological_process/input_text/","title":"Slot: input_text","text":"

URI: bp:input_text

"},{"location":"biological_process/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/input_text/#properties","title":"Properties","text":""},{"location":"biological_process/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/input_text/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biological_process/input_title/","title":"Slot: input_title","text":"

URI: bp:input_title

"},{"location":"biological_process/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/input_title/#properties","title":"Properties","text":""},{"location":"biological_process/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/input_title/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biological_process/inputs/","title":"Slot: inputs","text":"

the inputs of the biological process

URI: bp:inputs

"},{"location":"biological_process/inputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/inputs/#properties","title":"Properties","text":""},{"location":"biological_process/inputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/inputs/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/inputs/#linkml-source","title":"LinkML Source","text":"
name: inputs\ndescription: the inputs of the biological process\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: inputs\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: ChemicalEntity\n\n
"},{"location":"biological_process/label/","title":"Slot: label","text":"

URI: bp:label

"},{"location":"biological_process/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no Gene no MolecularActivity no ChemicalEntity no NamedEntity no RelationshipType no"},{"location":"biological_process/label/#properties","title":"Properties","text":""},{"location":"biological_process/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- BiologicalProcess\n- NamedEntity\nrange: string\n\n
"},{"location":"biological_process/molecular_activity/","title":"Slot: molecular_activity","text":"

URI: bp:molecular_activity

"},{"location":"biological_process/molecular_activity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship no"},{"location":"biological_process/molecular_activity/#properties","title":"Properties","text":""},{"location":"biological_process/molecular_activity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/molecular_activity/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/molecular_activity/#linkml-source","title":"LinkML Source","text":"
name: molecular_activity\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: molecular_activity\nowner: GeneMolecularActivityRelationship\ndomain_of:\n- GeneMolecularActivityRelationship\nrange: MolecularActivity\n\n
"},{"location":"biological_process/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: bp:named_entities

"},{"location":"biological_process/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/named_entities/#properties","title":"Properties","text":""},{"location":"biological_process/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biological_process/object/","title":"Slot: object","text":"

URI: bp:object

"},{"location":"biological_process/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/object/#properties","title":"Properties","text":""},{"location":"biological_process/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/object/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biological_process/object_id/","title":"Slot: object_id","text":"

URI: bp:object_id

"},{"location":"biological_process/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biological_process/object_id/#properties","title":"Properties","text":""},{"location":"biological_process/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/object_id/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biological_process/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: bp:object_qualifier

"},{"location":"biological_process/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/object_qualifier/#properties","title":"Properties","text":""},{"location":"biological_process/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biological_process/object_text/","title":"Slot: object_text","text":"

URI: bp:object_text

"},{"location":"biological_process/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biological_process/object_text/#properties","title":"Properties","text":""},{"location":"biological_process/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/object_text/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biological_process/outputs/","title":"Slot: outputs","text":"

the outputs of the biological process

URI: bp:outputs

"},{"location":"biological_process/outputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/outputs/#properties","title":"Properties","text":""},{"location":"biological_process/outputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/outputs/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/outputs/#linkml-source","title":"LinkML Source","text":"
name: outputs\ndescription: the outputs of the biological process\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: outputs\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: ChemicalEntity\n\n
"},{"location":"biological_process/predicate/","title":"Slot: predicate","text":"

URI: bp:predicate

"},{"location":"biological_process/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/predicate/#properties","title":"Properties","text":""},{"location":"biological_process/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/predicate/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"biological_process/prompt/","title":"Slot: prompt","text":"

URI: bp:prompt

"},{"location":"biological_process/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/prompt/#properties","title":"Properties","text":""},{"location":"biological_process/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/prompt/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biological_process/publication/","title":"Slot: publication","text":"

URI: bp:publication

"},{"location":"biological_process/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"biological_process/publication/#properties","title":"Properties","text":""},{"location":"biological_process/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"biological_process/publication/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"biological_process/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: bp:qualifier

"},{"location":"biological_process/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/qualifier/#properties","title":"Properties","text":""},{"location":"biological_process/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"biological_process/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: bp:raw_completion_output

"},{"location":"biological_process/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biological_process/raw_completion_output/#properties","title":"Properties","text":""},{"location":"biological_process/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biological_process/steps/","title":"Slot: steps","text":"

the steps involved in this biological process

URI: bp:steps

"},{"location":"biological_process/steps/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/steps/#properties","title":"Properties","text":""},{"location":"biological_process/steps/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/steps/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/steps/#linkml-source","title":"LinkML Source","text":"
name: steps\ndescription: the steps involved in this biological process\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: steps\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: MolecularActivity\n\n
"},{"location":"biological_process/subclass_of/","title":"Slot: subclass_of","text":"

the category to which this biological process belongs

URI: bp:subclass_of

"},{"location":"biological_process/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/subclass_of/#properties","title":"Properties","text":""},{"location":"biological_process/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\ndescription: the category to which this biological process belongs\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: subclass_of\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: BiologicalProcess\n\n
"},{"location":"biological_process/subject/","title":"Slot: subject","text":"

URI: bp:subject

"},{"location":"biological_process/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/subject/#properties","title":"Properties","text":""},{"location":"biological_process/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/subject/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biological_process/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: bp:subject_qualifier

"},{"location":"biological_process/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biological_process/subject_qualifier/#properties","title":"Properties","text":""},{"location":"biological_process/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biological_process/subject_text/","title":"Slot: subject_text","text":"

URI: bp:subject_text

"},{"location":"biological_process/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biological_process/subject_text/#properties","title":"Properties","text":""},{"location":"biological_process/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biological_process/synonyms/","title":"Slot: synonyms","text":"

alternative names of the biological process

URI: bp:synonyms

"},{"location":"biological_process/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiologicalProcess no"},{"location":"biological_process/synonyms/#properties","title":"Properties","text":""},{"location":"biological_process/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\ndescription: alternative names of the biological process\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: BiologicalProcess\ndomain_of:\n- BiologicalProcess\nrange: string\n\n
"},{"location":"biological_process/title/","title":"Slot: title","text":"

The title of the publication

URI: bp:title

"},{"location":"biological_process/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biological_process/title/#properties","title":"Properties","text":""},{"location":"biological_process/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/title/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biological_process/triples/","title":"Slot: triples","text":"

URI: bp:triples

"},{"location":"biological_process/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"biological_process/triples/#properties","title":"Properties","text":""},{"location":"biological_process/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biological_process/triples/#schema-source","title":"Schema Source","text":""},{"location":"biological_process/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/biological_process\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biotic_interaction/","title":"Biotic Interaction Template","text":"

A template for biotic interactions

URI: https://w3id.org/ontogpt/biotic_interaction

Name: biotic-interaction-template

"},{"location":"biotic_interaction/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nContainer {\n\n}\nBioticInteraction {\n\n}\nInteractionType {\n    string id  \n    string label  \n}\nTaxon {\n    string id  \n    string label  \n}\n\nContainer ||--}o BioticInteraction : \"interactions\"\nBioticInteraction ||--|o Taxon : \"source_taxon\"\nBioticInteraction ||--|o Taxon : \"target_taxon\"\nBioticInteraction ||--|o InteractionType : \"interaction_type\"\n\n
"},{"location":"biotic_interaction/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None BioticInteraction None CompoundExpression None Triple Abstract parent for Relation Extraction tasks Container None ExtractionResult A result of extracting knowledge on text NamedEntity None InteractionType None RelationshipType None Taxon None Publication None TextWithTriples None"},{"location":"biotic_interaction/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title interaction_type the type of interaction interactions label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output source_taxon the taxon that is the subject of the interaction subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text target_taxon the taxon that is the object of the interaction title The title of the publication triples"},{"location":"biotic_interaction/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"biotic_interaction/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"biotic_interaction/#subsets","title":"Subsets","text":"Subset Description"},{"location":"biotic_interaction/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: bp:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"biotic_interaction/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"biotic_interaction/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:AnnotatorResult native bp:AnnotatorResult"},{"location":"biotic_interaction/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n\n
"},{"location":"biotic_interaction/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"biotic_interaction/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"biotic_interaction/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"biotic_interaction/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"biotic_interaction/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Any/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native bp:Any"},{"location":"biotic_interaction/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nclass_uri: linkml:Any\n\n
"},{"location":"biotic_interaction/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nclass_uri: linkml:Any\n\n
"},{"location":"biotic_interaction/BioticInteraction/","title":"Class: BioticInteraction","text":"

URI: bp:BioticInteraction

erDiagram\nBioticInteraction {\n\n}\nInteractionType {\n    string id  \n    string label  \n}\nTaxon {\n    string id  \n    string label  \n}\n\nBioticInteraction ||--|o Taxon : \"source_taxon\"\nBioticInteraction ||--|o Taxon : \"target_taxon\"\nBioticInteraction ||--|o InteractionType : \"interaction_type\"\n\n
"},{"location":"biotic_interaction/BioticInteraction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance source_taxon 0..1 Taxon the taxon that is the subject of the interaction direct target_taxon 0..1 Taxon the taxon that is the object of the interaction direct interaction_type 0..1 InteractionType the type of interaction direct"},{"location":"biotic_interaction/BioticInteraction/#usages","title":"Usages","text":"used by used in type used Container interactions range BioticInteraction"},{"location":"biotic_interaction/BioticInteraction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/BioticInteraction/#annotations","title":"Annotations","text":"property value prompt A semi-colon separated list of taxon to taxon relationships"},{"location":"biotic_interaction/BioticInteraction/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/BioticInteraction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:BioticInteraction native bp:BioticInteraction"},{"location":"biotic_interaction/BioticInteraction/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/BioticInteraction/#direct","title":"Direct","text":"
name: BioticInteraction\nannotations:\n  prompt:\n    tag: prompt\n    value: A semi-colon separated list of taxon to taxon relationships\n  prompt.example:\n    tag: prompt.example\n    value: Carcharodon carcharias eats elephant seal; Pandarus sinuatus parasitizes\n      Carcharodon carcharias; orca eats Carcharodon carcharias\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  source_taxon:\n    name: source_taxon\n    description: the taxon that is the subject of the interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: Taxon\n  target_taxon:\n    name: target_taxon\n    description: the taxon that is the object of the interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: Taxon\n  interaction_type:\n    name: interaction_type\n    description: the type of interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: InteractionType\n\n
"},{"location":"biotic_interaction/BioticInteraction/#induced","title":"Induced","text":"
name: BioticInteraction\nannotations:\n  prompt:\n    tag: prompt\n    value: A semi-colon separated list of taxon to taxon relationships\n  prompt.example:\n    tag: prompt.example\n    value: Carcharodon carcharias eats elephant seal; Pandarus sinuatus parasitizes\n      Carcharodon carcharias; orca eats Carcharodon carcharias\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  source_taxon:\n    name: source_taxon\n    description: the taxon that is the subject of the interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: source_taxon\n    owner: BioticInteraction\n    domain_of:\n    - BioticInteraction\n    range: Taxon\n  target_taxon:\n    name: target_taxon\n    description: the taxon that is the object of the interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: target_taxon\n    owner: BioticInteraction\n    domain_of:\n    - BioticInteraction\n    range: Taxon\n  interaction_type:\n    name: interaction_type\n    description: the type of interaction\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: interaction_type\n    owner: BioticInteraction\n    domain_of:\n    - BioticInteraction\n    range: InteractionType\n\n
"},{"location":"biotic_interaction/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"biotic_interaction/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: bp:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"biotic_interaction/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"biotic_interaction/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:CompoundExpression native bp:CompoundExpression"},{"location":"biotic_interaction/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nabstract: true\n\n
"},{"location":"biotic_interaction/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nabstract: true\n\n
"},{"location":"biotic_interaction/Container/","title":"Class: Container","text":"

URI: bp:Container

erDiagram\nContainer {\n\n}\nBioticInteraction {\n\n}\nInteractionType {\n    string id  \n    string label  \n}\nTaxon {\n    string id  \n    string label  \n}\n\nContainer ||--}o BioticInteraction : \"interactions\"\nBioticInteraction ||--|o Taxon : \"source_taxon\"\nBioticInteraction ||--|o Taxon : \"target_taxon\"\nBioticInteraction ||--|o InteractionType : \"interaction_type\"\n\n
"},{"location":"biotic_interaction/Container/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance interactions 0..* BioticInteraction direct"},{"location":"biotic_interaction/Container/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Container/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Container/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Container native bp:Container"},{"location":"biotic_interaction/Container/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/Container/#direct","title":"Direct","text":"
name: Container\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  interactions:\n    name: interactions\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    range: BioticInteraction\n    inlined: true\n    inlined_as_list: true\ntree_root: true\n\n
"},{"location":"biotic_interaction/Container/#induced","title":"Induced","text":"
name: Container\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  interactions:\n    name: interactions\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    alias: interactions\n    owner: Container\n    domain_of:\n    - Container\n    range: BioticInteraction\n    inlined: true\n    inlined_as_list: true\ntree_root: true\n\n
"},{"location":"biotic_interaction/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"biotic_interaction/Curie/#comments","title":"Comments","text":""},{"location":"biotic_interaction/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Curie/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"biotic_interaction/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Date/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"biotic_interaction/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"biotic_interaction/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"biotic_interaction/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"biotic_interaction/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Double/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: bp:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"biotic_interaction/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"biotic_interaction/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ExtractionResult native bp:ExtractionResult"},{"location":"biotic_interaction/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biotic_interaction/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biotic_interaction/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"biotic_interaction/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Float/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"biotic_interaction/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Integer/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/InteractionType/","title":"Class: InteractionType","text":"

URI: bp:InteractionType

erDiagram\nInteractionType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biotic_interaction/InteractionType/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/InteractionType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biotic_interaction/InteractionType/#usages","title":"Usages","text":"used by used in type used BioticInteraction interaction_type range InteractionType"},{"location":"biotic_interaction/InteractionType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/InteractionType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biotic_interaction/InteractionType/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero"},{"location":"biotic_interaction/InteractionType/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/InteractionType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:InteractionType native bp:InteractionType"},{"location":"biotic_interaction/InteractionType/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/InteractionType/#direct","title":"Direct","text":"
name: InteractionType\nid_prefixes:\n- RO\n- MESH\n- ECOCORE\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\n\n
"},{"location":"biotic_interaction/InteractionType/#induced","title":"Induced","text":"
name: InteractionType\nid_prefixes:\n- RO\n- MESH\n- ECOCORE\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: InteractionType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: InteractionType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"biotic_interaction/NamedEntity/","title":"Class: NamedEntity","text":"

URI: bp:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biotic_interaction/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"biotic_interaction/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"biotic_interaction/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:NamedEntity native bp:NamedEntity"},{"location":"biotic_interaction/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"biotic_interaction/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"biotic_interaction/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"biotic_interaction/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"biotic_interaction/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"biotic_interaction/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"biotic_interaction/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"biotic_interaction/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"biotic_interaction/Objectidentifier/#comments","title":"Comments","text":""},{"location":"biotic_interaction/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Publication/","title":"Class: Publication","text":"

URI: bp:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"biotic_interaction/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"biotic_interaction/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"biotic_interaction/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Publication/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Publication native bp:Publication"},{"location":"biotic_interaction/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n\n
"},{"location":"biotic_interaction/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"biotic_interaction/RelationshipType/","title":"Class: RelationshipType","text":"

URI: bp:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biotic_interaction/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biotic_interaction/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"biotic_interaction/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biotic_interaction/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:RelationshipType native bp:RelationshipType"},{"location":"biotic_interaction/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\n\n
"},{"location":"biotic_interaction/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"biotic_interaction/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"biotic_interaction/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/String/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Taxon/","title":"Class: Taxon","text":"

URI: bp:Taxon

erDiagram\nTaxon {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"biotic_interaction/Taxon/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/Taxon/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"biotic_interaction/Taxon/#usages","title":"Usages","text":"used by used in type used BioticInteraction source_taxon range Taxon BioticInteraction target_taxon range Taxon"},{"location":"biotic_interaction/Taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Taxon/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"biotic_interaction/Taxon/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ncbitaxon, bioportal:SNOMEDCT"},{"location":"biotic_interaction/Taxon/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Taxon/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Taxon native bp:Taxon"},{"location":"biotic_interaction/Taxon/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/Taxon/#direct","title":"Direct","text":"
name: Taxon\nid_prefixes:\n- NCBITaxon\n- SNOMEDCT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ncbitaxon, bioportal:SNOMEDCT\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\n\n
"},{"location":"biotic_interaction/Taxon/#induced","title":"Induced","text":"
name: Taxon\nid_prefixes:\n- NCBITaxon\n- SNOMEDCT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ncbitaxon, bioportal:SNOMEDCT\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Taxon\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Taxon\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"biotic_interaction/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: bp:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"biotic_interaction/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"biotic_interaction/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:TextWithTriples native bp:TextWithTriples"},{"location":"biotic_interaction/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biotic_interaction/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"biotic_interaction/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"biotic_interaction/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Time/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: bp:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"biotic_interaction/Triple/#inheritance","title":"Inheritance","text":""},{"location":"biotic_interaction/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"biotic_interaction/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"biotic_interaction/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Triple/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Triple native bp:Triple"},{"location":"biotic_interaction/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"biotic_interaction/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"biotic_interaction/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/biotic_interaction\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"biotic_interaction/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"biotic_interaction/Uri/#comments","title":"Comments","text":""},{"location":"biotic_interaction/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Uri/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"biotic_interaction/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: bp:abstract

"},{"location":"biotic_interaction/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biotic_interaction/abstract/#properties","title":"Properties","text":""},{"location":"biotic_interaction/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/abstract/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biotic_interaction/biotic-interaction-template/","title":"biotic-interaction-template","text":"

A template for biotic interactions

URI: https://w3id.org/ontogpt/biotic_interaction

"},{"location":"biotic_interaction/combined_text/","title":"Slot: combined_text","text":"

URI: bp:combined_text

"},{"location":"biotic_interaction/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biotic_interaction/combined_text/#properties","title":"Properties","text":""},{"location":"biotic_interaction/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biotic_interaction/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: bp:extracted_object

"},{"location":"biotic_interaction/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/extracted_object/#properties","title":"Properties","text":""},{"location":"biotic_interaction/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"biotic_interaction/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: bp:full_text

"},{"location":"biotic_interaction/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biotic_interaction/full_text/#properties","title":"Properties","text":""},{"location":"biotic_interaction/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/full_text/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biotic_interaction/id/","title":"Slot: id","text":"

URI: bp:id

"},{"location":"biotic_interaction/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no InteractionType no NamedEntity no RelationshipType no Publication no"},{"location":"biotic_interaction/id/#properties","title":"Properties","text":""},{"location":"biotic_interaction/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"biotic_interaction/input_id/","title":"Slot: input_id","text":"

URI: bp:input_id

"},{"location":"biotic_interaction/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/input_id/#properties","title":"Properties","text":""},{"location":"biotic_interaction/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/input_id/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biotic_interaction/input_text/","title":"Slot: input_text","text":"

URI: bp:input_text

"},{"location":"biotic_interaction/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/input_text/#properties","title":"Properties","text":""},{"location":"biotic_interaction/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/input_text/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biotic_interaction/input_title/","title":"Slot: input_title","text":"

URI: bp:input_title

"},{"location":"biotic_interaction/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/input_title/#properties","title":"Properties","text":""},{"location":"biotic_interaction/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/input_title/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biotic_interaction/interaction_type/","title":"Slot: interaction_type","text":"

the type of interaction

URI: bp:interaction_type

"},{"location":"biotic_interaction/interaction_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BioticInteraction no"},{"location":"biotic_interaction/interaction_type/#properties","title":"Properties","text":""},{"location":"biotic_interaction/interaction_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/interaction_type/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/interaction_type/#linkml-source","title":"LinkML Source","text":"
name: interaction_type\ndescription: the type of interaction\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: interaction_type\nowner: BioticInteraction\ndomain_of:\n- BioticInteraction\nrange: InteractionType\n\n
"},{"location":"biotic_interaction/interactions/","title":"Slot: interactions","text":"

URI: bp:interactions

"},{"location":"biotic_interaction/interactions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Container no"},{"location":"biotic_interaction/interactions/#properties","title":"Properties","text":""},{"location":"biotic_interaction/interactions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/interactions/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/interactions/#linkml-source","title":"LinkML Source","text":"
name: interactions\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nmultivalued: true\nalias: interactions\nowner: Container\ndomain_of:\n- Container\nrange: BioticInteraction\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biotic_interaction/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"biotic_interaction/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no InteractionType no NamedEntity no RelationshipType no"},{"location":"biotic_interaction/label/#properties","title":"Properties","text":""},{"location":"biotic_interaction/label/#aliases","title":"Aliases","text":""},{"location":"biotic_interaction/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"biotic_interaction/label/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"biotic_interaction/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: bp:named_entities

"},{"location":"biotic_interaction/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/named_entities/#properties","title":"Properties","text":""},{"location":"biotic_interaction/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biotic_interaction/object/","title":"Slot: object","text":"

URI: bp:object

"},{"location":"biotic_interaction/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/object/#properties","title":"Properties","text":""},{"location":"biotic_interaction/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/object/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biotic_interaction/object_id/","title":"Slot: object_id","text":"

URI: bp:object_id

"},{"location":"biotic_interaction/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biotic_interaction/object_id/#properties","title":"Properties","text":""},{"location":"biotic_interaction/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/object_id/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biotic_interaction/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: bp:object_qualifier

"},{"location":"biotic_interaction/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/object_qualifier/#properties","title":"Properties","text":""},{"location":"biotic_interaction/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biotic_interaction/object_text/","title":"Slot: object_text","text":"

URI: bp:object_text

"},{"location":"biotic_interaction/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biotic_interaction/object_text/#properties","title":"Properties","text":""},{"location":"biotic_interaction/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/object_text/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biotic_interaction/predicate/","title":"Slot: predicate","text":"

URI: bp:predicate

"},{"location":"biotic_interaction/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/predicate/#properties","title":"Properties","text":""},{"location":"biotic_interaction/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/predicate/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"biotic_interaction/prompt/","title":"Slot: prompt","text":"

URI: bp:prompt

"},{"location":"biotic_interaction/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/prompt/#properties","title":"Properties","text":""},{"location":"biotic_interaction/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/prompt/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biotic_interaction/publication/","title":"Slot: publication","text":"

URI: bp:publication

"},{"location":"biotic_interaction/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"biotic_interaction/publication/#properties","title":"Properties","text":""},{"location":"biotic_interaction/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"biotic_interaction/publication/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"biotic_interaction/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: bp:qualifier

"},{"location":"biotic_interaction/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/qualifier/#properties","title":"Properties","text":""},{"location":"biotic_interaction/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"biotic_interaction/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: bp:raw_completion_output

"},{"location":"biotic_interaction/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"biotic_interaction/raw_completion_output/#properties","title":"Properties","text":""},{"location":"biotic_interaction/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"biotic_interaction/source_taxon/","title":"Slot: source_taxon","text":"

the taxon that is the subject of the interaction

URI: bp:source_taxon

"},{"location":"biotic_interaction/source_taxon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BioticInteraction no"},{"location":"biotic_interaction/source_taxon/#properties","title":"Properties","text":""},{"location":"biotic_interaction/source_taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/source_taxon/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/source_taxon/#linkml-source","title":"LinkML Source","text":"
name: source_taxon\ndescription: the taxon that is the subject of the interaction\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: source_taxon\nowner: BioticInteraction\ndomain_of:\n- BioticInteraction\nrange: Taxon\n\n
"},{"location":"biotic_interaction/subject/","title":"Slot: subject","text":"

URI: bp:subject

"},{"location":"biotic_interaction/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/subject/#properties","title":"Properties","text":""},{"location":"biotic_interaction/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/subject/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biotic_interaction/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: bp:subject_qualifier

"},{"location":"biotic_interaction/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"biotic_interaction/subject_qualifier/#properties","title":"Properties","text":""},{"location":"biotic_interaction/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"biotic_interaction/subject_text/","title":"Slot: subject_text","text":"

URI: bp:subject_text

"},{"location":"biotic_interaction/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"biotic_interaction/subject_text/#properties","title":"Properties","text":""},{"location":"biotic_interaction/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"biotic_interaction/target_taxon/","title":"Slot: target_taxon","text":"

the taxon that is the object of the interaction

URI: bp:target_taxon

"},{"location":"biotic_interaction/target_taxon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BioticInteraction no"},{"location":"biotic_interaction/target_taxon/#properties","title":"Properties","text":""},{"location":"biotic_interaction/target_taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/target_taxon/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/target_taxon/#linkml-source","title":"LinkML Source","text":"
name: target_taxon\ndescription: the taxon that is the object of the interaction\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: target_taxon\nowner: BioticInteraction\ndomain_of:\n- BioticInteraction\nrange: Taxon\n\n
"},{"location":"biotic_interaction/title/","title":"Slot: title","text":"

The title of the publication

URI: bp:title

"},{"location":"biotic_interaction/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"biotic_interaction/title/#properties","title":"Properties","text":""},{"location":"biotic_interaction/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/title/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"biotic_interaction/triples/","title":"Slot: triples","text":"

URI: bp:triples

"},{"location":"biotic_interaction/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"biotic_interaction/triples/#properties","title":"Properties","text":""},{"location":"biotic_interaction/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_interaction/triples/#schema-source","title":"Schema Source","text":""},{"location":"biotic_interaction/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/biotic_interaction\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"cell_type/","title":"Composite Disease","text":"

A template for representing cell types

URI: http://w3id.org/ontogpt/cell_type

Name: cell_type

"},{"location":"cell_type/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nCellType {\n    uriorcurie id  \n    string label  \n    string definition  \n}\nBiologicalProcess {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nAnatomicalStructure {\n    string id  \n    string label  \n}\nCellOntologyTerm {\n    string id  \n    string label  \n}\n\nCellType ||--|o CellOntologyTerm : \"equivalent_to\"\nCellType ||--}o CellOntologyTerm : \"parents\"\nCellType ||--}o CellOntologyTerm : \"subtypes\"\nCellType ||--}o AnatomicalStructure : \"localizations\"\nCellType ||--}o Gene : \"genes\"\nCellType ||--}o Disease : \"diseases\"\nCellType ||--}o BiologicalProcess : \"roles\"\n\n
"},{"location":"cell_type/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CellType Represents a cell type ImmuneCell None Neuron None Interneuron None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None AnatomicalStructure None BrainRegion None BiologicalProcess None CellOntologyTerm None ChemicalEntity None Neurotransmitter None Disease None Drug None Gene None Pathway None ProteinOrComplex None RelationshipType None Publication None TextWithTriples None"},{"location":"cell_type/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text definition diseases equivalent_to the the cell type described extracted_object The complex objects extracted from the text full_text The full text of the publication genes has_surface_markers id input_id input_text input_title label the concise name of the cell type localizations named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text parents categorization predicate projects_to_or_from Brain structures from which this cell type projects into or receives projecti... prompt publication qualifier A qualifier for the statements, e raw_completion_output releases_neurotransitter roles subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text subtypes title The title of the publication triples"},{"location":"cell_type/#enumerations","title":"Enumerations","text":"Enumeration Description BrainRegionIdentifier Brain region (or for now, any nervous system part) NeurotransmitterIdentifier NullDataOptions"},{"location":"cell_type/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"cell_type/#subsets","title":"Subsets","text":"Subset Description"},{"location":"cell_type/AnatomicalStructure/","title":"Class: AnatomicalStructure","text":"

URI: cell_type:AnatomicalStructure

erDiagram\nAnatomicalStructure {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/AnatomicalStructure/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/AnatomicalStructure/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/AnatomicalStructure/#usages","title":"Usages","text":"used by used in type used CellType localizations range AnatomicalStructure ImmuneCell localizations range AnatomicalStructure Neuron localizations range AnatomicalStructure Interneuron localizations range AnatomicalStructure"},{"location":"cell_type/AnatomicalStructure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/AnatomicalStructure/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/AnatomicalStructure/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt"},{"location":"cell_type/AnatomicalStructure/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/AnatomicalStructure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:AnatomicalStructure native cell_type:AnatomicalStructure"},{"location":"cell_type/AnatomicalStructure/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/AnatomicalStructure/#direct","title":"Direct","text":"
name: AnatomicalStructure\nid_prefixes:\n- UBERON\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/AnatomicalStructure/#induced","title":"Induced","text":"
name: AnatomicalStructure\nid_prefixes:\n- UBERON\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: AnatomicalStructure\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: AnatomicalStructure\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: cell_type:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"cell_type/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"cell_type/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:AnnotatorResult native cell_type:AnnotatorResult"},{"location":"cell_type/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n\n
"},{"location":"cell_type/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"cell_type/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"cell_type/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"cell_type/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"cell_type/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Any/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native cell_type:Any"},{"location":"cell_type/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/cell_type\nclass_uri: linkml:Any\n\n
"},{"location":"cell_type/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/cell_type\nclass_uri: linkml:Any\n\n
"},{"location":"cell_type/BiologicalProcess/","title":"Class: BiologicalProcess","text":"

URI: cell_type:BiologicalProcess

erDiagram\nBiologicalProcess {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/BiologicalProcess/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/BiologicalProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/BiologicalProcess/#usages","title":"Usages","text":"used by used in type used CellType roles range BiologicalProcess ImmuneCell roles range BiologicalProcess Neuron roles range BiologicalProcess Interneuron roles range BiologicalProcess"},{"location":"cell_type/BiologicalProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/BiologicalProcess/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/BiologicalProcess/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"cell_type/BiologicalProcess/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/BiologicalProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:BiologicalProcess native cell_type:BiologicalProcess"},{"location":"cell_type/BiologicalProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/BiologicalProcess/#direct","title":"Direct","text":"
name: BiologicalProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/BiologicalProcess/#induced","title":"Induced","text":"
name: BiologicalProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: BiologicalProcess\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: BiologicalProcess\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"cell_type/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/BrainRegion/","title":"Class: BrainRegion","text":"

URI: cell_type:BrainRegion

erDiagram\nBrainRegion {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/BrainRegion/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/BrainRegion/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/BrainRegion/#usages","title":"Usages","text":"used by used in type used Interneuron projects_to_or_from range BrainRegion"},{"location":"cell_type/BrainRegion/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/BrainRegion/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/BrainRegion/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt"},{"location":"cell_type/BrainRegion/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/BrainRegion/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:BrainRegion native cell_type:BrainRegion"},{"location":"cell_type/BrainRegion/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/BrainRegion/#direct","title":"Direct","text":"
name: BrainRegion\nid_prefixes:\n- UBERON\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: AnatomicalStructure\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - BrainRegionIdentifier\n    identifier: true\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n\n
"},{"location":"cell_type/BrainRegion/#induced","title":"Induced","text":"
name: BrainRegion\nid_prefixes:\n- UBERON\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: AnatomicalStructure\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - BrainRegionIdentifier\n    identifier: true\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/cell_type\n    values_from:\n    - BrainRegionIdentifier\n    identifier: true\n    alias: id\n    owner: BrainRegion\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: BrainRegion\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/BrainRegionIdentifier/","title":"Enum: BrainRegionIdentifier","text":"

Brain region (or for now, any nervous system part)

URI: BrainRegionIdentifier

This is a dynamic enum

"},{"location":"cell_type/BrainRegionIdentifier/#comments","title":"Comments","text":""},{"location":"cell_type/BrainRegionIdentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/BrainRegionIdentifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/BrainRegionIdentifier/#linkml-source","title":"LinkML Source","text":"
name: BrainRegionIdentifier\ndescription: Brain region (or for now, any nervous system part)\ncomments:\n- consider adding brain atlases here\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\ninclude:\n- reachable_from:\n    source_ontology: obo:uberon\n    source_nodes:\n    - UBERON:0001016\n    relationship_types:\n    - rdfs:subClassOf\n    - BFO:0000050\n- reachable_from:\n    source_ontology: obo:fbbt\n    source_nodes:\n    - FBbt:00005093\n    relationship_types:\n    - rdfs:subClassOf\n    - BFO:0000050\n- reachable_from:\n    source_ontology: obo:wbbt\n    source_nodes:\n    - WBbt:0005735\n    relationship_types:\n    - rdfs:subClassOf\n    - BFO:0000050\n\n
"},{"location":"cell_type/CellOntologyTerm/","title":"Class: CellOntologyTerm","text":"

URI: cell_type:CellOntologyTerm

erDiagram\nCellOntologyTerm {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/CellOntologyTerm/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/CellOntologyTerm/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/CellOntologyTerm/#usages","title":"Usages","text":"used by used in type used CellType equivalent_to range CellOntologyTerm CellType parents range CellOntologyTerm CellType subtypes range CellOntologyTerm ImmuneCell equivalent_to range CellOntologyTerm ImmuneCell parents range CellOntologyTerm ImmuneCell subtypes range CellOntologyTerm Neuron equivalent_to range CellOntologyTerm Neuron parents range CellOntologyTerm Neuron subtypes range CellOntologyTerm Interneuron equivalent_to range CellOntologyTerm Interneuron parents range CellOntologyTerm Interneuron subtypes range CellOntologyTerm"},{"location":"cell_type/CellOntologyTerm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/CellOntologyTerm/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/CellOntologyTerm/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:cl, sqlite:obo:fbbt, sqlite:obo:wbbt"},{"location":"cell_type/CellOntologyTerm/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/CellOntologyTerm/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:CellOntologyTerm native cell_type:CellOntologyTerm"},{"location":"cell_type/CellOntologyTerm/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/CellOntologyTerm/#direct","title":"Direct","text":"
name: CellOntologyTerm\nid_prefixes:\n- CL\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:cl, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/CellOntologyTerm/#induced","title":"Induced","text":"
name: CellOntologyTerm\nid_prefixes:\n- CL\n- FBbt\n- WBbt\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:cl, sqlite:obo:fbbt, sqlite:obo:wbbt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: CellOntologyTerm\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: CellOntologyTerm\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/CellType/","title":"Class: CellType","text":"

Represents a cell type

URI: cell_type:CellType

erDiagram\nCellType {\n    uriorcurie id  \n    string label  \n    string definition  \n}\nBiologicalProcess {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nAnatomicalStructure {\n    string id  \n    string label  \n}\nCellOntologyTerm {\n    string id  \n    string label  \n}\n\nCellType ||--|o CellOntologyTerm : \"equivalent_to\"\nCellType ||--}o CellOntologyTerm : \"parents\"\nCellType ||--}o CellOntologyTerm : \"subtypes\"\nCellType ||--}o AnatomicalStructure : \"localizations\"\nCellType ||--}o Gene : \"genes\"\nCellType ||--}o Disease : \"diseases\"\nCellType ||--}o BiologicalProcess : \"roles\"\n\n
"},{"location":"cell_type/CellType/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/CellType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 Uriorcurie direct label 0..1 String the concise name of the cell type direct equivalent_to 0..1 CellOntologyTerm the the cell type described direct definition 0..1 String direct parents 0..* CellOntologyTerm categorization direct subtypes 0..* CellOntologyTerm direct localizations 0..* AnatomicalStructure direct genes 0..* Gene direct diseases 0..* Disease direct roles 0..* BiologicalProcess direct"},{"location":"cell_type/CellType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/CellType/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/CellType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:CellType native cell_type:CellType"},{"location":"cell_type/CellType/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/CellType/#direct","title":"Direct","text":"
name: CellType\ndescription: Represents a cell type\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the concise name of the cell type\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n  equivalent_to:\n    name: equivalent_to\n    annotations:\n      prompt:\n        tag: prompt\n        value: the cell type described in the text\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the the cell type described\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: skos:exactMatch\n    range: CellOntologyTerm\n  definition:\n    name: definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n          that <differentiating characteristics>'\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: IAO:0000115\n  parents:\n    name: parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent (broader) cell types\n      owl:\n        tag: owl\n        value: SubClassOf\n    description: categorization\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: CellOntologyTerm\n  subtypes:\n    name: subtypes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of the subtypes (subclasses) of this cell\n          type. Use concise terms, and separate elements in a list using semicolon\n          (;)\n      owl.template:\n        tag: owl.template\n        value: '{% for subtype in subtypes %}\n\n          SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: CellOntologyTerm\n  localizations:\n    name: localizations\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures in which this cell\n          type is localized\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: BFO:0000050\n    multivalued: true\n    range: AnatomicalStructure\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of genes expressed in cells of this type\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002292\n    multivalued: true\n    range: Gene\n  diseases:\n    name: diseases\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of diseases in which this cell type is implicated\n      owl.template:\n        tag: owl.template\n        value: '{% for disease in diseases %}\n\n          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}\n          ))\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: Disease\n  roles:\n    name: roles\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of roles (e.g. biological processes) that\n          this cell type plays. These should be short descriptive terms corresponding\n          to ontology terms in the GO biological process hierarchy.\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002215\n    multivalued: true\n    range: BiologicalProcess\ntree_root: true\n\n
"},{"location":"cell_type/CellType/#induced","title":"Induced","text":"
name: CellType\ndescription: Represents a cell type\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    alias: id\n    owner: CellType\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the concise name of the cell type\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: CellType\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n  equivalent_to:\n    name: equivalent_to\n    annotations:\n      prompt:\n        tag: prompt\n        value: the cell type described in the text\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the the cell type described\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: skos:exactMatch\n    alias: equivalent_to\n    owner: CellType\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  definition:\n    name: definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n          that <differentiating characteristics>'\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: IAO:0000115\n    alias: definition\n    owner: CellType\n    domain_of:\n    - CellType\n    range: string\n  parents:\n    name: parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent (broader) cell types\n      owl:\n        tag: owl\n        value: SubClassOf\n    description: categorization\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: parents\n    owner: CellType\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  subtypes:\n    name: subtypes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of the subtypes (subclasses) of this cell\n          type. Use concise terms, and separate elements in a list using semicolon\n          (;)\n      owl.template:\n        tag: owl.template\n        value: '{% for subtype in subtypes %}\n\n          SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: CellType\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  localizations:\n    name: localizations\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures in which this cell\n          type is localized\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: localizations\n    owner: CellType\n    domain_of:\n    - CellType\n    range: AnatomicalStructure\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of genes expressed in cells of this type\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002292\n    multivalued: true\n    alias: genes\n    owner: CellType\n    domain_of:\n    - CellType\n    range: Gene\n  diseases:\n    name: diseases\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of diseases in which this cell type is implicated\n      owl.template:\n        tag: owl.template\n        value: '{% for disease in diseases %}\n\n          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}\n          ))\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: diseases\n    owner: CellType\n    domain_of:\n    - CellType\n    range: Disease\n  roles:\n    name: roles\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of roles (e.g. biological processes) that\n          this cell type plays. These should be short descriptive terms corresponding\n          to ontology terms in the GO biological process hierarchy.\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002215\n    multivalued: true\n    alias: roles\n    owner: CellType\n    domain_of:\n    - CellType\n    range: BiologicalProcess\ntree_root: true\n\n
"},{"location":"cell_type/ChemicalEntity/","title":"Class: ChemicalEntity","text":"

URI: cell_type:ChemicalEntity

erDiagram\nChemicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/ChemicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"cell_type/ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:ChemicalEntity native cell_type:ChemicalEntity"},{"location":"cell_type/ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalEntity\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: cell_type:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"cell_type/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"cell_type/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:CompoundExpression native cell_type:CompoundExpression"},{"location":"cell_type/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/cell_type\nabstract: true\n\n
"},{"location":"cell_type/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/cell_type\nabstract: true\n\n
"},{"location":"cell_type/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"cell_type/Curie/#comments","title":"Comments","text":""},{"location":"cell_type/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Curie/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"cell_type/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Date/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"cell_type/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"cell_type/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"cell_type/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Disease/","title":"Class: Disease","text":"

URI: cell_type:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/Disease/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/Disease/#usages","title":"Usages","text":"used by used in type used CellType diseases range Disease ImmuneCell diseases range Disease Neuron diseases range Disease Interneuron diseases range Disease"},{"location":"cell_type/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Disease/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo, sqlite:obo:hp"},{"location":"cell_type/Disease/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Disease native cell_type:Disease"},{"location":"cell_type/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Disease/#direct","title":"Direct","text":"
name: Disease\nid_prefixes:\n- MONDO\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo, sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/Disease/#induced","title":"Induced","text":"
name: Disease\nid_prefixes:\n- MONDO\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo, sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"cell_type/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Double/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Drug/","title":"Class: Drug","text":"

URI: cell_type:Drug

erDiagram\nDrug {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/Drug/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Drug/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/Drug/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Drug/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi, sqlite:obo:drugbank"},{"location":"cell_type/Drug/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Drug/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Drug native cell_type:Drug"},{"location":"cell_type/Drug/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Drug/#direct","title":"Direct","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/Drug/#induced","title":"Induced","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: Drug\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Drug\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: cell_type:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"cell_type/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"cell_type/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:ExtractionResult native cell_type:ExtractionResult"},{"location":"cell_type/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"cell_type/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"cell_type/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"cell_type/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Float/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Gene/","title":"Class: Gene","text":"

URI: cell_type:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/Gene/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/Gene/#usages","title":"Usages","text":"used by used in type used CellType genes range Gene ImmuneCell genes range Gene Neuron genes range Gene Interneuron genes range Gene"},{"location":"cell_type/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/Gene/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hgnc, bioportal:hgnc-nr"},{"location":"cell_type/Gene/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Gene native cell_type:Gene"},{"location":"cell_type/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\n- MGI\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\n- MGI\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/ImmuneCell/","title":"Class: ImmuneCell","text":"

URI: cell_type:ImmuneCell

erDiagram\nImmuneCell {\n    uriorcurie id  \n    string label  \n    string definition  \n}\nBiologicalProcess {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nAnatomicalStructure {\n    string id  \n    string label  \n}\nCellOntologyTerm {\n    string id  \n    string label  \n}\nProteinOrComplex {\n    string id  \n    string label  \n}\n\nImmuneCell ||--}o ProteinOrComplex : \"has_surface_markers\"\nImmuneCell ||--|o CellOntologyTerm : \"equivalent_to\"\nImmuneCell ||--}o CellOntologyTerm : \"parents\"\nImmuneCell ||--}o CellOntologyTerm : \"subtypes\"\nImmuneCell ||--}o AnatomicalStructure : \"localizations\"\nImmuneCell ||--}o Gene : \"genes\"\nImmuneCell ||--}o Disease : \"diseases\"\nImmuneCell ||--}o BiologicalProcess : \"roles\"\n\n
"},{"location":"cell_type/ImmuneCell/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/ImmuneCell/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_surface_markers 0..* ProteinOrComplex direct id 1..1 Uriorcurie CellType label 0..1 String the concise name of the cell type CellType equivalent_to 0..1 CellOntologyTerm the the cell type described CellType definition 0..1 String CellType parents 0..* CellOntologyTerm categorization CellType subtypes 0..* CellOntologyTerm CellType localizations 0..* AnatomicalStructure CellType genes 0..* Gene CellType diseases 0..* Disease CellType roles 0..* BiologicalProcess CellType"},{"location":"cell_type/ImmuneCell/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/ImmuneCell/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/ImmuneCell/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:ImmuneCell native cell_type:ImmuneCell"},{"location":"cell_type/ImmuneCell/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/ImmuneCell/#direct","title":"Direct","text":"
name: ImmuneCell\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CellType\nattributes:\n  has_surface_markers:\n    name: has_surface_markers\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of proteins or complexes expressed on the\n          surface of the cell\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: ProteinOrComplex\n\n
"},{"location":"cell_type/ImmuneCell/#induced","title":"Induced","text":"
name: ImmuneCell\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CellType\nattributes:\n  has_surface_markers:\n    name: has_surface_markers\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of proteins or complexes expressed on the\n          surface of the cell\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: has_surface_markers\n    owner: ImmuneCell\n    domain_of:\n    - ImmuneCell\n    range: ProteinOrComplex\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    alias: id\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the concise name of the cell type\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n  equivalent_to:\n    name: equivalent_to\n    annotations:\n      prompt:\n        tag: prompt\n        value: the cell type described in the text\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the the cell type described\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: skos:exactMatch\n    alias: equivalent_to\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  definition:\n    name: definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n          that <differentiating characteristics>'\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: IAO:0000115\n    alias: definition\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: string\n  parents:\n    name: parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent (broader) cell types\n      owl:\n        tag: owl\n        value: SubClassOf\n    description: categorization\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: parents\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  subtypes:\n    name: subtypes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of the subtypes (subclasses) of this cell\n          type. Use concise terms, and separate elements in a list using semicolon\n          (;)\n      owl.template:\n        tag: owl.template\n        value: '{% for subtype in subtypes %}\n\n          SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  localizations:\n    name: localizations\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures in which this cell\n          type is localized\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: localizations\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: AnatomicalStructure\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of genes expressed in cells of this type\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002292\n    multivalued: true\n    alias: genes\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: Gene\n  diseases:\n    name: diseases\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of diseases in which this cell type is implicated\n      owl.template:\n        tag: owl.template\n        value: '{% for disease in diseases %}\n\n          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}\n          ))\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: diseases\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: Disease\n  roles:\n    name: roles\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of roles (e.g. biological processes) that\n          this cell type plays. These should be short descriptive terms corresponding\n          to ontology terms in the GO biological process hierarchy.\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002215\n    multivalued: true\n    alias: roles\n    owner: ImmuneCell\n    domain_of:\n    - CellType\n    range: BiologicalProcess\n\n
"},{"location":"cell_type/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"cell_type/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Integer/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Interneuron/","title":"Class: Interneuron","text":"

URI: cell_type:Interneuron

erDiagram\nInterneuron {\n    uriorcurie id  \n    string label  \n    string definition  \n}\nBiologicalProcess {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nAnatomicalStructure {\n    string id  \n    string label  \n}\nCellOntologyTerm {\n    string id  \n    string label  \n}\nNeurotransmitter {\n    string id  \n    string label  \n}\nBrainRegion {\n    string id  \n    string label  \n}\n\nInterneuron ||--}o BrainRegion : \"projects_to_or_from\"\nInterneuron ||--}o Neurotransmitter : \"releases_neurotransitter\"\nInterneuron ||--|o CellOntologyTerm : \"equivalent_to\"\nInterneuron ||--}o CellOntologyTerm : \"parents\"\nInterneuron ||--}o CellOntologyTerm : \"subtypes\"\nInterneuron ||--}o AnatomicalStructure : \"localizations\"\nInterneuron ||--}o Gene : \"genes\"\nInterneuron ||--}o Disease : \"diseases\"\nInterneuron ||--}o BiologicalProcess : \"roles\"\n\n
"},{"location":"cell_type/Interneuron/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Interneuron/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance projects_to_or_from 0..* BrainRegion Brain structures from which this cell type projects into or receives projecti... direct releases_neurotransitter 0..* Neurotransmitter Neuron id 1..1 Uriorcurie CellType label 0..1 String the concise name of the cell type CellType equivalent_to 0..1 CellOntologyTerm the the cell type described CellType definition 0..1 String CellType parents 0..* CellOntologyTerm categorization CellType subtypes 0..* CellOntologyTerm CellType localizations 0..* AnatomicalStructure CellType genes 0..* Gene CellType diseases 0..* Disease CellType roles 0..* BiologicalProcess CellType"},{"location":"cell_type/Interneuron/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Interneuron/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Interneuron/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Interneuron native cell_type:Interneuron"},{"location":"cell_type/Interneuron/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Interneuron/#direct","title":"Direct","text":"
name: Interneuron\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: Neuron\nattributes:\n  projects_to_or_from:\n    name: projects_to_or_from\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures from which this cell\n          type projects from or into\n    description: Brain structures from which this cell type projects into or receives\n      projections from\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002170\n    multivalued: true\n    range: BrainRegion\n\n
"},{"location":"cell_type/Interneuron/#induced","title":"Induced","text":"
name: Interneuron\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: Neuron\nattributes:\n  projects_to_or_from:\n    name: projects_to_or_from\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures from which this cell\n          type projects from or into\n    description: Brain structures from which this cell type projects into or receives\n      projections from\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002170\n    multivalued: true\n    alias: projects_to_or_from\n    owner: Interneuron\n    domain_of:\n    - Interneuron\n    range: BrainRegion\n  releases_neurotransitter:\n    name: releases_neurotransitter\n    annotations:\n      prompt:\n        tag: prompt\n        value: named of chemical entity that this neuron releases\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002111\n    multivalued: true\n    alias: releases_neurotransitter\n    owner: Interneuron\n    domain_of:\n    - Neuron\n    range: Neurotransmitter\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    alias: id\n    owner: Interneuron\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the concise name of the cell type\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Interneuron\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n  equivalent_to:\n    name: equivalent_to\n    annotations:\n      prompt:\n        tag: prompt\n        value: the cell type described in the text\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the the cell type described\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: skos:exactMatch\n    alias: equivalent_to\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  definition:\n    name: definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n          that <differentiating characteristics>'\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: IAO:0000115\n    alias: definition\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: string\n  parents:\n    name: parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent (broader) cell types\n      owl:\n        tag: owl\n        value: SubClassOf\n    description: categorization\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: parents\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  subtypes:\n    name: subtypes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of the subtypes (subclasses) of this cell\n          type. Use concise terms, and separate elements in a list using semicolon\n          (;)\n      owl.template:\n        tag: owl.template\n        value: '{% for subtype in subtypes %}\n\n          SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  localizations:\n    name: localizations\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures in which this cell\n          type is localized\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: localizations\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: AnatomicalStructure\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of genes expressed in cells of this type\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002292\n    multivalued: true\n    alias: genes\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: Gene\n  diseases:\n    name: diseases\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of diseases in which this cell type is implicated\n      owl.template:\n        tag: owl.template\n        value: '{% for disease in diseases %}\n\n          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}\n          ))\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: diseases\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: Disease\n  roles:\n    name: roles\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of roles (e.g. biological processes) that\n          this cell type plays. These should be short descriptive terms corresponding\n          to ontology terms in the GO biological process hierarchy.\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002215\n    multivalued: true\n    alias: roles\n    owner: Interneuron\n    domain_of:\n    - CellType\n    range: BiologicalProcess\n\n
"},{"location":"cell_type/NamedEntity/","title":"Class: NamedEntity","text":"

URI: cell_type:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"cell_type/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"cell_type/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:NamedEntity native cell_type:NamedEntity"},{"location":"cell_type/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/cell_type\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"cell_type/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/cell_type\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"cell_type/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Neuron/","title":"Class: Neuron","text":"

URI: cell_type:Neuron

erDiagram\nNeuron {\n    uriorcurie id  \n    string label  \n    string definition  \n}\nBiologicalProcess {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nAnatomicalStructure {\n    string id  \n    string label  \n}\nCellOntologyTerm {\n    string id  \n    string label  \n}\nNeurotransmitter {\n    string id  \n    string label  \n}\n\nNeuron ||--}o Neurotransmitter : \"releases_neurotransitter\"\nNeuron ||--|o CellOntologyTerm : \"equivalent_to\"\nNeuron ||--}o CellOntologyTerm : \"parents\"\nNeuron ||--}o CellOntologyTerm : \"subtypes\"\nNeuron ||--}o AnatomicalStructure : \"localizations\"\nNeuron ||--}o Gene : \"genes\"\nNeuron ||--}o Disease : \"diseases\"\nNeuron ||--}o BiologicalProcess : \"roles\"\n\n
"},{"location":"cell_type/Neuron/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Neuron/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance releases_neurotransitter 0..* Neurotransmitter direct id 1..1 Uriorcurie CellType label 0..1 String the concise name of the cell type CellType equivalent_to 0..1 CellOntologyTerm the the cell type described CellType definition 0..1 String CellType parents 0..* CellOntologyTerm categorization CellType subtypes 0..* CellOntologyTerm CellType localizations 0..* AnatomicalStructure CellType genes 0..* Gene CellType diseases 0..* Disease CellType roles 0..* BiologicalProcess CellType"},{"location":"cell_type/Neuron/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Neuron/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Neuron/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Neuron native cell_type:Neuron"},{"location":"cell_type/Neuron/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Neuron/#direct","title":"Direct","text":"
name: Neuron\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CellType\nattributes:\n  releases_neurotransitter:\n    name: releases_neurotransitter\n    annotations:\n      prompt:\n        tag: prompt\n        value: named of chemical entity that this neuron releases\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002111\n    multivalued: true\n    range: Neurotransmitter\n\n
"},{"location":"cell_type/Neuron/#induced","title":"Induced","text":"
name: Neuron\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CellType\nattributes:\n  releases_neurotransitter:\n    name: releases_neurotransitter\n    annotations:\n      prompt:\n        tag: prompt\n        value: named of chemical entity that this neuron releases\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002111\n    multivalued: true\n    alias: releases_neurotransitter\n    owner: Neuron\n    domain_of:\n    - Neuron\n    range: Neurotransmitter\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    alias: id\n    owner: Neuron\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the concise name of the cell type\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Neuron\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n  equivalent_to:\n    name: equivalent_to\n    annotations:\n      prompt:\n        tag: prompt\n        value: the cell type described in the text\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: the the cell type described\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: skos:exactMatch\n    alias: equivalent_to\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  definition:\n    name: definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n          that <differentiating characteristics>'\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: IAO:0000115\n    alias: definition\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: string\n  parents:\n    name: parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent (broader) cell types\n      owl:\n        tag: owl\n        value: SubClassOf\n    description: categorization\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: parents\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  subtypes:\n    name: subtypes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of the subtypes (subclasses) of this cell\n          type. Use concise terms, and separate elements in a list using semicolon\n          (;)\n      owl.template:\n        tag: owl.template\n        value: '{% for subtype in subtypes %}\n\n          SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: CellOntologyTerm\n  localizations:\n    name: localizations\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of anatomical structures in which this cell\n          type is localized\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: localizations\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: AnatomicalStructure\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of genes expressed in cells of this type\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002292\n    multivalued: true\n    alias: genes\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: Gene\n  diseases:\n    name: diseases\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of diseases in which this cell type is implicated\n      owl.template:\n        tag: owl.template\n        value: '{% for disease in diseases %}\n\n          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}\n          ))\n\n          {% endfor %}\n\n          '\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: diseases\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: Disease\n  roles:\n    name: roles\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of roles (e.g. biological processes) that\n          this cell type plays. These should be short descriptive terms corresponding\n          to ontology terms in the GO biological process hierarchy.\n      owl:\n        tag: owl\n        value: SubClassOf, ObjectSomeValuesFrom\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    slot_uri: RO:0002215\n    multivalued: true\n    alias: roles\n    owner: Neuron\n    domain_of:\n    - CellType\n    range: BiologicalProcess\n\n
"},{"location":"cell_type/Neurotransmitter/","title":"Class: Neurotransmitter","text":"

URI: cell_type:Neurotransmitter

erDiagram\nNeurotransmitter {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/Neurotransmitter/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Neurotransmitter/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/Neurotransmitter/#usages","title":"Usages","text":"used by used in type used Neuron releases_neurotransitter range Neurotransmitter Interneuron releases_neurotransitter range Neurotransmitter"},{"location":"cell_type/Neurotransmitter/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Neurotransmitter/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/Neurotransmitter/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"cell_type/Neurotransmitter/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Neurotransmitter/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Neurotransmitter native cell_type:Neurotransmitter"},{"location":"cell_type/Neurotransmitter/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Neurotransmitter/#direct","title":"Direct","text":"
name: Neurotransmitter\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: ChemicalEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - NeurotransmitterIdentifier\n    identifier: true\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n\n
"},{"location":"cell_type/Neurotransmitter/#induced","title":"Induced","text":"
name: Neurotransmitter\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: ChemicalEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - NeurotransmitterIdentifier\n    identifier: true\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/cell_type\n    values_from:\n    - NeurotransmitterIdentifier\n    identifier: true\n    alias: id\n    owner: Neurotransmitter\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Neurotransmitter\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/NeurotransmitterIdentifier/","title":"Enum: NeurotransmitterIdentifier","text":"

URI: NeurotransmitterIdentifier

This is a dynamic enum

"},{"location":"cell_type/NeurotransmitterIdentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/NeurotransmitterIdentifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/NeurotransmitterIdentifier/#linkml-source","title":"LinkML Source","text":"
name: NeurotransmitterIdentifier\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nreachable_from:\n  source_ontology: obo:chebi\n  source_nodes:\n  - CHEBI:35942\n  relationship_types:\n  - rdfs:subClassOf\n  - RO:0000087\n\n
"},{"location":"cell_type/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"cell_type/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"cell_type/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"cell_type/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"cell_type/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"cell_type/Objectidentifier/#comments","title":"Comments","text":""},{"location":"cell_type/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Pathway/","title":"Class: Pathway","text":"

URI: cell_type:Pathway

erDiagram\nPathway {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/Pathway/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Pathway/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/Pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Pathway/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/Pathway/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:pw"},{"location":"cell_type/Pathway/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Pathway/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Pathway native cell_type:Pathway"},{"location":"cell_type/Pathway/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Pathway/#direct","title":"Direct","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/Pathway/#induced","title":"Induced","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: Pathway\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Pathway\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/ProteinOrComplex/","title":"Class: ProteinOrComplex","text":"

URI: cell_type:ProteinOrComplex

erDiagram\nProteinOrComplex {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/ProteinOrComplex/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/ProteinOrComplex/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/ProteinOrComplex/#usages","title":"Usages","text":"used by used in type used ImmuneCell has_surface_markers range ProteinOrComplex"},{"location":"cell_type/ProteinOrComplex/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/ProteinOrComplex/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/ProteinOrComplex/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hgnc, bioportal:hgnc-nr, sqlite:obo:go, sqlite:obo:pr"},{"location":"cell_type/ProteinOrComplex/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/ProteinOrComplex/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:ProteinOrComplex native cell_type:ProteinOrComplex"},{"location":"cell_type/ProteinOrComplex/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/ProteinOrComplex/#direct","title":"Direct","text":"
name: ProteinOrComplex\nid_prefixes:\n- HGNC\n- MGI\n- PR\n- UniProtKB\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, bioportal:hgnc-nr, sqlite:obo:go, sqlite:obo:pr\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/ProteinOrComplex/#induced","title":"Induced","text":"
name: ProteinOrComplex\nid_prefixes:\n- HGNC\n- MGI\n- PR\n- UniProtKB\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, bioportal:hgnc-nr, sqlite:obo:go, sqlite:obo:pr\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: ProteinOrComplex\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ProteinOrComplex\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/Publication/","title":"Class: Publication","text":"

URI: cell_type:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"cell_type/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"cell_type/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"cell_type/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Publication/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Publication native cell_type:Publication"},{"location":"cell_type/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/cell_type\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n\n
"},{"location":"cell_type/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/cell_type\n    alias: id\n    owner: Publication\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"cell_type/RelationshipType/","title":"Class: RelationshipType","text":"

URI: cell_type:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"cell_type/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"cell_type/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"cell_type/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"cell_type/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:RelationshipType native cell_type:RelationshipType"},{"location":"cell_type/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\n\n
"},{"location":"cell_type/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/cell_type\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - CellType\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/cell_type\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - CellType\n    - NamedEntity\n    range: string\n\n
"},{"location":"cell_type/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"cell_type/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/String/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: cell_type:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"cell_type/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"cell_type/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:TextWithTriples native cell_type:TextWithTriples"},{"location":"cell_type/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"cell_type/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/cell_type\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"cell_type/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"cell_type/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Time/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: cell_type:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"cell_type/Triple/#inheritance","title":"Inheritance","text":""},{"location":"cell_type/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"cell_type/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"cell_type/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Triple/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self cell_type:Triple native cell_type:Triple"},{"location":"cell_type/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"cell_type/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"cell_type/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/cell_type\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/cell_type\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"cell_type/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"cell_type/Uri/#comments","title":"Comments","text":""},{"location":"cell_type/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Uri/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"cell_type/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: cell_type:abstract

"},{"location":"cell_type/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"cell_type/abstract/#properties","title":"Properties","text":""},{"location":"cell_type/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/abstract/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"cell_type/cell_type/","title":"cell_type","text":"

A template for representing cell types

URI: http://w3id.org/ontogpt/cell_type

"},{"location":"cell_type/combined_text/","title":"Slot: combined_text","text":"

URI: cell_type:combined_text

"},{"location":"cell_type/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"cell_type/combined_text/#properties","title":"Properties","text":""},{"location":"cell_type/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"cell_type/definition/","title":"Slot: definition","text":"

URI: IAO:0000115

"},{"location":"cell_type/definition/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/definition/#properties","title":"Properties","text":""},{"location":"cell_type/definition/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/definition/#annotations","title":"Annotations","text":"property value prompt A concise textual definition in genus-differentia form, i.e 'A that '"},{"location":"cell_type/definition/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/definition/#linkml-source","title":"LinkML Source","text":"
name: definition\nannotations:\n  prompt:\n    tag: prompt\n    value: A concise textual definition in genus-differentia form, i.e  'A <genus>\n      that <differentiating characteristics>'\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: IAO:0000115\nalias: definition\nowner: CellType\ndomain_of:\n- CellType\nrange: string\n\n
"},{"location":"cell_type/diseases/","title":"Slot: diseases","text":"

URI: cell_type:diseases

"},{"location":"cell_type/diseases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/diseases/#properties","title":"Properties","text":""},{"location":"cell_type/diseases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/diseases/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of diseases in which this cell type is implicated SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }} )) {% endfor %}"},{"location":"cell_type/diseases/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/diseases/#linkml-source","title":"LinkML Source","text":"
name: diseases\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of diseases in which this cell type is implicated\n  owl.template:\n    tag: owl.template\n    value: '{% for disease in diseases %}\n\n      SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }} ))\n\n      {% endfor %}\n\n      '\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: diseases\nowner: CellType\ndomain_of:\n- CellType\nrange: Disease\n\n
"},{"location":"cell_type/equivalent_to/","title":"Slot: equivalent_to","text":"

the the cell type described

URI: skos:exactMatch

"},{"location":"cell_type/equivalent_to/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/equivalent_to/#properties","title":"Properties","text":""},{"location":"cell_type/equivalent_to/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/equivalent_to/#annotations","title":"Annotations","text":"property value prompt the cell type described in the text"},{"location":"cell_type/equivalent_to/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/equivalent_to/#linkml-source","title":"LinkML Source","text":"
name: equivalent_to\nannotations:\n  prompt:\n    tag: prompt\n    value: the cell type described in the text\n  owl:\n    tag: owl\n    value: AnnotationAssertion\ndescription: the the cell type described\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: skos:exactMatch\nalias: equivalent_to\nowner: CellType\ndomain_of:\n- CellType\nrange: CellOntologyTerm\n\n
"},{"location":"cell_type/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: cell_type:extracted_object

"},{"location":"cell_type/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/extracted_object/#properties","title":"Properties","text":""},{"location":"cell_type/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"cell_type/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: cell_type:full_text

"},{"location":"cell_type/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"cell_type/full_text/#properties","title":"Properties","text":""},{"location":"cell_type/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/full_text/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"cell_type/genes/","title":"Slot: genes","text":"

URI: RO:0002292

"},{"location":"cell_type/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/genes/#properties","title":"Properties","text":""},{"location":"cell_type/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/genes/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of genes expressed in cells of this type"},{"location":"cell_type/genes/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of genes expressed in cells of this type\n  owl:\n    tag: owl\n    value: SubClassOf, ObjectSomeValuesFrom\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: RO:0002292\nmultivalued: true\nalias: genes\nowner: CellType\ndomain_of:\n- CellType\nrange: Gene\n\n
"},{"location":"cell_type/has_surface_markers/","title":"Slot: has_surface_markers","text":"

URI: cell_type:has_surface_markers

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name: has_surface_markers\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of proteins or complexes expressed on the surface\n      of the cell\n  owl:\n    tag: owl\n    value: SubClassOf, ObjectSomeValuesFrom\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: has_surface_markers\nowner: ImmuneCell\ndomain_of:\n- ImmuneCell\nrange: ProteinOrComplex\n\n
"},{"location":"cell_type/id/","title":"Slot: id","text":"

URI: cell_type:id

"},{"location":"cell_type/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no Gene no ProteinOrComplex no BiologicalProcess no Pathway no AnatomicalStructure no ChemicalEntity no Neurotransmitter yes BrainRegion yes CellOntologyTerm no Disease no Drug no NamedEntity no RelationshipType no Publication no"},{"location":"cell_type/id/#properties","title":"Properties","text":""},{"location":"cell_type/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- CellType\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"cell_type/input_id/","title":"Slot: input_id","text":"

URI: cell_type:input_id

"},{"location":"cell_type/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/input_id/#properties","title":"Properties","text":""},{"location":"cell_type/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/input_id/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"cell_type/input_text/","title":"Slot: input_text","text":"

URI: cell_type:input_text

"},{"location":"cell_type/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/input_text/#properties","title":"Properties","text":""},{"location":"cell_type/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/input_text/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"cell_type/input_title/","title":"Slot: input_title","text":"

URI: cell_type:input_title

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name: input_title\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"cell_type/label/","title":"Slot: label","text":"

URI: cell_type:label

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name: label\nalias: label\ndomain_of:\n- CellType\n- NamedEntity\nrange: string\n\n
"},{"location":"cell_type/localizations/","title":"Slot: localizations","text":"

URI: BFO:0000050

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name: localizations\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of anatomical structures in which this cell type\n      is localized\n  owl:\n    tag: owl\n    value: SubClassOf, ObjectSomeValuesFrom\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: BFO:0000050\nmultivalued: true\nalias: localizations\nowner: CellType\ndomain_of:\n- CellType\nrange: AnatomicalStructure\n\n
"},{"location":"cell_type/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: cell_type:named_entities

"},{"location":"cell_type/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/named_entities/#properties","title":"Properties","text":""},{"location":"cell_type/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"cell_type/object/","title":"Slot: object","text":"

URI: cell_type:object

"},{"location":"cell_type/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/object/#properties","title":"Properties","text":""},{"location":"cell_type/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/object/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"cell_type/object_id/","title":"Slot: object_id","text":"

URI: cell_type:object_id

"},{"location":"cell_type/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"cell_type/object_id/#properties","title":"Properties","text":""},{"location":"cell_type/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/object_id/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"cell_type/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: cell_type:object_qualifier

"},{"location":"cell_type/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/object_qualifier/#properties","title":"Properties","text":""},{"location":"cell_type/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"cell_type/object_text/","title":"Slot: object_text","text":"

URI: cell_type:object_text

"},{"location":"cell_type/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"cell_type/object_text/#properties","title":"Properties","text":""},{"location":"cell_type/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/object_text/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"cell_type/parents/","title":"Slot: parents","text":"

categorization

URI: cell_type:parents

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name: parents\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of parent (broader) cell types\n  owl:\n    tag: owl\n    value: SubClassOf\ndescription: categorization\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: parents\nowner: CellType\ndomain_of:\n- CellType\nrange: CellOntologyTerm\n\n
"},{"location":"cell_type/predicate/","title":"Slot: predicate","text":"

URI: cell_type:predicate

"},{"location":"cell_type/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/predicate/#properties","title":"Properties","text":""},{"location":"cell_type/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/predicate/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"cell_type/projects_to_or_from/","title":"Slot: projects_to_or_from","text":"

Brain structures from which this cell type projects into or receives projections from

URI: RO:0002170

"},{"location":"cell_type/projects_to_or_from/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Interneuron no"},{"location":"cell_type/projects_to_or_from/#properties","title":"Properties","text":""},{"location":"cell_type/projects_to_or_from/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/projects_to_or_from/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of anatomical structures from which this cell type projects from or into"},{"location":"cell_type/projects_to_or_from/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/projects_to_or_from/#linkml-source","title":"LinkML Source","text":"
name: projects_to_or_from\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of anatomical structures from which this cell\n      type projects from or into\ndescription: Brain structures from which this cell type projects into or receives\n  projections from\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: RO:0002170\nmultivalued: true\nalias: projects_to_or_from\nowner: Interneuron\ndomain_of:\n- Interneuron\nrange: BrainRegion\n\n
"},{"location":"cell_type/prompt/","title":"Slot: prompt","text":"

URI: cell_type:prompt

"},{"location":"cell_type/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/prompt/#properties","title":"Properties","text":""},{"location":"cell_type/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/prompt/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"cell_type/publication/","title":"Slot: publication","text":"

URI: cell_type:publication

"},{"location":"cell_type/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"cell_type/publication/#properties","title":"Properties","text":""},{"location":"cell_type/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"cell_type/publication/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"cell_type/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: cell_type:qualifier

"},{"location":"cell_type/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/qualifier/#properties","title":"Properties","text":""},{"location":"cell_type/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"cell_type/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: cell_type:raw_completion_output

"},{"location":"cell_type/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"cell_type/raw_completion_output/#properties","title":"Properties","text":""},{"location":"cell_type/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"cell_type/releases_neurotransitter/","title":"Slot: releases_neurotransitter","text":"

URI: RO:0002111

"},{"location":"cell_type/releases_neurotransitter/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Neuron no Interneuron no"},{"location":"cell_type/releases_neurotransitter/#properties","title":"Properties","text":""},{"location":"cell_type/releases_neurotransitter/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/releases_neurotransitter/#annotations","title":"Annotations","text":"property value prompt named of chemical entity that this neuron releases"},{"location":"cell_type/releases_neurotransitter/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/releases_neurotransitter/#linkml-source","title":"LinkML Source","text":"
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"},{"location":"cell_type/roles/","title":"Slot: roles","text":"

URI: RO:0002215

"},{"location":"cell_type/roles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/roles/#properties","title":"Properties","text":""},{"location":"cell_type/roles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/roles/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of roles (e.g. biological processes) that this cell type plays. These should be short descriptive terms corresponding to ontology terms in the GO biological process hierarchy."},{"location":"cell_type/roles/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/roles/#linkml-source","title":"LinkML Source","text":"
name: roles\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of roles (e.g. biological processes) that this\n      cell type plays. These should be short descriptive terms corresponding to ontology\n      terms in the GO biological process hierarchy.\n  owl:\n    tag: owl\n    value: SubClassOf, ObjectSomeValuesFrom\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nslot_uri: RO:0002215\nmultivalued: true\nalias: roles\nowner: CellType\ndomain_of:\n- CellType\nrange: BiologicalProcess\n\n
"},{"location":"cell_type/subject/","title":"Slot: subject","text":"

URI: cell_type:subject

"},{"location":"cell_type/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/subject/#properties","title":"Properties","text":""},{"location":"cell_type/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/subject/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"cell_type/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: cell_type:subject_qualifier

"},{"location":"cell_type/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"cell_type/subject_qualifier/#properties","title":"Properties","text":""},{"location":"cell_type/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"cell_type/subject_text/","title":"Slot: subject_text","text":"

URI: cell_type:subject_text

"},{"location":"cell_type/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"cell_type/subject_text/#properties","title":"Properties","text":""},{"location":"cell_type/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"cell_type/subtypes/","title":"Slot: subtypes","text":"

URI: cell_type:subtypes

"},{"location":"cell_type/subtypes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CellType Represents a cell type no ImmuneCell no Neuron no Interneuron no"},{"location":"cell_type/subtypes/#properties","title":"Properties","text":""},{"location":"cell_type/subtypes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/subtypes/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of the subtypes (subclasses) of this cell type. Use concise terms, and separate elements in a list using semicolon (;) SubClassOf( {{ tr(subtype) }} {{ id }} ) {% endfor %}"},{"location":"cell_type/subtypes/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/subtypes/#linkml-source","title":"LinkML Source","text":"
name: subtypes\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of the subtypes (subclasses) of this cell type.\n      Use concise terms, and separate elements in a list using semicolon (;)\n  owl.template:\n    tag: owl.template\n    value: '{% for subtype in subtypes %}\n\n      SubClassOf( {{ tr(subtype) }} {{ id }} )\n\n      {% endfor %}\n\n      '\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: subtypes\nowner: CellType\ndomain_of:\n- CellType\nrange: CellOntologyTerm\n\n
"},{"location":"cell_type/title/","title":"Slot: title","text":"

The title of the publication

URI: cell_type:title

"},{"location":"cell_type/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"cell_type/title/#properties","title":"Properties","text":""},{"location":"cell_type/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/title/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"cell_type/triples/","title":"Slot: triples","text":"

URI: cell_type:triples

"},{"location":"cell_type/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"cell_type/triples/#properties","title":"Properties","text":""},{"location":"cell_type/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cell_type/triples/#schema-source","title":"Schema Source","text":""},{"location":"cell_type/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/cell_type\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"class_enrichment/","title":"Class Enrichment Datamodel","text":"

A datamodel for representing the results of class enrichment on gene sets

URI: https://w3id.org/oak/class-enrichment

Name: class-enrichment

"},{"location":"class_enrichment/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nClassEnrichmentConfiguration {\n    float p_value_cutoff  \n}\nClassEnrichmentResultSet {\n\n}\nClassEnrichmentResult {\n    uriorcurie class_id  \n    string class_label  \n    integer rank  \n    float p_value  \n    float p_value_adjusted  \n    float false_discovery_rate  \n    float fold_enrichment  \n    float probability  \n    integer sample_count  \n    integer sample_total  \n    integer background_count  \n    integer background_total  \n    boolean ancestor_of_more_informative_result  \n    boolean descendant_of_more_informative_result  \n}\n\nClassEnrichmentResultSet ||--}o ClassEnrichmentResult : \"results\"\n\n
"},{"location":"class_enrichment/#classes","title":"Classes","text":"Class Description ClassEnrichmentConfiguration configuration for search ClassEnrichmentResult A single enrichment result ClassEnrichmentResultSet A collection of enrichemt results"},{"location":"class_enrichment/#slots","title":"Slots","text":"Slot Description ancestor_of_more_informative_result This term is more general than a previously reported result background_count The background count background_total The background total class_id The class id class_label The class label descendant_of_more_informative_result This term is more specific than a previously reported result false_discovery_rate The false discovery rate fold_enrichment The fold enrichment p_value The p-value p_value_adjusted The adjusted p-value p_value_cutoff p-value cutoff for enrichment probability The probability, as estimated by model-based approaches rank The rank of this result results The enrichment results sample_count The number of entities in the sample with this class sample_total The total number of entities in the sample"},{"location":"class_enrichment/#enumerations","title":"Enumerations","text":"Enumeration Description SortFieldEnum The field to sort by"},{"location":"class_enrichment/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Position String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"class_enrichment/#subsets","title":"Subsets","text":"Subset Description"},{"location":"class_enrichment/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"class_enrichment/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ClassEnrichmentConfiguration/","title":"Class: ClassEnrichmentConfiguration","text":"

configuration for search

URI: ontoenrich:ClassEnrichmentConfiguration

erDiagram\nClassEnrichmentConfiguration {\n    float p_value_cutoff  \n}\n\n\n\n
"},{"location":"class_enrichment/ClassEnrichmentConfiguration/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance p_value_cutoff 1..1 Float p-value cutoff for enrichment direct"},{"location":"class_enrichment/ClassEnrichmentConfiguration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/ClassEnrichmentConfiguration/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ClassEnrichmentConfiguration/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ontoenrich:ClassEnrichmentConfiguration native ontoenrich:ClassEnrichmentConfiguration"},{"location":"class_enrichment/ClassEnrichmentConfiguration/#linkml-source","title":"LinkML Source","text":""},{"location":"class_enrichment/ClassEnrichmentConfiguration/#direct","title":"Direct","text":"
name: ClassEnrichmentConfiguration\ndescription: configuration for search\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  p_value_cutoff:\n    name: p_value_cutoff\n    description: p-value cutoff for enrichment\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: float\n    required: true\n\n
"},{"location":"class_enrichment/ClassEnrichmentConfiguration/#induced","title":"Induced","text":"
name: ClassEnrichmentConfiguration\ndescription: configuration for search\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  p_value_cutoff:\n    name: p_value_cutoff\n    description: p-value cutoff for enrichment\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: p_value_cutoff\n    owner: ClassEnrichmentConfiguration\n    domain_of:\n    - ClassEnrichmentConfiguration\n    range: float\n    required: true\n\n
"},{"location":"class_enrichment/ClassEnrichmentResult/","title":"Class: ClassEnrichmentResult","text":"

A single enrichment result

URI: ontoenrich:ClassEnrichmentResult

erDiagram\nClassEnrichmentResult {\n    uriorcurie class_id  \n    string class_label  \n    integer rank  \n    float p_value  \n    float p_value_adjusted  \n    float false_discovery_rate  \n    float fold_enrichment  \n    float probability  \n    integer sample_count  \n    integer sample_total  \n    integer background_count  \n    integer background_total  \n    boolean ancestor_of_more_informative_result  \n    boolean descendant_of_more_informative_result  \n}\n\n\n\n
"},{"location":"class_enrichment/ClassEnrichmentResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance class_id 1..1 Uriorcurie The class id direct class_label 0..1 String The class label direct rank 0..1 Integer The rank of this result direct p_value 1..1 Float The p-value direct p_value_adjusted 0..1 Float The adjusted p-value direct false_discovery_rate 0..1 Float The false discovery rate direct fold_enrichment 0..1 Float The fold enrichment direct probability 0..1 Float The probability, as estimated by model-based approaches direct sample_count 0..1 Integer The number of entities in the sample with this class direct sample_total 0..1 Integer The total number of entities in the sample direct background_count 0..1 Integer The background count direct background_total 0..1 Integer The background total direct ancestor_of_more_informative_result 0..1 Boolean This term is more general than a previously reported result direct descendant_of_more_informative_result 0..1 Boolean This term is more specific than a previously reported result direct"},{"location":"class_enrichment/ClassEnrichmentResult/#usages","title":"Usages","text":"used by used in type used ClassEnrichmentResultSet results range ClassEnrichmentResult"},{"location":"class_enrichment/ClassEnrichmentResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/ClassEnrichmentResult/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ClassEnrichmentResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ontoenrich:ClassEnrichmentResult native ontoenrich:ClassEnrichmentResult"},{"location":"class_enrichment/ClassEnrichmentResult/#linkml-source","title":"LinkML Source","text":""},{"location":"class_enrichment/ClassEnrichmentResult/#direct","title":"Direct","text":"
name: ClassEnrichmentResult\ndescription: A single enrichment result\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  class_id:\n    name: class_id\n    description: The class id\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: uriorcurie\n    required: true\n  class_label:\n    name: class_label\n    description: The class label\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: string\n  rank:\n    name: rank\n    description: The rank of this result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: integer\n  p_value:\n    name: p_value\n    description: The p-value\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    slot_uri: OBI:0000175\n    range: float\n    required: true\n  p_value_adjusted:\n    name: p_value_adjusted\n    description: The adjusted p-value\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: float\n  false_discovery_rate:\n    name: false_discovery_rate\n    description: The false discovery rate\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: float\n  fold_enrichment:\n    name: fold_enrichment\n    description: The fold enrichment\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: float\n  probability:\n    name: probability\n    description: The probability, as estimated by model-based approaches\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: float\n    minimum_value: 0\n    maximum_value: 1\n  sample_count:\n    name: sample_count\n    description: The number of entities in the sample with this class\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: integer\n  sample_total:\n    name: sample_total\n    description: The total number of entities in the sample\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: integer\n  background_count:\n    name: background_count\n    description: The background count\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: integer\n  background_total:\n    name: background_total\n    description: The background total\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: integer\n  ancestor_of_more_informative_result:\n    name: ancestor_of_more_informative_result\n    description: This term is more general than a previously reported result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: boolean\n  descendant_of_more_informative_result:\n    name: descendant_of_more_informative_result\n    description: This term is more specific than a previously reported result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    range: boolean\n\n
"},{"location":"class_enrichment/ClassEnrichmentResult/#induced","title":"Induced","text":"
name: ClassEnrichmentResult\ndescription: A single enrichment result\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  class_id:\n    name: class_id\n    description: The class id\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: class_id\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: uriorcurie\n    required: true\n  class_label:\n    name: class_label\n    description: The class label\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: class_label\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: string\n  rank:\n    name: rank\n    description: The rank of this result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: rank\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: integer\n  p_value:\n    name: p_value\n    description: The p-value\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    slot_uri: OBI:0000175\n    alias: p_value\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: float\n    required: true\n  p_value_adjusted:\n    name: p_value_adjusted\n    description: The adjusted p-value\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: p_value_adjusted\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: float\n  false_discovery_rate:\n    name: false_discovery_rate\n    description: The false discovery rate\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: false_discovery_rate\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: float\n  fold_enrichment:\n    name: fold_enrichment\n    description: The fold enrichment\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: fold_enrichment\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: float\n  probability:\n    name: probability\n    description: The probability, as estimated by model-based approaches\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: probability\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: float\n    minimum_value: 0\n    maximum_value: 1\n  sample_count:\n    name: sample_count\n    description: The number of entities in the sample with this class\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: sample_count\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: integer\n  sample_total:\n    name: sample_total\n    description: The total number of entities in the sample\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: sample_total\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: integer\n  background_count:\n    name: background_count\n    description: The background count\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: background_count\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: integer\n  background_total:\n    name: background_total\n    description: The background total\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: background_total\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: integer\n  ancestor_of_more_informative_result:\n    name: ancestor_of_more_informative_result\n    description: This term is more general than a previously reported result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: ancestor_of_more_informative_result\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: boolean\n  descendant_of_more_informative_result:\n    name: descendant_of_more_informative_result\n    description: This term is more specific than a previously reported result\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    alias: descendant_of_more_informative_result\n    owner: ClassEnrichmentResult\n    domain_of:\n    - ClassEnrichmentResult\n    range: boolean\n\n
"},{"location":"class_enrichment/ClassEnrichmentResultSet/","title":"Class: ClassEnrichmentResultSet","text":"

A collection of enrichemt results

URI: ontoenrich:ClassEnrichmentResultSet

erDiagram\nClassEnrichmentResultSet {\n\n}\nClassEnrichmentResult {\n    uriorcurie class_id  \n    string class_label  \n    integer rank  \n    float p_value  \n    float p_value_adjusted  \n    float false_discovery_rate  \n    float fold_enrichment  \n    float probability  \n    integer sample_count  \n    integer sample_total  \n    integer background_count  \n    integer background_total  \n    boolean ancestor_of_more_informative_result  \n    boolean descendant_of_more_informative_result  \n}\n\nClassEnrichmentResultSet ||--}o ClassEnrichmentResult : \"results\"\n\n
"},{"location":"class_enrichment/ClassEnrichmentResultSet/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance results 0..* ClassEnrichmentResult The enrichment results direct"},{"location":"class_enrichment/ClassEnrichmentResultSet/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/ClassEnrichmentResultSet/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ClassEnrichmentResultSet/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ontoenrich:ClassEnrichmentResultSet native ontoenrich:ClassEnrichmentResultSet"},{"location":"class_enrichment/ClassEnrichmentResultSet/#linkml-source","title":"LinkML Source","text":""},{"location":"class_enrichment/ClassEnrichmentResultSet/#direct","title":"Direct","text":"
name: ClassEnrichmentResultSet\ndescription: A collection of enrichemt results\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  results:\n    name: results\n    description: The enrichment results\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    multivalued: true\n    range: ClassEnrichmentResult\n\n
"},{"location":"class_enrichment/ClassEnrichmentResultSet/#induced","title":"Induced","text":"
name: ClassEnrichmentResultSet\ndescription: A collection of enrichemt results\nfrom_schema: https://w3id.org/oak/class-enrichment\nattributes:\n  results:\n    name: results\n    description: The enrichment results\n    from_schema: https://w3id.org/oak/class-enrichment\n    rank: 1000\n    multivalued: true\n    alias: results\n    owner: ClassEnrichmentResultSet\n    domain_of:\n    - ClassEnrichmentResultSet\n    range: ClassEnrichmentResult\n\n
"},{"location":"class_enrichment/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"class_enrichment/Curie/#comments","title":"Comments","text":""},{"location":"class_enrichment/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Curie/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"class_enrichment/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Date/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"class_enrichment/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"class_enrichment/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"class_enrichment/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"class_enrichment/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Double/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"class_enrichment/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Float/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"class_enrichment/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Integer/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"class_enrichment/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"class_enrichment/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"class_enrichment/Objectidentifier/#comments","title":"Comments","text":""},{"location":"class_enrichment/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Position/","title":"Type: Position","text":"

URI: xsd:integer

"},{"location":"class_enrichment/Position/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Position/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/SortFieldEnum/","title":"Enum: SortFieldEnum","text":"

The field to sort by

URI: SortFieldEnum

"},{"location":"class_enrichment/SortFieldEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ANY None P_VALUE None"},{"location":"class_enrichment/SortFieldEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/SortFieldEnum/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/SortFieldEnum/#linkml-source","title":"LinkML Source","text":"
name: SortFieldEnum\ndescription: The field to sort by\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\npermissible_values:\n  ANY:\n    text: ANY\n  P_VALUE:\n    text: P_VALUE\n\n
"},{"location":"class_enrichment/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"class_enrichment/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/String/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"class_enrichment/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Time/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"class_enrichment/Uri/#comments","title":"Comments","text":""},{"location":"class_enrichment/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Uri/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"class_enrichment/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ancestor_of_more_informative_result/","title":"Slot: ancestor_of_more_informative_result","text":"

This term is more general than a previously reported result

URI: ontoenrich:ancestor_of_more_informative_result

"},{"location":"class_enrichment/ancestor_of_more_informative_result/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/ancestor_of_more_informative_result/#properties","title":"Properties","text":""},{"location":"class_enrichment/ancestor_of_more_informative_result/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/ancestor_of_more_informative_result/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/ancestor_of_more_informative_result/#linkml-source","title":"LinkML Source","text":"
name: ancestor_of_more_informative_result\ndescription: This term is more general than a previously reported result\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: ancestor_of_more_informative_result\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: boolean\n\n
"},{"location":"class_enrichment/background_count/","title":"Slot: background_count","text":"

The background count

URI: ontoenrich:background_count

"},{"location":"class_enrichment/background_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/background_count/#properties","title":"Properties","text":""},{"location":"class_enrichment/background_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/background_count/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/background_count/#linkml-source","title":"LinkML Source","text":"
name: background_count\ndescription: The background count\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: background_count\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: integer\n\n
"},{"location":"class_enrichment/background_total/","title":"Slot: background_total","text":"

The background total

URI: ontoenrich:background_total

"},{"location":"class_enrichment/background_total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/background_total/#properties","title":"Properties","text":""},{"location":"class_enrichment/background_total/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/background_total/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/background_total/#linkml-source","title":"LinkML Source","text":"
name: background_total\ndescription: The background total\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: background_total\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: integer\n\n
"},{"location":"class_enrichment/class-enrichment/","title":"class-enrichment","text":"

A datamodel for representing the results of class enrichment on gene sets

URI: https://w3id.org/oak/class-enrichment

"},{"location":"class_enrichment/class_id/","title":"Slot: class_id","text":"

The class id

URI: ontoenrich:class_id

"},{"location":"class_enrichment/class_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/class_id/#properties","title":"Properties","text":""},{"location":"class_enrichment/class_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/class_id/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/class_id/#linkml-source","title":"LinkML Source","text":"
name: class_id\ndescription: The class id\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: class_id\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: uriorcurie\nrequired: true\n\n
"},{"location":"class_enrichment/class_label/","title":"Slot: class_label","text":"

The class label

URI: ontoenrich:class_label

"},{"location":"class_enrichment/class_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/class_label/#properties","title":"Properties","text":""},{"location":"class_enrichment/class_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/class_label/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/class_label/#linkml-source","title":"LinkML Source","text":"
name: class_label\ndescription: The class label\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: class_label\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: string\n\n
"},{"location":"class_enrichment/descendant_of_more_informative_result/","title":"Slot: descendant_of_more_informative_result","text":"

This term is more specific than a previously reported result

URI: ontoenrich:descendant_of_more_informative_result

"},{"location":"class_enrichment/descendant_of_more_informative_result/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/descendant_of_more_informative_result/#properties","title":"Properties","text":""},{"location":"class_enrichment/descendant_of_more_informative_result/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/descendant_of_more_informative_result/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/descendant_of_more_informative_result/#linkml-source","title":"LinkML Source","text":"
name: descendant_of_more_informative_result\ndescription: This term is more specific than a previously reported result\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: descendant_of_more_informative_result\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: boolean\n\n
"},{"location":"class_enrichment/false_discovery_rate/","title":"Slot: false_discovery_rate","text":"

The false discovery rate

URI: ontoenrich:false_discovery_rate

"},{"location":"class_enrichment/false_discovery_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/false_discovery_rate/#properties","title":"Properties","text":""},{"location":"class_enrichment/false_discovery_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/false_discovery_rate/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/false_discovery_rate/#linkml-source","title":"LinkML Source","text":"
name: false_discovery_rate\ndescription: The false discovery rate\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: false_discovery_rate\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: float\n\n
"},{"location":"class_enrichment/fold_enrichment/","title":"Slot: fold_enrichment","text":"

The fold enrichment

URI: ontoenrich:fold_enrichment

"},{"location":"class_enrichment/fold_enrichment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/fold_enrichment/#properties","title":"Properties","text":""},{"location":"class_enrichment/fold_enrichment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/fold_enrichment/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/fold_enrichment/#linkml-source","title":"LinkML Source","text":"
name: fold_enrichment\ndescription: The fold enrichment\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: fold_enrichment\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: float\n\n
"},{"location":"class_enrichment/p_value/","title":"Slot: p_value","text":"

The p-value

URI: OBI:0000175

"},{"location":"class_enrichment/p_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/p_value/#properties","title":"Properties","text":""},{"location":"class_enrichment/p_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/p_value/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/p_value/#linkml-source","title":"LinkML Source","text":"
name: p_value\ndescription: The p-value\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nslot_uri: OBI:0000175\nalias: p_value\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: float\nrequired: true\n\n
"},{"location":"class_enrichment/p_value_adjusted/","title":"Slot: p_value_adjusted","text":"

The adjusted p-value

URI: ontoenrich:p_value_adjusted

"},{"location":"class_enrichment/p_value_adjusted/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/p_value_adjusted/#properties","title":"Properties","text":""},{"location":"class_enrichment/p_value_adjusted/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/p_value_adjusted/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/p_value_adjusted/#linkml-source","title":"LinkML Source","text":"
name: p_value_adjusted\ndescription: The adjusted p-value\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: p_value_adjusted\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: float\n\n
"},{"location":"class_enrichment/p_value_cutoff/","title":"Slot: p_value_cutoff","text":"

p-value cutoff for enrichment

URI: ontoenrich:p_value_cutoff

"},{"location":"class_enrichment/p_value_cutoff/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentConfiguration configuration for search no"},{"location":"class_enrichment/p_value_cutoff/#properties","title":"Properties","text":""},{"location":"class_enrichment/p_value_cutoff/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/p_value_cutoff/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/p_value_cutoff/#linkml-source","title":"LinkML Source","text":"
name: p_value_cutoff\ndescription: p-value cutoff for enrichment\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: p_value_cutoff\nowner: ClassEnrichmentConfiguration\ndomain_of:\n- ClassEnrichmentConfiguration\nrange: float\nrequired: true\n\n
"},{"location":"class_enrichment/probability/","title":"Slot: probability","text":"

The probability, as estimated by model-based approaches

URI: ontoenrich:probability

"},{"location":"class_enrichment/probability/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/probability/#properties","title":"Properties","text":""},{"location":"class_enrichment/probability/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/probability/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/probability/#linkml-source","title":"LinkML Source","text":"
name: probability\ndescription: The probability, as estimated by model-based approaches\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: probability\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: float\nminimum_value: 0\nmaximum_value: 1\n\n
"},{"location":"class_enrichment/rank/","title":"Slot: rank","text":"

The rank of this result

URI: ontoenrich:rank

"},{"location":"class_enrichment/rank/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/rank/#properties","title":"Properties","text":""},{"location":"class_enrichment/rank/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/rank/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/rank/#linkml-source","title":"LinkML Source","text":"
name: rank\ndescription: The rank of this result\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: rank\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: integer\n\n
"},{"location":"class_enrichment/results/","title":"Slot: results","text":"

The enrichment results

URI: ontoenrich:results

"},{"location":"class_enrichment/results/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResultSet A collection of enrichemt results no"},{"location":"class_enrichment/results/#properties","title":"Properties","text":""},{"location":"class_enrichment/results/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/results/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/results/#linkml-source","title":"LinkML Source","text":"
name: results\ndescription: The enrichment results\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nmultivalued: true\nalias: results\nowner: ClassEnrichmentResultSet\ndomain_of:\n- ClassEnrichmentResultSet\nrange: ClassEnrichmentResult\n\n
"},{"location":"class_enrichment/sample_count/","title":"Slot: sample_count","text":"

The number of entities in the sample with this class

URI: ontoenrich:sample_count

"},{"location":"class_enrichment/sample_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/sample_count/#properties","title":"Properties","text":""},{"location":"class_enrichment/sample_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/sample_count/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/sample_count/#linkml-source","title":"LinkML Source","text":"
name: sample_count\ndescription: The number of entities in the sample with this class\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: sample_count\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: integer\n\n
"},{"location":"class_enrichment/sample_total/","title":"Slot: sample_total","text":"

The total number of entities in the sample

URI: ontoenrich:sample_total

"},{"location":"class_enrichment/sample_total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClassEnrichmentResult A single enrichment result no"},{"location":"class_enrichment/sample_total/#properties","title":"Properties","text":""},{"location":"class_enrichment/sample_total/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"class_enrichment/sample_total/#schema-source","title":"Schema Source","text":""},{"location":"class_enrichment/sample_total/#linkml-source","title":"LinkML Source","text":"
name: sample_total\ndescription: The total number of entities in the sample\nfrom_schema: https://w3id.org/oak/class-enrichment\nrank: 1000\nalias: sample_total\nowner: ClassEnrichmentResult\ndomain_of:\n- ClassEnrichmentResult\nrange: integer\n\n
"},{"location":"coffee/","title":"Coffee Template","text":"

A template for extracting information about coffee beverages.

URI: http://w3id.org/ontogpt/coffee

Name: coffee-template

"},{"location":"coffee/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nBeverageSet {\n\n}\nBeverage {\n    string name  \n    stringList other_names  \n    string description  \n}\nIngredient {\n    string id  \n    string label  \n}\n\nBeverageSet ||--}o Beverage : \"beverages\"\nBeverage ||--}o Ingredient : \"ingredients\"\n\n
"},{"location":"coffee/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None Beverage None BeverageSet None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None Ingredient None RelationshipType None Publication None TextWithTriples None"},{"location":"coffee/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication beverages combined_text description A one sentence description of the beverage extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity ingredients A semicolon-separated list of ingredients in the beverage, without volumes or... input_id input_text input_title label The label (name) of the named thing name The common name of the beverage, for example, caff\u00e8 macchiato named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text other_names A semicolon-separated list of alternative names for the beverage, including E... predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"coffee/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"coffee/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"coffee/#subsets","title":"Subsets","text":"Subset Description"},{"location":"coffee/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: coffee:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"coffee/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"coffee/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"coffee/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:AnnotatorResult native coffee:AnnotatorResult"},{"location":"coffee/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n\n
"},{"location":"coffee/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"coffee/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"coffee/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"coffee/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"coffee/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Any/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native coffee:Any"},{"location":"coffee/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/coffee\nclass_uri: linkml:Any\n\n
"},{"location":"coffee/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/coffee\nclass_uri: linkml:Any\n\n
"},{"location":"coffee/Beverage/","title":"Class: Beverage","text":"

URI: coffee:Beverage

erDiagram\nBeverage {\n    string name  \n    stringList other_names  \n    string description  \n}\nIngredient {\n    string id  \n    string label  \n}\n\nBeverage ||--}o Ingredient : \"ingredients\"\n\n
"},{"location":"coffee/Beverage/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance name 0..1 String The common name of the beverage, for example, caff\u00e8 macchiato direct other_names 0..* String A semicolon-separated list of alternative names for the beverage, including E... direct description 0..1 String A one sentence description of the beverage direct ingredients 0..* Ingredient A semicolon-separated list of ingredients in the beverage, without volumes or... direct"},{"location":"coffee/Beverage/#usages","title":"Usages","text":"used by used in type used BeverageSet beverages range Beverage"},{"location":"coffee/Beverage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Beverage/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Beverage/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:Beverage native coffee:Beverage"},{"location":"coffee/Beverage/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/Beverage/#direct","title":"Direct","text":"
name: Beverage\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  name:\n    name: name\n    description: The common name of the beverage, for example, caff\u00e8 macchiato.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  other_names:\n    name: other_names\n    description: A semicolon-separated list of alternative names for the beverage,\n      including English names like 'stained coffee' or regional variations.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n  description:\n    name: description\n    description: A one sentence description of the beverage.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  ingredients:\n    name: ingredients\n    description: A semicolon-separated list of ingredients in the beverage, without\n      volumes or units.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    range: Ingredient\n\n
"},{"location":"coffee/Beverage/#induced","title":"Induced","text":"
name: Beverage\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  name:\n    name: name\n    description: The common name of the beverage, for example, caff\u00e8 macchiato.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: name\n    owner: Beverage\n    domain_of:\n    - Beverage\n    range: string\n  other_names:\n    name: other_names\n    description: A semicolon-separated list of alternative names for the beverage,\n      including English names like 'stained coffee' or regional variations.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    alias: other_names\n    owner: Beverage\n    domain_of:\n    - Beverage\n    range: string\n  description:\n    name: description\n    description: A one sentence description of the beverage.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: description\n    owner: Beverage\n    domain_of:\n    - Beverage\n    range: string\n  ingredients:\n    name: ingredients\n    description: A semicolon-separated list of ingredients in the beverage, without\n      volumes or units.\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    alias: ingredients\n    owner: Beverage\n    domain_of:\n    - Beverage\n    range: Ingredient\n\n
"},{"location":"coffee/BeverageSet/","title":"Class: BeverageSet","text":"

URI: coffee:BeverageSet

erDiagram\nBeverageSet {\n\n}\nBeverage {\n    string name  \n    stringList other_names  \n    string description  \n}\nIngredient {\n    string id  \n    string label  \n}\n\nBeverageSet ||--}o Beverage : \"beverages\"\nBeverage ||--}o Ingredient : \"ingredients\"\n\n
"},{"location":"coffee/BeverageSet/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance beverages 0..* Beverage direct"},{"location":"coffee/BeverageSet/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/BeverageSet/#schema-source","title":"Schema Source","text":""},{"location":"coffee/BeverageSet/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:BeverageSet native coffee:BeverageSet"},{"location":"coffee/BeverageSet/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/BeverageSet/#direct","title":"Direct","text":"
name: BeverageSet\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  beverages:\n    name: beverages\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    range: Beverage\n    inlined: true\n    inlined_as_list: true\ntree_root: true\n\n
"},{"location":"coffee/BeverageSet/#induced","title":"Induced","text":"
name: BeverageSet\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  beverages:\n    name: beverages\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    alias: beverages\n    owner: BeverageSet\n    domain_of:\n    - BeverageSet\n    range: Beverage\n    inlined: true\n    inlined_as_list: true\ntree_root: true\n\n
"},{"location":"coffee/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"coffee/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"coffee/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: coffee:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"coffee/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"coffee/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"coffee/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"coffee/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:CompoundExpression native coffee:CompoundExpression"},{"location":"coffee/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/coffee\nabstract: true\n\n
"},{"location":"coffee/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/coffee\nabstract: true\n\n
"},{"location":"coffee/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"coffee/Curie/#comments","title":"Comments","text":""},{"location":"coffee/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Curie/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"coffee/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Date/#schema-source","title":"Schema Source","text":""},{"location":"coffee/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"coffee/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"coffee/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"coffee/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"coffee/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Double/#schema-source","title":"Schema Source","text":""},{"location":"coffee/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: coffee:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"coffee/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"coffee/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"coffee/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:ExtractionResult native coffee:ExtractionResult"},{"location":"coffee/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"coffee/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"coffee/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"coffee/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Float/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Ingredient/","title":"Class: Ingredient","text":"

URI: coffee:Ingredient

erDiagram\nIngredient {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"coffee/Ingredient/#inheritance","title":"Inheritance","text":""},{"location":"coffee/Ingredient/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"coffee/Ingredient/#usages","title":"Usages","text":"used by used in type used Beverage ingredients range Ingredient"},{"location":"coffee/Ingredient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Ingredient/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"coffee/Ingredient/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:foodon"},{"location":"coffee/Ingredient/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Ingredient/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:Ingredient native coffee:Ingredient"},{"location":"coffee/Ingredient/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/Ingredient/#direct","title":"Direct","text":"
name: Ingredient\nid_prefixes:\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: NamedEntity\n\n
"},{"location":"coffee/Ingredient/#induced","title":"Induced","text":"
name: Ingredient\nid_prefixes:\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Ingredient\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/coffee\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Ingredient\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"coffee/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"coffee/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Integer/#schema-source","title":"Schema Source","text":""},{"location":"coffee/NamedEntity/","title":"Class: NamedEntity","text":"

URI: coffee:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"coffee/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"coffee/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"coffee/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"coffee/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"coffee/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:NamedEntity native coffee:NamedEntity"},{"location":"coffee/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/coffee\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/coffee\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"coffee/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/coffee\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/coffee\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"coffee/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"coffee/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"coffee/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"coffee/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"coffee/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"coffee/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"coffee/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"coffee/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"coffee/Objectidentifier/#comments","title":"Comments","text":""},{"location":"coffee/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Publication/","title":"Class: Publication","text":"

URI: coffee:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"coffee/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"coffee/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"coffee/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Publication/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:Publication native coffee:Publication"},{"location":"coffee/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/coffee\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n\n
"},{"location":"coffee/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/coffee\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"coffee/RelationshipType/","title":"Class: RelationshipType","text":"

URI: coffee:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"coffee/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"coffee/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"coffee/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"coffee/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"coffee/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"coffee/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:RelationshipType native coffee:RelationshipType"},{"location":"coffee/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: NamedEntity\n\n
"},{"location":"coffee/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/coffee\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"coffee/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"coffee/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/String/#schema-source","title":"Schema Source","text":""},{"location":"coffee/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: coffee:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"coffee/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"coffee/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"coffee/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:TextWithTriples native coffee:TextWithTriples"},{"location":"coffee/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"coffee/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/coffee\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"coffee/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"coffee/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Time/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: coffee:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"coffee/Triple/#inheritance","title":"Inheritance","text":""},{"location":"coffee/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"coffee/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"coffee/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Triple/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self coffee:Triple native coffee:Triple"},{"location":"coffee/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"coffee/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"coffee/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/coffee\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/coffee\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"coffee/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"coffee/Uri/#comments","title":"Comments","text":""},{"location":"coffee/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Uri/#schema-source","title":"Schema Source","text":""},{"location":"coffee/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"coffee/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"coffee/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: coffee:abstract

"},{"location":"coffee/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"coffee/abstract/#properties","title":"Properties","text":""},{"location":"coffee/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/abstract/#schema-source","title":"Schema Source","text":""},{"location":"coffee/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"coffee/beverages/","title":"Slot: beverages","text":"

URI: coffee:beverages

"},{"location":"coffee/beverages/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BeverageSet no"},{"location":"coffee/beverages/#properties","title":"Properties","text":""},{"location":"coffee/beverages/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/beverages/#schema-source","title":"Schema Source","text":""},{"location":"coffee/beverages/#linkml-source","title":"LinkML Source","text":"
name: beverages\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nmultivalued: true\nalias: beverages\nowner: BeverageSet\ndomain_of:\n- BeverageSet\nrange: Beverage\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"coffee/coffee-template/","title":"coffee-template","text":"

A template for extracting information about coffee beverages.

URI: http://w3id.org/ontogpt/coffee

"},{"location":"coffee/combined_text/","title":"Slot: combined_text","text":"

URI: coffee:combined_text

"},{"location":"coffee/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"coffee/combined_text/#properties","title":"Properties","text":""},{"location":"coffee/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"coffee/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"coffee/description/","title":"Slot: description","text":"

A one sentence description of the beverage.

URI: coffee:description

"},{"location":"coffee/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Beverage no"},{"location":"coffee/description/#properties","title":"Properties","text":""},{"location":"coffee/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/description/#schema-source","title":"Schema Source","text":""},{"location":"coffee/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: A one sentence description of the beverage.\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: description\nowner: Beverage\ndomain_of:\n- Beverage\nrange: string\n\n
"},{"location":"coffee/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: coffee:extracted_object

"},{"location":"coffee/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/extracted_object/#properties","title":"Properties","text":""},{"location":"coffee/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"coffee/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"coffee/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: coffee:full_text

"},{"location":"coffee/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"coffee/full_text/#properties","title":"Properties","text":""},{"location":"coffee/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/full_text/#schema-source","title":"Schema Source","text":""},{"location":"coffee/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"coffee/id/","title":"Slot: id","text":"

URI: coffee:id

"},{"location":"coffee/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Ingredient no NamedEntity no RelationshipType no Publication no"},{"location":"coffee/id/#properties","title":"Properties","text":""},{"location":"coffee/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"coffee/ingredients/","title":"Slot: ingredients","text":"

A semicolon-separated list of ingredients in the beverage, without volumes or units.

URI: coffee:ingredients

"},{"location":"coffee/ingredients/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Beverage no"},{"location":"coffee/ingredients/#properties","title":"Properties","text":""},{"location":"coffee/ingredients/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/ingredients/#schema-source","title":"Schema Source","text":""},{"location":"coffee/ingredients/#linkml-source","title":"LinkML Source","text":"
name: ingredients\ndescription: A semicolon-separated list of ingredients in the beverage, without volumes\n  or units.\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nmultivalued: true\nalias: ingredients\nowner: Beverage\ndomain_of:\n- Beverage\nrange: Ingredient\n\n
"},{"location":"coffee/input_id/","title":"Slot: input_id","text":"

URI: coffee:input_id

"},{"location":"coffee/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/input_id/#properties","title":"Properties","text":""},{"location":"coffee/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/input_id/#schema-source","title":"Schema Source","text":""},{"location":"coffee/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"coffee/input_text/","title":"Slot: input_text","text":"

URI: coffee:input_text

"},{"location":"coffee/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/input_text/#properties","title":"Properties","text":""},{"location":"coffee/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/input_text/#schema-source","title":"Schema Source","text":""},{"location":"coffee/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"coffee/input_title/","title":"Slot: input_title","text":"

URI: coffee:input_title

"},{"location":"coffee/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/input_title/#properties","title":"Properties","text":""},{"location":"coffee/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/input_title/#schema-source","title":"Schema Source","text":""},{"location":"coffee/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"coffee/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"coffee/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Ingredient no NamedEntity no RelationshipType no"},{"location":"coffee/label/#properties","title":"Properties","text":""},{"location":"coffee/label/#aliases","title":"Aliases","text":""},{"location":"coffee/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"coffee/label/#schema-source","title":"Schema Source","text":""},{"location":"coffee/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/coffee\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"coffee/name/","title":"Slot: name","text":"

The common name of the beverage, for example, caff\u00e8 macchiato.

URI: coffee:name

"},{"location":"coffee/name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Beverage no"},{"location":"coffee/name/#properties","title":"Properties","text":""},{"location":"coffee/name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/name/#schema-source","title":"Schema Source","text":""},{"location":"coffee/name/#linkml-source","title":"LinkML Source","text":"
name: name\ndescription: The common name of the beverage, for example, caff\u00e8 macchiato.\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: name\nowner: Beverage\ndomain_of:\n- Beverage\nrange: string\n\n
"},{"location":"coffee/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: coffee:named_entities

"},{"location":"coffee/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/named_entities/#properties","title":"Properties","text":""},{"location":"coffee/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"coffee/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"coffee/object/","title":"Slot: object","text":"

URI: coffee:object

"},{"location":"coffee/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/object/#properties","title":"Properties","text":""},{"location":"coffee/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/object/#schema-source","title":"Schema Source","text":""},{"location":"coffee/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"coffee/object_id/","title":"Slot: object_id","text":"

URI: coffee:object_id

"},{"location":"coffee/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"coffee/object_id/#properties","title":"Properties","text":""},{"location":"coffee/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/object_id/#schema-source","title":"Schema Source","text":""},{"location":"coffee/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"coffee/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: coffee:object_qualifier

"},{"location":"coffee/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/object_qualifier/#properties","title":"Properties","text":""},{"location":"coffee/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"coffee/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"coffee/object_text/","title":"Slot: object_text","text":"

URI: coffee:object_text

"},{"location":"coffee/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"coffee/object_text/#properties","title":"Properties","text":""},{"location":"coffee/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/object_text/#schema-source","title":"Schema Source","text":""},{"location":"coffee/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"coffee/other_names/","title":"Slot: other_names","text":"

A semicolon-separated list of alternative names for the beverage, including English names like 'stained coffee' or regional variations.

URI: coffee:other_names

"},{"location":"coffee/other_names/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Beverage no"},{"location":"coffee/other_names/#properties","title":"Properties","text":""},{"location":"coffee/other_names/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/other_names/#schema-source","title":"Schema Source","text":""},{"location":"coffee/other_names/#linkml-source","title":"LinkML Source","text":"
name: other_names\ndescription: A semicolon-separated list of alternative names for the beverage, including\n  English names like 'stained coffee' or regional variations.\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nmultivalued: true\nalias: other_names\nowner: Beverage\ndomain_of:\n- Beverage\nrange: string\n\n
"},{"location":"coffee/predicate/","title":"Slot: predicate","text":"

URI: coffee:predicate

"},{"location":"coffee/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/predicate/#properties","title":"Properties","text":""},{"location":"coffee/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/predicate/#schema-source","title":"Schema Source","text":""},{"location":"coffee/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"coffee/prompt/","title":"Slot: prompt","text":"

URI: coffee:prompt

"},{"location":"coffee/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/prompt/#properties","title":"Properties","text":""},{"location":"coffee/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/prompt/#schema-source","title":"Schema Source","text":""},{"location":"coffee/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"coffee/publication/","title":"Slot: publication","text":"

URI: coffee:publication

"},{"location":"coffee/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"coffee/publication/#properties","title":"Properties","text":""},{"location":"coffee/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"coffee/publication/#schema-source","title":"Schema Source","text":""},{"location":"coffee/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"coffee/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: coffee:qualifier

"},{"location":"coffee/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/qualifier/#properties","title":"Properties","text":""},{"location":"coffee/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"coffee/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"coffee/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: coffee:raw_completion_output

"},{"location":"coffee/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"coffee/raw_completion_output/#properties","title":"Properties","text":""},{"location":"coffee/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"coffee/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"coffee/subject/","title":"Slot: subject","text":"

URI: coffee:subject

"},{"location":"coffee/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/subject/#properties","title":"Properties","text":""},{"location":"coffee/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/subject/#schema-source","title":"Schema Source","text":""},{"location":"coffee/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"coffee/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: coffee:subject_qualifier

"},{"location":"coffee/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"coffee/subject_qualifier/#properties","title":"Properties","text":""},{"location":"coffee/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"coffee/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"coffee/subject_text/","title":"Slot: subject_text","text":"

URI: coffee:subject_text

"},{"location":"coffee/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"coffee/subject_text/#properties","title":"Properties","text":""},{"location":"coffee/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"coffee/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"coffee/title/","title":"Slot: title","text":"

The title of the publication

URI: coffee:title

"},{"location":"coffee/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"coffee/title/#properties","title":"Properties","text":""},{"location":"coffee/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/title/#schema-source","title":"Schema Source","text":""},{"location":"coffee/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"coffee/triples/","title":"Slot: triples","text":"

URI: coffee:triples

"},{"location":"coffee/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"coffee/triples/#properties","title":"Properties","text":""},{"location":"coffee/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"coffee/triples/#schema-source","title":"Schema Source","text":""},{"location":"coffee/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/coffee\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"composite_disease/","title":"Composite Disease","text":"

A template for representing composite disease concepts

URI: http://w3id.org/ontogpt/composite_disease

Name: composite_disease

"},{"location":"composite_disease/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nCompositeDisease {\n\n}\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nCompositeDisease ||--|o Disease : \"main_disease\"\nCompositeDisease ||--}o Drug : \"drugs\"\nCompositeDisease ||--}o Treatment : \"treatments\"\nCompositeDisease ||--}o Treatment : \"contraindications\"\nCompositeDisease ||--}o TreatmentMechanism : \"treatment_mechanisms\"\nCompositeDisease ||--}o TreatmentEfficacy : \"treatment_efficacies\"\nCompositeDisease ||--}o TreatmentAdverseEffect : \"treatment_adverse_effects\"\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"composite_disease/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompositeDisease None CompoundExpression None TreatmentAdverseEffect None TreatmentEfficacy None TreatmentMechanism None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None AdverseEffect None Disease None Drug None Gene None Mechanism None RelationshipType None Symptom None Treatment None Publication None TextWithTriples None"},{"location":"composite_disease/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication adverse_effects combined_text contraindications semicolon-separated list of therapies and treatments that are contra-indicate... drugs semicolon-separated list of named small molecule drugs efficacy extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing main_disease the name of the disease that is treated mechanism named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication treatment treatment_adverse_effects semicolon-separated list of treatment to adverse effect associations, e treatment_efficacies semicolon-separated list of treatment to efficacy associations, e treatment_mechanisms semicolon-separated list of treatment to asterisk-separated mechanism associa... treatments semicolon-separated list of therapies and treatments are indicated for treati... triples"},{"location":"composite_disease/#enumerations","title":"Enumerations","text":"Enumeration Description CHEBIDrugType MAXOActionType MESHTherapeuticType NCITDrugType NCITTActivityType NCITTreatmentType NullDataOptions"},{"location":"composite_disease/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"composite_disease/#subsets","title":"Subsets","text":"Subset Description"},{"location":"composite_disease/AdverseEffect/","title":"Class: AdverseEffect","text":"

URI: composite_disease:AdverseEffect

erDiagram\nAdverseEffect {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/AdverseEffect/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/AdverseEffect/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/AdverseEffect/#usages","title":"Usages","text":"used by used in type used TreatmentAdverseEffect adverse_effects range AdverseEffect"},{"location":"composite_disease/AdverseEffect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/AdverseEffect/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:ncit"},{"location":"composite_disease/AdverseEffect/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/AdverseEffect/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:AdverseEffect native composite_disease:AdverseEffect"},{"location":"composite_disease/AdverseEffect/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/AdverseEffect/#direct","title":"Direct","text":"
name: AdverseEffect\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/AdverseEffect/#induced","title":"Induced","text":"
name: AdverseEffect\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: AdverseEffect\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: AdverseEffect\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: composite_disease:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"composite_disease/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"composite_disease/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:AnnotatorResult native composite_disease:AnnotatorResult"},{"location":"composite_disease/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n\n
"},{"location":"composite_disease/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"composite_disease/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"composite_disease/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"composite_disease/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"composite_disease/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Any/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native composite_disease:Any"},{"location":"composite_disease/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nclass_uri: linkml:Any\n\n
"},{"location":"composite_disease/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nclass_uri: linkml:Any\n\n
"},{"location":"composite_disease/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"composite_disease/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/CHEBIDrugType/","title":"Enum: CHEBIDrugType","text":"

URI: CHEBIDrugType

This is a dynamic enum

"},{"location":"composite_disease/CHEBIDrugType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/CHEBIDrugType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/CHEBIDrugType/#linkml-source","title":"LinkML Source","text":"
name: CHEBIDrugType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:chebi\n  source_nodes:\n  - CHEBI:23888\n  relationship_types:\n  - rdfs:subClassOf\n  - RO:0000087\n\n
"},{"location":"composite_disease/CompositeDisease/","title":"Class: CompositeDisease","text":"

URI: composite_disease:CompositeDisease

erDiagram\nCompositeDisease {\n\n}\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nCompositeDisease ||--|o Disease : \"main_disease\"\nCompositeDisease ||--}o Drug : \"drugs\"\nCompositeDisease ||--}o Treatment : \"treatments\"\nCompositeDisease ||--}o Treatment : \"contraindications\"\nCompositeDisease ||--}o TreatmentMechanism : \"treatment_mechanisms\"\nCompositeDisease ||--}o TreatmentEfficacy : \"treatment_efficacies\"\nCompositeDisease ||--}o TreatmentAdverseEffect : \"treatment_adverse_effects\"\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"composite_disease/CompositeDisease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance main_disease 0..1 Disease the name of the disease that is treated direct drugs 0..* Drug semicolon-separated list of named small molecule drugs direct treatments 0..* Treatment semicolon-separated list of therapies and treatments are indicated for treati... direct contraindications 0..* Treatment semicolon-separated list of therapies and treatments that are contra-indicate... direct treatment_mechanisms 0..* TreatmentMechanism semicolon-separated list of treatment to asterisk-separated mechanism associa... direct treatment_efficacies 0..* TreatmentEfficacy semicolon-separated list of treatment to efficacy associations, e direct treatment_adverse_effects 0..* TreatmentAdverseEffect semicolon-separated list of treatment to adverse effect associations, e direct"},{"location":"composite_disease/CompositeDisease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/CompositeDisease/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/CompositeDisease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:CompositeDisease native composite_disease:CompositeDisease"},{"location":"composite_disease/CompositeDisease/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/CompositeDisease/#direct","title":"Direct","text":"
name: CompositeDisease\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  main_disease:\n    name: main_disease\n    description: the name of the disease that is treated.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: Disease\n  drugs:\n    name: drugs\n    description: semicolon-separated list of named small molecule drugs\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: Drug\n  treatments:\n    name: treatments\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Imatinib, exercise, surgery\n    description: semicolon-separated list of therapies and treatments are indicated\n      for treating the disease.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: Treatment\n  contraindications:\n    name: contraindications\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Beta-blockers, exercise, surgery\n    description: semicolon-separated list of therapies and treatments that are contra-indicated\n      for the disease, and should not be used, due to risk of adverse effects.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: Treatment\n  treatment_mechanisms:\n    name: treatment_mechanisms\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to asterisk-separated mechanism\n      associations\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: TreatmentMechanism\n  treatment_efficacies:\n    name: treatment_efficacies\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to efficacy associations, e.g.\n      Imatinib*effective\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: TreatmentEfficacy\n  treatment_adverse_effects:\n    name: treatment_adverse_effects\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to adverse effect associations,\n      e.g. Imatinib*nausea\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: TreatmentAdverseEffect\ntree_root: true\n\n
"},{"location":"composite_disease/CompositeDisease/#induced","title":"Induced","text":"
name: CompositeDisease\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  main_disease:\n    name: main_disease\n    description: the name of the disease that is treated.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: main_disease\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: Disease\n  drugs:\n    name: drugs\n    description: semicolon-separated list of named small molecule drugs\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: drugs\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: Drug\n  treatments:\n    name: treatments\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Imatinib, exercise, surgery\n    description: semicolon-separated list of therapies and treatments are indicated\n      for treating the disease.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: treatments\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: Treatment\n  contraindications:\n    name: contraindications\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Beta-blockers, exercise, surgery\n    description: semicolon-separated list of therapies and treatments that are contra-indicated\n      for the disease, and should not be used, due to risk of adverse effects.\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: contraindications\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: Treatment\n  treatment_mechanisms:\n    name: treatment_mechanisms\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to asterisk-separated mechanism\n      associations\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: treatment_mechanisms\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: TreatmentMechanism\n  treatment_efficacies:\n    name: treatment_efficacies\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to efficacy associations, e.g.\n      Imatinib*effective\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: treatment_efficacies\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: TreatmentEfficacy\n  treatment_adverse_effects:\n    name: treatment_adverse_effects\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to adverse effect associations,\n      e.g. Imatinib*nausea\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: treatment_adverse_effects\n    owner: CompositeDisease\n    domain_of:\n    - CompositeDisease\n    range: TreatmentAdverseEffect\ntree_root: true\n\n
"},{"location":"composite_disease/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: composite_disease:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"composite_disease/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"composite_disease/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:CompoundExpression native composite_disease:CompoundExpression"},{"location":"composite_disease/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nabstract: true\n\n
"},{"location":"composite_disease/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nabstract: true\n\n
"},{"location":"composite_disease/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"composite_disease/Curie/#comments","title":"Comments","text":""},{"location":"composite_disease/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Curie/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"composite_disease/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Date/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"composite_disease/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"composite_disease/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"composite_disease/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Disease/","title":"Class: Disease","text":"

URI: composite_disease:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Disease/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Disease/#usages","title":"Usages","text":"used by used in type used CompositeDisease main_disease range Disease"},{"location":"composite_disease/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo"},{"location":"composite_disease/Disease/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Disease native composite_disease:Disease"},{"location":"composite_disease/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Disease/#direct","title":"Direct","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/Disease/#induced","title":"Induced","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"composite_disease/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Double/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Drug/","title":"Class: Drug","text":"

URI: composite_disease:Drug

erDiagram\nDrug {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Drug/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Drug/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Drug/#usages","title":"Usages","text":"used by used in type used CompositeDisease drugs range Drug"},{"location":"composite_disease/Drug/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Drug/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi, sqlite:obo:drugbank"},{"location":"composite_disease/Drug/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Drug/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Drug native composite_disease:Drug"},{"location":"composite_disease/Drug/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Drug/#direct","title":"Direct","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/Drug/#induced","title":"Induced","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: composite_disease:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"composite_disease/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"composite_disease/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:ExtractionResult native composite_disease:ExtractionResult"},{"location":"composite_disease/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"composite_disease/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"composite_disease/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"composite_disease/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Float/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Gene/","title":"Class: Gene","text":"

URI: composite_disease:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Gene/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"composite_disease/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, obo:sql:hgnc, bioportal:hgnc-nr"},{"location":"composite_disease/Gene/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Gene native composite_disease:Gene"},{"location":"composite_disease/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, obo:sql:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, obo:sql:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"composite_disease/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Integer/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/MAXOActionType/","title":"Enum: MAXOActionType","text":"

URI: MAXOActionType

This is a dynamic enum

"},{"location":"composite_disease/MAXOActionType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/MAXOActionType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/MAXOActionType/#linkml-source","title":"LinkML Source","text":"
name: MAXOActionType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:maxo\n  source_nodes:\n  - MAXO:0000001\n\n
"},{"location":"composite_disease/MESHTherapeuticType/","title":"Enum: MESHTherapeuticType","text":"

URI: MESHTherapeuticType

This is a dynamic enum

"},{"location":"composite_disease/MESHTherapeuticType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/MESHTherapeuticType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/MESHTherapeuticType/#linkml-source","title":"LinkML Source","text":"
name: MESHTherapeuticType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:mesh\n  source_nodes:\n  - MESH:D013812\n\n
"},{"location":"composite_disease/Mechanism/","title":"Class: Mechanism","text":"

URI: composite_disease:Mechanism

erDiagram\nMechanism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Mechanism/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Mechanism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Mechanism/#usages","title":"Usages","text":"used by used in type used TreatmentMechanism mechanism range Mechanism"},{"location":"composite_disease/Mechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Mechanism/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh"},{"location":"composite_disease/Mechanism/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Mechanism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Mechanism native composite_disease:Mechanism"},{"location":"composite_disease/Mechanism/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Mechanism/#direct","title":"Direct","text":"
name: Mechanism\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/Mechanism/#induced","title":"Induced","text":"
name: Mechanism\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Mechanism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Mechanism\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/NCITDrugType/","title":"Enum: NCITDrugType","text":"

URI: NCITDrugType

This is a dynamic enum

"},{"location":"composite_disease/NCITDrugType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/NCITDrugType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NCITDrugType/#linkml-source","title":"LinkML Source","text":"
name: NCITDrugType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C1908\n\n
"},{"location":"composite_disease/NCITTActivityType/","title":"Enum: NCITTActivityType","text":"

URI: NCITTActivityType

This is a dynamic enum

"},{"location":"composite_disease/NCITTActivityType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/NCITTActivityType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NCITTActivityType/#linkml-source","title":"LinkML Source","text":"
name: NCITTActivityType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C43431\n\n
"},{"location":"composite_disease/NCITTreatmentType/","title":"Enum: NCITTreatmentType","text":"

URI: NCITTreatmentType

This is a dynamic enum

"},{"location":"composite_disease/NCITTreatmentType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/NCITTreatmentType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NCITTreatmentType/#linkml-source","title":"LinkML Source","text":"
name: NCITTreatmentType\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C25218\n\n
"},{"location":"composite_disease/NamedEntity/","title":"Class: NamedEntity","text":"

URI: composite_disease:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"composite_disease/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"composite_disease/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:NamedEntity native composite_disease:NamedEntity"},{"location":"composite_disease/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"composite_disease/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"composite_disease/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"composite_disease/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"composite_disease/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"composite_disease/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"composite_disease/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"composite_disease/Objectidentifier/#comments","title":"Comments","text":""},{"location":"composite_disease/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Publication/","title":"Class: Publication","text":"

URI: composite_disease:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"composite_disease/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"composite_disease/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"composite_disease/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Publication/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Publication native composite_disease:Publication"},{"location":"composite_disease/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/composite_disease\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n\n
"},{"location":"composite_disease/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"composite_disease/RelationshipType/","title":"Class: RelationshipType","text":"

URI: composite_disease:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"composite_disease/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"composite_disease/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:RelationshipType native composite_disease:RelationshipType"},{"location":"composite_disease/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"composite_disease/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/String/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Symptom/","title":"Class: Symptom","text":"

URI: composite_disease:Symptom

erDiagram\nSymptom {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Symptom/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Symptom/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Symptom/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"composite_disease/Symptom/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp"},{"location":"composite_disease/Symptom/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Symptom/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Symptom native composite_disease:Symptom"},{"location":"composite_disease/Symptom/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Symptom/#direct","title":"Direct","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\n\n
"},{"location":"composite_disease/Symptom/#induced","title":"Induced","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: composite_disease:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"composite_disease/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"composite_disease/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:TextWithTriples native composite_disease:TextWithTriples"},{"location":"composite_disease/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"composite_disease/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"composite_disease/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"composite_disease/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Time/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Treatment/","title":"Class: Treatment","text":"

URI: composite_disease:Treatment

erDiagram\nTreatment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"composite_disease/Treatment/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Treatment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"composite_disease/Treatment/#usages","title":"Usages","text":"used by used in type used CompositeDisease treatments range Treatment CompositeDisease contraindications range Treatment TreatmentMechanism treatment range Treatment TreatmentAdverseEffect treatment range Treatment TreatmentEfficacy treatment range Treatment"},{"location":"composite_disease/Treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Treatment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi"},{"location":"composite_disease/Treatment/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Treatment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Treatment native composite_disease:Treatment"},{"location":"composite_disease/Treatment/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Treatment/#direct","title":"Direct","text":"
name: Treatment\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nvalues_from:\n- NCITDrugType\n- NCITTreatmentType\n- NCITActivityType\n- MAXOTreatmentType\n- MESHTherapeuticType\n- CHEBIDrugType\n\n
"},{"location":"composite_disease/Treatment/#induced","title":"Induced","text":"
name: Treatment\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: NamedEntity\nvalues_from:\n- NCITDrugType\n- NCITTreatmentType\n- NCITActivityType\n- MAXOTreatmentType\n- MESHTherapeuticType\n- CHEBIDrugType\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"composite_disease/TreatmentAdverseEffect/","title":"Class: TreatmentAdverseEffect","text":"

URI: composite_disease:TreatmentAdverseEffect

erDiagram\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\n\n
"},{"location":"composite_disease/TreatmentAdverseEffect/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/TreatmentAdverseEffect/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct adverse_effects 0..* AdverseEffect direct"},{"location":"composite_disease/TreatmentAdverseEffect/#usages","title":"Usages","text":"used by used in type used CompositeDisease treatment_adverse_effects range TreatmentAdverseEffect"},{"location":"composite_disease/TreatmentAdverseEffect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/TreatmentAdverseEffect/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/TreatmentAdverseEffect/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:TreatmentAdverseEffect native composite_disease:TreatmentAdverseEffect"},{"location":"composite_disease/TreatmentAdverseEffect/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/TreatmentAdverseEffect/#direct","title":"Direct","text":"
name: TreatmentAdverseEffect\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    range: Treatment\n  adverse_effects:\n    name: adverse_effects\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    range: AdverseEffect\n\n
"},{"location":"composite_disease/TreatmentAdverseEffect/#induced","title":"Induced","text":"
name: TreatmentAdverseEffect\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    alias: treatment\n    owner: TreatmentAdverseEffect\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  adverse_effects:\n    name: adverse_effects\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    multivalued: true\n    alias: adverse_effects\n    owner: TreatmentAdverseEffect\n    domain_of:\n    - TreatmentAdverseEffect\n    range: AdverseEffect\n\n
"},{"location":"composite_disease/TreatmentEfficacy/","title":"Class: TreatmentEfficacy","text":"

URI: composite_disease:TreatmentEfficacy

erDiagram\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\n\n
"},{"location":"composite_disease/TreatmentEfficacy/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/TreatmentEfficacy/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct efficacy 0..1 String direct"},{"location":"composite_disease/TreatmentEfficacy/#usages","title":"Usages","text":"used by used in type used CompositeDisease treatment_efficacies range TreatmentEfficacy"},{"location":"composite_disease/TreatmentEfficacy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/TreatmentEfficacy/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/TreatmentEfficacy/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:TreatmentEfficacy native composite_disease:TreatmentEfficacy"},{"location":"composite_disease/TreatmentEfficacy/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/TreatmentEfficacy/#direct","title":"Direct","text":"
name: TreatmentEfficacy\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    range: Treatment\n  efficacy:\n    name: efficacy\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: string\n\n
"},{"location":"composite_disease/TreatmentEfficacy/#induced","title":"Induced","text":"
name: TreatmentEfficacy\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    alias: treatment\n    owner: TreatmentEfficacy\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  efficacy:\n    name: efficacy\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: efficacy\n    owner: TreatmentEfficacy\n    domain_of:\n    - TreatmentEfficacy\n    range: string\n\n
"},{"location":"composite_disease/TreatmentMechanism/","title":"Class: TreatmentMechanism","text":"

URI: composite_disease:TreatmentMechanism

erDiagram\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"composite_disease/TreatmentMechanism/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/TreatmentMechanism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct mechanism 0..1 Mechanism direct"},{"location":"composite_disease/TreatmentMechanism/#usages","title":"Usages","text":"used by used in type used CompositeDisease treatment_mechanisms range TreatmentMechanism"},{"location":"composite_disease/TreatmentMechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/TreatmentMechanism/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/TreatmentMechanism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:TreatmentMechanism native composite_disease:TreatmentMechanism"},{"location":"composite_disease/TreatmentMechanism/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/TreatmentMechanism/#direct","title":"Direct","text":"
name: TreatmentMechanism\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: Treatment\n  mechanism:\n    name: mechanism\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: Mechanism\n\n
"},{"location":"composite_disease/TreatmentMechanism/#induced","title":"Induced","text":"
name: TreatmentMechanism\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: treatment\n    owner: TreatmentMechanism\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  mechanism:\n    name: mechanism\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: mechanism\n    owner: TreatmentMechanism\n    domain_of:\n    - TreatmentMechanism\n    range: Mechanism\n\n
"},{"location":"composite_disease/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: composite_disease:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"composite_disease/Triple/#inheritance","title":"Inheritance","text":""},{"location":"composite_disease/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"composite_disease/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"composite_disease/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Triple/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self composite_disease:Triple native composite_disease:Triple"},{"location":"composite_disease/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"composite_disease/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"composite_disease/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/composite_disease\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"composite_disease/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"composite_disease/Uri/#comments","title":"Comments","text":""},{"location":"composite_disease/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Uri/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"composite_disease/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: composite_disease:abstract

"},{"location":"composite_disease/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"composite_disease/abstract/#properties","title":"Properties","text":""},{"location":"composite_disease/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/abstract/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"composite_disease/adverse_effects/","title":"Slot: adverse_effects","text":"

URI: composite_disease:adverse_effects

"},{"location":"composite_disease/adverse_effects/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentAdverseEffect no"},{"location":"composite_disease/adverse_effects/#properties","title":"Properties","text":""},{"location":"composite_disease/adverse_effects/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/adverse_effects/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/adverse_effects/#linkml-source","title":"LinkML Source","text":"
name: adverse_effects\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: adverse_effects\nowner: TreatmentAdverseEffect\ndomain_of:\n- TreatmentAdverseEffect\nrange: AdverseEffect\n\n
"},{"location":"composite_disease/combined_text/","title":"Slot: combined_text","text":"

URI: composite_disease:combined_text

"},{"location":"composite_disease/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"composite_disease/combined_text/#properties","title":"Properties","text":""},{"location":"composite_disease/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"composite_disease/composite_disease/","title":"composite_disease","text":"

A template for representing composite disease concepts

URI: http://w3id.org/ontogpt/composite_disease

"},{"location":"composite_disease/contraindications/","title":"Slot: contraindications","text":"

semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.

URI: composite_disease:contraindications

"},{"location":"composite_disease/contraindications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/contraindications/#properties","title":"Properties","text":""},{"location":"composite_disease/contraindications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/contraindications/#annotations","title":"Annotations","text":"property value prompt.examples Beta-blockers, exercise, surgery"},{"location":"composite_disease/contraindications/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/contraindications/#linkml-source","title":"LinkML Source","text":"
name: contraindications\nannotations:\n  prompt.examples:\n    tag: prompt.examples\n    value: Beta-blockers, exercise, surgery\ndescription: semicolon-separated list of therapies and treatments that are contra-indicated\n  for the disease, and should not be used, due to risk of adverse effects.\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: contraindications\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: Treatment\n\n
"},{"location":"composite_disease/drugs/","title":"Slot: drugs","text":"

semicolon-separated list of named small molecule drugs

URI: composite_disease:drugs

"},{"location":"composite_disease/drugs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/drugs/#properties","title":"Properties","text":""},{"location":"composite_disease/drugs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/drugs/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/drugs/#linkml-source","title":"LinkML Source","text":"
name: drugs\ndescription: semicolon-separated list of named small molecule drugs\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: drugs\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: Drug\n\n
"},{"location":"composite_disease/efficacy/","title":"Slot: efficacy","text":"

URI: composite_disease:efficacy

"},{"location":"composite_disease/efficacy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentEfficacy no"},{"location":"composite_disease/efficacy/#properties","title":"Properties","text":""},{"location":"composite_disease/efficacy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/efficacy/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/efficacy/#linkml-source","title":"LinkML Source","text":"
name: efficacy\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: efficacy\nowner: TreatmentEfficacy\ndomain_of:\n- TreatmentEfficacy\nrange: string\n\n
"},{"location":"composite_disease/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: composite_disease:extracted_object

"},{"location":"composite_disease/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/extracted_object/#properties","title":"Properties","text":""},{"location":"composite_disease/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"composite_disease/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: composite_disease:full_text

"},{"location":"composite_disease/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"composite_disease/full_text/#properties","title":"Properties","text":""},{"location":"composite_disease/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/full_text/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"composite_disease/id/","title":"Slot: id","text":"

URI: composite_disease:id

"},{"location":"composite_disease/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Symptom no Disease no AdverseEffect no Treatment no Mechanism no Drug no NamedEntity no RelationshipType no Publication no"},{"location":"composite_disease/id/#properties","title":"Properties","text":""},{"location":"composite_disease/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"composite_disease/input_id/","title":"Slot: input_id","text":"

URI: composite_disease:input_id

"},{"location":"composite_disease/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/input_id/#properties","title":"Properties","text":""},{"location":"composite_disease/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/input_id/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"composite_disease/input_text/","title":"Slot: input_text","text":"

URI: composite_disease:input_text

"},{"location":"composite_disease/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/input_text/#properties","title":"Properties","text":""},{"location":"composite_disease/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/input_text/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"composite_disease/input_title/","title":"Slot: input_title","text":"

URI: composite_disease:input_title

"},{"location":"composite_disease/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/input_title/#properties","title":"Properties","text":""},{"location":"composite_disease/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/input_title/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"composite_disease/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"composite_disease/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Symptom no Disease no AdverseEffect no Treatment no Mechanism no Drug no NamedEntity no RelationshipType no"},{"location":"composite_disease/label/#properties","title":"Properties","text":""},{"location":"composite_disease/label/#aliases","title":"Aliases","text":""},{"location":"composite_disease/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"composite_disease/label/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/composite_disease\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"composite_disease/main_disease/","title":"Slot: main_disease","text":"

the name of the disease that is treated.

URI: composite_disease:main_disease

"},{"location":"composite_disease/main_disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/main_disease/#properties","title":"Properties","text":""},{"location":"composite_disease/main_disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/main_disease/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/main_disease/#linkml-source","title":"LinkML Source","text":"
name: main_disease\ndescription: the name of the disease that is treated.\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: main_disease\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: Disease\n\n
"},{"location":"composite_disease/mechanism/","title":"Slot: mechanism","text":"

URI: composite_disease:mechanism

"},{"location":"composite_disease/mechanism/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentMechanism no"},{"location":"composite_disease/mechanism/#properties","title":"Properties","text":""},{"location":"composite_disease/mechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/mechanism/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/mechanism/#linkml-source","title":"LinkML Source","text":"
name: mechanism\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: mechanism\nowner: TreatmentMechanism\ndomain_of:\n- TreatmentMechanism\nrange: Mechanism\n\n
"},{"location":"composite_disease/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: composite_disease:named_entities

"},{"location":"composite_disease/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/named_entities/#properties","title":"Properties","text":""},{"location":"composite_disease/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"composite_disease/object/","title":"Slot: object","text":"

URI: composite_disease:object

"},{"location":"composite_disease/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/object/#properties","title":"Properties","text":""},{"location":"composite_disease/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/object/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"composite_disease/object_id/","title":"Slot: object_id","text":"

URI: composite_disease:object_id

"},{"location":"composite_disease/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"composite_disease/object_id/#properties","title":"Properties","text":""},{"location":"composite_disease/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/object_id/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"composite_disease/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: composite_disease:object_qualifier

"},{"location":"composite_disease/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/object_qualifier/#properties","title":"Properties","text":""},{"location":"composite_disease/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"composite_disease/object_text/","title":"Slot: object_text","text":"

URI: composite_disease:object_text

"},{"location":"composite_disease/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"composite_disease/object_text/#properties","title":"Properties","text":""},{"location":"composite_disease/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/object_text/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"composite_disease/predicate/","title":"Slot: predicate","text":"

URI: composite_disease:predicate

"},{"location":"composite_disease/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/predicate/#properties","title":"Properties","text":""},{"location":"composite_disease/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/predicate/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"composite_disease/prompt/","title":"Slot: prompt","text":"

URI: composite_disease:prompt

"},{"location":"composite_disease/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/prompt/#properties","title":"Properties","text":""},{"location":"composite_disease/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/prompt/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"composite_disease/publication/","title":"Slot: publication","text":"

URI: composite_disease:publication

"},{"location":"composite_disease/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"composite_disease/publication/#properties","title":"Properties","text":""},{"location":"composite_disease/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"composite_disease/publication/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"composite_disease/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: composite_disease:qualifier

"},{"location":"composite_disease/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/qualifier/#properties","title":"Properties","text":""},{"location":"composite_disease/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"composite_disease/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: composite_disease:raw_completion_output

"},{"location":"composite_disease/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"composite_disease/raw_completion_output/#properties","title":"Properties","text":""},{"location":"composite_disease/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"composite_disease/subject/","title":"Slot: subject","text":"

URI: composite_disease:subject

"},{"location":"composite_disease/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/subject/#properties","title":"Properties","text":""},{"location":"composite_disease/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/subject/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"composite_disease/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: composite_disease:subject_qualifier

"},{"location":"composite_disease/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"composite_disease/subject_qualifier/#properties","title":"Properties","text":""},{"location":"composite_disease/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"composite_disease/subject_text/","title":"Slot: subject_text","text":"

URI: composite_disease:subject_text

"},{"location":"composite_disease/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"composite_disease/subject_text/#properties","title":"Properties","text":""},{"location":"composite_disease/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"composite_disease/title/","title":"Slot: title","text":"

The title of the publication

URI: composite_disease:title

"},{"location":"composite_disease/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"composite_disease/title/#properties","title":"Properties","text":""},{"location":"composite_disease/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/title/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"composite_disease/treatment/","title":"Slot: treatment","text":"

URI: composite_disease:treatment

"},{"location":"composite_disease/treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentMechanism no TreatmentAdverseEffect no TreatmentEfficacy no"},{"location":"composite_disease/treatment/#properties","title":"Properties","text":""},{"location":"composite_disease/treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/treatment/#linkml-source","title":"LinkML Source","text":"
name: treatment\nalias: treatment\ndomain_of:\n- TreatmentMechanism\n- TreatmentAdverseEffect\n- TreatmentEfficacy\nrange: string\n\n
"},{"location":"composite_disease/treatment_adverse_effects/","title":"Slot: treatment_adverse_effects","text":"

semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea

URI: composite_disease:treatment_adverse_effects

"},{"location":"composite_disease/treatment_adverse_effects/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/treatment_adverse_effects/#properties","title":"Properties","text":""},{"location":"composite_disease/treatment_adverse_effects/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/treatment_adverse_effects/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"composite_disease/treatment_adverse_effects/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/treatment_adverse_effects/#linkml-source","title":"LinkML Source","text":"
name: treatment_adverse_effects\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to adverse effect associations,\n  e.g. Imatinib*nausea\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: treatment_adverse_effects\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: TreatmentAdverseEffect\n\n
"},{"location":"composite_disease/treatment_efficacies/","title":"Slot: treatment_efficacies","text":"

semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective

URI: composite_disease:treatment_efficacies

"},{"location":"composite_disease/treatment_efficacies/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/treatment_efficacies/#properties","title":"Properties","text":""},{"location":"composite_disease/treatment_efficacies/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/treatment_efficacies/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"composite_disease/treatment_efficacies/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/treatment_efficacies/#linkml-source","title":"LinkML Source","text":"
name: treatment_efficacies\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to efficacy associations, e.g.\n  Imatinib*effective\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: treatment_efficacies\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: TreatmentEfficacy\n\n
"},{"location":"composite_disease/treatment_mechanisms/","title":"Slot: treatment_mechanisms","text":"

semicolon-separated list of treatment to asterisk-separated mechanism associations

URI: composite_disease:treatment_mechanisms

"},{"location":"composite_disease/treatment_mechanisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/treatment_mechanisms/#properties","title":"Properties","text":""},{"location":"composite_disease/treatment_mechanisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/treatment_mechanisms/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"composite_disease/treatment_mechanisms/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/treatment_mechanisms/#linkml-source","title":"LinkML Source","text":"
name: treatment_mechanisms\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to asterisk-separated mechanism\n  associations\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: treatment_mechanisms\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: TreatmentMechanism\n\n
"},{"location":"composite_disease/treatments/","title":"Slot: treatments","text":"

semicolon-separated list of therapies and treatments are indicated for treating the disease.

URI: composite_disease:treatments

"},{"location":"composite_disease/treatments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompositeDisease no"},{"location":"composite_disease/treatments/#properties","title":"Properties","text":""},{"location":"composite_disease/treatments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/treatments/#annotations","title":"Annotations","text":"property value prompt.examples Imatinib, exercise, surgery"},{"location":"composite_disease/treatments/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/treatments/#linkml-source","title":"LinkML Source","text":"
name: treatments\nannotations:\n  prompt.examples:\n    tag: prompt.examples\n    value: Imatinib, exercise, surgery\ndescription: semicolon-separated list of therapies and treatments are indicated for\n  treating the disease.\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: treatments\nowner: CompositeDisease\ndomain_of:\n- CompositeDisease\nrange: Treatment\n\n
"},{"location":"composite_disease/triples/","title":"Slot: triples","text":"

URI: composite_disease:triples

"},{"location":"composite_disease/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"composite_disease/triples/#properties","title":"Properties","text":""},{"location":"composite_disease/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"composite_disease/triples/#schema-source","title":"Schema Source","text":""},{"location":"composite_disease/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/composite_disease\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"core/","title":"AI core Template","text":"

Core upper level

URI: http://w3id.org/ontogpt/core

Name: core

"},{"location":"core/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"core/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None RelationshipType None Publication None TextWithTriples None"},{"location":"core/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"core/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"core/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"core/#subsets","title":"Subsets","text":"Subset Description"},{"location":"core/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: core:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"core/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"core/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"core/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:AnnotatorResult native core:AnnotatorResult"},{"location":"core/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"core/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n\n
"},{"location":"core/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"core/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"core/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"core/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"core/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Any/#schema-source","title":"Schema Source","text":""},{"location":"core/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native core:Any"},{"location":"core/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"core/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/core\nclass_uri: linkml:Any\n\n
"},{"location":"core/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/core\nclass_uri: linkml:Any\n\n
"},{"location":"core/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"core/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"core/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: core:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"core/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"core/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"core/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"core/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:CompoundExpression native core:CompoundExpression"},{"location":"core/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"core/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/core\nabstract: true\n\n
"},{"location":"core/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/core\nabstract: true\n\n
"},{"location":"core/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"core/Curie/#comments","title":"Comments","text":""},{"location":"core/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Curie/#schema-source","title":"Schema Source","text":""},{"location":"core/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"core/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Date/#schema-source","title":"Schema Source","text":""},{"location":"core/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"core/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"core/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"core/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"core/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"core/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"core/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"core/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Double/#schema-source","title":"Schema Source","text":""},{"location":"core/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: core:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"core/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"core/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"core/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:ExtractionResult native core:ExtractionResult"},{"location":"core/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"core/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"core/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"core/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"core/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Float/#schema-source","title":"Schema Source","text":""},{"location":"core/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"core/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Integer/#schema-source","title":"Schema Source","text":""},{"location":"core/NamedEntity/","title":"Class: NamedEntity","text":"

URI: core:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"core/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"core/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"core/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"core/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"core/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:NamedEntity native core:NamedEntity"},{"location":"core/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"core/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/core\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/core\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"core/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/core\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/core\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"core/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"core/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"core/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"core/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"core/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"core/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"core/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"core/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"core/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"core/Objectidentifier/#comments","title":"Comments","text":""},{"location":"core/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"core/Publication/","title":"Class: Publication","text":"

URI: core:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"core/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"core/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"core/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Publication/#schema-source","title":"Schema Source","text":""},{"location":"core/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:Publication native core:Publication"},{"location":"core/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"core/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/core\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n\n
"},{"location":"core/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/core\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"core/RelationshipType/","title":"Class: RelationshipType","text":"

URI: core:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"core/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"core/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"core/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"core/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"core/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"core/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:RelationshipType native core:RelationshipType"},{"location":"core/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"core/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/core\nis_a: NamedEntity\n\n
"},{"location":"core/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/core\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/core\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"core/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"core/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/String/#schema-source","title":"Schema Source","text":""},{"location":"core/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: core:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"core/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"core/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"core/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:TextWithTriples native core:TextWithTriples"},{"location":"core/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"core/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"core/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/core\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"core/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"core/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Time/#schema-source","title":"Schema Source","text":""},{"location":"core/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: core:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"core/Triple/#inheritance","title":"Inheritance","text":""},{"location":"core/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"core/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"core/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Triple/#schema-source","title":"Schema Source","text":""},{"location":"core/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self core:Triple native core:Triple"},{"location":"core/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"core/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/core\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"core/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/core\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/core\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"core/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"core/Uri/#comments","title":"Comments","text":""},{"location":"core/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Uri/#schema-source","title":"Schema Source","text":""},{"location":"core/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"core/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"core/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: core:abstract

"},{"location":"core/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"core/abstract/#properties","title":"Properties","text":""},{"location":"core/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/abstract/#schema-source","title":"Schema Source","text":""},{"location":"core/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"core/combined_text/","title":"Slot: combined_text","text":"

URI: core:combined_text

"},{"location":"core/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"core/combined_text/#properties","title":"Properties","text":""},{"location":"core/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"core/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"core/core/","title":"core","text":"

Core upper level

URI: http://w3id.org/ontogpt/core

"},{"location":"core/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: core:extracted_object

"},{"location":"core/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/extracted_object/#properties","title":"Properties","text":""},{"location":"core/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"core/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"core/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: core:full_text

"},{"location":"core/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"core/full_text/#properties","title":"Properties","text":""},{"location":"core/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/full_text/#schema-source","title":"Schema Source","text":""},{"location":"core/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"core/id/","title":"Slot: id","text":"

URI: core:id

"},{"location":"core/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NamedEntity no RelationshipType no Publication no"},{"location":"core/id/#properties","title":"Properties","text":""},{"location":"core/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"core/input_id/","title":"Slot: input_id","text":"

URI: core:input_id

"},{"location":"core/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/input_id/#properties","title":"Properties","text":""},{"location":"core/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/input_id/#schema-source","title":"Schema Source","text":""},{"location":"core/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"core/input_text/","title":"Slot: input_text","text":"

URI: core:input_text

"},{"location":"core/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/input_text/#properties","title":"Properties","text":""},{"location":"core/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/input_text/#schema-source","title":"Schema Source","text":""},{"location":"core/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"core/input_title/","title":"Slot: input_title","text":"

URI: core:input_title

"},{"location":"core/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/input_title/#properties","title":"Properties","text":""},{"location":"core/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/input_title/#schema-source","title":"Schema Source","text":""},{"location":"core/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"core/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"core/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NamedEntity no RelationshipType no"},{"location":"core/label/#properties","title":"Properties","text":""},{"location":"core/label/#aliases","title":"Aliases","text":""},{"location":"core/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"core/label/#schema-source","title":"Schema Source","text":""},{"location":"core/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/core\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"core/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: core:named_entities

"},{"location":"core/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/named_entities/#properties","title":"Properties","text":""},{"location":"core/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"core/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"core/object/","title":"Slot: object","text":"

URI: core:object

"},{"location":"core/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/object/#properties","title":"Properties","text":""},{"location":"core/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/object/#schema-source","title":"Schema Source","text":""},{"location":"core/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"core/object_id/","title":"Slot: object_id","text":"

URI: core:object_id

"},{"location":"core/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"core/object_id/#properties","title":"Properties","text":""},{"location":"core/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/object_id/#schema-source","title":"Schema Source","text":""},{"location":"core/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"core/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: core:object_qualifier

"},{"location":"core/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/object_qualifier/#properties","title":"Properties","text":""},{"location":"core/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"core/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"core/object_text/","title":"Slot: object_text","text":"

URI: core:object_text

"},{"location":"core/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"core/object_text/#properties","title":"Properties","text":""},{"location":"core/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/object_text/#schema-source","title":"Schema Source","text":""},{"location":"core/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"core/predicate/","title":"Slot: predicate","text":"

URI: core:predicate

"},{"location":"core/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/predicate/#properties","title":"Properties","text":""},{"location":"core/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/predicate/#schema-source","title":"Schema Source","text":""},{"location":"core/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"core/prompt/","title":"Slot: prompt","text":"

URI: core:prompt

"},{"location":"core/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/prompt/#properties","title":"Properties","text":""},{"location":"core/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/prompt/#schema-source","title":"Schema Source","text":""},{"location":"core/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"core/publication/","title":"Slot: publication","text":"

URI: core:publication

"},{"location":"core/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"core/publication/#properties","title":"Properties","text":""},{"location":"core/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"core/publication/#schema-source","title":"Schema Source","text":""},{"location":"core/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"core/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: core:qualifier

"},{"location":"core/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/qualifier/#properties","title":"Properties","text":""},{"location":"core/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"core/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"core/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: core:raw_completion_output

"},{"location":"core/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"core/raw_completion_output/#properties","title":"Properties","text":""},{"location":"core/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"core/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"core/subject/","title":"Slot: subject","text":"

URI: core:subject

"},{"location":"core/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/subject/#properties","title":"Properties","text":""},{"location":"core/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/subject/#schema-source","title":"Schema Source","text":""},{"location":"core/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"core/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: core:subject_qualifier

"},{"location":"core/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"core/subject_qualifier/#properties","title":"Properties","text":""},{"location":"core/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"core/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"core/subject_text/","title":"Slot: subject_text","text":"

URI: core:subject_text

"},{"location":"core/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"core/subject_text/#properties","title":"Properties","text":""},{"location":"core/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"core/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"core/title/","title":"Slot: title","text":"

The title of the publication

URI: core:title

"},{"location":"core/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"core/title/#properties","title":"Properties","text":""},{"location":"core/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/title/#schema-source","title":"Schema Source","text":""},{"location":"core/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"core/triples/","title":"Slot: triples","text":"

URI: core:triples

"},{"location":"core/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"core/triples/#properties","title":"Properties","text":""},{"location":"core/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core/triples/#schema-source","title":"Schema Source","text":""},{"location":"core/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/core\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ctd/","title":"Chemical to Disease Template","text":"

A template for Chemical to Disease associations. This template is intended to represent associations between chemicals and diseases, and for evaluating Semantic Llama against BioCreative V Chemical Disease Relation (CDR) Task (BC5CDR).

URI: http://w3id.org/ontogpt/ctd

Name: ctd

"},{"location":"ctd/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nChemicalToDiseaseDocument {\n\n}\nChemicalToDiseaseRelationship {\n    string qualifier  \n}\nDisease {\n    string id  \n    string label  \n}\nChemical {\n    string id  \n    string label  \n}\nChemicalToDiseasePredicate {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nChemicalToDiseaseDocument ||--|o Publication : \"publication\"\nChemicalToDiseaseDocument ||--}o ChemicalToDiseaseRelationship : \"triples\"\nChemicalToDiseaseRelationship ||--|o Chemical : \"subject\"\nChemicalToDiseaseRelationship ||--|o ChemicalToDiseasePredicate : \"predicate\"\nChemicalToDiseaseRelationship ||--|o Disease : \"object\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"ctd/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease. ExtractionResult A result of extracting knowledge on text NamedEntity None Chemical None Disease None RelationshipType None ChemicalToDiseasePredicate A predicate for chemical to disease relationships Publication None TextWithTriples None ChemicalToDiseaseDocument A document that contains chemical to disease relations."},{"location":"ctd/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"ctd/#enumerations","title":"Enumerations","text":"Enumeration Description MeshChemicalIdentifier MeshDiseaseIdentifier NullDataOptions"},{"location":"ctd/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"ctd/#subsets","title":"Subsets","text":"Subset Description"},{"location":"ctd/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: drug:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"ctd/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"ctd/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"ctd/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:AnnotatorResult native drug:AnnotatorResult"},{"location":"ctd/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n\n
"},{"location":"ctd/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"ctd/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"ctd/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ctd/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"ctd/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Any/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native drug:Any"},{"location":"ctd/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/ctd\nclass_uri: linkml:Any\n\n
"},{"location":"ctd/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/ctd\nclass_uri: linkml:Any\n\n
"},{"location":"ctd/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"ctd/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Chemical/","title":"Class: Chemical","text":"

URI: drug:Chemical

erDiagram\nChemical {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ctd/Chemical/#inheritance","title":"Inheritance","text":""},{"location":"ctd/Chemical/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ctd/Chemical/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseRelationship subject range Chemical"},{"location":"ctd/Chemical/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Chemical/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ctd/Chemical/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:"},{"location":"ctd/Chemical/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Chemical/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Chemical native drug:Chemical"},{"location":"ctd/Chemical/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/Chemical/#direct","title":"Direct","text":"
name: Chemical\nid_prefixes:\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: 'sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank,\n      gilda:'\n  prompt.examples:\n    tag: prompt.examples\n    value: Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - MeshChemicalIdentifier\n    domain_of:\n    - NamedEntity\n    - Publication\n    pattern: ^MESH:[CD][0-9]{6}$\n\n
"},{"location":"ctd/Chemical/#induced","title":"Induced","text":"
name: Chemical\nid_prefixes:\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: 'sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank,\n      gilda:'\n  prompt.examples:\n    tag: prompt.examples\n    value: Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - MeshChemicalIdentifier\n    domain_of:\n    - NamedEntity\n    - Publication\n    pattern: ^MESH:[CD][0-9]{6}$\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    values_from:\n    - MeshChemicalIdentifier\n    identifier: true\n    alias: id\n    owner: Chemical\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n    pattern: ^MESH:[CD][0-9]{6}$\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Chemical\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ctd/ChemicalToDiseaseDocument/","title":"Class: ChemicalToDiseaseDocument","text":"

A document that contains chemical to disease relations.

URI: drug:ChemicalToDiseaseDocument

erDiagram\nChemicalToDiseaseDocument {\n\n}\nChemicalToDiseaseRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nChemicalToDiseasePredicate {\n    string id  \n    string label  \n}\nChemical {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nChemicalToDiseaseDocument ||--|o Publication : \"publication\"\nChemicalToDiseaseDocument ||--}o ChemicalToDiseaseRelationship : \"triples\"\nChemicalToDiseaseRelationship ||--|o Chemical : \"subject\"\nChemicalToDiseaseRelationship ||--|o ChemicalToDiseasePredicate : \"predicate\"\nChemicalToDiseaseRelationship ||--|o Disease : \"object\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ctd/ChemicalToDiseaseDocument/#inheritance","title":"Inheritance","text":""},{"location":"ctd/ChemicalToDiseaseDocument/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication TextWithTriples triples 0..* ChemicalToDiseaseRelationship TextWithTriples"},{"location":"ctd/ChemicalToDiseaseDocument/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/ChemicalToDiseaseDocument/#schema-source","title":"Schema Source","text":""},{"location":"ctd/ChemicalToDiseaseDocument/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:ChemicalToDiseaseDocument native drug:ChemicalToDiseaseDocument"},{"location":"ctd/ChemicalToDiseaseDocument/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/ChemicalToDiseaseDocument/#direct","title":"Direct","text":"
name: ChemicalToDiseaseDocument\ndescription: A document that contains chemical to disease relations.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: TextWithTriples\nslot_usage:\n  triples:\n    name: triples\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'A semi-colon separated list of chemical to disease relationships,\n          where the relationship is either INDUCES or TREATS. for example: Lidocaine\n          INDUCES cardiac asystole;  Hydroxychloroquine NOT TREATS COVID-19; Methyldopa\n          INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib\n          TREATS cancer'\n      exclude:\n        tag: exclude\n        value: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa,\n          Headache, Imatinib, cancer\n    domain_of:\n    - TextWithTriples\n    range: ChemicalToDiseaseRelationship\n\n
"},{"location":"ctd/ChemicalToDiseaseDocument/#induced","title":"Induced","text":"
name: ChemicalToDiseaseDocument\ndescription: A document that contains chemical to disease relations.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: TextWithTriples\nslot_usage:\n  triples:\n    name: triples\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'A semi-colon separated list of chemical to disease relationships,\n          where the relationship is either INDUCES or TREATS. for example: Lidocaine\n          INDUCES cardiac asystole;  Hydroxychloroquine NOT TREATS COVID-19; Methyldopa\n          INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib\n          TREATS cancer'\n      exclude:\n        tag: exclude\n        value: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa,\n          Headache, Imatinib, cancer\n    domain_of:\n    - TextWithTriples\n    range: ChemicalToDiseaseRelationship\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: publication\n    owner: ChemicalToDiseaseDocument\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'A semi-colon separated list of chemical to disease relationships,\n          where the relationship is either INDUCES or TREATS. for example: Lidocaine\n          INDUCES cardiac asystole;  Hydroxychloroquine NOT TREATS COVID-19; Methyldopa\n          INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib\n          TREATS cancer'\n      exclude:\n        tag: exclude\n        value: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa,\n          Headache, Imatinib, cancer\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: ChemicalToDiseaseDocument\n    domain_of:\n    - TextWithTriples\n    range: ChemicalToDiseaseRelationship\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ctd/ChemicalToDiseasePredicate/","title":"Class: ChemicalToDiseasePredicate","text":"

A predicate for chemical to disease relationships

URI: drug:ChemicalToDiseasePredicate

erDiagram\nChemicalToDiseasePredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ctd/ChemicalToDiseasePredicate/#inheritance","title":"Inheritance","text":""},{"location":"ctd/ChemicalToDiseasePredicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ctd/ChemicalToDiseasePredicate/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseRelationship predicate range ChemicalToDiseasePredicate"},{"location":"ctd/ChemicalToDiseasePredicate/#comments","title":"Comments","text":""},{"location":"ctd/ChemicalToDiseasePredicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/ChemicalToDiseasePredicate/#schema-source","title":"Schema Source","text":""},{"location":"ctd/ChemicalToDiseasePredicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:ChemicalToDiseasePredicate native drug:ChemicalToDiseasePredicate"},{"location":"ctd/ChemicalToDiseasePredicate/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/ChemicalToDiseasePredicate/#direct","title":"Direct","text":"
name: ChemicalToDiseasePredicate\ndescription: A predicate for chemical to disease relationships\ncomments:\n- for the purposes of evaluation against BC5CDR, any predicate other than INDUCES\n  is ignored.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: RelationshipType\n\n
"},{"location":"ctd/ChemicalToDiseasePredicate/#induced","title":"Induced","text":"
name: ChemicalToDiseasePredicate\ndescription: A predicate for chemical to disease relationships\ncomments:\n- for the purposes of evaluation against BC5CDR, any predicate other than INDUCES\n  is ignored.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: RelationshipType\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalToDiseasePredicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalToDiseasePredicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ctd/ChemicalToDiseaseRelationship/","title":"Class: ChemicalToDiseaseRelationship","text":"

A triple where the subject is a chemical and the object is a disease.

URI: drug:ChemicalToDiseaseRelationship

erDiagram\nChemicalToDiseaseRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nChemicalToDiseasePredicate {\n    string id  \n    string label  \n}\nChemical {\n    string id  \n    string label  \n}\n\nChemicalToDiseaseRelationship ||--|o Chemical : \"subject\"\nChemicalToDiseaseRelationship ||--|o ChemicalToDiseasePredicate : \"predicate\"\nChemicalToDiseaseRelationship ||--|o Disease : \"object\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nChemicalToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ctd/ChemicalToDiseaseRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ctd/ChemicalToDiseaseRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 Chemical The chemical substance, drug, or small molecule Triple predicate 0..1 ChemicalToDiseasePredicate The relationship type, e Triple object 0..1 Disease The disease or condition that is being treated or induced by the chemical Triple qualifier 0..1 String A qualifier for the statements, e Triple subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the chemical, e Triple object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the disease, e Triple"},{"location":"ctd/ChemicalToDiseaseRelationship/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseDocument triples range ChemicalToDiseaseRelationship"},{"location":"ctd/ChemicalToDiseaseRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/ChemicalToDiseaseRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ctd/ChemicalToDiseaseRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:ChemicalToDiseaseRelationship native drug:ChemicalToDiseaseRelationship"},{"location":"ctd/ChemicalToDiseaseRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/ChemicalToDiseaseRelationship/#direct","title":"Direct","text":"
name: ChemicalToDiseaseRelationship\ndescription: A triple where the subject is a chemical and the object is a disease.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: 'The chemical substance, drug, or small molecule.  For example: Lidocaine,\n      Monosodium Glutamate, Imatinib.'\n    domain_of:\n    - Triple\n    range: Chemical\n  object:\n    name: object\n    description: The disease or condition that is being treated or induced by the\n      chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension,\n      Headache.\n    domain_of:\n    - Triple\n    range: Disease\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. INDUCES, TREATS.\n    domain_of:\n    - Triple\n    range: ChemicalToDiseasePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the chemical, e.g. \"high dose\"\n      or \"intravenously administered\"\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease, e.g. \"severe\"\n      or \"with additional complications\"\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ctd/ChemicalToDiseaseRelationship/#induced","title":"Induced","text":"
name: ChemicalToDiseaseRelationship\ndescription: A triple where the subject is a chemical and the object is a disease.\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: 'The chemical substance, drug, or small molecule.  For example: Lidocaine,\n      Monosodium Glutamate, Imatinib.'\n    domain_of:\n    - Triple\n    range: Chemical\n  object:\n    name: object\n    description: The disease or condition that is being treated or induced by the\n      chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension,\n      Headache.\n    domain_of:\n    - Triple\n    range: Disease\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. INDUCES, TREATS.\n    domain_of:\n    - Triple\n    range: ChemicalToDiseasePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the chemical, e.g. \"high dose\"\n      or \"intravenously administered\"\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease, e.g. \"severe\"\n      or \"with additional complications\"\n    domain_of:\n    - Triple\n    range: NamedEntity\nattributes:\n  subject:\n    name: subject\n    description: 'The chemical substance, drug, or small molecule.  For example: Lidocaine,\n      Monosodium Glutamate, Imatinib.'\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: subject\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: Chemical\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. INDUCES, TREATS.\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: predicate\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: ChemicalToDiseasePredicate\n  object:\n    name: object\n    description: The disease or condition that is being treated or induced by the\n      chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension,\n      Headache.\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: Disease\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: qualifier\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the chemical, e.g. \"high dose\"\n      or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: subject_qualifier\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease, e.g. \"severe\"\n      or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object_qualifier\n    owner: ChemicalToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ctd/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: drug:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"ctd/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"ctd/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ctd/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"ctd/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:CompoundExpression native drug:CompoundExpression"},{"location":"ctd/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/ctd\nabstract: true\n\n
"},{"location":"ctd/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/ctd\nabstract: true\n\n
"},{"location":"ctd/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"ctd/Curie/#comments","title":"Comments","text":""},{"location":"ctd/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Curie/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"ctd/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Date/#schema-source","title":"Schema Source","text":""},{"location":"ctd/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"ctd/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"ctd/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"ctd/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Disease/","title":"Class: Disease","text":"

URI: drug:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ctd/Disease/#inheritance","title":"Inheritance","text":""},{"location":"ctd/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ctd/Disease/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseRelationship object range Disease"},{"location":"ctd/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Disease/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ctd/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra"},{"location":"ctd/Disease/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Disease native drug:Disease"},{"location":"ctd/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/Disease/#direct","title":"Direct","text":"
name: Disease\nid_prefixes:\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid,\n      bioportal:meddra\n  prompt.examples:\n    tag: prompt.examples\n    value: cardiac asystole, COVID-19, Headache, cancer\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - MeshDiseaseIdentifier\n    domain_of:\n    - NamedEntity\n    - Publication\n    pattern: ^MESH:[CD][0-9]{6}$\n\n
"},{"location":"ctd/Disease/#induced","title":"Induced","text":"
name: Disease\nid_prefixes:\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid,\n      bioportal:meddra\n  prompt.examples:\n    tag: prompt.examples\n    value: cardiac asystole, COVID-19, Headache, cancer\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - MeshDiseaseIdentifier\n    domain_of:\n    - NamedEntity\n    - Publication\n    pattern: ^MESH:[CD][0-9]{6}$\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    values_from:\n    - MeshDiseaseIdentifier\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n    pattern: ^MESH:[CD][0-9]{6}$\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ctd/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"ctd/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Double/#schema-source","title":"Schema Source","text":""},{"location":"ctd/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: drug:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"ctd/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"ctd/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"ctd/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:ExtractionResult native drug:ExtractionResult"},{"location":"ctd/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ctd/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ctd/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"ctd/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Float/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"ctd/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Integer/#schema-source","title":"Schema Source","text":""},{"location":"ctd/MeshChemicalIdentifier/","title":"Enum: MeshChemicalIdentifier","text":"

URI: MeshChemicalIdentifier

This is a dynamic enum

"},{"location":"ctd/MeshChemicalIdentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/MeshChemicalIdentifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/MeshChemicalIdentifier/#linkml-source","title":"LinkML Source","text":"
name: MeshChemicalIdentifier\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nreachable_from:\n  source_ontology: obo:mesh\n  source_nodes:\n  - MESH:D000602\n  - MESH:D001685\n  - MESH:D002241\n  - MESH:D004364\n  - MESH:D006571\n  - MESH:D007287\n  - MESH:D008055\n  - MESH:D009706\n  - MESH:D009930\n  - MESH:D011083\n  - MESH:D013812\n  - MESH:D019602\n  - MESH:D045424\n  - MESH:D045762\n  - MESH:D046911\n\n
"},{"location":"ctd/MeshDiseaseIdentifier/","title":"Enum: MeshDiseaseIdentifier","text":"

URI: MeshDiseaseIdentifier

This is a dynamic enum

"},{"location":"ctd/MeshDiseaseIdentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/MeshDiseaseIdentifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/MeshDiseaseIdentifier/#linkml-source","title":"LinkML Source","text":"
name: MeshDiseaseIdentifier\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nreachable_from:\n  source_ontology: obo:mesh\n  source_nodes:\n  - MESH:D001423\n  - MESH:D001523\n  - MESH:D002318\n  - MESH:D002943\n  - MESH:D004066\n  - MESH:D004700\n  - MESH:D005128\n  - MESH:D005261\n  - MESH:D006425\n  - MESH:D007154\n  - MESH:D007280\n  - MESH:D009057\n  - MESH:D009140\n  - MESH:D009358\n  - MESH:D009369\n  - MESH:D009422\n  - MESH:D009750\n  - MESH:D009784\n  - MESH:D010038\n  - MESH:D010272\n  - MESH:D012140\n  - MESH:D013568\n  - MESH:D014777\n  - MESH:D014947\n  - MESH:D017437\n  - MESH:D052801\n  - MESH:D064419\n\n
"},{"location":"ctd/NamedEntity/","title":"Class: NamedEntity","text":"

URI: drug:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ctd/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"ctd/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"ctd/NamedEntity/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseRelationship subject_qualifier range NamedEntity ChemicalToDiseaseRelationship object_qualifier range NamedEntity Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"ctd/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"ctd/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:NamedEntity native drug:NamedEntity"},{"location":"ctd/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/ctd\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"ctd/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/ctd\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ctd/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"ctd/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"ctd/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"ctd/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"ctd/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"ctd/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"ctd/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"ctd/Objectidentifier/#comments","title":"Comments","text":""},{"location":"ctd/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Publication/","title":"Class: Publication","text":"

URI: drug:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"ctd/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"ctd/Publication/#usages","title":"Usages","text":"used by used in type used ChemicalToDiseaseDocument publication range Publication TextWithTriples publication range Publication"},{"location":"ctd/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Publication/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Publication native drug:Publication"},{"location":"ctd/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/ctd\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n\n
"},{"location":"ctd/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/ctd\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"ctd/RelationshipType/","title":"Class: RelationshipType","text":"

URI: drug:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ctd/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"ctd/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ctd/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"ctd/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ctd/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"ctd/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:RelationshipType native drug:RelationshipType"},{"location":"ctd/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\n\n
"},{"location":"ctd/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ctd\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ctd/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"ctd/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/String/#schema-source","title":"Schema Source","text":""},{"location":"ctd/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: drug:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ctd/TextWithTriples/#inheritance","title":"Inheritance","text":""},{"location":"ctd/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"ctd/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"ctd/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:TextWithTriples native drug:TextWithTriples"},{"location":"ctd/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ctd/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/ctd\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ctd/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"ctd/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Time/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: drug:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ctd/Triple/#inheritance","title":"Inheritance","text":""},{"location":"ctd/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"ctd/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"ctd/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Triple/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Triple native drug:Triple"},{"location":"ctd/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"ctd/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"ctd/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/ctd\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/ctd\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ctd/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"ctd/Uri/#comments","title":"Comments","text":""},{"location":"ctd/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Uri/#schema-source","title":"Schema Source","text":""},{"location":"ctd/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"ctd/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"ctd/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: drug:abstract

"},{"location":"ctd/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ctd/abstract/#properties","title":"Properties","text":""},{"location":"ctd/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/abstract/#schema-source","title":"Schema Source","text":""},{"location":"ctd/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ctd/combined_text/","title":"Slot: combined_text","text":"

URI: drug:combined_text

"},{"location":"ctd/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ctd/combined_text/#properties","title":"Properties","text":""},{"location":"ctd/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"ctd/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ctd/ctd/","title":"ctd","text":"

A template for Chemical to Disease associations. This template is intended to represent associations between chemicals and diseases, and for evaluating Semantic Llama against BioCreative V Chemical Disease Relation (CDR) Task (BC5CDR).

URI: http://w3id.org/ontogpt/ctd

"},{"location":"ctd/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: drug:extracted_object

"},{"location":"ctd/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/extracted_object/#properties","title":"Properties","text":""},{"location":"ctd/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"ctd/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"ctd/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: drug:full_text

"},{"location":"ctd/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ctd/full_text/#properties","title":"Properties","text":""},{"location":"ctd/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/full_text/#schema-source","title":"Schema Source","text":""},{"location":"ctd/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ctd/id/","title":"Slot: id","text":"

URI: drug:id

"},{"location":"ctd/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Disease yes Chemical yes ChemicalToDiseasePredicate A predicate for chemical to disease relationships no NamedEntity no RelationshipType no Publication no"},{"location":"ctd/id/#properties","title":"Properties","text":""},{"location":"ctd/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"ctd/input_id/","title":"Slot: input_id","text":"

URI: drug:input_id

"},{"location":"ctd/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/input_id/#properties","title":"Properties","text":""},{"location":"ctd/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/input_id/#schema-source","title":"Schema Source","text":""},{"location":"ctd/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ctd/input_text/","title":"Slot: input_text","text":"

URI: drug:input_text

"},{"location":"ctd/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/input_text/#properties","title":"Properties","text":""},{"location":"ctd/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/input_text/#schema-source","title":"Schema Source","text":""},{"location":"ctd/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ctd/input_title/","title":"Slot: input_title","text":"

URI: drug:input_title

"},{"location":"ctd/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/input_title/#properties","title":"Properties","text":""},{"location":"ctd/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/input_title/#schema-source","title":"Schema Source","text":""},{"location":"ctd/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ctd/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"ctd/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Disease no Chemical no ChemicalToDiseasePredicate A predicate for chemical to disease relationships no NamedEntity no RelationshipType no"},{"location":"ctd/label/#properties","title":"Properties","text":""},{"location":"ctd/label/#aliases","title":"Aliases","text":""},{"location":"ctd/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"ctd/label/#schema-source","title":"Schema Source","text":""},{"location":"ctd/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/ctd\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"ctd/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: drug:named_entities

"},{"location":"ctd/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/named_entities/#properties","title":"Properties","text":""},{"location":"ctd/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"ctd/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ctd/object/","title":"Slot: object","text":"

URI: drug:object

"},{"location":"ctd/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/object/#properties","title":"Properties","text":""},{"location":"ctd/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/object/#schema-source","title":"Schema Source","text":""},{"location":"ctd/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ctd/object_id/","title":"Slot: object_id","text":"

URI: drug:object_id

"},{"location":"ctd/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ctd/object_id/#properties","title":"Properties","text":""},{"location":"ctd/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/object_id/#schema-source","title":"Schema Source","text":""},{"location":"ctd/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ctd/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: drug:object_qualifier

"},{"location":"ctd/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/object_qualifier/#properties","title":"Properties","text":""},{"location":"ctd/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ctd/object_text/","title":"Slot: object_text","text":"

URI: drug:object_text

"},{"location":"ctd/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ctd/object_text/#properties","title":"Properties","text":""},{"location":"ctd/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/object_text/#schema-source","title":"Schema Source","text":""},{"location":"ctd/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ctd/predicate/","title":"Slot: predicate","text":"

URI: drug:predicate

"},{"location":"ctd/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/predicate/#properties","title":"Properties","text":""},{"location":"ctd/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/predicate/#schema-source","title":"Schema Source","text":""},{"location":"ctd/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"ctd/prompt/","title":"Slot: prompt","text":"

URI: drug:prompt

"},{"location":"ctd/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/prompt/#properties","title":"Properties","text":""},{"location":"ctd/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/prompt/#schema-source","title":"Schema Source","text":""},{"location":"ctd/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ctd/publication/","title":"Slot: publication","text":"

URI: drug:publication

"},{"location":"ctd/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseDocument A document that contains chemical to disease relations no TextWithTriples no"},{"location":"ctd/publication/#properties","title":"Properties","text":""},{"location":"ctd/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"ctd/publication/#schema-source","title":"Schema Source","text":""},{"location":"ctd/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"ctd/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: drug:qualifier

"},{"location":"ctd/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/qualifier/#properties","title":"Properties","text":""},{"location":"ctd/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"ctd/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: drug:raw_completion_output

"},{"location":"ctd/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ctd/raw_completion_output/#properties","title":"Properties","text":""},{"location":"ctd/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"ctd/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ctd/subject/","title":"Slot: subject","text":"

URI: drug:subject

"},{"location":"ctd/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/subject/#properties","title":"Properties","text":""},{"location":"ctd/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/subject/#schema-source","title":"Schema Source","text":""},{"location":"ctd/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ctd/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: drug:subject_qualifier

"},{"location":"ctd/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseRelationship A triple where the subject is a chemical and the object is a disease yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"ctd/subject_qualifier/#properties","title":"Properties","text":""},{"location":"ctd/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ctd/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ctd/subject_text/","title":"Slot: subject_text","text":"

URI: drug:subject_text

"},{"location":"ctd/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ctd/subject_text/#properties","title":"Properties","text":""},{"location":"ctd/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"ctd/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ctd/title/","title":"Slot: title","text":"

The title of the publication

URI: drug:title

"},{"location":"ctd/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ctd/title/#properties","title":"Properties","text":""},{"location":"ctd/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/title/#schema-source","title":"Schema Source","text":""},{"location":"ctd/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ctd/triples/","title":"Slot: triples","text":"

URI: drug:triples

"},{"location":"ctd/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalToDiseaseDocument A document that contains chemical to disease relations yes TextWithTriples no"},{"location":"ctd/triples/#properties","title":"Properties","text":""},{"location":"ctd/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctd/triples/#schema-source","title":"Schema Source","text":""},{"location":"ctd/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/ctd\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/","title":"Diagnostic Procedure Template","text":"

A template for clinical diagnostic procedures and the phenotypes they may contribute to.

URI: http://w3id.org/ontogpt/diagnostic_procedure

Name: diagnostic_procedure

"},{"location":"diagnostic_procedure/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nDiagnosticProceduretoPhenotypeAssociation {\n    string qualifier  \n}\nDiagnosticProceduretoAttributeAssociation {\n    string qualifier  \n}\nDiagnosticProcedure {\n    string id  \n    string label  \n}\nPhenotype {\n    string id  \n    string label  \n}\nClinicalAttribute {\n    string id  \n    string label  \n}\nQuality {\n    string id  \n    string label  \n}\nProcedureToPhenotypePredicate {\n    string id  \n    string label  \n}\nProcedureToAttributePredicate {\n    string id  \n    string label  \n}\nUnit {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nDiagnosticProceduretoPhenotypeAssociation ||--|o DiagnosticProcedure : \"subject\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o ProcedureToPhenotypePredicate : \"predicate\"\nDiagnosticProceduretoPhenotypeAssociation ||--}o Phenotype : \"object\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o NamedEntity : \"subject_qualifier\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o NamedEntity : \"object_qualifier\"\nDiagnosticProceduretoAttributeAssociation ||--|o DiagnosticProcedure : \"subject\"\nDiagnosticProceduretoAttributeAssociation ||--|o ProcedureToAttributePredicate : \"predicate\"\nDiagnosticProceduretoAttributeAssociation ||--}o ClinicalAttribute : \"object\"\nDiagnosticProceduretoAttributeAssociation ||--|o NamedEntity : \"subject_qualifier\"\nDiagnosticProceduretoAttributeAssociation ||--|o Quality : \"object_qualifier\"\nClinicalAttribute ||--|o Unit : \"unit\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"diagnostic_procedure/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\"). DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\". ExtractionResult A result of extracting knowledge on text NamedEntity None ClinicalAttribute None DiagnosticProcedure None Phenotype None Quality None RelationshipType None ProcedureToAttributePredicate A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\". ProcedureToPhenotypePredicate A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\". Unit None Publication None TextWithTriples None"},{"location":"diagnostic_procedure/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples unit the unit used to measure the attribute"},{"location":"diagnostic_procedure/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"diagnostic_procedure/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"diagnostic_procedure/#subsets","title":"Subsets","text":"Subset Description"},{"location":"diagnostic_procedure/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: diag:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"diagnostic_procedure/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:AnnotatorResult native diag:AnnotatorResult"},{"location":"diagnostic_procedure/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n\n
"},{"location":"diagnostic_procedure/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"diagnostic_procedure/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"diagnostic_procedure/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"diagnostic_procedure/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"diagnostic_procedure/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Any/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native diag:Any"},{"location":"diagnostic_procedure/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nclass_uri: linkml:Any\n\n
"},{"location":"diagnostic_procedure/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nclass_uri: linkml:Any\n\n
"},{"location":"diagnostic_procedure/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"diagnostic_procedure/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ClinicalAttribute/","title":"Class: ClinicalAttribute","text":"

URI: diag:ClinicalAttribute

erDiagram\nClinicalAttribute {\n    string id  \n    string label  \n}\nUnit {\n    string id  \n    string label  \n}\n\nClinicalAttribute ||--|o Unit : \"unit\"\n\n
"},{"location":"diagnostic_procedure/ClinicalAttribute/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/ClinicalAttribute/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance unit 0..1 Unit the unit used to measure the attribute direct id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/ClinicalAttribute/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoAttributeAssociation object range ClinicalAttribute"},{"location":"diagnostic_procedure/ClinicalAttribute/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/ClinicalAttribute/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/ClinicalAttribute/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:oba, sqlite:obo:ncit"},{"location":"diagnostic_procedure/ClinicalAttribute/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ClinicalAttribute/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:ClinicalAttribute native diag:ClinicalAttribute"},{"location":"diagnostic_procedure/ClinicalAttribute/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/ClinicalAttribute/#direct","title":"Direct","text":"
name: ClinicalAttribute\nid_prefixes:\n- OBA\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:oba, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  unit:\n    name: unit\n    description: the unit used to measure the attribute\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: Unit\n\n
"},{"location":"diagnostic_procedure/ClinicalAttribute/#induced","title":"Induced","text":"
name: ClinicalAttribute\nid_prefixes:\n- OBA\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:oba, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  unit:\n    name: unit\n    description: the unit used to measure the attribute\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: unit\n    owner: ClinicalAttribute\n    domain_of:\n    - ClinicalAttribute\n    range: Unit\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ClinicalAttribute\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ClinicalAttribute\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: diag:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"diagnostic_procedure/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"diagnostic_procedure/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:CompoundExpression native diag:CompoundExpression"},{"location":"diagnostic_procedure/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nabstract: true\n\n
"},{"location":"diagnostic_procedure/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nabstract: true\n\n
"},{"location":"diagnostic_procedure/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"diagnostic_procedure/Curie/#comments","title":"Comments","text":""},{"location":"diagnostic_procedure/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Curie/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"diagnostic_procedure/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Date/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"diagnostic_procedure/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"diagnostic_procedure/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"diagnostic_procedure/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/DiagnosticProcedure/","title":"Class: DiagnosticProcedure","text":"

URI: diag:DiagnosticProcedure

erDiagram\nDiagnosticProcedure {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/DiagnosticProcedure/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/DiagnosticProcedure/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/DiagnosticProcedure/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoPhenotypeAssociation subject range DiagnosticProcedure DiagnosticProceduretoAttributeAssociation subject range DiagnosticProcedure"},{"location":"diagnostic_procedure/DiagnosticProcedure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/DiagnosticProcedure/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/DiagnosticProcedure/#annotations","title":"Annotations","text":"property value annotators bioportal:loinc, sqlite:obo:ncit"},{"location":"diagnostic_procedure/DiagnosticProcedure/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/DiagnosticProcedure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:DiagnosticProcedure native diag:DiagnosticProcedure"},{"location":"diagnostic_procedure/DiagnosticProcedure/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/DiagnosticProcedure/#direct","title":"Direct","text":"
name: DiagnosticProcedure\nid_prefixes:\n- LOINC\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:loinc, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\n\n
"},{"location":"diagnostic_procedure/DiagnosticProcedure/#induced","title":"Induced","text":"
name: DiagnosticProcedure\nid_prefixes:\n- LOINC\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:loinc, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DiagnosticProcedure\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: DiagnosticProcedure\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/","title":"Class: DiagnosticProceduretoAttributeAssociation","text":"

A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").

URI: diag:DiagnosticProceduretoAttributeAssociation

erDiagram\nDiagnosticProceduretoAttributeAssociation {\n    string qualifier  \n}\nQuality {\n    string id  \n    string label  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nClinicalAttribute {\n    string id  \n    string label  \n}\nUnit {\n    string id  \n    string label  \n}\nProcedureToAttributePredicate {\n    string id  \n    string label  \n}\nDiagnosticProcedure {\n    string id  \n    string label  \n}\n\nDiagnosticProceduretoAttributeAssociation ||--|o DiagnosticProcedure : \"subject\"\nDiagnosticProceduretoAttributeAssociation ||--|o ProcedureToAttributePredicate : \"predicate\"\nDiagnosticProceduretoAttributeAssociation ||--}o ClinicalAttribute : \"object\"\nDiagnosticProceduretoAttributeAssociation ||--|o NamedEntity : \"subject_qualifier\"\nDiagnosticProceduretoAttributeAssociation ||--|o Quality : \"object_qualifier\"\nClinicalAttribute ||--|o Unit : \"unit\"\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 DiagnosticProcedure A diagnostic procedure yielding a result, which in turn may be interpreted as... Triple predicate 0..1 ProcedureToAttributePredicate The relationship type, e Triple object 0..* ClinicalAttribute Any measurable clinical attribute Triple qualifier 0..1 String A qualifier for the statements, e Triple subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the procedure Triple object_qualifier 0..1 Quality An optional qualifier or modifier for the phenotype Triple"},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:DiagnosticProceduretoAttributeAssociation native diag:DiagnosticProceduretoAttributeAssociation"},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#direct","title":"Direct","text":"
name: DiagnosticProceduretoAttributeAssociation\ndescription: A triple representing a relationship between a diagnostic procedure and\n  a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood\n  pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  object:\n    name: object\n    description: Any measurable clinical attribute.\n    multivalued: true\n    domain_of:\n    - Triple\n    range: ClinicalAttribute\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    domain_of:\n    - Triple\n    range: ProcedureToAttributePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    domain_of:\n    - Triple\n    range: Quality\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoAttributeAssociation/#induced","title":"Induced","text":"
name: DiagnosticProceduretoAttributeAssociation\ndescription: A triple representing a relationship between a diagnostic procedure and\n  a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood\n  pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  object:\n    name: object\n    description: Any measurable clinical attribute.\n    multivalued: true\n    domain_of:\n    - Triple\n    range: ClinicalAttribute\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    domain_of:\n    - Triple\n    range: ProcedureToAttributePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    domain_of:\n    - Triple\n    range: Quality\nattributes:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: predicate\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: ProcedureToAttributePredicate\n  object:\n    name: object\n    description: Any measurable clinical attribute.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    alias: object\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: ClinicalAttribute\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: qualifier\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject_qualifier\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object_qualifier\n    owner: DiagnosticProceduretoAttributeAssociation\n    domain_of:\n    - Triple\n    range: Quality\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/","title":"Class: DiagnosticProceduretoPhenotypeAssociation","text":"

A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\".

URI: diag:DiagnosticProceduretoPhenotypeAssociation

erDiagram\nDiagnosticProceduretoPhenotypeAssociation {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nPhenotype {\n    string id  \n    string label  \n}\nProcedureToPhenotypePredicate {\n    string id  \n    string label  \n}\nDiagnosticProcedure {\n    string id  \n    string label  \n}\n\nDiagnosticProceduretoPhenotypeAssociation ||--|o DiagnosticProcedure : \"subject\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o ProcedureToPhenotypePredicate : \"predicate\"\nDiagnosticProceduretoPhenotypeAssociation ||--}o Phenotype : \"object\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o NamedEntity : \"subject_qualifier\"\nDiagnosticProceduretoPhenotypeAssociation ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 DiagnosticProcedure A diagnostic procedure yielding a result, which in turn may be interpreted as... Triple predicate 0..1 ProcedureToPhenotypePredicate The relationship type, e Triple object 0..* Phenotype The observable physical or biochemical characteristics of a patient Triple qualifier 0..1 String A qualifier for the statements, e Triple subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the procedure Triple object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the phenotype Triple"},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:DiagnosticProceduretoPhenotypeAssociation native diag:DiagnosticProceduretoPhenotypeAssociation"},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#direct","title":"Direct","text":"
name: DiagnosticProceduretoPhenotypeAssociation\ndescription: A triple representing a relationship between a diagnostic procedure and\n  an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high\n  blood pressure\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  object:\n    name: object\n    description: The observable physical or biochemical characteristics of a patient.\n      Not equivalent to a disease state, but may contribute to a diagnosis.\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Phenotype\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    domain_of:\n    - Triple\n    range: ProcedureToPhenotypePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation/#induced","title":"Induced","text":"
name: DiagnosticProceduretoPhenotypeAssociation\ndescription: A triple representing a relationship between a diagnostic procedure and\n  an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high\n  blood pressure\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  object:\n    name: object\n    description: The observable physical or biochemical characteristics of a patient.\n      Not equivalent to a disease state, but may contribute to a diagnosis.\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Phenotype\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    domain_of:\n    - Triple\n    range: ProcedureToPhenotypePredicate\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    domain_of:\n    - Triple\n    range: NamedEntity\nattributes:\n  subject:\n    name: subject\n    description: A diagnostic procedure yielding a result, which in turn may be interpreted\n      as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure\n      measurement\", \"oxygen saturation measurement\", etc. In practice, procedures\n      may be named based on what they measure, with the \"measurement\" part left implicit.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: DiagnosticProcedure\n  predicate:\n    name: predicate\n    description: The relationship type, e.g. RELATED_TO\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: predicate\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: ProcedureToPhenotypePredicate\n  object:\n    name: object\n    description: The observable physical or biochemical characteristics of a patient.\n      Not equivalent to a disease state, but may contribute to a diagnosis.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    alias: object\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: Phenotype\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: qualifier\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the procedure.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject_qualifier\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the phenotype.\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object_qualifier\n    owner: DiagnosticProceduretoPhenotypeAssociation\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"diagnostic_procedure/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Double/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: diag:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"diagnostic_procedure/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"diagnostic_procedure/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:ExtractionResult native diag:ExtractionResult"},{"location":"diagnostic_procedure/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"diagnostic_procedure/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Float/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"diagnostic_procedure/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Integer/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/NamedEntity/","title":"Class: NamedEntity","text":"

URI: diag:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"diagnostic_procedure/NamedEntity/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoPhenotypeAssociation subject_qualifier range NamedEntity DiagnosticProceduretoPhenotypeAssociation object_qualifier range NamedEntity DiagnosticProceduretoAttributeAssociation subject_qualifier range NamedEntity Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"diagnostic_procedure/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:NamedEntity native diag:NamedEntity"},{"location":"diagnostic_procedure/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"diagnostic_procedure/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"diagnostic_procedure/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"diagnostic_procedure/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"diagnostic_procedure/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"diagnostic_procedure/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"diagnostic_procedure/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"diagnostic_procedure/Objectidentifier/#comments","title":"Comments","text":""},{"location":"diagnostic_procedure/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Phenotype/","title":"Class: Phenotype","text":"

URI: diag:Phenotype

erDiagram\nPhenotype {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/Phenotype/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/Phenotype/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/Phenotype/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoPhenotypeAssociation object range Phenotype"},{"location":"diagnostic_procedure/Phenotype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Phenotype/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/Phenotype/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp"},{"location":"diagnostic_procedure/Phenotype/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Phenotype/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:Phenotype native diag:Phenotype"},{"location":"diagnostic_procedure/Phenotype/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Phenotype/#direct","title":"Direct","text":"
name: Phenotype\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Phenotype/#induced","title":"Induced","text":"
name: Phenotype\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Phenotype\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Phenotype\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/","title":"Class: ProcedureToAttributePredicate","text":"

A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\".

URI: diag:ProcedureToAttributePredicate

erDiagram\nProcedureToAttributePredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoAttributeAssociation predicate range ProcedureToAttributePredicate"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:ProcedureToAttributePredicate native diag:ProcedureToAttributePredicate"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#direct","title":"Direct","text":"
name: ProcedureToAttributePredicate\ndescription: A predicate for procedure to attribute relationships, defining \"this\n  procedure is a measurement of this attribute\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: RelationshipType\n\n
"},{"location":"diagnostic_procedure/ProcedureToAttributePredicate/#induced","title":"Induced","text":"
name: ProcedureToAttributePredicate\ndescription: A predicate for procedure to attribute relationships, defining \"this\n  procedure is a measurement of this attribute\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: RelationshipType\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ProcedureToAttributePredicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ProcedureToAttributePredicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/","title":"Class: ProcedureToPhenotypePredicate","text":"

A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\".

URI: diag:ProcedureToPhenotypePredicate

erDiagram\nProcedureToPhenotypePredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoPhenotypeAssociation predicate range ProcedureToPhenotypePredicate"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:ProcedureToPhenotypePredicate native diag:ProcedureToPhenotypePredicate"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#direct","title":"Direct","text":"
name: ProcedureToPhenotypePredicate\ndescription: A predicate for procedure to phenotype relationships, defining \"this\n  procedure is intended to provide support for/against this phenotype\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: RelationshipType\n\n
"},{"location":"diagnostic_procedure/ProcedureToPhenotypePredicate/#induced","title":"Induced","text":"
name: ProcedureToPhenotypePredicate\ndescription: A predicate for procedure to phenotype relationships, defining \"this\n  procedure is intended to provide support for/against this phenotype\".\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: RelationshipType\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ProcedureToPhenotypePredicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ProcedureToPhenotypePredicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/Publication/","title":"Class: Publication","text":"

URI: diag:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"diagnostic_procedure/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"diagnostic_procedure/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Publication/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:Publication native diag:Publication"},{"location":"diagnostic_procedure/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n\n
"},{"location":"diagnostic_procedure/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"diagnostic_procedure/Quality/","title":"Class: Quality","text":"

URI: diag:Quality

erDiagram\nQuality {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/Quality/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/Quality/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/Quality/#usages","title":"Usages","text":"used by used in type used DiagnosticProceduretoAttributeAssociation object_qualifier range Quality"},{"location":"diagnostic_procedure/Quality/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Quality/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/Quality/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:pato"},{"location":"diagnostic_procedure/Quality/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Quality/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:Quality native diag:Quality"},{"location":"diagnostic_procedure/Quality/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Quality/#direct","title":"Direct","text":"
name: Quality\nid_prefixes:\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:pato\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Quality/#induced","title":"Induced","text":"
name: Quality\nid_prefixes:\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:pato\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Quality\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Quality\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/RelationshipType/","title":"Class: RelationshipType","text":"

URI: diag:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"diagnostic_procedure/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:RelationshipType native diag:RelationshipType"},{"location":"diagnostic_procedure/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\n\n
"},{"location":"diagnostic_procedure/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"diagnostic_procedure/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/String/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: diag:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"diagnostic_procedure/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"diagnostic_procedure/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:TextWithTriples native diag:TextWithTriples"},{"location":"diagnostic_procedure/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"diagnostic_procedure/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Time/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: diag:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"diagnostic_procedure/Triple/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"diagnostic_procedure/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"diagnostic_procedure/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Triple/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:Triple native diag:Triple"},{"location":"diagnostic_procedure/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Unit/","title":"Class: Unit","text":"

URI: diag:Unit

erDiagram\nUnit {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"diagnostic_procedure/Unit/#inheritance","title":"Inheritance","text":""},{"location":"diagnostic_procedure/Unit/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"diagnostic_procedure/Unit/#usages","title":"Usages","text":"used by used in type used ClinicalAttribute unit range Unit"},{"location":"diagnostic_procedure/Unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Unit/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"diagnostic_procedure/Unit/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uo"},{"location":"diagnostic_procedure/Unit/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Unit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self diag:Unit native diag:Unit"},{"location":"diagnostic_procedure/Unit/#linkml-source","title":"LinkML Source","text":""},{"location":"diagnostic_procedure/Unit/#direct","title":"Direct","text":"
name: Unit\nid_prefixes:\n- UO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\n\n
"},{"location":"diagnostic_procedure/Unit/#induced","title":"Induced","text":"
name: Unit\nid_prefixes:\n- UO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/diagnostic_procedure\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"diagnostic_procedure/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"diagnostic_procedure/Uri/#comments","title":"Comments","text":""},{"location":"diagnostic_procedure/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Uri/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"diagnostic_procedure/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: diag:abstract

"},{"location":"diagnostic_procedure/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"diagnostic_procedure/abstract/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/abstract/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"diagnostic_procedure/combined_text/","title":"Slot: combined_text","text":"

URI: diag:combined_text

"},{"location":"diagnostic_procedure/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"diagnostic_procedure/combined_text/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"diagnostic_procedure/diagnostic_procedure/","title":"diagnostic_procedure","text":"

A template for clinical diagnostic procedures and the phenotypes they may contribute to.

URI: http://w3id.org/ontogpt/diagnostic_procedure

"},{"location":"diagnostic_procedure/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: diag:extracted_object

"},{"location":"diagnostic_procedure/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/extracted_object/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"diagnostic_procedure/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: diag:full_text

"},{"location":"diagnostic_procedure/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"diagnostic_procedure/full_text/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/full_text/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"diagnostic_procedure/id/","title":"Slot: id","text":"

URI: diag:id

"},{"location":"diagnostic_procedure/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProcedure no Phenotype no ClinicalAttribute no Quality no ProcedureToPhenotypePredicate A predicate for procedure to phenotype relationships, defining \"this procedur... no ProcedureToAttributePredicate A predicate for procedure to attribute relationships, defining \"this procedur... no Unit no NamedEntity no RelationshipType no Publication no"},{"location":"diagnostic_procedure/id/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"diagnostic_procedure/input_id/","title":"Slot: input_id","text":"

URI: diag:input_id

"},{"location":"diagnostic_procedure/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/input_id/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/input_id/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/input_text/","title":"Slot: input_text","text":"

URI: diag:input_text

"},{"location":"diagnostic_procedure/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/input_text/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/input_text/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/input_title/","title":"Slot: input_title","text":"

URI: diag:input_title

"},{"location":"diagnostic_procedure/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/input_title/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/input_title/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"diagnostic_procedure/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProcedure no Phenotype no ClinicalAttribute no Quality no ProcedureToPhenotypePredicate A predicate for procedure to phenotype relationships, defining \"this procedur... no ProcedureToAttributePredicate A predicate for procedure to attribute relationships, defining \"this procedur... no Unit no NamedEntity no RelationshipType no"},{"location":"diagnostic_procedure/label/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/label/#aliases","title":"Aliases","text":""},{"location":"diagnostic_procedure/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"diagnostic_procedure/label/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"diagnostic_procedure/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: diag:named_entities

"},{"location":"diagnostic_procedure/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/named_entities/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/object/","title":"Slot: object","text":"

URI: diag:object

"},{"location":"diagnostic_procedure/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... yes DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/object/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/object/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"diagnostic_procedure/object_id/","title":"Slot: object_id","text":"

URI: diag:object_id

"},{"location":"diagnostic_procedure/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"diagnostic_procedure/object_id/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/object_id/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: diag:object_qualifier

"},{"location":"diagnostic_procedure/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... yes DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/object_qualifier/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"diagnostic_procedure/object_text/","title":"Slot: object_text","text":"

URI: diag:object_text

"},{"location":"diagnostic_procedure/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"diagnostic_procedure/object_text/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/object_text/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/predicate/","title":"Slot: predicate","text":"

URI: diag:predicate

"},{"location":"diagnostic_procedure/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... yes DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/predicate/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/predicate/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"diagnostic_procedure/prompt/","title":"Slot: prompt","text":"

URI: diag:prompt

"},{"location":"diagnostic_procedure/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/prompt/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/prompt/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/publication/","title":"Slot: publication","text":"

URI: diag:publication

"},{"location":"diagnostic_procedure/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"diagnostic_procedure/publication/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"diagnostic_procedure/publication/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"diagnostic_procedure/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: diag:qualifier

"},{"location":"diagnostic_procedure/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... no DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... no Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/qualifier/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"diagnostic_procedure/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: diag:raw_completion_output

"},{"location":"diagnostic_procedure/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"diagnostic_procedure/raw_completion_output/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/subject/","title":"Slot: subject","text":"

URI: diag:subject

"},{"location":"diagnostic_procedure/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... yes DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/subject/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/subject/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"diagnostic_procedure/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: diag:subject_qualifier

"},{"location":"diagnostic_procedure/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an as... yes DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a mea... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"diagnostic_procedure/subject_qualifier/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"diagnostic_procedure/subject_text/","title":"Slot: subject_text","text":"

URI: diag:subject_text

"},{"location":"diagnostic_procedure/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"diagnostic_procedure/subject_text/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"diagnostic_procedure/title/","title":"Slot: title","text":"

The title of the publication

URI: diag:title

"},{"location":"diagnostic_procedure/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"diagnostic_procedure/title/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/title/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"diagnostic_procedure/triples/","title":"Slot: triples","text":"

URI: diag:triples

"},{"location":"diagnostic_procedure/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"diagnostic_procedure/triples/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/triples/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"diagnostic_procedure/unit/","title":"Slot: unit","text":"

the unit used to measure the attribute

URI: diag:unit

"},{"location":"diagnostic_procedure/unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ClinicalAttribute no"},{"location":"diagnostic_procedure/unit/#properties","title":"Properties","text":""},{"location":"diagnostic_procedure/unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diagnostic_procedure/unit/#schema-source","title":"Schema Source","text":""},{"location":"diagnostic_procedure/unit/#linkml-source","title":"LinkML Source","text":"
name: unit\ndescription: the unit used to measure the attribute\nfrom_schema: http://w3id.org/ontogpt/diagnostic_procedure\nrank: 1000\nalias: unit\nowner: ClinicalAttribute\ndomain_of:\n- ClinicalAttribute\nrange: Unit\n\n
"},{"location":"drug/","title":"Drug Template","text":"

A template for Drugs and drug mechanism

URI: http://w3id.org/ontogpt/drug

Name: drug

"},{"location":"drug/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nDrugMechanism {\n    stringList references  \n    string source_text  \n}\nMechanismLink {\n\n}\nMechanismElement {\n    string id  \n    string label  \n}\nPredicate {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nDrugMechanism ||--|o Disease : \"disease\"\nDrugMechanism ||--|o Drug : \"drug\"\nDrugMechanism ||--}o MechanismLink : \"mechanism_links\"\nMechanismLink ||--|o MechanismElement : \"subject\"\nMechanismLink ||--|o Predicate : \"predicate\"\nMechanismLink ||--|o MechanismElement : \"object\"\n\n
"},{"location":"drug/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None MechanismLink None Triple Abstract parent for Relation Extraction tasks DrugMechanism None ExtractionResult A result of extracting knowledge on text NamedEntity None Disease None Drug None MechanismElement None Predicate None RelationshipType None Publication None TextWithTriples None"},{"location":"drug/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text disease the name of the disease that is treated drug the name of the drug that treats the disease extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing mechanism_links semicolon-separated list of links, where each link is a triple connecting two... named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output references source_text subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"drug/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"drug/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"drug/#subsets","title":"Subsets","text":"Subset Description"},{"location":"drug/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: drug:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"drug/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"drug/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"drug/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:AnnotatorResult native drug:AnnotatorResult"},{"location":"drug/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n\n
"},{"location":"drug/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"drug/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"drug/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"drug/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"drug/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Any/#schema-source","title":"Schema Source","text":""},{"location":"drug/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native drug:Any"},{"location":"drug/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/drug\nclass_uri: linkml:Any\n\n
"},{"location":"drug/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/drug\nclass_uri: linkml:Any\n\n
"},{"location":"drug/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"drug/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"drug/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: drug:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"drug/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"drug/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"drug/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"drug/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:CompoundExpression native drug:CompoundExpression"},{"location":"drug/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/drug\nabstract: true\n\n
"},{"location":"drug/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/drug\nabstract: true\n\n
"},{"location":"drug/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"drug/Curie/#comments","title":"Comments","text":""},{"location":"drug/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Curie/#schema-source","title":"Schema Source","text":""},{"location":"drug/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"drug/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Date/#schema-source","title":"Schema Source","text":""},{"location":"drug/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"drug/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"drug/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"drug/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"drug/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"drug/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"drug/Disease/","title":"Class: Disease","text":"

URI: drug:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/Disease/#inheritance","title":"Inheritance","text":""},{"location":"drug/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"drug/Disease/#usages","title":"Usages","text":"used by used in type used DrugMechanism disease range Disease"},{"location":"drug/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mesh, sqlite:obo:mondo"},{"location":"drug/Disease/#schema-source","title":"Schema Source","text":""},{"location":"drug/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Disease native drug:Disease"},{"location":"drug/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Disease/#direct","title":"Direct","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mesh, sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\n\n
"},{"location":"drug/Disease/#induced","title":"Induced","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mesh, sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"drug/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Double/#schema-source","title":"Schema Source","text":""},{"location":"drug/Drug/","title":"Class: Drug","text":"

URI: drug:Drug

erDiagram\nDrug {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/Drug/#inheritance","title":"Inheritance","text":""},{"location":"drug/Drug/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"drug/Drug/#usages","title":"Usages","text":"used by used in type used DrugMechanism drug range Drug"},{"location":"drug/Drug/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Drug/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh"},{"location":"drug/Drug/#schema-source","title":"Schema Source","text":""},{"location":"drug/Drug/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Drug native drug:Drug"},{"location":"drug/Drug/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Drug/#direct","title":"Direct","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\n\n
"},{"location":"drug/Drug/#induced","title":"Induced","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/DrugMechanism/","title":"Class: DrugMechanism","text":"

URI: drug:DrugMechanism

erDiagram\nDrugMechanism {\n    stringList references  \n    string source_text  \n}\nMechanismLink {\n\n}\nMechanismElement {\n    string id  \n    string label  \n}\nPredicate {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nDrugMechanism ||--|o Disease : \"disease\"\nDrugMechanism ||--|o Drug : \"drug\"\nDrugMechanism ||--}o MechanismLink : \"mechanism_links\"\nMechanismLink ||--|o MechanismElement : \"subject\"\nMechanismLink ||--|o Predicate : \"predicate\"\nMechanismLink ||--|o MechanismElement : \"object\"\n\n
"},{"location":"drug/DrugMechanism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance disease 0..1 Disease the name of the disease that is treated direct drug 0..1 Drug the name of the drug that treats the disease direct mechanism_links 0..* MechanismLink semicolon-separated list of links, where each link is a triple connecting two... direct references 0..* String direct source_text 0..1 String direct"},{"location":"drug/DrugMechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/DrugMechanism/#schema-source","title":"Schema Source","text":""},{"location":"drug/DrugMechanism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:DrugMechanism native drug:DrugMechanism"},{"location":"drug/DrugMechanism/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/DrugMechanism/#direct","title":"Direct","text":"
name: DrugMechanism\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  disease:\n    name: disease\n    description: the name of the disease that is treated\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: Disease\n  drug:\n    name: drug\n    description: the name of the drug that treats the disease\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: Drug\n  mechanism_links:\n    name: mechanism_links\n    description: semicolon-separated list of links, where each link is a triple connecting\n      two entities via a relationship type\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    range: MechanismLink\n  references:\n    name: references\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    range: string\n  source_text:\n    name: source_text\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: string\ntree_root: true\n\n
"},{"location":"drug/DrugMechanism/#induced","title":"Induced","text":"
name: DrugMechanism\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  disease:\n    name: disease\n    description: the name of the disease that is treated\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: disease\n    owner: DrugMechanism\n    domain_of:\n    - DrugMechanism\n    range: Disease\n  drug:\n    name: drug\n    description: the name of the drug that treats the disease\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: drug\n    owner: DrugMechanism\n    domain_of:\n    - DrugMechanism\n    range: Drug\n  mechanism_links:\n    name: mechanism_links\n    description: semicolon-separated list of links, where each link is a triple connecting\n      two entities via a relationship type\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    alias: mechanism_links\n    owner: DrugMechanism\n    domain_of:\n    - DrugMechanism\n    range: MechanismLink\n  references:\n    name: references\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    alias: references\n    owner: DrugMechanism\n    domain_of:\n    - DrugMechanism\n    range: string\n  source_text:\n    name: source_text\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: source_text\n    owner: DrugMechanism\n    domain_of:\n    - DrugMechanism\n    range: string\ntree_root: true\n\n
"},{"location":"drug/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: drug:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"drug/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"drug/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"drug/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:ExtractionResult native drug:ExtractionResult"},{"location":"drug/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"drug/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"drug/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"drug/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Float/#schema-source","title":"Schema Source","text":""},{"location":"drug/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"drug/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Integer/#schema-source","title":"Schema Source","text":""},{"location":"drug/MechanismElement/","title":"Class: MechanismElement","text":"

URI: drug:MechanismElement

erDiagram\nMechanismElement {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/MechanismElement/#inheritance","title":"Inheritance","text":""},{"location":"drug/MechanismElement/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"drug/MechanismElement/#usages","title":"Usages","text":"used by used in type used MechanismLink subject range MechanismElement MechanismLink object range MechanismElement"},{"location":"drug/MechanismElement/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/MechanismElement/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"drug/MechanismElement/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon, sqlite:obo:cl"},{"location":"drug/MechanismElement/#schema-source","title":"Schema Source","text":""},{"location":"drug/MechanismElement/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:MechanismElement native drug:MechanismElement"},{"location":"drug/MechanismElement/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/MechanismElement/#direct","title":"Direct","text":"
name: MechanismElement\nid_prefixes:\n- HGNC\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon,\n      sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\n\n
"},{"location":"drug/MechanismElement/#induced","title":"Induced","text":"
name: MechanismElement\nid_prefixes:\n- HGNC\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon,\n      sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MechanismElement\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: MechanismElement\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/MechanismLink/","title":"Class: MechanismLink","text":"

URI: drug:MechanismLink

erDiagram\nMechanismLink {\n\n}\nMechanismElement {\n    string id  \n    string label  \n}\nPredicate {\n    string id  \n    string label  \n}\n\nMechanismLink ||--|o MechanismElement : \"subject\"\nMechanismLink ||--|o Predicate : \"predicate\"\nMechanismLink ||--|o MechanismElement : \"object\"\n\n
"},{"location":"drug/MechanismLink/#inheritance","title":"Inheritance","text":""},{"location":"drug/MechanismLink/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 MechanismElement direct predicate 0..1 Predicate direct object 0..1 MechanismElement direct"},{"location":"drug/MechanismLink/#usages","title":"Usages","text":"used by used in type used DrugMechanism mechanism_links range MechanismLink"},{"location":"drug/MechanismLink/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/MechanismLink/#schema-source","title":"Schema Source","text":""},{"location":"drug/MechanismLink/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:MechanismLink native drug:MechanismLink"},{"location":"drug/MechanismLink/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/MechanismLink/#direct","title":"Direct","text":"
name: MechanismLink\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: MechanismElement\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: Predicate\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: MechanismElement\n\n
"},{"location":"drug/MechanismLink/#induced","title":"Induced","text":"
name: MechanismLink\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: subject\n    owner: MechanismLink\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: MechanismElement\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: predicate\n    owner: MechanismLink\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: Predicate\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: object\n    owner: MechanismLink\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: MechanismElement\n\n
"},{"location":"drug/NamedEntity/","title":"Class: NamedEntity","text":"

URI: drug:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"drug/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"drug/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"drug/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"drug/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:NamedEntity native drug:NamedEntity"},{"location":"drug/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/drug\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"drug/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/drug\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"drug/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"drug/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"drug/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"drug/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"drug/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"drug/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"drug/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"drug/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"drug/Objectidentifier/#comments","title":"Comments","text":""},{"location":"drug/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"drug/Predicate/","title":"Class: Predicate","text":"

URI: drug:Predicate

erDiagram\nPredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/Predicate/#inheritance","title":"Inheritance","text":""},{"location":"drug/Predicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"drug/Predicate/#usages","title":"Usages","text":"used by used in type used MechanismLink predicate range Predicate"},{"location":"drug/Predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Predicate/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:biolink, sqlite:obo:ro"},{"location":"drug/Predicate/#schema-source","title":"Schema Source","text":""},{"location":"drug/Predicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Predicate native drug:Predicate"},{"location":"drug/Predicate/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Predicate/#direct","title":"Direct","text":"
name: Predicate\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:biolink, sqlite:obo:ro\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\n\n
"},{"location":"drug/Predicate/#induced","title":"Induced","text":"
name: Predicate\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:biolink, sqlite:obo:ro\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Predicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Predicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/Publication/","title":"Class: Publication","text":"

URI: drug:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"drug/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"drug/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"drug/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Publication/#schema-source","title":"Schema Source","text":""},{"location":"drug/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Publication native drug:Publication"},{"location":"drug/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/drug\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n\n
"},{"location":"drug/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/drug\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"drug/RelationshipType/","title":"Class: RelationshipType","text":"

URI: drug:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"drug/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"drug/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"drug/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"drug/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"drug/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"drug/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:RelationshipType native drug:RelationshipType"},{"location":"drug/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\n\n
"},{"location":"drug/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/drug\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"drug/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"drug/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/String/#schema-source","title":"Schema Source","text":""},{"location":"drug/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: drug:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"drug/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"drug/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"drug/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:TextWithTriples native drug:TextWithTriples"},{"location":"drug/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"drug/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/drug\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"drug/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"drug/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Time/#schema-source","title":"Schema Source","text":""},{"location":"drug/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: drug:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"drug/Triple/#inheritance","title":"Inheritance","text":""},{"location":"drug/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"drug/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"drug/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Triple/#schema-source","title":"Schema Source","text":""},{"location":"drug/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self drug:Triple native drug:Triple"},{"location":"drug/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"drug/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/drug\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/drug\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/drug\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"drug/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/drug\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/drug\n    alias: subject\n    owner: Triple\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/drug\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/drug\n    alias: object\n    owner: Triple\n    domain_of:\n    - MechanismLink\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/drug\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"drug/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"drug/Uri/#comments","title":"Comments","text":""},{"location":"drug/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Uri/#schema-source","title":"Schema Source","text":""},{"location":"drug/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"drug/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"drug/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: drug:abstract

"},{"location":"drug/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"drug/abstract/#properties","title":"Properties","text":""},{"location":"drug/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/abstract/#schema-source","title":"Schema Source","text":""},{"location":"drug/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"drug/combined_text/","title":"Slot: combined_text","text":"

URI: drug:combined_text

"},{"location":"drug/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"drug/combined_text/#properties","title":"Properties","text":""},{"location":"drug/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"drug/disease/","title":"Slot: disease","text":"

the name of the disease that is treated

URI: drug:disease

"},{"location":"drug/disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DrugMechanism no"},{"location":"drug/disease/#properties","title":"Properties","text":""},{"location":"drug/disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/disease/#schema-source","title":"Schema Source","text":""},{"location":"drug/disease/#linkml-source","title":"LinkML Source","text":"
name: disease\ndescription: the name of the disease that is treated\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: disease\nowner: DrugMechanism\ndomain_of:\n- DrugMechanism\nrange: Disease\n\n
"},{"location":"drug/drug/","title":"Slot: drug","text":"

the name of the drug that treats the disease

URI: drug:drug

"},{"location":"drug/drug/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DrugMechanism no"},{"location":"drug/drug/#properties","title":"Properties","text":""},{"location":"drug/drug/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/drug/#schema-source","title":"Schema Source","text":""},{"location":"drug/drug/#linkml-source","title":"LinkML Source","text":"
name: drug\ndescription: the name of the drug that treats the disease\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: drug\nowner: DrugMechanism\ndomain_of:\n- DrugMechanism\nrange: Drug\n\n
"},{"location":"drug/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: drug:extracted_object

"},{"location":"drug/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/extracted_object/#properties","title":"Properties","text":""},{"location":"drug/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"drug/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"drug/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: drug:full_text

"},{"location":"drug/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"drug/full_text/#properties","title":"Properties","text":""},{"location":"drug/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/full_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"drug/id/","title":"Slot: id","text":"

URI: drug:id

"},{"location":"drug/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MechanismElement no Disease no Drug no Predicate no NamedEntity no RelationshipType no Publication no"},{"location":"drug/id/#properties","title":"Properties","text":""},{"location":"drug/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"drug/input_id/","title":"Slot: input_id","text":"

URI: drug:input_id

"},{"location":"drug/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/input_id/#properties","title":"Properties","text":""},{"location":"drug/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/input_id/#schema-source","title":"Schema Source","text":""},{"location":"drug/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"drug/input_text/","title":"Slot: input_text","text":"

URI: drug:input_text

"},{"location":"drug/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/input_text/#properties","title":"Properties","text":""},{"location":"drug/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/input_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"drug/input_title/","title":"Slot: input_title","text":"

URI: drug:input_title

"},{"location":"drug/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/input_title/#properties","title":"Properties","text":""},{"location":"drug/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/input_title/#schema-source","title":"Schema Source","text":""},{"location":"drug/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"drug/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"drug/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MechanismElement no Disease no Drug no Predicate no NamedEntity no RelationshipType no"},{"location":"drug/label/#properties","title":"Properties","text":""},{"location":"drug/label/#aliases","title":"Aliases","text":""},{"location":"drug/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"drug/label/#schema-source","title":"Schema Source","text":""},{"location":"drug/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/drug\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"drug/mechanism_links/","title":"Slot: mechanism_links","text":"

semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type

URI: drug:mechanism_links

"},{"location":"drug/mechanism_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DrugMechanism no"},{"location":"drug/mechanism_links/#properties","title":"Properties","text":""},{"location":"drug/mechanism_links/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/mechanism_links/#schema-source","title":"Schema Source","text":""},{"location":"drug/mechanism_links/#linkml-source","title":"LinkML Source","text":"
name: mechanism_links\ndescription: semicolon-separated list of links, where each link is a triple connecting\n  two entities via a relationship type\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nmultivalued: true\nalias: mechanism_links\nowner: DrugMechanism\ndomain_of:\n- DrugMechanism\nrange: MechanismLink\n\n
"},{"location":"drug/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: drug:named_entities

"},{"location":"drug/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/named_entities/#properties","title":"Properties","text":""},{"location":"drug/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"drug/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"drug/object/","title":"Slot: object","text":"

URI: drug:object

"},{"location":"drug/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MechanismLink no Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/object/#properties","title":"Properties","text":""},{"location":"drug/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/object/#linkml-source","title":"LinkML Source","text":"
name: object\nalias: object\ndomain_of:\n- MechanismLink\n- Triple\nrange: string\n\n
"},{"location":"drug/object_id/","title":"Slot: object_id","text":"

URI: drug:object_id

"},{"location":"drug/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"drug/object_id/#properties","title":"Properties","text":""},{"location":"drug/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/object_id/#schema-source","title":"Schema Source","text":""},{"location":"drug/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"drug/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: drug:object_qualifier

"},{"location":"drug/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/object_qualifier/#properties","title":"Properties","text":""},{"location":"drug/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"drug/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"drug/object_text/","title":"Slot: object_text","text":"

URI: drug:object_text

"},{"location":"drug/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"drug/object_text/#properties","title":"Properties","text":""},{"location":"drug/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/object_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"drug/predicate/","title":"Slot: predicate","text":"

URI: drug:predicate

"},{"location":"drug/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MechanismLink no Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/predicate/#properties","title":"Properties","text":""},{"location":"drug/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nalias: predicate\ndomain_of:\n- MechanismLink\n- Triple\nrange: string\n\n
"},{"location":"drug/prompt/","title":"Slot: prompt","text":"

URI: drug:prompt

"},{"location":"drug/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/prompt/#properties","title":"Properties","text":""},{"location":"drug/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/prompt/#schema-source","title":"Schema Source","text":""},{"location":"drug/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"drug/publication/","title":"Slot: publication","text":"

URI: drug:publication

"},{"location":"drug/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"drug/publication/#properties","title":"Properties","text":""},{"location":"drug/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"drug/publication/#schema-source","title":"Schema Source","text":""},{"location":"drug/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"drug/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: drug:qualifier

"},{"location":"drug/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/qualifier/#properties","title":"Properties","text":""},{"location":"drug/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"drug/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"drug/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: drug:raw_completion_output

"},{"location":"drug/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"drug/raw_completion_output/#properties","title":"Properties","text":""},{"location":"drug/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"drug/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"drug/references/","title":"Slot: references","text":"

URI: drug:references

"},{"location":"drug/references/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DrugMechanism no"},{"location":"drug/references/#properties","title":"Properties","text":""},{"location":"drug/references/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/references/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"drug/references/#schema-source","title":"Schema Source","text":""},{"location":"drug/references/#linkml-source","title":"LinkML Source","text":"
name: references\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nmultivalued: true\nalias: references\nowner: DrugMechanism\ndomain_of:\n- DrugMechanism\nrange: string\n\n
"},{"location":"drug/source_text/","title":"Slot: source_text","text":"

URI: drug:source_text

"},{"location":"drug/source_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DrugMechanism no"},{"location":"drug/source_text/#properties","title":"Properties","text":""},{"location":"drug/source_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/source_text/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"drug/source_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/source_text/#linkml-source","title":"LinkML Source","text":"
name: source_text\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: source_text\nowner: DrugMechanism\ndomain_of:\n- DrugMechanism\nrange: string\n\n
"},{"location":"drug/subject/","title":"Slot: subject","text":"

URI: drug:subject

"},{"location":"drug/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MechanismLink no Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/subject/#properties","title":"Properties","text":""},{"location":"drug/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nalias: subject\ndomain_of:\n- MechanismLink\n- Triple\nrange: string\n\n
"},{"location":"drug/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: drug:subject_qualifier

"},{"location":"drug/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"drug/subject_qualifier/#properties","title":"Properties","text":""},{"location":"drug/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"drug/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"drug/subject_text/","title":"Slot: subject_text","text":"

URI: drug:subject_text

"},{"location":"drug/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"drug/subject_text/#properties","title":"Properties","text":""},{"location":"drug/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"drug/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"drug/title/","title":"Slot: title","text":"

The title of the publication

URI: drug:title

"},{"location":"drug/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"drug/title/#properties","title":"Properties","text":""},{"location":"drug/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/title/#schema-source","title":"Schema Source","text":""},{"location":"drug/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"drug/triples/","title":"Slot: triples","text":"

URI: drug:triples

"},{"location":"drug/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"drug/triples/#properties","title":"Properties","text":""},{"location":"drug/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drug/triples/#schema-source","title":"Schema Source","text":""},{"location":"drug/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/drug\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"environmental_metadata/","title":"Environmental sample metadata","text":"

A template for categorizing Environmental Data Initiative data entries. See https://github.com/EDIorg/EDIorg-repository-index

URI: http://w3id.org/ontogpt/environmental-metadata

Name: environmental-metadata

"},{"location":"environmental_metadata/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nDataset {\n    string packageid  \n}\nMethod {\n    string id  \n    string label  \n}\nEnvironment {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nLocation {\n    string id  \n    string label  \n}\nTopic {\n    string id  \n    string label  \n}\n\nDataset ||--}o Topic : \"topic\"\nDataset ||--}o Location : \"location\"\nDataset ||--}o EnvironmentalMaterial : \"environmental_material\"\nDataset ||--}o Environment : \"environments\"\nDataset ||--}o Method : \"methods\"\n\n
"},{"location":"environmental_metadata/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks Dataset None ExtractionResult A result of extracting knowledge on text NamedEntity None Environment None EnvironmentalMaterial None Location None Method None RelationshipType None Topic None Publication None TextWithTriples None"},{"location":"environmental_metadata/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text environmental_material the environmental material that was sampled environments the environmental context in which the study was conducted extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing location the geographic location where the sample was isolated methods named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text packageid The internal identifier for the dataset predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication topic the general scientific area of study concerning the sample(s) triples"},{"location":"environmental_metadata/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"environmental_metadata/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"environmental_metadata/#subsets","title":"Subsets","text":"Subset Description"},{"location":"environmental_metadata/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: envmd:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"environmental_metadata/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"environmental_metadata/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:AnnotatorResult native envmd:AnnotatorResult"},{"location":"environmental_metadata/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n\n
"},{"location":"environmental_metadata/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"environmental_metadata/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"environmental_metadata/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"environmental_metadata/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"environmental_metadata/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Any/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native envmd:Any"},{"location":"environmental_metadata/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nclass_uri: linkml:Any\n\n
"},{"location":"environmental_metadata/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nclass_uri: linkml:Any\n\n
"},{"location":"environmental_metadata/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"environmental_metadata/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: envmd:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"environmental_metadata/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"environmental_metadata/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:CompoundExpression native envmd:CompoundExpression"},{"location":"environmental_metadata/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nabstract: true\n\n
"},{"location":"environmental_metadata/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nabstract: true\n\n
"},{"location":"environmental_metadata/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"environmental_metadata/Curie/#comments","title":"Comments","text":""},{"location":"environmental_metadata/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Curie/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Dataset/","title":"Class: Dataset","text":"

URI: envmd:Dataset

erDiagram\nDataset {\n    string packageid  \n}\nMethod {\n    string id  \n    string label  \n}\nEnvironment {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nLocation {\n    string id  \n    string label  \n}\nTopic {\n    string id  \n    string label  \n}\n\nDataset ||--}o Topic : \"topic\"\nDataset ||--}o Location : \"location\"\nDataset ||--}o EnvironmentalMaterial : \"environmental_material\"\nDataset ||--}o Environment : \"environments\"\nDataset ||--}o Method : \"methods\"\n\n
"},{"location":"environmental_metadata/Dataset/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance packageid 0..1 String The internal identifier for the dataset direct topic 0..* Topic the general scientific area of study concerning the sample(s) direct location 0..* Location the geographic location where the sample was isolated direct environmental_material 0..* EnvironmentalMaterial the environmental material that was sampled direct environments 0..* Environment the environmental context in which the study was conducted direct methods 0..* Method direct"},{"location":"environmental_metadata/Dataset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Dataset/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Dataset/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Dataset native envmd:Dataset"},{"location":"environmental_metadata/Dataset/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Dataset/#direct","title":"Direct","text":"
name: Dataset\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  packageid:\n    name: packageid\n    annotations:\n      prompt:\n        tag: prompt\n        value: single unique identifier for the dataset\n    description: The internal identifier for the dataset\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: false\n    range: string\n  topic:\n    name: topic\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of scientific areas of study concerning the\n          sample(s)\n    description: the general scientific area of study concerning the sample(s)\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Topic\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of geographic locations of sample isolations\n    description: the geographic location where the sample was isolated\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: EnvironmentalMaterial\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental contexts in which the study\n          was conducted\n    description: the environmental context in which the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Environment\n  methods:\n    name: methods\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of methods used in measuring sample variables\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Method\ntree_root: true\n\n
"},{"location":"environmental_metadata/Dataset/#induced","title":"Induced","text":"
name: Dataset\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  packageid:\n    name: packageid\n    annotations:\n      prompt:\n        tag: prompt\n        value: single unique identifier for the dataset\n    description: The internal identifier for the dataset\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: false\n    alias: packageid\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: string\n  topic:\n    name: topic\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of scientific areas of study concerning the\n          sample(s)\n    description: the general scientific area of study concerning the sample(s)\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: topic\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: Topic\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of geographic locations of sample isolations\n    description: the geographic location where the sample was isolated\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: location\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: environmental_material\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: EnvironmentalMaterial\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental contexts in which the study\n          was conducted\n    description: the environmental context in which the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: environments\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: Environment\n  methods:\n    name: methods\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of methods used in measuring sample variables\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: methods\n    owner: Dataset\n    domain_of:\n    - Dataset\n    range: Method\ntree_root: true\n\n
"},{"location":"environmental_metadata/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"environmental_metadata/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Date/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"environmental_metadata/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"environmental_metadata/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"environmental_metadata/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"environmental_metadata/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Double/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Environment/","title":"Class: Environment","text":"

URI: envmd:Environment

erDiagram\nEnvironment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/Environment/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/Environment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/Environment/#usages","title":"Usages","text":"used by used in type used Dataset environments range Environment"},{"location":"environmental_metadata/Environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Environment/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/Environment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:ENVTHES"},{"location":"environmental_metadata/Environment/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Environment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Environment native envmd:Environment"},{"location":"environmental_metadata/Environment/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Environment/#direct","title":"Direct","text":"
name: Environment\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/Environment/#induced","title":"Induced","text":"
name: Environment\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/EnvironmentalMaterial/","title":"Class: EnvironmentalMaterial","text":"

URI: envmd:EnvironmentalMaterial

erDiagram\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/EnvironmentalMaterial/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/EnvironmentalMaterial/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/EnvironmentalMaterial/#usages","title":"Usages","text":"used by used in type used Dataset environmental_material range EnvironmentalMaterial"},{"location":"environmental_metadata/EnvironmentalMaterial/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/EnvironmentalMaterial/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/EnvironmentalMaterial/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:ENVTHES"},{"location":"environmental_metadata/EnvironmentalMaterial/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/EnvironmentalMaterial/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:EnvironmentalMaterial native envmd:EnvironmentalMaterial"},{"location":"environmental_metadata/EnvironmentalMaterial/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/EnvironmentalMaterial/#direct","title":"Direct","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/EnvironmentalMaterial/#induced","title":"Induced","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: envmd:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"environmental_metadata/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"environmental_metadata/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:ExtractionResult native envmd:ExtractionResult"},{"location":"environmental_metadata/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_metadata/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_metadata/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"environmental_metadata/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Float/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"environmental_metadata/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Integer/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Location/","title":"Class: Location","text":"

URI: envmd:Location

erDiagram\nLocation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/Location/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/Location/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/Location/#usages","title":"Usages","text":"used by used in type used Dataset location range Location"},{"location":"environmental_metadata/Location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Location/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/Location/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:GAZ"},{"location":"environmental_metadata/Location/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Location/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Location native envmd:Location"},{"location":"environmental_metadata/Location/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Location/#direct","title":"Direct","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:GAZ\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/Location/#induced","title":"Induced","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:GAZ\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Location\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Location\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/Method/","title":"Class: Method","text":"

URI: envmd:Method

erDiagram\nMethod {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/Method/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/Method/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/Method/#usages","title":"Usages","text":"used by used in type used Dataset methods range Method"},{"location":"environmental_metadata/Method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Method/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/Method/#annotations","title":"Annotations","text":"property value annotators bioportal:ENVTHES"},{"location":"environmental_metadata/Method/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Method/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Method native envmd:Method"},{"location":"environmental_metadata/Method/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Method/#direct","title":"Direct","text":"
name: Method\nid_prefixes:\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/Method/#induced","title":"Induced","text":"
name: Method\nid_prefixes:\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Method\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Method\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/NamedEntity/","title":"Class: NamedEntity","text":"

URI: envmd:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"environmental_metadata/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"environmental_metadata/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:NamedEntity native envmd:NamedEntity"},{"location":"environmental_metadata/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"environmental_metadata/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"environmental_metadata/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"environmental_metadata/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"environmental_metadata/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"environmental_metadata/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"environmental_metadata/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"environmental_metadata/Objectidentifier/#comments","title":"Comments","text":""},{"location":"environmental_metadata/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Publication/","title":"Class: Publication","text":"

URI: envmd:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"environmental_metadata/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"environmental_metadata/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"environmental_metadata/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Publication/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Publication native envmd:Publication"},{"location":"environmental_metadata/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n\n
"},{"location":"environmental_metadata/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"environmental_metadata/RelationshipType/","title":"Class: RelationshipType","text":"

URI: envmd:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"environmental_metadata/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:RelationshipType native envmd:RelationshipType"},{"location":"environmental_metadata/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"environmental_metadata/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/String/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: envmd:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"environmental_metadata/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"environmental_metadata/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:TextWithTriples native envmd:TextWithTriples"},{"location":"environmental_metadata/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_metadata/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_metadata/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"environmental_metadata/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Time/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Topic/","title":"Class: Topic","text":"

URI: envmd:Topic

erDiagram\nTopic {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_metadata/Topic/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/Topic/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_metadata/Topic/#usages","title":"Usages","text":"used by used in type used Dataset topic range Topic"},{"location":"environmental_metadata/Topic/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Topic/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_metadata/Topic/#annotations","title":"Annotations","text":"property value annotators bioportal:ENVTHES"},{"location":"environmental_metadata/Topic/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Topic/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Topic native envmd:Topic"},{"location":"environmental_metadata/Topic/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Topic/#direct","title":"Direct","text":"
name: Topic\nid_prefixes:\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\n\n
"},{"location":"environmental_metadata/Topic/#induced","title":"Induced","text":"
name: Topic\nid_prefixes:\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: bioportal:ENVTHES\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Topic\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Topic\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_metadata/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: envmd:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"environmental_metadata/Triple/#inheritance","title":"Inheritance","text":""},{"location":"environmental_metadata/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"environmental_metadata/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"environmental_metadata/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Triple/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self envmd:Triple native envmd:Triple"},{"location":"environmental_metadata/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_metadata/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"environmental_metadata/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/environmental-metadata\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"environmental_metadata/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"environmental_metadata/Uri/#comments","title":"Comments","text":""},{"location":"environmental_metadata/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Uri/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"environmental_metadata/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: envmd:abstract

"},{"location":"environmental_metadata/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_metadata/abstract/#properties","title":"Properties","text":""},{"location":"environmental_metadata/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/abstract/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_metadata/combined_text/","title":"Slot: combined_text","text":"

URI: envmd:combined_text

"},{"location":"environmental_metadata/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_metadata/combined_text/#properties","title":"Properties","text":""},{"location":"environmental_metadata/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_metadata/environmental-metadata/","title":"environmental-metadata","text":"

A template for categorizing Environmental Data Initiative data entries. See https://github.com/EDIorg/EDIorg-repository-index

URI: http://w3id.org/ontogpt/environmental-metadata

"},{"location":"environmental_metadata/environmental_material/","title":"Slot: environmental_material","text":"

the environmental material that was sampled

URI: envmd:environmental_material

"},{"location":"environmental_metadata/environmental_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/environmental_material/#properties","title":"Properties","text":""},{"location":"environmental_metadata/environmental_material/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/environmental_material/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental materials"},{"location":"environmental_metadata/environmental_material/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/environmental_material/#linkml-source","title":"LinkML Source","text":"
name: environmental_material\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental materials\ndescription: the environmental material that was sampled\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: environmental_material\nowner: Dataset\ndomain_of:\n- Dataset\nrange: EnvironmentalMaterial\n\n
"},{"location":"environmental_metadata/environments/","title":"Slot: environments","text":"

the environmental context in which the study was conducted

URI: envmd:environments

"},{"location":"environmental_metadata/environments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/environments/#properties","title":"Properties","text":""},{"location":"environmental_metadata/environments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/environments/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental contexts in which the study was conducted"},{"location":"environmental_metadata/environments/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/environments/#linkml-source","title":"LinkML Source","text":"
name: environments\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental contexts in which the study was\n      conducted\ndescription: the environmental context in which the study was conducted\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: environments\nowner: Dataset\ndomain_of:\n- Dataset\nrange: Environment\n\n
"},{"location":"environmental_metadata/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: envmd:extracted_object

"},{"location":"environmental_metadata/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/extracted_object/#properties","title":"Properties","text":""},{"location":"environmental_metadata/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"environmental_metadata/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: envmd:full_text

"},{"location":"environmental_metadata/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_metadata/full_text/#properties","title":"Properties","text":""},{"location":"environmental_metadata/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/full_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_metadata/id/","title":"Slot: id","text":"

URI: envmd:id

"},{"location":"environmental_metadata/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Topic no Location no EnvironmentalMaterial no Environment no Method no NamedEntity no RelationshipType no Publication no"},{"location":"environmental_metadata/id/#properties","title":"Properties","text":""},{"location":"environmental_metadata/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"environmental_metadata/input_id/","title":"Slot: input_id","text":"

URI: envmd:input_id

"},{"location":"environmental_metadata/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/input_id/#properties","title":"Properties","text":""},{"location":"environmental_metadata/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/input_id/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_metadata/input_text/","title":"Slot: input_text","text":"

URI: envmd:input_text

"},{"location":"environmental_metadata/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/input_text/#properties","title":"Properties","text":""},{"location":"environmental_metadata/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/input_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_metadata/input_title/","title":"Slot: input_title","text":"

URI: envmd:input_title

"},{"location":"environmental_metadata/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/input_title/#properties","title":"Properties","text":""},{"location":"environmental_metadata/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/input_title/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_metadata/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"environmental_metadata/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Topic no Location no EnvironmentalMaterial no Environment no Method no NamedEntity no RelationshipType no"},{"location":"environmental_metadata/label/#properties","title":"Properties","text":""},{"location":"environmental_metadata/label/#aliases","title":"Aliases","text":""},{"location":"environmental_metadata/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"environmental_metadata/label/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"environmental_metadata/location/","title":"Slot: location","text":"

the geographic location where the sample was isolated

URI: envmd:location

"},{"location":"environmental_metadata/location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/location/#properties","title":"Properties","text":""},{"location":"environmental_metadata/location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/location/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of geographic locations of sample isolations"},{"location":"environmental_metadata/location/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/location/#linkml-source","title":"LinkML Source","text":"
name: location\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of geographic locations of sample isolations\ndescription: the geographic location where the sample was isolated\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: location\nowner: Dataset\ndomain_of:\n- Dataset\nrange: Location\n\n
"},{"location":"environmental_metadata/methods/","title":"Slot: methods","text":"

URI: envmd:methods

"},{"location":"environmental_metadata/methods/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/methods/#properties","title":"Properties","text":""},{"location":"environmental_metadata/methods/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/methods/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of methods used in measuring sample variables"},{"location":"environmental_metadata/methods/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/methods/#linkml-source","title":"LinkML Source","text":"
name: methods\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of methods used in measuring sample variables\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: methods\nowner: Dataset\ndomain_of:\n- Dataset\nrange: Method\n\n
"},{"location":"environmental_metadata/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: envmd:named_entities

"},{"location":"environmental_metadata/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/named_entities/#properties","title":"Properties","text":""},{"location":"environmental_metadata/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"environmental_metadata/object/","title":"Slot: object","text":"

URI: envmd:object

"},{"location":"environmental_metadata/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/object/#properties","title":"Properties","text":""},{"location":"environmental_metadata/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/object/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_metadata/object_id/","title":"Slot: object_id","text":"

URI: envmd:object_id

"},{"location":"environmental_metadata/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_metadata/object_id/#properties","title":"Properties","text":""},{"location":"environmental_metadata/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/object_id/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_metadata/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: envmd:object_qualifier

"},{"location":"environmental_metadata/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/object_qualifier/#properties","title":"Properties","text":""},{"location":"environmental_metadata/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_metadata/object_text/","title":"Slot: object_text","text":"

URI: envmd:object_text

"},{"location":"environmental_metadata/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_metadata/object_text/#properties","title":"Properties","text":""},{"location":"environmental_metadata/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/object_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_metadata/packageid/","title":"Slot: packageid","text":"

The internal identifier for the dataset

URI: envmd:packageid

"},{"location":"environmental_metadata/packageid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/packageid/#properties","title":"Properties","text":""},{"location":"environmental_metadata/packageid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/packageid/#annotations","title":"Annotations","text":"property value prompt single unique identifier for the dataset"},{"location":"environmental_metadata/packageid/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/packageid/#linkml-source","title":"LinkML Source","text":"
name: packageid\nannotations:\n  prompt:\n    tag: prompt\n    value: single unique identifier for the dataset\ndescription: The internal identifier for the dataset\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: false\nalias: packageid\nowner: Dataset\ndomain_of:\n- Dataset\nrange: string\n\n
"},{"location":"environmental_metadata/predicate/","title":"Slot: predicate","text":"

URI: envmd:predicate

"},{"location":"environmental_metadata/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/predicate/#properties","title":"Properties","text":""},{"location":"environmental_metadata/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/predicate/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"environmental_metadata/prompt/","title":"Slot: prompt","text":"

URI: envmd:prompt

"},{"location":"environmental_metadata/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/prompt/#properties","title":"Properties","text":""},{"location":"environmental_metadata/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/prompt/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_metadata/publication/","title":"Slot: publication","text":"

URI: envmd:publication

"},{"location":"environmental_metadata/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"environmental_metadata/publication/#properties","title":"Properties","text":""},{"location":"environmental_metadata/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"environmental_metadata/publication/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"environmental_metadata/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: envmd:qualifier

"},{"location":"environmental_metadata/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/qualifier/#properties","title":"Properties","text":""},{"location":"environmental_metadata/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"environmental_metadata/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: envmd:raw_completion_output

"},{"location":"environmental_metadata/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_metadata/raw_completion_output/#properties","title":"Properties","text":""},{"location":"environmental_metadata/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_metadata/subject/","title":"Slot: subject","text":"

URI: envmd:subject

"},{"location":"environmental_metadata/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/subject/#properties","title":"Properties","text":""},{"location":"environmental_metadata/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/subject/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_metadata/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: envmd:subject_qualifier

"},{"location":"environmental_metadata/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_metadata/subject_qualifier/#properties","title":"Properties","text":""},{"location":"environmental_metadata/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_metadata/subject_text/","title":"Slot: subject_text","text":"

URI: envmd:subject_text

"},{"location":"environmental_metadata/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_metadata/subject_text/#properties","title":"Properties","text":""},{"location":"environmental_metadata/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_metadata/title/","title":"Slot: title","text":"

The title of the publication

URI: envmd:title

"},{"location":"environmental_metadata/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_metadata/title/#properties","title":"Properties","text":""},{"location":"environmental_metadata/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/title/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_metadata/topic/","title":"Slot: topic","text":"

the general scientific area of study concerning the sample(s)

URI: envmd:topic

"},{"location":"environmental_metadata/topic/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Dataset no"},{"location":"environmental_metadata/topic/#properties","title":"Properties","text":""},{"location":"environmental_metadata/topic/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/topic/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of scientific areas of study concerning the sample(s)"},{"location":"environmental_metadata/topic/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/topic/#linkml-source","title":"LinkML Source","text":"
name: topic\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of scientific areas of study concerning the sample(s)\ndescription: the general scientific area of study concerning the sample(s)\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: topic\nowner: Dataset\ndomain_of:\n- Dataset\nrange: Topic\n\n
"},{"location":"environmental_metadata/triples/","title":"Slot: triples","text":"

URI: envmd:triples

"},{"location":"environmental_metadata/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"environmental_metadata/triples/#properties","title":"Properties","text":""},{"location":"environmental_metadata/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_metadata/triples/#schema-source","title":"Schema Source","text":""},{"location":"environmental_metadata/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/environmental-metadata\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"environmental_sample/","title":"Environmental Sample Template","text":"

A template for Environmental Samples

URI: http://w3id.org/ontogpt/environmental-sample

Name: environmental-sample

"},{"location":"environmental_sample/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nStudy {\n\n}\nMeasurement {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\nVariable {\n    string id  \n    string label  \n}\nCausalRelationship {\n\n}\nEnvironment {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nLocation {\n    string id  \n    string label  \n}\n\nStudy ||--}o Location : \"location\"\nStudy ||--}o EnvironmentalMaterial : \"environmental_material\"\nStudy ||--}o Environment : \"environments\"\nStudy ||--}o CausalRelationship : \"causal_relationships\"\nStudy ||--}o Variable : \"variables\"\nStudy ||--}o Measurement : \"measurements\"\nMeasurement ||--|o Unit : \"unit\"\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\n\n
"},{"location":"environmental_sample/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None CausalRelationship None Measurement None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None Environment None EnvironmentalMaterial None Location None RelationshipType None Unit None Variable None Publication None Study None TextWithTriples None"},{"location":"environmental_sample/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication causal_relationships cause the variable that is the cause of the effect combined_text effect the things that is affected environmental_material the environmental material that was sampled environments extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing location the sites at which the study was conducted measurements named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples unit the unit of the measurement value the value of the measurement variables"},{"location":"environmental_sample/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"environmental_sample/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"environmental_sample/#subsets","title":"Subsets","text":"Subset Description"},{"location":"environmental_sample/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: sample:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"environmental_sample/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"environmental_sample/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:AnnotatorResult native sample:AnnotatorResult"},{"location":"environmental_sample/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n\n
"},{"location":"environmental_sample/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"environmental_sample/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"environmental_sample/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"environmental_sample/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"environmental_sample/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Any/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native sample:Any"},{"location":"environmental_sample/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nclass_uri: linkml:Any\n\n
"},{"location":"environmental_sample/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nclass_uri: linkml:Any\n\n
"},{"location":"environmental_sample/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"environmental_sample/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/CausalRelationship/","title":"Class: CausalRelationship","text":"

URI: sample:CausalRelationship

erDiagram\nCausalRelationship {\n\n}\nVariable {\n    string id  \n    string label  \n}\n\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\n\n
"},{"location":"environmental_sample/CausalRelationship/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/CausalRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance cause 0..1 Variable the variable that is the cause of the effect direct effect 0..1 Variable the things that is affected direct"},{"location":"environmental_sample/CausalRelationship/#usages","title":"Usages","text":"used by used in type used Study causal_relationships range CausalRelationship"},{"location":"environmental_sample/CausalRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/CausalRelationship/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/CausalRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:CausalRelationship native sample:CausalRelationship"},{"location":"environmental_sample/CausalRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/CausalRelationship/#direct","title":"Direct","text":"
name: CausalRelationship\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nattributes:\n  cause:\n    name: cause\n    description: the variable that is the cause of the effect\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: Variable\n  effect:\n    name: effect\n    description: the things that is affected\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: Variable\n\n
"},{"location":"environmental_sample/CausalRelationship/#induced","title":"Induced","text":"
name: CausalRelationship\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nattributes:\n  cause:\n    name: cause\n    description: the variable that is the cause of the effect\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: cause\n    owner: CausalRelationship\n    domain_of:\n    - CausalRelationship\n    range: Variable\n  effect:\n    name: effect\n    description: the things that is affected\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: effect\n    owner: CausalRelationship\n    domain_of:\n    - CausalRelationship\n    range: Variable\n\n
"},{"location":"environmental_sample/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: sample:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"environmental_sample/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"environmental_sample/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:CompoundExpression native sample:CompoundExpression"},{"location":"environmental_sample/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nabstract: true\n\n
"},{"location":"environmental_sample/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nabstract: true\n\n
"},{"location":"environmental_sample/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"environmental_sample/Curie/#comments","title":"Comments","text":""},{"location":"environmental_sample/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Curie/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"environmental_sample/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Date/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"environmental_sample/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"environmental_sample/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"environmental_sample/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"environmental_sample/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Double/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Environment/","title":"Class: Environment","text":"

URI: sample:Environment

erDiagram\nEnvironment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/Environment/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Environment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/Environment/#usages","title":"Usages","text":"used by used in type used Study environments range Environment"},{"location":"environmental_sample/Environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Environment/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/Environment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:envthes"},{"location":"environmental_sample/Environment/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Environment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Environment native sample:Environment"},{"location":"environmental_sample/Environment/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Environment/#direct","title":"Direct","text":"
name: Environment\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/Environment/#induced","title":"Induced","text":"
name: Environment\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/EnvironmentalMaterial/","title":"Class: EnvironmentalMaterial","text":"

URI: sample:EnvironmentalMaterial

erDiagram\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/EnvironmentalMaterial/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/EnvironmentalMaterial/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/EnvironmentalMaterial/#usages","title":"Usages","text":"used by used in type used Study environmental_material range EnvironmentalMaterial"},{"location":"environmental_sample/EnvironmentalMaterial/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/EnvironmentalMaterial/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/EnvironmentalMaterial/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:envthes"},{"location":"environmental_sample/EnvironmentalMaterial/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/EnvironmentalMaterial/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:EnvironmentalMaterial native sample:EnvironmentalMaterial"},{"location":"environmental_sample/EnvironmentalMaterial/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/EnvironmentalMaterial/#direct","title":"Direct","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/EnvironmentalMaterial/#induced","title":"Induced","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: sample:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"environmental_sample/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"environmental_sample/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:ExtractionResult native sample:ExtractionResult"},{"location":"environmental_sample/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_sample/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_sample/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"environmental_sample/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Float/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"environmental_sample/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Integer/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Location/","title":"Class: Location","text":"

URI: sample:Location

erDiagram\nLocation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/Location/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Location/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/Location/#usages","title":"Usages","text":"used by used in type used Study location range Location"},{"location":"environmental_sample/Location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Location/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/Location/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:gaz, bioportal:envthes"},{"location":"environmental_sample/Location/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Location/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Location native sample:Location"},{"location":"environmental_sample/Location/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Location/#direct","title":"Direct","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:gaz, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/Location/#induced","title":"Induced","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:gaz, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Location\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Location\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/Measurement/","title":"Class: Measurement","text":"

URI: sample:Measurement

erDiagram\nMeasurement {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\n\nMeasurement ||--|o Unit : \"unit\"\n\n
"},{"location":"environmental_sample/Measurement/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Measurement/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance value 0..1 String the value of the measurement direct unit 0..1 Unit the unit of the measurement direct"},{"location":"environmental_sample/Measurement/#usages","title":"Usages","text":"used by used in type used Study measurements range Measurement"},{"location":"environmental_sample/Measurement/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Measurement/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Measurement/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Measurement native sample:Measurement"},{"location":"environmental_sample/Measurement/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Measurement/#direct","title":"Direct","text":"
name: Measurement\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    description: the value of the measurement\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  unit:\n    name: unit\n    description: the unit of the measurement\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: Unit\n\n
"},{"location":"environmental_sample/Measurement/#induced","title":"Induced","text":"
name: Measurement\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    description: the value of the measurement\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: value\n    owner: Measurement\n    domain_of:\n    - Measurement\n    range: string\n  unit:\n    name: unit\n    description: the unit of the measurement\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: unit\n    owner: Measurement\n    domain_of:\n    - Measurement\n    range: Unit\n\n
"},{"location":"environmental_sample/NamedEntity/","title":"Class: NamedEntity","text":"

URI: sample:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"environmental_sample/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"environmental_sample/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:NamedEntity native sample:NamedEntity"},{"location":"environmental_sample/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"environmental_sample/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"environmental_sample/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"environmental_sample/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"environmental_sample/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"environmental_sample/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"environmental_sample/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"environmental_sample/Objectidentifier/#comments","title":"Comments","text":""},{"location":"environmental_sample/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Publication/","title":"Class: Publication","text":"

URI: sample:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"environmental_sample/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"environmental_sample/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"environmental_sample/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Publication/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Publication native sample:Publication"},{"location":"environmental_sample/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n\n
"},{"location":"environmental_sample/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"environmental_sample/RelationshipType/","title":"Class: RelationshipType","text":"

URI: sample:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"environmental_sample/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:RelationshipType native sample:RelationshipType"},{"location":"environmental_sample/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"environmental_sample/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/String/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Study/","title":"Class: Study","text":"

URI: sample:Study

erDiagram\nStudy {\n\n}\nMeasurement {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\nVariable {\n    string id  \n    string label  \n}\nCausalRelationship {\n\n}\nEnvironment {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nLocation {\n    string id  \n    string label  \n}\n\nStudy ||--}o Location : \"location\"\nStudy ||--}o EnvironmentalMaterial : \"environmental_material\"\nStudy ||--}o Environment : \"environments\"\nStudy ||--}o CausalRelationship : \"causal_relationships\"\nStudy ||--}o Variable : \"variables\"\nStudy ||--}o Measurement : \"measurements\"\nMeasurement ||--|o Unit : \"unit\"\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\n\n
"},{"location":"environmental_sample/Study/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance location 0..* Location the sites at which the study was conducted direct environmental_material 0..* EnvironmentalMaterial the environmental material that was sampled direct environments 0..* Environment direct causal_relationships 0..* CausalRelationship direct variables 0..* Variable direct measurements 0..* Measurement direct"},{"location":"environmental_sample/Study/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Study/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Study/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Study native sample:Study"},{"location":"environmental_sample/Study/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Study/#direct","title":"Direct","text":"
name: Study\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of sites at which the study was conducted.\n          give specific place names. if you cannot find a specific place name leave\n          the field as empty.\n    description: the sites at which the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: EnvironmentalMaterial\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environment terms for the location in which\n          the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Environment\n  causal_relationships:\n    name: causal_relationships\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of cause-effect pairs, for example, effect\n          of temperature on growth\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: CausalRelationship\n  variables:\n    name: variables\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of study variables\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Variable\n  measurements:\n    name: measurements\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of value-measurement pairs\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Measurement\ntree_root: true\n\n
"},{"location":"environmental_sample/Study/#induced","title":"Induced","text":"
name: Study\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of sites at which the study was conducted.\n          give specific place names. if you cannot find a specific place name leave\n          the field as empty.\n    description: the sites at which the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: location\n    owner: Study\n    domain_of:\n    - Study\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: environmental_material\n    owner: Study\n    domain_of:\n    - Study\n    range: EnvironmentalMaterial\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environment terms for the location in which\n          the study was conducted\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: environments\n    owner: Study\n    domain_of:\n    - Study\n    range: Environment\n  causal_relationships:\n    name: causal_relationships\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of cause-effect pairs, for example, effect\n          of temperature on growth\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: causal_relationships\n    owner: Study\n    domain_of:\n    - Study\n    range: CausalRelationship\n  variables:\n    name: variables\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of study variables\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: variables\n    owner: Study\n    domain_of:\n    - Study\n    range: Variable\n  measurements:\n    name: measurements\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of value-measurement pairs\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: measurements\n    owner: Study\n    domain_of:\n    - Study\n    range: Measurement\ntree_root: true\n\n
"},{"location":"environmental_sample/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: sample:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"environmental_sample/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"environmental_sample/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:TextWithTriples native sample:TextWithTriples"},{"location":"environmental_sample/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_sample/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"environmental_sample/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"environmental_sample/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Time/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: sample:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"environmental_sample/Triple/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"environmental_sample/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"environmental_sample/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Triple/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Triple native sample:Triple"},{"location":"environmental_sample/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"environmental_sample/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"environmental_sample/Unit/","title":"Class: Unit","text":"

URI: sample:Unit

erDiagram\nUnit {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/Unit/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Unit/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/Unit/#usages","title":"Usages","text":"used by used in type used Measurement unit range Unit"},{"location":"environmental_sample/Unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Unit/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/Unit/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uo, bioportal:ncit"},{"location":"environmental_sample/Unit/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Unit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Unit native sample:Unit"},{"location":"environmental_sample/Unit/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Unit/#direct","title":"Direct","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, bioportal:ncit\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/Unit/#induced","title":"Induced","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, bioportal:ncit\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"environmental_sample/Uri/#comments","title":"Comments","text":""},{"location":"environmental_sample/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Uri/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"environmental_sample/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Variable/","title":"Class: Variable","text":"

URI: sample:Variable

erDiagram\nVariable {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"environmental_sample/Variable/#inheritance","title":"Inheritance","text":""},{"location":"environmental_sample/Variable/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"environmental_sample/Variable/#usages","title":"Usages","text":"used by used in type used Study variables range Variable CausalRelationship cause range Variable CausalRelationship effect range Variable"},{"location":"environmental_sample/Variable/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/Variable/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"environmental_sample/Variable/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:bero, bioportal:envthes"},{"location":"environmental_sample/Variable/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/Variable/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sample:Variable native sample:Variable"},{"location":"environmental_sample/Variable/#linkml-source","title":"LinkML Source","text":""},{"location":"environmental_sample/Variable/#direct","title":"Direct","text":"
name: Variable\nid_prefixes:\n- ENVO\n- MIXS\n- PATO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:bero, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\n\n
"},{"location":"environmental_sample/Variable/#induced","title":"Induced","text":"
name: Variable\nid_prefixes:\n- ENVO\n- MIXS\n- PATO\n- ENVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:bero, bioportal:envthes\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Variable\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/environmental-sample\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Variable\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"environmental_sample/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: sample:abstract

"},{"location":"environmental_sample/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_sample/abstract/#properties","title":"Properties","text":""},{"location":"environmental_sample/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/abstract/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_sample/causal_relationships/","title":"Slot: causal_relationships","text":"

URI: sample:causal_relationships

"},{"location":"environmental_sample/causal_relationships/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/causal_relationships/#properties","title":"Properties","text":""},{"location":"environmental_sample/causal_relationships/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/causal_relationships/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth"},{"location":"environmental_sample/causal_relationships/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/causal_relationships/#linkml-source","title":"LinkML Source","text":"
name: causal_relationships\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of cause-effect pairs, for example, effect of\n      temperature on growth\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: causal_relationships\nowner: Study\ndomain_of:\n- Study\nrange: CausalRelationship\n\n
"},{"location":"environmental_sample/cause/","title":"Slot: cause","text":"

the variable that is the cause of the effect

URI: sample:cause

"},{"location":"environmental_sample/cause/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CausalRelationship no"},{"location":"environmental_sample/cause/#properties","title":"Properties","text":""},{"location":"environmental_sample/cause/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/cause/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/cause/#linkml-source","title":"LinkML Source","text":"
name: cause\ndescription: the variable that is the cause of the effect\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: cause\nowner: CausalRelationship\ndomain_of:\n- CausalRelationship\nrange: Variable\n\n
"},{"location":"environmental_sample/combined_text/","title":"Slot: combined_text","text":"

URI: sample:combined_text

"},{"location":"environmental_sample/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_sample/combined_text/#properties","title":"Properties","text":""},{"location":"environmental_sample/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_sample/effect/","title":"Slot: effect","text":"

the things that is affected

URI: sample:effect

"},{"location":"environmental_sample/effect/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CausalRelationship no"},{"location":"environmental_sample/effect/#properties","title":"Properties","text":""},{"location":"environmental_sample/effect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/effect/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/effect/#linkml-source","title":"LinkML Source","text":"
name: effect\ndescription: the things that is affected\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: effect\nowner: CausalRelationship\ndomain_of:\n- CausalRelationship\nrange: Variable\n\n
"},{"location":"environmental_sample/environmental-sample/","title":"environmental-sample","text":"

A template for Environmental Samples

URI: http://w3id.org/ontogpt/environmental-sample

"},{"location":"environmental_sample/environmental_material/","title":"Slot: environmental_material","text":"

the environmental material that was sampled

URI: sample:environmental_material

"},{"location":"environmental_sample/environmental_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/environmental_material/#properties","title":"Properties","text":""},{"location":"environmental_sample/environmental_material/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/environmental_material/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental materials"},{"location":"environmental_sample/environmental_material/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/environmental_material/#linkml-source","title":"LinkML Source","text":"
name: environmental_material\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental materials\ndescription: the environmental material that was sampled\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: environmental_material\nowner: Study\ndomain_of:\n- Study\nrange: EnvironmentalMaterial\n\n
"},{"location":"environmental_sample/environments/","title":"Slot: environments","text":"

URI: sample:environments

"},{"location":"environmental_sample/environments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/environments/#properties","title":"Properties","text":""},{"location":"environmental_sample/environments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/environments/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environment terms for the location in which the study was conducted"},{"location":"environmental_sample/environments/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/environments/#linkml-source","title":"LinkML Source","text":"
name: environments\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environment terms for the location in which\n      the study was conducted\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: environments\nowner: Study\ndomain_of:\n- Study\nrange: Environment\n\n
"},{"location":"environmental_sample/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: sample:extracted_object

"},{"location":"environmental_sample/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/extracted_object/#properties","title":"Properties","text":""},{"location":"environmental_sample/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"environmental_sample/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: sample:full_text

"},{"location":"environmental_sample/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_sample/full_text/#properties","title":"Properties","text":""},{"location":"environmental_sample/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/full_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_sample/id/","title":"Slot: id","text":"

URI: sample:id

"},{"location":"environmental_sample/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Location no EnvironmentalMaterial no Environment no Variable no Unit no NamedEntity no RelationshipType no Publication no"},{"location":"environmental_sample/id/#properties","title":"Properties","text":""},{"location":"environmental_sample/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"environmental_sample/input_id/","title":"Slot: input_id","text":"

URI: sample:input_id

"},{"location":"environmental_sample/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/input_id/#properties","title":"Properties","text":""},{"location":"environmental_sample/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/input_id/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_sample/input_text/","title":"Slot: input_text","text":"

URI: sample:input_text

"},{"location":"environmental_sample/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/input_text/#properties","title":"Properties","text":""},{"location":"environmental_sample/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/input_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_sample/input_title/","title":"Slot: input_title","text":"

URI: sample:input_title

"},{"location":"environmental_sample/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/input_title/#properties","title":"Properties","text":""},{"location":"environmental_sample/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/input_title/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_sample/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"environmental_sample/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Location no EnvironmentalMaterial no Environment no Variable no Unit no NamedEntity no RelationshipType no"},{"location":"environmental_sample/label/#properties","title":"Properties","text":""},{"location":"environmental_sample/label/#aliases","title":"Aliases","text":""},{"location":"environmental_sample/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"environmental_sample/label/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"environmental_sample/location/","title":"Slot: location","text":"

the sites at which the study was conducted

URI: sample:location

"},{"location":"environmental_sample/location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/location/#properties","title":"Properties","text":""},{"location":"environmental_sample/location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/location/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty."},{"location":"environmental_sample/location/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/location/#linkml-source","title":"LinkML Source","text":"
name: location\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of sites at which the study was conducted. give\n      specific place names. if you cannot find a specific place name leave the field\n      as empty.\ndescription: the sites at which the study was conducted\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: location\nowner: Study\ndomain_of:\n- Study\nrange: Location\n\n
"},{"location":"environmental_sample/measurements/","title":"Slot: measurements","text":"

URI: sample:measurements

"},{"location":"environmental_sample/measurements/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/measurements/#properties","title":"Properties","text":""},{"location":"environmental_sample/measurements/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/measurements/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of value-measurement pairs"},{"location":"environmental_sample/measurements/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/measurements/#linkml-source","title":"LinkML Source","text":"
name: measurements\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of value-measurement pairs\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: measurements\nowner: Study\ndomain_of:\n- Study\nrange: Measurement\n\n
"},{"location":"environmental_sample/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: sample:named_entities

"},{"location":"environmental_sample/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/named_entities/#properties","title":"Properties","text":""},{"location":"environmental_sample/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"environmental_sample/object/","title":"Slot: object","text":"

URI: sample:object

"},{"location":"environmental_sample/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/object/#properties","title":"Properties","text":""},{"location":"environmental_sample/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/object/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_sample/object_id/","title":"Slot: object_id","text":"

URI: sample:object_id

"},{"location":"environmental_sample/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_sample/object_id/#properties","title":"Properties","text":""},{"location":"environmental_sample/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/object_id/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_sample/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: sample:object_qualifier

"},{"location":"environmental_sample/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/object_qualifier/#properties","title":"Properties","text":""},{"location":"environmental_sample/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_sample/object_text/","title":"Slot: object_text","text":"

URI: sample:object_text

"},{"location":"environmental_sample/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_sample/object_text/#properties","title":"Properties","text":""},{"location":"environmental_sample/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/object_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_sample/predicate/","title":"Slot: predicate","text":"

URI: sample:predicate

"},{"location":"environmental_sample/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/predicate/#properties","title":"Properties","text":""},{"location":"environmental_sample/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/predicate/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"environmental_sample/prompt/","title":"Slot: prompt","text":"

URI: sample:prompt

"},{"location":"environmental_sample/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/prompt/#properties","title":"Properties","text":""},{"location":"environmental_sample/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/prompt/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_sample/publication/","title":"Slot: publication","text":"

URI: sample:publication

"},{"location":"environmental_sample/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"environmental_sample/publication/#properties","title":"Properties","text":""},{"location":"environmental_sample/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"environmental_sample/publication/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"environmental_sample/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: sample:qualifier

"},{"location":"environmental_sample/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/qualifier/#properties","title":"Properties","text":""},{"location":"environmental_sample/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"environmental_sample/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: sample:raw_completion_output

"},{"location":"environmental_sample/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"environmental_sample/raw_completion_output/#properties","title":"Properties","text":""},{"location":"environmental_sample/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"environmental_sample/subject/","title":"Slot: subject","text":"

URI: sample:subject

"},{"location":"environmental_sample/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/subject/#properties","title":"Properties","text":""},{"location":"environmental_sample/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/subject/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_sample/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: sample:subject_qualifier

"},{"location":"environmental_sample/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"environmental_sample/subject_qualifier/#properties","title":"Properties","text":""},{"location":"environmental_sample/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"environmental_sample/subject_text/","title":"Slot: subject_text","text":"

URI: sample:subject_text

"},{"location":"environmental_sample/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"environmental_sample/subject_text/#properties","title":"Properties","text":""},{"location":"environmental_sample/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"environmental_sample/title/","title":"Slot: title","text":"

The title of the publication

URI: sample:title

"},{"location":"environmental_sample/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"environmental_sample/title/#properties","title":"Properties","text":""},{"location":"environmental_sample/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/title/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"environmental_sample/triples/","title":"Slot: triples","text":"

URI: sample:triples

"},{"location":"environmental_sample/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"environmental_sample/triples/#properties","title":"Properties","text":""},{"location":"environmental_sample/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/triples/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"environmental_sample/unit/","title":"Slot: unit","text":"

the unit of the measurement

URI: sample:unit

"},{"location":"environmental_sample/unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Measurement no"},{"location":"environmental_sample/unit/#properties","title":"Properties","text":""},{"location":"environmental_sample/unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/unit/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/unit/#linkml-source","title":"LinkML Source","text":"
name: unit\ndescription: the unit of the measurement\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: unit\nowner: Measurement\ndomain_of:\n- Measurement\nrange: Unit\n\n
"},{"location":"environmental_sample/value/","title":"Slot: value","text":"

the value of the measurement

URI: sample:value

"},{"location":"environmental_sample/value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Measurement no"},{"location":"environmental_sample/value/#properties","title":"Properties","text":""},{"location":"environmental_sample/value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/value/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/value/#linkml-source","title":"LinkML Source","text":"
name: value\ndescription: the value of the measurement\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nalias: value\nowner: Measurement\ndomain_of:\n- Measurement\nrange: string\n\n
"},{"location":"environmental_sample/variables/","title":"Slot: variables","text":"

URI: sample:variables

"},{"location":"environmental_sample/variables/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"environmental_sample/variables/#properties","title":"Properties","text":""},{"location":"environmental_sample/variables/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environmental_sample/variables/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of study variables"},{"location":"environmental_sample/variables/#schema-source","title":"Schema Source","text":""},{"location":"environmental_sample/variables/#linkml-source","title":"LinkML Source","text":"
name: variables\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of study variables\nfrom_schema: http://w3id.org/ontogpt/environmental-sample\nrank: 1000\nmultivalued: true\nalias: variables\nowner: Study\ndomain_of:\n- Study\nrange: Variable\n\n
"},{"location":"gene_description_term/","title":"GO Term Template","text":"

A simple GO term template for NER

URI: https://w3id.org/ontogpt/go_term

Name: go-term-template

"},{"location":"gene_description_term/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nGeneDescriptionTerm {\n    string label  \n    string id  \n}\n\n\n\n
"},{"location":"gene_description_term/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text GeneDescription A summarization of an individual gene NamedEntity None Gene None GeneDescriptionTerm None RelationshipType None Publication None TextWithTriples None"},{"location":"gene_description_term/#slots","title":"Slots","text":"Slot Description about The official symbol of the gene that is described abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label the name of the GO term named_entities Named entities extracted from the text narrative_summary A free text summary describing the function of the gene object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text terms A semicolon separated list of controlled terms drawn from the Gene Ontology t... title The title of the publication triples"},{"location":"gene_description_term/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"gene_description_term/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"gene_description_term/#subsets","title":"Subsets","text":"Subset Description"},{"location":"gene_description_term/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: bp:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"gene_description_term/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"gene_description_term/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:AnnotatorResult native bp:AnnotatorResult"},{"location":"gene_description_term/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n\n
"},{"location":"gene_description_term/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"gene_description_term/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"gene_description_term/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"gene_description_term/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"gene_description_term/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Any/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native bp:Any"},{"location":"gene_description_term/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/go_term\nclass_uri: linkml:Any\n\n
"},{"location":"gene_description_term/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/go_term\nclass_uri: linkml:Any\n\n
"},{"location":"gene_description_term/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"gene_description_term/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: bp:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"gene_description_term/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"gene_description_term/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:CompoundExpression native bp:CompoundExpression"},{"location":"gene_description_term/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/go_term\nabstract: true\n\n
"},{"location":"gene_description_term/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/go_term\nabstract: true\n\n
"},{"location":"gene_description_term/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"gene_description_term/Curie/#comments","title":"Comments","text":""},{"location":"gene_description_term/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Curie/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"gene_description_term/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Date/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"gene_description_term/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"gene_description_term/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"gene_description_term/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"gene_description_term/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Double/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: bp:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"gene_description_term/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"gene_description_term/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ExtractionResult native bp:ExtractionResult"},{"location":"gene_description_term/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gene_description_term/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gene_description_term/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"gene_description_term/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Float/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Gene/","title":"Class: Gene","text":"

URI: bp:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gene_description_term/Gene/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gene_description_term/Gene/#usages","title":"Usages","text":"used by used in type used GeneDescription about range Gene"},{"location":"gene_description_term/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gene_description_term/Gene/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hgnc"},{"location":"gene_description_term/Gene/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Gene native bp:Gene"},{"location":"gene_description_term/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\n\n
"},{"location":"gene_description_term/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/go_term\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - GeneDescriptionTerm\n    - NamedEntity\n    range: string\n\n
"},{"location":"gene_description_term/GeneDescription/","title":"Class: GeneDescription","text":"

A summarization of an individual gene

URI: bp:GeneDescription

erDiagram\nGeneDescription {\n    string narrative_summary  \n}\nGeneDescriptionTerm {\n    string label  \n    string id  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneDescription ||--|o Gene : \"about\"\nGeneDescription ||--}o GeneDescriptionTerm : \"terms\"\n\n
"},{"location":"gene_description_term/GeneDescription/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance about 0..1 Gene The official symbol of the gene that is described direct narrative_summary 0..1 String A free text summary describing the function of the gene direct terms 0..* GeneDescriptionTerm A semicolon separated list of controlled terms drawn from the Gene Ontology t... direct"},{"location":"gene_description_term/GeneDescription/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/GeneDescription/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/GeneDescription/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:GeneDescription native bp:GeneDescription"},{"location":"gene_description_term/GeneDescription/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/GeneDescription/#direct","title":"Direct","text":"
name: GeneDescription\ndescription: A summarization of an individual gene\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  about:\n    name: about\n    description: The official symbol of the gene that is described. For example \"TP53\".\n      Do not include the word \"gene\" in the answer.\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: Gene\n  narrative_summary:\n    name: narrative_summary\n    description: A free text summary describing the function of the gene\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: string\n  terms:\n    name: terms\n    description: A semicolon separated list of controlled terms drawn from the Gene\n      Ontology that describe the function of the gene\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    range: GeneDescriptionTerm\n\n
"},{"location":"gene_description_term/GeneDescription/#induced","title":"Induced","text":"
name: GeneDescription\ndescription: A summarization of an individual gene\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  about:\n    name: about\n    description: The official symbol of the gene that is described. For example \"TP53\".\n      Do not include the word \"gene\" in the answer.\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: about\n    owner: GeneDescription\n    domain_of:\n    - GeneDescription\n    range: Gene\n  narrative_summary:\n    name: narrative_summary\n    description: A free text summary describing the function of the gene\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: narrative_summary\n    owner: GeneDescription\n    domain_of:\n    - GeneDescription\n    range: string\n  terms:\n    name: terms\n    description: A semicolon separated list of controlled terms drawn from the Gene\n      Ontology that describe the function of the gene\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    alias: terms\n    owner: GeneDescription\n    domain_of:\n    - GeneDescription\n    range: GeneDescriptionTerm\n\n
"},{"location":"gene_description_term/GeneDescriptionTerm/","title":"Class: GeneDescriptionTerm","text":"

URI: bp:GeneDescriptionTerm

erDiagram\nGeneDescriptionTerm {\n    string label  \n    string id  \n}\n\n\n\n
"},{"location":"gene_description_term/GeneDescriptionTerm/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/GeneDescriptionTerm/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 0..1 String the name of the GO term direct id 1..1 String A unique identifier for the named entity NamedEntity"},{"location":"gene_description_term/GeneDescriptionTerm/#usages","title":"Usages","text":"used by used in type used GeneDescription terms range GeneDescriptionTerm"},{"location":"gene_description_term/GeneDescriptionTerm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/GeneDescriptionTerm/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gene_description_term/GeneDescriptionTerm/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh"},{"location":"gene_description_term/GeneDescriptionTerm/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/GeneDescriptionTerm/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:GeneDescriptionTerm native bp:GeneDescriptionTerm"},{"location":"gene_description_term/GeneDescriptionTerm/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/GeneDescriptionTerm/#direct","title":"Direct","text":"
name: GeneDescriptionTerm\nid_prefixes:\n- GO\n- MONDO\n- UBERON\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the GO term\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\ntree_root: true\n\n
"},{"location":"gene_description_term/GeneDescriptionTerm/#induced","title":"Induced","text":"
name: GeneDescriptionTerm\nid_prefixes:\n- GO\n- MONDO\n- UBERON\n- MESH\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the GO term\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: label\n    owner: GeneDescriptionTerm\n    domain_of:\n    - GeneDescriptionTerm\n    - NamedEntity\n    range: string\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: GeneDescriptionTerm\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\ntree_root: true\n\n
"},{"location":"gene_description_term/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"gene_description_term/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Integer/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/NamedEntity/","title":"Class: NamedEntity","text":"

URI: bp:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gene_description_term/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"gene_description_term/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"gene_description_term/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:NamedEntity native bp:NamedEntity"},{"location":"gene_description_term/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/go_term\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/go_term\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"gene_description_term/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/go_term\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/go_term\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - GeneDescriptionTerm\n    - NamedEntity\n    range: string\n\n
"},{"location":"gene_description_term/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"gene_description_term/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"gene_description_term/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"gene_description_term/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"gene_description_term/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"gene_description_term/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"gene_description_term/Objectidentifier/#comments","title":"Comments","text":""},{"location":"gene_description_term/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Publication/","title":"Class: Publication","text":"

URI: bp:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"gene_description_term/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"gene_description_term/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"gene_description_term/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Publication/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Publication native bp:Publication"},{"location":"gene_description_term/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/go_term\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n\n
"},{"location":"gene_description_term/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/go_term\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"gene_description_term/RelationshipType/","title":"Class: RelationshipType","text":"

URI: bp:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gene_description_term/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gene_description_term/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"gene_description_term/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gene_description_term/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:RelationshipType native bp:RelationshipType"},{"location":"gene_description_term/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\n\n
"},{"location":"gene_description_term/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/go_term\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - GeneDescriptionTerm\n    - NamedEntity\n    range: string\n\n
"},{"location":"gene_description_term/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"gene_description_term/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/String/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: bp:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"gene_description_term/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"gene_description_term/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:TextWithTriples native bp:TextWithTriples"},{"location":"gene_description_term/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gene_description_term/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/go_term\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gene_description_term/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"gene_description_term/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Time/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: bp:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"gene_description_term/Triple/#inheritance","title":"Inheritance","text":""},{"location":"gene_description_term/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"gene_description_term/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"gene_description_term/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Triple/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Triple native bp:Triple"},{"location":"gene_description_term/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"gene_description_term/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"gene_description_term/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/go_term\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/go_term\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"gene_description_term/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"gene_description_term/Uri/#comments","title":"Comments","text":""},{"location":"gene_description_term/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Uri/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"gene_description_term/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/about/","title":"Slot: about","text":"

The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.

URI: bp:about

"},{"location":"gene_description_term/about/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneDescription A summarization of an individual gene no"},{"location":"gene_description_term/about/#properties","title":"Properties","text":""},{"location":"gene_description_term/about/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/about/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/about/#linkml-source","title":"LinkML Source","text":"
name: about\ndescription: The official symbol of the gene that is described. For example \"TP53\".\n  Do not include the word \"gene\" in the answer.\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: about\nowner: GeneDescription\ndomain_of:\n- GeneDescription\nrange: Gene\n\n
"},{"location":"gene_description_term/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: bp:abstract

"},{"location":"gene_description_term/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gene_description_term/abstract/#properties","title":"Properties","text":""},{"location":"gene_description_term/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/abstract/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gene_description_term/combined_text/","title":"Slot: combined_text","text":"

URI: bp:combined_text

"},{"location":"gene_description_term/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gene_description_term/combined_text/#properties","title":"Properties","text":""},{"location":"gene_description_term/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gene_description_term/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: bp:extracted_object

"},{"location":"gene_description_term/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/extracted_object/#properties","title":"Properties","text":""},{"location":"gene_description_term/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"gene_description_term/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: bp:full_text

"},{"location":"gene_description_term/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gene_description_term/full_text/#properties","title":"Properties","text":""},{"location":"gene_description_term/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/full_text/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gene_description_term/go-term-template/","title":"go-term-template","text":"

A simple GO term template for NER

URI: https://w3id.org/ontogpt/go_term

"},{"location":"gene_description_term/id/","title":"Slot: id","text":"

URI: bp:id

"},{"location":"gene_description_term/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no GeneDescriptionTerm no NamedEntity no RelationshipType no Publication no"},{"location":"gene_description_term/id/#properties","title":"Properties","text":""},{"location":"gene_description_term/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"gene_description_term/input_id/","title":"Slot: input_id","text":"

URI: bp:input_id

"},{"location":"gene_description_term/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/input_id/#properties","title":"Properties","text":""},{"location":"gene_description_term/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/input_id/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gene_description_term/input_text/","title":"Slot: input_text","text":"

URI: bp:input_text

"},{"location":"gene_description_term/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/input_text/#properties","title":"Properties","text":""},{"location":"gene_description_term/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/input_text/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gene_description_term/input_title/","title":"Slot: input_title","text":"

URI: bp:input_title

"},{"location":"gene_description_term/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/input_title/#properties","title":"Properties","text":""},{"location":"gene_description_term/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/input_title/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gene_description_term/label/","title":"Slot: label","text":"

URI: bp:label

"},{"location":"gene_description_term/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no GeneDescriptionTerm no NamedEntity no RelationshipType no"},{"location":"gene_description_term/label/#properties","title":"Properties","text":""},{"location":"gene_description_term/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- GeneDescriptionTerm\n- NamedEntity\nrange: string\n\n
"},{"location":"gene_description_term/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: bp:named_entities

"},{"location":"gene_description_term/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/named_entities/#properties","title":"Properties","text":""},{"location":"gene_description_term/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gene_description_term/narrative_summary/","title":"Slot: narrative_summary","text":"

A free text summary describing the function of the gene

URI: bp:narrative_summary

"},{"location":"gene_description_term/narrative_summary/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneDescription A summarization of an individual gene no"},{"location":"gene_description_term/narrative_summary/#properties","title":"Properties","text":""},{"location":"gene_description_term/narrative_summary/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/narrative_summary/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/narrative_summary/#linkml-source","title":"LinkML Source","text":"
name: narrative_summary\ndescription: A free text summary describing the function of the gene\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: narrative_summary\nowner: GeneDescription\ndomain_of:\n- GeneDescription\nrange: string\n\n
"},{"location":"gene_description_term/object/","title":"Slot: object","text":"

URI: bp:object

"},{"location":"gene_description_term/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/object/#properties","title":"Properties","text":""},{"location":"gene_description_term/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/object/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gene_description_term/object_id/","title":"Slot: object_id","text":"

URI: bp:object_id

"},{"location":"gene_description_term/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gene_description_term/object_id/#properties","title":"Properties","text":""},{"location":"gene_description_term/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/object_id/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gene_description_term/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: bp:object_qualifier

"},{"location":"gene_description_term/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/object_qualifier/#properties","title":"Properties","text":""},{"location":"gene_description_term/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gene_description_term/object_text/","title":"Slot: object_text","text":"

URI: bp:object_text

"},{"location":"gene_description_term/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gene_description_term/object_text/#properties","title":"Properties","text":""},{"location":"gene_description_term/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/object_text/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gene_description_term/predicate/","title":"Slot: predicate","text":"

URI: bp:predicate

"},{"location":"gene_description_term/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/predicate/#properties","title":"Properties","text":""},{"location":"gene_description_term/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/predicate/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"gene_description_term/prompt/","title":"Slot: prompt","text":"

URI: bp:prompt

"},{"location":"gene_description_term/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/prompt/#properties","title":"Properties","text":""},{"location":"gene_description_term/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/prompt/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gene_description_term/publication/","title":"Slot: publication","text":"

URI: bp:publication

"},{"location":"gene_description_term/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"gene_description_term/publication/#properties","title":"Properties","text":""},{"location":"gene_description_term/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"gene_description_term/publication/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"gene_description_term/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: bp:qualifier

"},{"location":"gene_description_term/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/qualifier/#properties","title":"Properties","text":""},{"location":"gene_description_term/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"gene_description_term/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: bp:raw_completion_output

"},{"location":"gene_description_term/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gene_description_term/raw_completion_output/#properties","title":"Properties","text":""},{"location":"gene_description_term/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gene_description_term/subject/","title":"Slot: subject","text":"

URI: bp:subject

"},{"location":"gene_description_term/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/subject/#properties","title":"Properties","text":""},{"location":"gene_description_term/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/subject/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gene_description_term/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: bp:subject_qualifier

"},{"location":"gene_description_term/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gene_description_term/subject_qualifier/#properties","title":"Properties","text":""},{"location":"gene_description_term/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gene_description_term/subject_text/","title":"Slot: subject_text","text":"

URI: bp:subject_text

"},{"location":"gene_description_term/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gene_description_term/subject_text/#properties","title":"Properties","text":""},{"location":"gene_description_term/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gene_description_term/terms/","title":"Slot: terms","text":"

A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene

URI: bp:terms

"},{"location":"gene_description_term/terms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneDescription A summarization of an individual gene no"},{"location":"gene_description_term/terms/#properties","title":"Properties","text":""},{"location":"gene_description_term/terms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/terms/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/terms/#linkml-source","title":"LinkML Source","text":"
name: terms\ndescription: A semicolon separated list of controlled terms drawn from the Gene Ontology\n  that describe the function of the gene\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nmultivalued: true\nalias: terms\nowner: GeneDescription\ndomain_of:\n- GeneDescription\nrange: GeneDescriptionTerm\n\n
"},{"location":"gene_description_term/title/","title":"Slot: title","text":"

The title of the publication

URI: bp:title

"},{"location":"gene_description_term/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gene_description_term/title/#properties","title":"Properties","text":""},{"location":"gene_description_term/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/title/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gene_description_term/triples/","title":"Slot: triples","text":"

URI: bp:triples

"},{"location":"gene_description_term/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"gene_description_term/triples/#properties","title":"Properties","text":""},{"location":"gene_description_term/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_description_term/triples/#schema-source","title":"Schema Source","text":""},{"location":"gene_description_term/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/go_term\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gocam/","title":"GO-CAM Template","text":"

A template for GO-CAMs

URI: http://w3id.org/ontogpt/gocam

Name: gocam-template

"},{"location":"gocam/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nGoCamAnnotations {\n\n}\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nGeneGeneInteraction {\n\n}\nPathway {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\n\nGoCamAnnotations ||--}o Gene : \"genes\"\nGoCamAnnotations ||--}o Organism : \"organisms\"\nGoCamAnnotations ||--}o GeneOrganismRelationship : \"gene_organisms\"\nGoCamAnnotations ||--}o MolecularActivity : \"activities\"\nGoCamAnnotations ||--}o GeneMolecularActivityRelationship : \"gene_functions\"\nGoCamAnnotations ||--}o CellularProcess : \"cellular_processes\"\nGoCamAnnotations ||--}o Pathway : \"pathways\"\nGoCamAnnotations ||--}o GeneGeneInteraction : \"gene_gene_interactions\"\nGoCamAnnotations ||--}o GeneSubcellularLocalizationRelationship : \"gene_localizations\"\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"gocam/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None GeneGeneInteraction None GeneMolecularActivityRelationship None GeneMolecularActivityRelationship2 None GeneOrganismRelationship None GeneSubcellularLocalizationRelationship None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text GoCamAnnotations None NamedEntity None CellularProcess None Gene None GeneLocation None MolecularActivity None Molecule None Organism None Pathway None RelationshipType None Publication None TextWithTriples None"},{"location":"gocam/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication activities semicolon-separated list of molecular activities cellular_processes semicolon-separated list of cellular processes combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication gene gene1 gene2 gene_functions semicolon-separated list of gene to molecular activity relationships gene_gene_interactions semicolon-separated list of gene to gene interactions gene_localizations semicolon-separated list of genes plus their location in the cell; for exampl... gene_organisms genes semicolon-separated list of genes id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing location molecular_activity named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text organism organisms semicolon-separated list of organism taxons pathways semicolon-separated list of pathways predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text target title The title of the publication triples"},{"location":"gocam/#enumerations","title":"Enumerations","text":"Enumeration Description CellType GeneLocationEnum GOCellComponentType NullDataOptions"},{"location":"gocam/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"gocam/#subsets","title":"Subsets","text":"Subset Description"},{"location":"gocam/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: gocam:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"gocam/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"gocam/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"gocam/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:AnnotatorResult native gocam:AnnotatorResult"},{"location":"gocam/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n\n
"},{"location":"gocam/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"gocam/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"gocam/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"gocam/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"gocam/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Any/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native gocam:Any"},{"location":"gocam/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/gocam\nclass_uri: linkml:Any\n\n
"},{"location":"gocam/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/gocam\nclass_uri: linkml:Any\n\n
"},{"location":"gocam/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"gocam/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"gocam/CellType/","title":"Enum: CellType","text":"

URI: CellType

This is a dynamic enum

"},{"location":"gocam/CellType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/CellType/#schema-source","title":"Schema Source","text":""},{"location":"gocam/CellType/#linkml-source","title":"LinkML Source","text":"
name: CellType\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nreachable_from:\n  source_ontology: obo:cl\n  source_nodes:\n  - CL:0000000\n\n
"},{"location":"gocam/CellularProcess/","title":"Class: CellularProcess","text":"

URI: gocam:CellularProcess

erDiagram\nCellularProcess {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/CellularProcess/#inheritance","title":"Inheritance","text":""},{"location":"gocam/CellularProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/CellularProcess/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations cellular_processes range CellularProcess"},{"location":"gocam/CellularProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/CellularProcess/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/CellularProcess/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"gocam/CellularProcess/#schema-source","title":"Schema Source","text":""},{"location":"gocam/CellularProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:CellularProcess native gocam:CellularProcess"},{"location":"gocam/CellularProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/CellularProcess/#direct","title":"Direct","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/CellularProcess/#induced","title":"Induced","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: gocam:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"gocam/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"gocam/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"gocam/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"gocam/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:CompoundExpression native gocam:CompoundExpression"},{"location":"gocam/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\n\n
"},{"location":"gocam/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\n\n
"},{"location":"gocam/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"gocam/Curie/#comments","title":"Comments","text":""},{"location":"gocam/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Curie/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"gocam/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Date/#schema-source","title":"Schema Source","text":""},{"location":"gocam/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"gocam/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"gocam/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"gocam/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"gocam/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Double/#schema-source","title":"Schema Source","text":""},{"location":"gocam/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: gocam:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"gocam/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"gocam/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"gocam/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:ExtractionResult native gocam:ExtractionResult"},{"location":"gocam/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gocam/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gocam/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"gocam/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Float/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GOCellComponentType/","title":"Enum: GOCellComponentType","text":"

URI: GOCellComponentType

This is a dynamic enum

"},{"location":"gocam/GOCellComponentType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GOCellComponentType/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GOCellComponentType/#linkml-source","title":"LinkML Source","text":"
name: GOCellComponentType\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nreachable_from:\n  source_ontology: obo:go\n  source_nodes:\n  - GO:0005575\n\n
"},{"location":"gocam/Gene/","title":"Class: Gene","text":"

URI: gocam:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/Gene/#inheritance","title":"Inheritance","text":""},{"location":"gocam/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/Gene/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations genes range Gene GeneOrganismRelationship gene range Gene GeneMolecularActivityRelationship gene range Gene GeneMolecularActivityRelationship2 gene range Gene GeneSubcellularLocalizationRelationship gene range Gene GeneGeneInteraction gene1 range Gene GeneGeneInteraction gene2 range Gene"},{"location":"gocam/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, bioportal:hgnc-nr"},{"location":"gocam/Gene/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Gene native gocam:Gene"},{"location":"gocam/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/GeneGeneInteraction/","title":"Class: GeneGeneInteraction","text":"

URI: gocam:GeneGeneInteraction

erDiagram\nGeneGeneInteraction {\n\n}\nGene {\n    string id  \n    string label  \n}\n\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\n\n
"},{"location":"gocam/GeneGeneInteraction/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneGeneInteraction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene1 0..1 Gene direct gene2 0..1 Gene direct"},{"location":"gocam/GeneGeneInteraction/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations gene_gene_interactions range GeneGeneInteraction"},{"location":"gocam/GeneGeneInteraction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneGeneInteraction/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneGeneInteraction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneGeneInteraction native gocam:GeneGeneInteraction"},{"location":"gocam/GeneGeneInteraction/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneGeneInteraction/#direct","title":"Direct","text":"
name: GeneGeneInteraction\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene1:\n    name: gene1\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n  gene2:\n    name: gene2\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n\n
"},{"location":"gocam/GeneGeneInteraction/#induced","title":"Induced","text":"
name: GeneGeneInteraction\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene1:\n    name: gene1\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene1\n    owner: GeneGeneInteraction\n    domain_of:\n    - GeneGeneInteraction\n    range: Gene\n  gene2:\n    name: gene2\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene2\n    owner: GeneGeneInteraction\n    domain_of:\n    - GeneGeneInteraction\n    range: Gene\n\n
"},{"location":"gocam/GeneLocation/","title":"Class: GeneLocation","text":"

URI: gocam:GeneLocation

erDiagram\nGeneLocation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/GeneLocation/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneLocation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/GeneLocation/#usages","title":"Usages","text":"used by used in type used GeneSubcellularLocalizationRelationship location range GeneLocation"},{"location":"gocam/GeneLocation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneLocation/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/GeneLocation/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:cl"},{"location":"gocam/GeneLocation/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneLocation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneLocation native gocam:GeneLocation"},{"location":"gocam/GeneLocation/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneLocation/#direct","title":"Direct","text":"
name: GeneLocation\nid_prefixes:\n- GO\n- CL\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - GOCellComponentType\n    - CellType\n    domain_of:\n    - NamedEntity\n    - Publication\n\n
"},{"location":"gocam/GeneLocation/#induced","title":"Induced","text":"
name: GeneLocation\nid_prefixes:\n- GO\n- CL\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - GOCellComponentType\n    - CellType\n    domain_of:\n    - NamedEntity\n    - Publication\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    values_from:\n    - GOCellComponentType\n    - CellType\n    identifier: true\n    alias: id\n    owner: GeneLocation\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: GeneLocation\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/GeneLocationEnum/","title":"Enum: GeneLocationEnum","text":"

URI: GeneLocationEnum

This is a dynamic enum

"},{"location":"gocam/GeneLocationEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneLocationEnum/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneLocationEnum/#linkml-source","title":"LinkML Source","text":"
name: GeneLocationEnum\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\ninherits:\n- GOCellComponent\n- CellType\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship/","title":"Class: GeneMolecularActivityRelationship","text":"

URI: gocam:GeneMolecularActivityRelationship

erDiagram\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneMolecularActivityRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct molecular_activity 0..1 MolecularActivity direct"},{"location":"gocam/GeneMolecularActivityRelationship/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations gene_functions range GeneMolecularActivityRelationship"},{"location":"gocam/GeneMolecularActivityRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneMolecularActivityRelationship/#annotations","title":"Annotations","text":"property value prompt.example TODO

gene: HGNC:1234 molecular_activity: GO:0003674 |

"},{"location":"gocam/GeneMolecularActivityRelationship/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneMolecularActivityRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneMolecularActivityRelationship native gocam:GeneMolecularActivityRelationship"},{"location":"gocam/GeneMolecularActivityRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneMolecularActivityRelationship/#direct","title":"Direct","text":"
name: GeneMolecularActivityRelationship\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: 'TODO\n\n\n      gene: HGNC:1234\n\n      molecular_activity: GO:0003674'\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene in the pair. This comes first.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular function in the pair. This comes second.\n          May be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: MolecularActivity\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship/#induced","title":"Induced","text":"
name: GeneMolecularActivityRelationship\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: 'TODO\n\n\n      gene: HGNC:1234\n\n      molecular_activity: GO:0003674'\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene in the pair. This comes first.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular function in the pair. This comes second.\n          May be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: molecular_activity\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    range: MolecularActivity\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship2/","title":"Class: GeneMolecularActivityRelationship2","text":"

URI: gocam:GeneMolecularActivityRelationship2

erDiagram\nGeneMolecularActivityRelationship2 {\n\n}\nMolecule {\n    string id  \n    string label  \n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneMolecularActivityRelationship2 ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship2 ||--|o MolecularActivity : \"molecular_activity\"\nGeneMolecularActivityRelationship2 ||--|o Molecule : \"target\"\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship2/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneMolecularActivityRelationship2/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct molecular_activity 0..1 MolecularActivity direct target 0..1 Molecule direct"},{"location":"gocam/GeneMolecularActivityRelationship2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneMolecularActivityRelationship2/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneMolecularActivityRelationship2/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneMolecularActivityRelationship2 native gocam:GeneMolecularActivityRelationship2"},{"location":"gocam/GeneMolecularActivityRelationship2/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneMolecularActivityRelationship2/#direct","title":"Direct","text":"
name: GeneMolecularActivityRelationship2\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular activity, for example, ubiquitination. May\n          be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: MolecularActivity\n  target:\n    name: target\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular entity that is the target of the molecular\n          activity.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Molecule\n\n
"},{"location":"gocam/GeneMolecularActivityRelationship2/#induced","title":"Induced","text":"
name: GeneMolecularActivityRelationship2\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular activity, for example, ubiquitination. May\n          be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: molecular_activity\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    range: MolecularActivity\n  target:\n    name: target\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular entity that is the target of the molecular\n          activity.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: target\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneMolecularActivityRelationship2\n    range: Molecule\n\n
"},{"location":"gocam/GeneOrganismRelationship/","title":"Class: GeneOrganismRelationship","text":"

URI: gocam:GeneOrganismRelationship

erDiagram\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"gocam/GeneOrganismRelationship/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneOrganismRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct organism 0..1 Organism direct"},{"location":"gocam/GeneOrganismRelationship/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations gene_organisms range GeneOrganismRelationship"},{"location":"gocam/GeneOrganismRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneOrganismRelationship/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneOrganismRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneOrganismRelationship native gocam:GeneOrganismRelationship"},{"location":"gocam/GeneOrganismRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneOrganismRelationship/#direct","title":"Direct","text":"
name: GeneOrganismRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n  organism:\n    name: organism\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Organism\n\n
"},{"location":"gocam/GeneOrganismRelationship/#induced","title":"Induced","text":"
name: GeneOrganismRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene\n    owner: GeneOrganismRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  organism:\n    name: organism\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: organism\n    owner: GeneOrganismRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    range: Organism\n\n
"},{"location":"gocam/GeneSubcellularLocalizationRelationship/","title":"Class: GeneSubcellularLocalizationRelationship","text":"

URI: gocam:GeneSubcellularLocalizationRelationship

erDiagram\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\n\n
"},{"location":"gocam/GeneSubcellularLocalizationRelationship/#inheritance","title":"Inheritance","text":""},{"location":"gocam/GeneSubcellularLocalizationRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct location 0..1 GeneLocation direct"},{"location":"gocam/GeneSubcellularLocalizationRelationship/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations gene_localizations range GeneSubcellularLocalizationRelationship"},{"location":"gocam/GeneSubcellularLocalizationRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GeneSubcellularLocalizationRelationship/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GeneSubcellularLocalizationRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneSubcellularLocalizationRelationship native gocam:GeneSubcellularLocalizationRelationship"},{"location":"gocam/GeneSubcellularLocalizationRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GeneSubcellularLocalizationRelationship/#direct","title":"Direct","text":"
name: GeneSubcellularLocalizationRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  location:\n    name: location\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: GeneLocation\n\n
"},{"location":"gocam/GeneSubcellularLocalizationRelationship/#induced","title":"Induced","text":"
name: GeneSubcellularLocalizationRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneSubcellularLocalizationRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  location:\n    name: location\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: location\n    owner: GeneSubcellularLocalizationRelationship\n    domain_of:\n    - GeneSubcellularLocalizationRelationship\n    range: GeneLocation\n\n
"},{"location":"gocam/GoCamAnnotations/","title":"Class: GoCamAnnotations","text":"

URI: gocam:GoCamAnnotations

erDiagram\nGoCamAnnotations {\n\n}\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nGeneGeneInteraction {\n\n}\nPathway {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\n\nGoCamAnnotations ||--}o Gene : \"genes\"\nGoCamAnnotations ||--}o Organism : \"organisms\"\nGoCamAnnotations ||--}o GeneOrganismRelationship : \"gene_organisms\"\nGoCamAnnotations ||--}o MolecularActivity : \"activities\"\nGoCamAnnotations ||--}o GeneMolecularActivityRelationship : \"gene_functions\"\nGoCamAnnotations ||--}o CellularProcess : \"cellular_processes\"\nGoCamAnnotations ||--}o Pathway : \"pathways\"\nGoCamAnnotations ||--}o GeneGeneInteraction : \"gene_gene_interactions\"\nGoCamAnnotations ||--}o GeneSubcellularLocalizationRelationship : \"gene_localizations\"\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"gocam/GoCamAnnotations/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance genes 0..* Gene semicolon-separated list of genes direct organisms 0..* Organism semicolon-separated list of organism taxons direct gene_organisms 0..* GeneOrganismRelationship direct activities 0..* MolecularActivity semicolon-separated list of molecular activities direct gene_functions 0..* GeneMolecularActivityRelationship semicolon-separated list of gene to molecular activity relationships direct cellular_processes 0..* CellularProcess semicolon-separated list of cellular processes direct pathways 0..* Pathway semicolon-separated list of pathways direct gene_gene_interactions 0..* GeneGeneInteraction semicolon-separated list of gene to gene interactions direct gene_localizations 0..* GeneSubcellularLocalizationRelationship semicolon-separated list of genes plus their location in the cell; for exampl... direct"},{"location":"gocam/GoCamAnnotations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/GoCamAnnotations/#schema-source","title":"Schema Source","text":""},{"location":"gocam/GoCamAnnotations/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GoCamAnnotations native gocam:GoCamAnnotations"},{"location":"gocam/GoCamAnnotations/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/GoCamAnnotations/#direct","title":"Direct","text":"
name: GoCamAnnotations\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Gene\n  organisms:\n    name: organisms\n    description: semicolon-separated list of organism taxons\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Organism\n  gene_organisms:\n    name: gene_organisms\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of asterisk separated gene to organism relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneOrganismRelationship\n  activities:\n    name: activities\n    description: semicolon-separated list of molecular activities\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: MolecularActivity\n  gene_functions:\n    name: gene_functions\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneMolecularActivityRelationship\n  cellular_processes:\n    name: cellular_processes\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: CellularProcess\n  pathways:\n    name: pathways\n    description: semicolon-separated list of pathways\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Pathway\n  gene_gene_interactions:\n    name: gene_gene_interactions\n    description: semicolon-separated list of gene to gene interactions\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneGeneInteraction\n  gene_localizations:\n    name: gene_localizations\n    description: semicolon-separated list of genes plus their location in the cell;\n      for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneSubcellularLocalizationRelationship\ntree_root: true\n\n
"},{"location":"gocam/GoCamAnnotations/#induced","title":"Induced","text":"
name: GoCamAnnotations\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: Gene\n  organisms:\n    name: organisms\n    description: semicolon-separated list of organism taxons\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: organisms\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: Organism\n  gene_organisms:\n    name: gene_organisms\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of asterisk separated gene to organism relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_organisms\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: GeneOrganismRelationship\n  activities:\n    name: activities\n    description: semicolon-separated list of molecular activities\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: activities\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: MolecularActivity\n  gene_functions:\n    name: gene_functions\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_functions\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: GeneMolecularActivityRelationship\n  cellular_processes:\n    name: cellular_processes\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: cellular_processes\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: CellularProcess\n  pathways:\n    name: pathways\n    description: semicolon-separated list of pathways\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: pathways\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: Pathway\n  gene_gene_interactions:\n    name: gene_gene_interactions\n    description: semicolon-separated list of gene to gene interactions\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_gene_interactions\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: GeneGeneInteraction\n  gene_localizations:\n    name: gene_localizations\n    description: semicolon-separated list of genes plus their location in the cell;\n      for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_localizations\n    owner: GoCamAnnotations\n    domain_of:\n    - GoCamAnnotations\n    range: GeneSubcellularLocalizationRelationship\ntree_root: true\n\n
"},{"location":"gocam/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"gocam/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Integer/#schema-source","title":"Schema Source","text":""},{"location":"gocam/MolecularActivity/","title":"Class: MolecularActivity","text":"

URI: gocam:MolecularActivity

erDiagram\nMolecularActivity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/MolecularActivity/#inheritance","title":"Inheritance","text":""},{"location":"gocam/MolecularActivity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/MolecularActivity/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations activities range MolecularActivity GeneMolecularActivityRelationship molecular_activity range MolecularActivity GeneMolecularActivityRelationship2 molecular_activity range MolecularActivity"},{"location":"gocam/MolecularActivity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/MolecularActivity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/MolecularActivity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"gocam/MolecularActivity/#schema-source","title":"Schema Source","text":""},{"location":"gocam/MolecularActivity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:MolecularActivity native gocam:MolecularActivity"},{"location":"gocam/MolecularActivity/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/MolecularActivity/#direct","title":"Direct","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/MolecularActivity/#induced","title":"Induced","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MolecularActivity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: MolecularActivity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/Molecule/","title":"Class: Molecule","text":"

URI: gocam:Molecule

erDiagram\nMolecule {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/Molecule/#inheritance","title":"Inheritance","text":""},{"location":"gocam/Molecule/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/Molecule/#usages","title":"Usages","text":"used by used in type used GeneMolecularActivityRelationship2 target range Molecule"},{"location":"gocam/Molecule/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Molecule/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/Molecule/#annotations","title":"Annotations","text":"property value annotators gilda:, sqlite:obo:chebi"},{"location":"gocam/Molecule/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Molecule/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Molecule native gocam:Molecule"},{"location":"gocam/Molecule/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Molecule/#direct","title":"Direct","text":"
name: Molecule\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/Molecule/#induced","title":"Induced","text":"
name: Molecule\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Molecule\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Molecule\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/NamedEntity/","title":"Class: NamedEntity","text":"

URI: gocam:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"gocam/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"gocam/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"gocam/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"gocam/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:NamedEntity native gocam:NamedEntity"},{"location":"gocam/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"gocam/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"gocam/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"gocam/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"gocam/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"gocam/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"gocam/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"gocam/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"gocam/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"gocam/Objectidentifier/#comments","title":"Comments","text":""},{"location":"gocam/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Organism/","title":"Class: Organism","text":"

URI: gocam:Organism

erDiagram\nOrganism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/Organism/#inheritance","title":"Inheritance","text":""},{"location":"gocam/Organism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/Organism/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations organisms range Organism GeneOrganismRelationship organism range Organism"},{"location":"gocam/Organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Organism/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/Organism/#annotations","title":"Annotations","text":"property value annotators gilda:, sqlite:obo:ncbitaxon"},{"location":"gocam/Organism/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Organism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Organism native gocam:Organism"},{"location":"gocam/Organism/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Organism/#direct","title":"Direct","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/Organism/#induced","title":"Induced","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/Pathway/","title":"Class: Pathway","text":"

URI: gocam:Pathway

erDiagram\nPathway {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/Pathway/#inheritance","title":"Inheritance","text":""},{"location":"gocam/Pathway/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/Pathway/#usages","title":"Usages","text":"used by used in type used GoCamAnnotations pathways range Pathway"},{"location":"gocam/Pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Pathway/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/Pathway/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:pw"},{"location":"gocam/Pathway/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Pathway/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Pathway native gocam:Pathway"},{"location":"gocam/Pathway/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Pathway/#direct","title":"Direct","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/Pathway/#induced","title":"Induced","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Pathway\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Pathway\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/Publication/","title":"Class: Publication","text":"

URI: gocam:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"gocam/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"gocam/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"gocam/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Publication/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Publication native gocam:Publication"},{"location":"gocam/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/gocam\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n\n
"},{"location":"gocam/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"gocam/RelationshipType/","title":"Class: RelationshipType","text":"

URI: gocam:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"gocam/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"gocam/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"gocam/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"gocam/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"gocam/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"gocam/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:RelationshipType native gocam:RelationshipType"},{"location":"gocam/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"gocam/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"gocam/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"gocam/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/String/#schema-source","title":"Schema Source","text":""},{"location":"gocam/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: gocam:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"gocam/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"gocam/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"gocam/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:TextWithTriples native gocam:TextWithTriples"},{"location":"gocam/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gocam/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"gocam/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"gocam/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Time/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: gocam:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"gocam/Triple/#inheritance","title":"Inheritance","text":""},{"location":"gocam/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"gocam/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"gocam/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Triple/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Triple native gocam:Triple"},{"location":"gocam/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"gocam/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"gocam/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"gocam/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"gocam/Uri/#comments","title":"Comments","text":""},{"location":"gocam/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Uri/#schema-source","title":"Schema Source","text":""},{"location":"gocam/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"gocam/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"gocam/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: gocam:abstract

"},{"location":"gocam/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gocam/abstract/#properties","title":"Properties","text":""},{"location":"gocam/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/abstract/#schema-source","title":"Schema Source","text":""},{"location":"gocam/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gocam/activities/","title":"Slot: activities","text":"

semicolon-separated list of molecular activities

URI: gocam:activities

"},{"location":"gocam/activities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/activities/#properties","title":"Properties","text":""},{"location":"gocam/activities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/activities/#schema-source","title":"Schema Source","text":""},{"location":"gocam/activities/#linkml-source","title":"LinkML Source","text":"
name: activities\ndescription: semicolon-separated list of molecular activities\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: activities\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: MolecularActivity\n\n
"},{"location":"gocam/cellular_processes/","title":"Slot: cellular_processes","text":"

semicolon-separated list of cellular processes

URI: gocam:cellular_processes

"},{"location":"gocam/cellular_processes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/cellular_processes/#properties","title":"Properties","text":""},{"location":"gocam/cellular_processes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/cellular_processes/#schema-source","title":"Schema Source","text":""},{"location":"gocam/cellular_processes/#linkml-source","title":"LinkML Source","text":"
name: cellular_processes\ndescription: semicolon-separated list of cellular processes\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: cellular_processes\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: CellularProcess\n\n
"},{"location":"gocam/combined_text/","title":"Slot: combined_text","text":"

URI: gocam:combined_text

"},{"location":"gocam/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gocam/combined_text/#properties","title":"Properties","text":""},{"location":"gocam/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"gocam/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gocam/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: gocam:extracted_object

"},{"location":"gocam/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/extracted_object/#properties","title":"Properties","text":""},{"location":"gocam/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"gocam/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"gocam/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: gocam:full_text

"},{"location":"gocam/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gocam/full_text/#properties","title":"Properties","text":""},{"location":"gocam/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/full_text/#schema-source","title":"Schema Source","text":""},{"location":"gocam/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gocam/gene/","title":"Slot: gene","text":"

URI: gocam:gene

"},{"location":"gocam/gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneOrganismRelationship no GeneMolecularActivityRelationship no GeneMolecularActivityRelationship2 no GeneSubcellularLocalizationRelationship no"},{"location":"gocam/gene/#properties","title":"Properties","text":""},{"location":"gocam/gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene/#linkml-source","title":"LinkML Source","text":"
name: gene\nalias: gene\ndomain_of:\n- GeneOrganismRelationship\n- GeneMolecularActivityRelationship\n- GeneMolecularActivityRelationship2\n- GeneSubcellularLocalizationRelationship\nrange: string\n\n
"},{"location":"gocam/gene1/","title":"Slot: gene1","text":"

URI: gocam:gene1

"},{"location":"gocam/gene1/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneGeneInteraction no"},{"location":"gocam/gene1/#properties","title":"Properties","text":""},{"location":"gocam/gene1/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene1/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene1/#linkml-source","title":"LinkML Source","text":"
name: gene1\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: gene1\nowner: GeneGeneInteraction\ndomain_of:\n- GeneGeneInteraction\nrange: Gene\n\n
"},{"location":"gocam/gene2/","title":"Slot: gene2","text":"

URI: gocam:gene2

"},{"location":"gocam/gene2/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneGeneInteraction no"},{"location":"gocam/gene2/#properties","title":"Properties","text":""},{"location":"gocam/gene2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene2/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene2/#linkml-source","title":"LinkML Source","text":"
name: gene2\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: gene2\nowner: GeneGeneInteraction\ndomain_of:\n- GeneGeneInteraction\nrange: Gene\n\n
"},{"location":"gocam/gene_functions/","title":"Slot: gene_functions","text":"

semicolon-separated list of gene to molecular activity relationships

URI: gocam:gene_functions

"},{"location":"gocam/gene_functions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/gene_functions/#properties","title":"Properties","text":""},{"location":"gocam/gene_functions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene_functions/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene_functions/#linkml-source","title":"LinkML Source","text":"
name: gene_functions\ndescription: semicolon-separated list of gene to molecular activity relationships\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_functions\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: GeneMolecularActivityRelationship\n\n
"},{"location":"gocam/gene_gene_interactions/","title":"Slot: gene_gene_interactions","text":"

semicolon-separated list of gene to gene interactions

URI: gocam:gene_gene_interactions

"},{"location":"gocam/gene_gene_interactions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/gene_gene_interactions/#properties","title":"Properties","text":""},{"location":"gocam/gene_gene_interactions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene_gene_interactions/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene_gene_interactions/#linkml-source","title":"LinkML Source","text":"
name: gene_gene_interactions\ndescription: semicolon-separated list of gene to gene interactions\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_gene_interactions\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: GeneGeneInteraction\n\n
"},{"location":"gocam/gene_localizations/","title":"Slot: gene_localizations","text":"

semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"

URI: gocam:gene_localizations

"},{"location":"gocam/gene_localizations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/gene_localizations/#properties","title":"Properties","text":""},{"location":"gocam/gene_localizations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene_localizations/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene_localizations/#linkml-source","title":"LinkML Source","text":"
name: gene_localizations\ndescription: semicolon-separated list of genes plus their location in the cell; for\n  example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_localizations\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: GeneSubcellularLocalizationRelationship\n\n
"},{"location":"gocam/gene_organisms/","title":"Slot: gene_organisms","text":"

URI: gocam:gene_organisms

"},{"location":"gocam/gene_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/gene_organisms/#properties","title":"Properties","text":""},{"location":"gocam/gene_organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/gene_organisms/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of asterisk separated gene to organism relationships"},{"location":"gocam/gene_organisms/#schema-source","title":"Schema Source","text":""},{"location":"gocam/gene_organisms/#linkml-source","title":"LinkML Source","text":"
name: gene_organisms\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of asterisk separated gene to organism relationships\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_organisms\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: GeneOrganismRelationship\n\n
"},{"location":"gocam/genes/","title":"Slot: genes","text":"

semicolon-separated list of genes

URI: gocam:genes

"},{"location":"gocam/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/genes/#properties","title":"Properties","text":""},{"location":"gocam/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/genes/#schema-source","title":"Schema Source","text":""},{"location":"gocam/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\ndescription: semicolon-separated list of genes\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: genes\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: Gene\n\n
"},{"location":"gocam/gocam-template/","title":"gocam-template","text":"

A template for GO-CAMs

URI: http://w3id.org/ontogpt/gocam

"},{"location":"gocam/id/","title":"Slot: id","text":"

URI: gocam:id

"},{"location":"gocam/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Pathway no CellularProcess no MolecularActivity no GeneLocation yes Organism no Molecule no NamedEntity no RelationshipType no Publication no"},{"location":"gocam/id/#properties","title":"Properties","text":""},{"location":"gocam/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"gocam/input_id/","title":"Slot: input_id","text":"

URI: gocam:input_id

"},{"location":"gocam/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/input_id/#properties","title":"Properties","text":""},{"location":"gocam/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/input_id/#schema-source","title":"Schema Source","text":""},{"location":"gocam/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gocam/input_text/","title":"Slot: input_text","text":"

URI: gocam:input_text

"},{"location":"gocam/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/input_text/#properties","title":"Properties","text":""},{"location":"gocam/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/input_text/#schema-source","title":"Schema Source","text":""},{"location":"gocam/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gocam/input_title/","title":"Slot: input_title","text":"

URI: gocam:input_title

"},{"location":"gocam/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/input_title/#properties","title":"Properties","text":""},{"location":"gocam/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/input_title/#schema-source","title":"Schema Source","text":""},{"location":"gocam/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gocam/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"gocam/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Pathway no CellularProcess no MolecularActivity no GeneLocation no Organism no Molecule no NamedEntity no RelationshipType no"},{"location":"gocam/label/#properties","title":"Properties","text":""},{"location":"gocam/label/#aliases","title":"Aliases","text":""},{"location":"gocam/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"gocam/label/#schema-source","title":"Schema Source","text":""},{"location":"gocam/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/gocam\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"gocam/location/","title":"Slot: location","text":"

URI: gocam:location

"},{"location":"gocam/location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneSubcellularLocalizationRelationship no"},{"location":"gocam/location/#properties","title":"Properties","text":""},{"location":"gocam/location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/location/#schema-source","title":"Schema Source","text":""},{"location":"gocam/location/#linkml-source","title":"LinkML Source","text":"
name: location\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: location\nowner: GeneSubcellularLocalizationRelationship\ndomain_of:\n- GeneSubcellularLocalizationRelationship\nrange: GeneLocation\n\n
"},{"location":"gocam/molecular_activity/","title":"Slot: molecular_activity","text":"

URI: gocam:molecular_activity

"},{"location":"gocam/molecular_activity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship no GeneMolecularActivityRelationship2 no"},{"location":"gocam/molecular_activity/#properties","title":"Properties","text":""},{"location":"gocam/molecular_activity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/molecular_activity/#linkml-source","title":"LinkML Source","text":"
name: molecular_activity\nalias: molecular_activity\ndomain_of:\n- GeneMolecularActivityRelationship\n- GeneMolecularActivityRelationship2\nrange: string\n\n
"},{"location":"gocam/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: gocam:named_entities

"},{"location":"gocam/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/named_entities/#properties","title":"Properties","text":""},{"location":"gocam/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"gocam/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gocam/object/","title":"Slot: object","text":"

URI: gocam:object

"},{"location":"gocam/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/object/#properties","title":"Properties","text":""},{"location":"gocam/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/object/#schema-source","title":"Schema Source","text":""},{"location":"gocam/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gocam/object_id/","title":"Slot: object_id","text":"

URI: gocam:object_id

"},{"location":"gocam/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gocam/object_id/#properties","title":"Properties","text":""},{"location":"gocam/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/object_id/#schema-source","title":"Schema Source","text":""},{"location":"gocam/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gocam/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: gocam:object_qualifier

"},{"location":"gocam/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/object_qualifier/#properties","title":"Properties","text":""},{"location":"gocam/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gocam/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gocam/object_text/","title":"Slot: object_text","text":"

URI: gocam:object_text

"},{"location":"gocam/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gocam/object_text/#properties","title":"Properties","text":""},{"location":"gocam/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/object_text/#schema-source","title":"Schema Source","text":""},{"location":"gocam/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gocam/organism/","title":"Slot: organism","text":"

URI: gocam:organism

"},{"location":"gocam/organism/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneOrganismRelationship no"},{"location":"gocam/organism/#properties","title":"Properties","text":""},{"location":"gocam/organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/organism/#schema-source","title":"Schema Source","text":""},{"location":"gocam/organism/#linkml-source","title":"LinkML Source","text":"
name: organism\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: organism\nowner: GeneOrganismRelationship\ndomain_of:\n- GeneOrganismRelationship\nrange: Organism\n\n
"},{"location":"gocam/organisms/","title":"Slot: organisms","text":"

semicolon-separated list of organism taxons

URI: gocam:organisms

"},{"location":"gocam/organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/organisms/#properties","title":"Properties","text":""},{"location":"gocam/organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/organisms/#schema-source","title":"Schema Source","text":""},{"location":"gocam/organisms/#linkml-source","title":"LinkML Source","text":"
name: organisms\ndescription: semicolon-separated list of organism taxons\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: organisms\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: Organism\n\n
"},{"location":"gocam/pathways/","title":"Slot: pathways","text":"

semicolon-separated list of pathways

URI: gocam:pathways

"},{"location":"gocam/pathways/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GoCamAnnotations no"},{"location":"gocam/pathways/#properties","title":"Properties","text":""},{"location":"gocam/pathways/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/pathways/#schema-source","title":"Schema Source","text":""},{"location":"gocam/pathways/#linkml-source","title":"LinkML Source","text":"
name: pathways\ndescription: semicolon-separated list of pathways\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: pathways\nowner: GoCamAnnotations\ndomain_of:\n- GoCamAnnotations\nrange: Pathway\n\n
"},{"location":"gocam/predicate/","title":"Slot: predicate","text":"

URI: gocam:predicate

"},{"location":"gocam/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/predicate/#properties","title":"Properties","text":""},{"location":"gocam/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/predicate/#schema-source","title":"Schema Source","text":""},{"location":"gocam/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"gocam/prompt/","title":"Slot: prompt","text":"

URI: gocam:prompt

"},{"location":"gocam/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/prompt/#properties","title":"Properties","text":""},{"location":"gocam/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/prompt/#schema-source","title":"Schema Source","text":""},{"location":"gocam/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gocam/publication/","title":"Slot: publication","text":"

URI: gocam:publication

"},{"location":"gocam/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"gocam/publication/#properties","title":"Properties","text":""},{"location":"gocam/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"gocam/publication/#schema-source","title":"Schema Source","text":""},{"location":"gocam/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"gocam/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: gocam:qualifier

"},{"location":"gocam/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/qualifier/#properties","title":"Properties","text":""},{"location":"gocam/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gocam/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"gocam/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: gocam:raw_completion_output

"},{"location":"gocam/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"gocam/raw_completion_output/#properties","title":"Properties","text":""},{"location":"gocam/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"gocam/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"gocam/subject/","title":"Slot: subject","text":"

URI: gocam:subject

"},{"location":"gocam/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/subject/#properties","title":"Properties","text":""},{"location":"gocam/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/subject/#schema-source","title":"Schema Source","text":""},{"location":"gocam/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gocam/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: gocam:subject_qualifier

"},{"location":"gocam/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"gocam/subject_qualifier/#properties","title":"Properties","text":""},{"location":"gocam/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"gocam/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"gocam/subject_text/","title":"Slot: subject_text","text":"

URI: gocam:subject_text

"},{"location":"gocam/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"gocam/subject_text/#properties","title":"Properties","text":""},{"location":"gocam/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"gocam/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"gocam/target/","title":"Slot: target","text":"

URI: gocam:target

"},{"location":"gocam/target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship2 no"},{"location":"gocam/target/#properties","title":"Properties","text":""},{"location":"gocam/target/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/target/#annotations","title":"Annotations","text":"property value prompt the name of the molecular entity that is the target of the molecular activity."},{"location":"gocam/target/#schema-source","title":"Schema Source","text":""},{"location":"gocam/target/#linkml-source","title":"LinkML Source","text":"
name: target\nannotations:\n  prompt:\n    tag: prompt\n    value: the name of the molecular entity that is the target of the molecular activity.\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: target\nowner: GeneMolecularActivityRelationship2\ndomain_of:\n- GeneMolecularActivityRelationship2\nrange: Molecule\n\n
"},{"location":"gocam/title/","title":"Slot: title","text":"

The title of the publication

URI: gocam:title

"},{"location":"gocam/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"gocam/title/#properties","title":"Properties","text":""},{"location":"gocam/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/title/#schema-source","title":"Schema Source","text":""},{"location":"gocam/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"gocam/triples/","title":"Slot: triples","text":"

URI: gocam:triples

"},{"location":"gocam/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"gocam/triples/#properties","title":"Properties","text":""},{"location":"gocam/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gocam/triples/#schema-source","title":"Schema Source","text":""},{"location":"gocam/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"halo/","title":"Ontology Class Template","text":"

A template for Ontology Classes

URI: https://w3id.org/ontogpt/halo

Name: ontology-class

"},{"location":"halo/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nOntology {\n\n}\nOntologyElement {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\nCategory {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nOntology ||--}o OntologyElement : \"elements\"\nOntologyElement ||--}o Category : \"categories\"\nOntologyElement ||--}o OntologyElement : \"subclass_of\"\nOntologyElement ||--}o OntologyElement : \"part_of\"\nOntologyElement ||--}o OntologyElement : \"subtypes\"\nOntologyElement ||--}o OntologyElement : \"parts\"\nCategory ||--}o Category : \"categories\"\nCategory ||--}o OntologyElement : \"subclass_of\"\nCategory ||--}o OntologyElement : \"part_of\"\nCategory ||--}o OntologyElement : \"subtypes\"\nCategory ||--}o OntologyElement : \"parts\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"halo/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None RelationshipType None Ontology None OntologyElement None Category None Publication None TextWithTriples None"},{"location":"halo/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication categories a list of the categories to which this entity belongs combined_text context the ontology to which this belongs (single-valued) description a textual description of the entity (single-valued) elements equivalent_to an OWL class expression with the necessary and sufficient conditions for this... extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing name the name of the entity named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text part_of a list of things this element is part of parts a list of names of things this element has as parts (components) predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subclass_of a list of parent class (superclasses) of this entity subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text subtypes a list of child classes (subclasses) of this entity synonyms a list of alternative names of the entity title The title of the publication triples"},{"location":"halo/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"halo/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"halo/#subsets","title":"Subsets","text":"Subset Description"},{"location":"halo/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: oc:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"halo/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"halo/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"halo/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:AnnotatorResult native oc:AnnotatorResult"},{"location":"halo/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n\n
"},{"location":"halo/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"halo/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"halo/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"halo/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"halo/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Any/#schema-source","title":"Schema Source","text":""},{"location":"halo/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native oc:Any"},{"location":"halo/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/halo\nclass_uri: linkml:Any\n\n
"},{"location":"halo/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/halo\nclass_uri: linkml:Any\n\n
"},{"location":"halo/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"halo/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"halo/Category/","title":"Class: Category","text":"

URI: oc:Category

erDiagram\nCategory {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\nOntologyElement {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\n\nCategory ||--}o Category : \"categories\"\nCategory ||--}o OntologyElement : \"subclass_of\"\nCategory ||--}o OntologyElement : \"part_of\"\nCategory ||--}o OntologyElement : \"subtypes\"\nCategory ||--}o OntologyElement : \"parts\"\nOntologyElement ||--}o Category : \"categories\"\nOntologyElement ||--}o OntologyElement : \"subclass_of\"\nOntologyElement ||--}o OntologyElement : \"part_of\"\nOntologyElement ||--}o OntologyElement : \"subtypes\"\nOntologyElement ||--}o OntologyElement : \"parts\"\n\n
"},{"location":"halo/Category/#inheritance","title":"Inheritance","text":""},{"location":"halo/Category/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance name 1..1 String the name of the entity OntologyElement context 0..1 String the ontology to which this belongs (single-valued) OntologyElement description 0..1 String a textual description of the entity (single-valued) OntologyElement synonyms 0..* String a list of alternative names of the entity OntologyElement categories 0..* Category a list of the categories to which this entity belongs OntologyElement subclass_of 0..* OntologyElement a list of parent class (superclasses) of this entity OntologyElement part_of 0..* OntologyElement a list of things this element is part of OntologyElement subtypes 0..* OntologyElement a list of child classes (subclasses) of this entity OntologyElement parts 0..* OntologyElement a list of names of things this element has as parts (components) OntologyElement equivalent_to 0..1 String an OWL class expression with the necessary and sufficient conditions for this... OntologyElement"},{"location":"halo/Category/#usages","title":"Usages","text":"used by used in type used OntologyElement categories range Category Category categories range Category"},{"location":"halo/Category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Category/#schema-source","title":"Schema Source","text":""},{"location":"halo/Category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Category native oc:Category"},{"location":"halo/Category/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/Category/#direct","title":"Direct","text":"
name: Category\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: OntologyElement\n\n
"},{"location":"halo/Category/#induced","title":"Induced","text":"
name: Category\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: OntologyElement\nattributes:\n  name:\n    name: name\n    description: the name of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    alias: name\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: string\n    required: true\n  context:\n    name: context\n    description: the ontology to which this belongs (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: context\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: string\n  description:\n    name: description\n    description: a textual description of the entity (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: description\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: string\n  synonyms:\n    name: synonyms\n    description: a list of alternative names of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: string\n  categories:\n    name: categories\n    description: a list of the categories to which this entity belongs\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: categories\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: Category\n  subclass_of:\n    name: subclass_of\n    description: a list of parent class (superclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: rdfs:subClassOf\n    multivalued: true\n    alias: subclass_of\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: OntologyElement\n  part_of:\n    name: part_of\n    description: a list of things this element is part of\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: part_of\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: OntologyElement\n  subtypes:\n    name: subtypes\n    description: a list of child classes (subclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: Category\n    domain_of:\n    - OntologyElement\n    inverse: subclass_of\n    range: OntologyElement\n  parts:\n    name: parts\n    description: a list of names of things this element has as parts (components)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: parts\n    owner: Category\n    domain_of:\n    - OntologyElement\n    inverse: part_of\n    range: OntologyElement\n  equivalent_to:\n    name: equivalent_to\n    description: an OWL class expression with the necessary and sufficient conditions\n      for this entity to be an instance of this class\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: equivalent_to\n    owner: Category\n    domain_of:\n    - OntologyElement\n    range: string\n\n
"},{"location":"halo/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: oc:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"halo/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"halo/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"halo/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"halo/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:CompoundExpression native oc:CompoundExpression"},{"location":"halo/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/halo\nabstract: true\n\n
"},{"location":"halo/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/halo\nabstract: true\n\n
"},{"location":"halo/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"halo/Curie/#comments","title":"Comments","text":""},{"location":"halo/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Curie/#schema-source","title":"Schema Source","text":""},{"location":"halo/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"halo/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Date/#schema-source","title":"Schema Source","text":""},{"location":"halo/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"halo/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"halo/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"halo/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"halo/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"halo/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"halo/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"halo/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Double/#schema-source","title":"Schema Source","text":""},{"location":"halo/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: oc:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"halo/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"halo/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"halo/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:ExtractionResult native oc:ExtractionResult"},{"location":"halo/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"halo/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Float/#schema-source","title":"Schema Source","text":""},{"location":"halo/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"halo/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Integer/#schema-source","title":"Schema Source","text":""},{"location":"halo/NamedEntity/","title":"Class: NamedEntity","text":"

URI: oc:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"halo/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"halo/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"halo/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"halo/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"halo/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:NamedEntity native oc:NamedEntity"},{"location":"halo/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/halo\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/halo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"halo/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/halo\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/halo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"halo/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"halo/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"halo/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"halo/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"halo/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"halo/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"halo/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"halo/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"halo/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"halo/Objectidentifier/#comments","title":"Comments","text":""},{"location":"halo/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"halo/Ontology/","title":"Class: Ontology","text":"

URI: oc:Ontology

erDiagram\nOntology {\n\n}\nOntologyElement {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\nCategory {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\n\nOntology ||--}o OntologyElement : \"elements\"\nOntologyElement ||--}o Category : \"categories\"\nOntologyElement ||--}o OntologyElement : \"subclass_of\"\nOntologyElement ||--}o OntologyElement : \"part_of\"\nOntologyElement ||--}o OntologyElement : \"subtypes\"\nOntologyElement ||--}o OntologyElement : \"parts\"\nCategory ||--}o Category : \"categories\"\nCategory ||--}o OntologyElement : \"subclass_of\"\nCategory ||--}o OntologyElement : \"part_of\"\nCategory ||--}o OntologyElement : \"subtypes\"\nCategory ||--}o OntologyElement : \"parts\"\n\n
"},{"location":"halo/Ontology/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance elements 0..* OntologyElement direct"},{"location":"halo/Ontology/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Ontology/#schema-source","title":"Schema Source","text":""},{"location":"halo/Ontology/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Ontology native oc:Ontology"},{"location":"halo/Ontology/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/Ontology/#direct","title":"Direct","text":"
name: Ontology\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  elements:\n    name: elements\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    range: OntologyElement\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/Ontology/#induced","title":"Induced","text":"
name: Ontology\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  elements:\n    name: elements\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: elements\n    owner: Ontology\n    domain_of:\n    - Ontology\n    range: OntologyElement\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/OntologyElement/","title":"Class: OntologyElement","text":"

URI: oc:OntologyElement

erDiagram\nOntologyElement {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\nCategory {\n    string name  \n    string context  \n    string description  \n    stringList synonyms  \n    string equivalent_to  \n}\n\nOntologyElement ||--}o Category : \"categories\"\nOntologyElement ||--}o OntologyElement : \"subclass_of\"\nOntologyElement ||--}o OntologyElement : \"part_of\"\nOntologyElement ||--}o OntologyElement : \"subtypes\"\nOntologyElement ||--}o OntologyElement : \"parts\"\nCategory ||--}o Category : \"categories\"\nCategory ||--}o OntologyElement : \"subclass_of\"\nCategory ||--}o OntologyElement : \"part_of\"\nCategory ||--}o OntologyElement : \"subtypes\"\nCategory ||--}o OntologyElement : \"parts\"\n\n
"},{"location":"halo/OntologyElement/#inheritance","title":"Inheritance","text":""},{"location":"halo/OntologyElement/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance name 1..1 String the name of the entity direct context 0..1 String the ontology to which this belongs (single-valued) direct description 0..1 String a textual description of the entity (single-valued) direct synonyms 0..* String a list of alternative names of the entity direct categories 0..* Category a list of the categories to which this entity belongs direct subclass_of 0..* OntologyElement a list of parent class (superclasses) of this entity direct part_of 0..* OntologyElement a list of things this element is part of direct subtypes 0..* OntologyElement a list of child classes (subclasses) of this entity direct parts 0..* OntologyElement a list of names of things this element has as parts (components) direct equivalent_to 0..1 String an OWL class expression with the necessary and sufficient conditions for this... direct"},{"location":"halo/OntologyElement/#usages","title":"Usages","text":"used by used in type used Ontology elements range OntologyElement OntologyElement subclass_of range OntologyElement OntologyElement part_of range OntologyElement OntologyElement subtypes range OntologyElement OntologyElement parts range OntologyElement Category subclass_of range OntologyElement Category part_of range OntologyElement Category subtypes range OntologyElement Category parts range OntologyElement"},{"location":"halo/OntologyElement/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/OntologyElement/#schema-source","title":"Schema Source","text":""},{"location":"halo/OntologyElement/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyElement native oc:OntologyElement"},{"location":"halo/OntologyElement/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/OntologyElement/#direct","title":"Direct","text":"
name: OntologyElement\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  name:\n    name: name\n    description: the name of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    required: true\n  context:\n    name: context\n    description: the ontology to which this belongs (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  description:\n    name: description\n    description: a textual description of the entity (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  synonyms:\n    name: synonyms\n    description: a list of alternative names of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n  categories:\n    name: categories\n    description: a list of the categories to which this entity belongs\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    range: Category\n  subclass_of:\n    name: subclass_of\n    description: a list of parent class (superclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: rdfs:subClassOf\n    multivalued: true\n    range: OntologyElement\n  part_of:\n    name: part_of\n    description: a list of things this element is part of\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: BFO:0000050\n    multivalued: true\n    range: OntologyElement\n  subtypes:\n    name: subtypes\n    description: a list of child classes (subclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    inverse: subclass_of\n    range: OntologyElement\n  parts:\n    name: parts\n    description: a list of names of things this element has as parts (components)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    inverse: part_of\n    range: OntologyElement\n  equivalent_to:\n    name: equivalent_to\n    description: an OWL class expression with the necessary and sufficient conditions\n      for this entity to be an instance of this class\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: string\n\n
"},{"location":"halo/OntologyElement/#induced","title":"Induced","text":"
name: OntologyElement\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  name:\n    name: name\n    description: the name of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    alias: name\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: string\n    required: true\n  context:\n    name: context\n    description: the ontology to which this belongs (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: context\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: string\n  description:\n    name: description\n    description: a textual description of the entity (single-valued)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: description\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: string\n  synonyms:\n    name: synonyms\n    description: a list of alternative names of the entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: string\n  categories:\n    name: categories\n    description: a list of the categories to which this entity belongs\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: categories\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: Category\n  subclass_of:\n    name: subclass_of\n    description: a list of parent class (superclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: rdfs:subClassOf\n    multivalued: true\n    alias: subclass_of\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: OntologyElement\n  part_of:\n    name: part_of\n    description: a list of things this element is part of\n    from_schema: https://w3id.org/ontogpt/halo\n    slot_uri: BFO:0000050\n    multivalued: true\n    alias: part_of\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: OntologyElement\n  subtypes:\n    name: subtypes\n    description: a list of child classes (subclasses) of this entity\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: subtypes\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    inverse: subclass_of\n    range: OntologyElement\n  parts:\n    name: parts\n    description: a list of names of things this element has as parts (components)\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: parts\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    inverse: part_of\n    range: OntologyElement\n  equivalent_to:\n    name: equivalent_to\n    description: an OWL class expression with the necessary and sufficient conditions\n      for this entity to be an instance of this class\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: equivalent_to\n    owner: OntologyElement\n    domain_of:\n    - OntologyElement\n    range: string\n\n
"},{"location":"halo/Publication/","title":"Class: Publication","text":"

URI: oc:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"halo/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"halo/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"halo/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Publication/#schema-source","title":"Schema Source","text":""},{"location":"halo/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Publication native oc:Publication"},{"location":"halo/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/halo\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n\n
"},{"location":"halo/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/halo\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"halo/RelationshipType/","title":"Class: RelationshipType","text":"

URI: oc:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"halo/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"halo/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"halo/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"halo/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"halo/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"halo/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:RelationshipType native oc:RelationshipType"},{"location":"halo/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: NamedEntity\n\n
"},{"location":"halo/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/halo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"halo/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"halo/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/String/#schema-source","title":"Schema Source","text":""},{"location":"halo/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: oc:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"halo/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"halo/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"halo/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:TextWithTriples native oc:TextWithTriples"},{"location":"halo/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/halo\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"halo/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"halo/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Time/#schema-source","title":"Schema Source","text":""},{"location":"halo/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: oc:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"halo/Triple/#inheritance","title":"Inheritance","text":""},{"location":"halo/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"halo/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"halo/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Triple/#schema-source","title":"Schema Source","text":""},{"location":"halo/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Triple native oc:Triple"},{"location":"halo/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"halo/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"halo/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/halo\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/halo\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"halo/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"halo/Uri/#comments","title":"Comments","text":""},{"location":"halo/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Uri/#schema-source","title":"Schema Source","text":""},{"location":"halo/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"halo/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"halo/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: oc:abstract

"},{"location":"halo/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"halo/abstract/#properties","title":"Properties","text":""},{"location":"halo/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/abstract/#schema-source","title":"Schema Source","text":""},{"location":"halo/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"halo/categories/","title":"Slot: categories","text":"

a list of the categories to which this entity belongs

URI: oc:categories

"},{"location":"halo/categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/categories/#properties","title":"Properties","text":""},{"location":"halo/categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/categories/#schema-source","title":"Schema Source","text":""},{"location":"halo/categories/#linkml-source","title":"LinkML Source","text":"
name: categories\ndescription: a list of the categories to which this entity belongs\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: categories\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: Category\n\n
"},{"location":"halo/combined_text/","title":"Slot: combined_text","text":"

URI: oc:combined_text

"},{"location":"halo/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"halo/combined_text/#properties","title":"Properties","text":""},{"location":"halo/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"halo/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"halo/context/","title":"Slot: context","text":"

the ontology to which this belongs (single-valued)

URI: oc:context

"},{"location":"halo/context/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/context/#properties","title":"Properties","text":""},{"location":"halo/context/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/context/#schema-source","title":"Schema Source","text":""},{"location":"halo/context/#linkml-source","title":"LinkML Source","text":"
name: context\ndescription: the ontology to which this belongs (single-valued)\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: context\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: string\n\n
"},{"location":"halo/description/","title":"Slot: description","text":"

a textual description of the entity (single-valued)

URI: oc:description

"},{"location":"halo/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/description/#properties","title":"Properties","text":""},{"location":"halo/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/description/#schema-source","title":"Schema Source","text":""},{"location":"halo/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a textual description of the entity (single-valued)\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: description\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: string\n\n
"},{"location":"halo/elements/","title":"Slot: elements","text":"

URI: oc:elements

"},{"location":"halo/elements/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Ontology no"},{"location":"halo/elements/#properties","title":"Properties","text":""},{"location":"halo/elements/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/elements/#schema-source","title":"Schema Source","text":""},{"location":"halo/elements/#linkml-source","title":"LinkML Source","text":"
name: elements\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: elements\nowner: Ontology\ndomain_of:\n- Ontology\nrange: OntologyElement\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"halo/equivalent_to/","title":"Slot: equivalent_to","text":"

an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class

URI: oc:equivalent_to

"},{"location":"halo/equivalent_to/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/equivalent_to/#properties","title":"Properties","text":""},{"location":"halo/equivalent_to/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/equivalent_to/#schema-source","title":"Schema Source","text":""},{"location":"halo/equivalent_to/#linkml-source","title":"LinkML Source","text":"
name: equivalent_to\ndescription: an OWL class expression with the necessary and sufficient conditions\n  for this entity to be an instance of this class\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: equivalent_to\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: string\n\n
"},{"location":"halo/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: oc:extracted_object

"},{"location":"halo/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/extracted_object/#properties","title":"Properties","text":""},{"location":"halo/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"halo/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"halo/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: oc:full_text

"},{"location":"halo/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"halo/full_text/#properties","title":"Properties","text":""},{"location":"halo/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/full_text/#schema-source","title":"Schema Source","text":""},{"location":"halo/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"halo/id/","title":"Slot: id","text":"

URI: oc:id

"},{"location":"halo/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NamedEntity no RelationshipType no Publication no"},{"location":"halo/id/#properties","title":"Properties","text":""},{"location":"halo/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"halo/input_id/","title":"Slot: input_id","text":"

URI: oc:input_id

"},{"location":"halo/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/input_id/#properties","title":"Properties","text":""},{"location":"halo/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/input_id/#schema-source","title":"Schema Source","text":""},{"location":"halo/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"halo/input_text/","title":"Slot: input_text","text":"

URI: oc:input_text

"},{"location":"halo/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/input_text/#properties","title":"Properties","text":""},{"location":"halo/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/input_text/#schema-source","title":"Schema Source","text":""},{"location":"halo/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"halo/input_title/","title":"Slot: input_title","text":"

URI: oc:input_title

"},{"location":"halo/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/input_title/#properties","title":"Properties","text":""},{"location":"halo/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/input_title/#schema-source","title":"Schema Source","text":""},{"location":"halo/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"halo/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"halo/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NamedEntity no RelationshipType no"},{"location":"halo/label/#properties","title":"Properties","text":""},{"location":"halo/label/#aliases","title":"Aliases","text":""},{"location":"halo/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"halo/label/#schema-source","title":"Schema Source","text":""},{"location":"halo/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: https://w3id.org/ontogpt/halo\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"halo/name/","title":"Slot: name","text":"

the name of the entity

URI: oc:name

"},{"location":"halo/name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/name/#properties","title":"Properties","text":""},{"location":"halo/name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/name/#schema-source","title":"Schema Source","text":""},{"location":"halo/name/#linkml-source","title":"LinkML Source","text":"
name: name\ndescription: the name of the entity\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nidentifier: true\nalias: name\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: string\nrequired: true\n\n
"},{"location":"halo/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: oc:named_entities

"},{"location":"halo/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/named_entities/#properties","title":"Properties","text":""},{"location":"halo/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"halo/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"halo/object/","title":"Slot: object","text":"

URI: oc:object

"},{"location":"halo/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/object/#properties","title":"Properties","text":""},{"location":"halo/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/object/#schema-source","title":"Schema Source","text":""},{"location":"halo/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"halo/object_id/","title":"Slot: object_id","text":"

URI: oc:object_id

"},{"location":"halo/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"halo/object_id/#properties","title":"Properties","text":""},{"location":"halo/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/object_id/#schema-source","title":"Schema Source","text":""},{"location":"halo/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"halo/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: oc:object_qualifier

"},{"location":"halo/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/object_qualifier/#properties","title":"Properties","text":""},{"location":"halo/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"halo/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"halo/object_text/","title":"Slot: object_text","text":"

URI: oc:object_text

"},{"location":"halo/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"halo/object_text/#properties","title":"Properties","text":""},{"location":"halo/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/object_text/#schema-source","title":"Schema Source","text":""},{"location":"halo/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"halo/ontology-class/","title":"ontology-class","text":"

A template for Ontology Classes

URI: https://w3id.org/ontogpt/halo

"},{"location":"halo/part_of/","title":"Slot: part_of","text":"

a list of things this element is part of

URI: BFO:0000050

"},{"location":"halo/part_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/part_of/#properties","title":"Properties","text":""},{"location":"halo/part_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/part_of/#schema-source","title":"Schema Source","text":""},{"location":"halo/part_of/#linkml-source","title":"LinkML Source","text":"
name: part_of\ndescription: a list of things this element is part of\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nslot_uri: BFO:0000050\nmultivalued: true\nalias: part_of\ndomain_of:\n- OntologyElement\nrange: OntologyElement\n\n
"},{"location":"halo/parts/","title":"Slot: parts","text":"

a list of names of things this element has as parts (components)

URI: oc:parts

"},{"location":"halo/parts/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/parts/#properties","title":"Properties","text":""},{"location":"halo/parts/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/parts/#schema-source","title":"Schema Source","text":""},{"location":"halo/parts/#linkml-source","title":"LinkML Source","text":"
name: parts\ndescription: a list of names of things this element has as parts (components)\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: parts\nowner: OntologyElement\ndomain_of:\n- OntologyElement\ninverse: part_of\nrange: OntologyElement\n\n
"},{"location":"halo/predicate/","title":"Slot: predicate","text":"

URI: oc:predicate

"},{"location":"halo/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/predicate/#properties","title":"Properties","text":""},{"location":"halo/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/predicate/#schema-source","title":"Schema Source","text":""},{"location":"halo/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"halo/prompt/","title":"Slot: prompt","text":"

URI: oc:prompt

"},{"location":"halo/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/prompt/#properties","title":"Properties","text":""},{"location":"halo/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/prompt/#schema-source","title":"Schema Source","text":""},{"location":"halo/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"halo/publication/","title":"Slot: publication","text":"

URI: oc:publication

"},{"location":"halo/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"halo/publication/#properties","title":"Properties","text":""},{"location":"halo/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"halo/publication/#schema-source","title":"Schema Source","text":""},{"location":"halo/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"halo/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: oc:qualifier

"},{"location":"halo/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/qualifier/#properties","title":"Properties","text":""},{"location":"halo/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"halo/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"halo/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: oc:raw_completion_output

"},{"location":"halo/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"halo/raw_completion_output/#properties","title":"Properties","text":""},{"location":"halo/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"halo/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"halo/subclass_of/","title":"Slot: subclass_of","text":"

a list of parent class (superclasses) of this entity

URI: rdfs:subClassOf

"},{"location":"halo/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/subclass_of/#properties","title":"Properties","text":""},{"location":"halo/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"halo/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\ndescription: a list of parent class (superclasses) of this entity\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nslot_uri: rdfs:subClassOf\nmultivalued: true\nalias: subclass_of\ndomain_of:\n- OntologyElement\nrange: OntologyElement\n\n
"},{"location":"halo/subject/","title":"Slot: subject","text":"

URI: oc:subject

"},{"location":"halo/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/subject/#properties","title":"Properties","text":""},{"location":"halo/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/subject/#schema-source","title":"Schema Source","text":""},{"location":"halo/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"halo/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: oc:subject_qualifier

"},{"location":"halo/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"halo/subject_qualifier/#properties","title":"Properties","text":""},{"location":"halo/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"halo/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"halo/subject_text/","title":"Slot: subject_text","text":"

URI: oc:subject_text

"},{"location":"halo/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"halo/subject_text/#properties","title":"Properties","text":""},{"location":"halo/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"halo/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"halo/subtypes/","title":"Slot: subtypes","text":"

a list of child classes (subclasses) of this entity

URI: oc:subtypes

"},{"location":"halo/subtypes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/subtypes/#properties","title":"Properties","text":""},{"location":"halo/subtypes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/subtypes/#schema-source","title":"Schema Source","text":""},{"location":"halo/subtypes/#linkml-source","title":"LinkML Source","text":"
name: subtypes\ndescription: a list of child classes (subclasses) of this entity\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: subtypes\nowner: OntologyElement\ndomain_of:\n- OntologyElement\ninverse: subclass_of\nrange: OntologyElement\n\n
"},{"location":"halo/synonyms/","title":"Slot: synonyms","text":"

a list of alternative names of the entity

URI: oc:synonyms

"},{"location":"halo/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyElement no Category no"},{"location":"halo/synonyms/#properties","title":"Properties","text":""},{"location":"halo/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"halo/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\ndescription: a list of alternative names of the entity\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: OntologyElement\ndomain_of:\n- OntologyElement\nrange: string\n\n
"},{"location":"halo/title/","title":"Slot: title","text":"

The title of the publication

URI: oc:title

"},{"location":"halo/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"halo/title/#properties","title":"Properties","text":""},{"location":"halo/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/title/#schema-source","title":"Schema Source","text":""},{"location":"halo/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"halo/triples/","title":"Slot: triples","text":"

URI: oc:triples

"},{"location":"halo/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"halo/triples/#properties","title":"Properties","text":""},{"location":"halo/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"halo/triples/#schema-source","title":"Schema Source","text":""},{"location":"halo/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/halo\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"human_phenotype/","title":"Human Phenotype Extraction Template","text":"

A template for extracting human phenotypes to HPO terms

URI: http://w3id.org/ontogpt/human_phenotype

Name: human_phenotype-template

"},{"location":"human_phenotype/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nHumanPhenotypeSet {\n    string id  \n    string label  \n}\nHumanPhenotype {\n    string id  \n    string label  \n}\n\nHumanPhenotypeSet ||--}o HumanPhenotype : \"phenotypes\"\n\n
"},{"location":"human_phenotype/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None HumanPhenotype None HumanPhenotypeSet None RelationshipType None Publication None TextWithTriples None"},{"location":"human_phenotype/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text phenotypes A semicolon-separated list of human phenotypes, including symptoms of disease predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"human_phenotype/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"human_phenotype/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"human_phenotype/#subsets","title":"Subsets","text":"Subset Description"},{"location":"human_phenotype/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: human_phenotype:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"human_phenotype/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"human_phenotype/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:AnnotatorResult native human_phenotype:AnnotatorResult"},{"location":"human_phenotype/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n\n
"},{"location":"human_phenotype/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"human_phenotype/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"human_phenotype/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"human_phenotype/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"human_phenotype/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Any/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native human_phenotype:Any"},{"location":"human_phenotype/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nclass_uri: linkml:Any\n\n
"},{"location":"human_phenotype/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nclass_uri: linkml:Any\n\n
"},{"location":"human_phenotype/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"human_phenotype/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: human_phenotype:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"human_phenotype/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"human_phenotype/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:CompoundExpression native human_phenotype:CompoundExpression"},{"location":"human_phenotype/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nabstract: true\n\n
"},{"location":"human_phenotype/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nabstract: true\n\n
"},{"location":"human_phenotype/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"human_phenotype/Curie/#comments","title":"Comments","text":""},{"location":"human_phenotype/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Curie/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"human_phenotype/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Date/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"human_phenotype/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"human_phenotype/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"human_phenotype/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"human_phenotype/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Double/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: human_phenotype:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"human_phenotype/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"human_phenotype/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:ExtractionResult native human_phenotype:ExtractionResult"},{"location":"human_phenotype/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"human_phenotype/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"human_phenotype/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"human_phenotype/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Float/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/HumanPhenotype/","title":"Class: HumanPhenotype","text":"

URI: human_phenotype:HumanPhenotype

erDiagram\nHumanPhenotype {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"human_phenotype/HumanPhenotype/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/HumanPhenotype/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"human_phenotype/HumanPhenotype/#usages","title":"Usages","text":"used by used in type used HumanPhenotypeSet phenotypes range HumanPhenotype"},{"location":"human_phenotype/HumanPhenotype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/HumanPhenotype/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"human_phenotype/HumanPhenotype/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:mondo, sqlite:obo:mesh, sqlite:obo:ncit Examples are ascites, fever, pain, seizure, increased intracranial pressure, lactic acidosis."},{"location":"human_phenotype/HumanPhenotype/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/HumanPhenotype/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:HumanPhenotype native human_phenotype:HumanPhenotype"},{"location":"human_phenotype/HumanPhenotype/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/HumanPhenotype/#direct","title":"Direct","text":"
name: HumanPhenotype\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:mondo, sqlite:obo:mesh, sqlite:obo:ncit\n  prompt:\n    tag: prompt\n    value: \"the name of a human phenotype or symptom.\\n Examples are ascites, fever,\\\n      \\ pain, seizure, increased intracranial pressure, lactic acidosis.\"\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\n\n
"},{"location":"human_phenotype/HumanPhenotype/#induced","title":"Induced","text":"
name: HumanPhenotype\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:mondo, sqlite:obo:mesh, sqlite:obo:ncit\n  prompt:\n    tag: prompt\n    value: \"the name of a human phenotype or symptom.\\n Examples are ascites, fever,\\\n      \\ pain, seizure, increased intracranial pressure, lactic acidosis.\"\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: HumanPhenotype\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: HumanPhenotype\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"human_phenotype/HumanPhenotypeSet/","title":"Class: HumanPhenotypeSet","text":"

URI: human_phenotype:HumanPhenotypeSet

erDiagram\nHumanPhenotypeSet {\n    string id  \n    string label  \n}\nHumanPhenotype {\n    string id  \n    string label  \n}\n\nHumanPhenotypeSet ||--}o HumanPhenotype : \"phenotypes\"\n\n
"},{"location":"human_phenotype/HumanPhenotypeSet/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/HumanPhenotypeSet/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance phenotypes 0..* HumanPhenotype A semicolon-separated list of human phenotypes, including symptoms of disease direct id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"human_phenotype/HumanPhenotypeSet/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/HumanPhenotypeSet/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/HumanPhenotypeSet/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:HumanPhenotypeSet native human_phenotype:HumanPhenotypeSet"},{"location":"human_phenotype/HumanPhenotypeSet/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/HumanPhenotypeSet/#direct","title":"Direct","text":"
name: HumanPhenotypeSet\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\nattributes:\n  phenotypes:\n    name: phenotypes\n    description: A semicolon-separated list of human phenotypes, including symptoms\n      of disease. It must be semicolon-separated. Labels containing the word 'with'\n      should be split into multiple phenotypes.\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    range: HumanPhenotype\ntree_root: true\n\n
"},{"location":"human_phenotype/HumanPhenotypeSet/#induced","title":"Induced","text":"
name: HumanPhenotypeSet\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\nattributes:\n  phenotypes:\n    name: phenotypes\n    description: A semicolon-separated list of human phenotypes, including symptoms\n      of disease. It must be semicolon-separated. Labels containing the word 'with'\n      should be split into multiple phenotypes.\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    alias: phenotypes\n    owner: HumanPhenotypeSet\n    domain_of:\n    - HumanPhenotypeSet\n    range: HumanPhenotype\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: HumanPhenotypeSet\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: HumanPhenotypeSet\n    domain_of:\n    - NamedEntity\n    range: string\ntree_root: true\n\n
"},{"location":"human_phenotype/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"human_phenotype/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Integer/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/NamedEntity/","title":"Class: NamedEntity","text":"

URI: human_phenotype:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"human_phenotype/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"human_phenotype/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"human_phenotype/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:NamedEntity native human_phenotype:NamedEntity"},{"location":"human_phenotype/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"human_phenotype/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"human_phenotype/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"human_phenotype/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"human_phenotype/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"human_phenotype/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"human_phenotype/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"human_phenotype/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"human_phenotype/Objectidentifier/#comments","title":"Comments","text":""},{"location":"human_phenotype/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Publication/","title":"Class: Publication","text":"

URI: human_phenotype:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"human_phenotype/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"human_phenotype/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"human_phenotype/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Publication/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:Publication native human_phenotype:Publication"},{"location":"human_phenotype/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n\n
"},{"location":"human_phenotype/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"human_phenotype/RelationshipType/","title":"Class: RelationshipType","text":"

URI: human_phenotype:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"human_phenotype/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"human_phenotype/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"human_phenotype/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"human_phenotype/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:RelationshipType native human_phenotype:RelationshipType"},{"location":"human_phenotype/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\n\n
"},{"location":"human_phenotype/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"human_phenotype/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"human_phenotype/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/String/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: human_phenotype:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"human_phenotype/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"human_phenotype/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:TextWithTriples native human_phenotype:TextWithTriples"},{"location":"human_phenotype/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"human_phenotype/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"human_phenotype/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"human_phenotype/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Time/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: human_phenotype:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"human_phenotype/Triple/#inheritance","title":"Inheritance","text":""},{"location":"human_phenotype/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"human_phenotype/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"human_phenotype/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Triple/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self human_phenotype:Triple native human_phenotype:Triple"},{"location":"human_phenotype/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"human_phenotype/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"human_phenotype/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/human_phenotype\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"human_phenotype/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"human_phenotype/Uri/#comments","title":"Comments","text":""},{"location":"human_phenotype/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Uri/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"human_phenotype/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: human_phenotype:abstract

"},{"location":"human_phenotype/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"human_phenotype/abstract/#properties","title":"Properties","text":""},{"location":"human_phenotype/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/abstract/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"human_phenotype/combined_text/","title":"Slot: combined_text","text":"

URI: human_phenotype:combined_text

"},{"location":"human_phenotype/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"human_phenotype/combined_text/#properties","title":"Properties","text":""},{"location":"human_phenotype/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"human_phenotype/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: human_phenotype:extracted_object

"},{"location":"human_phenotype/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/extracted_object/#properties","title":"Properties","text":""},{"location":"human_phenotype/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"human_phenotype/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: human_phenotype:full_text

"},{"location":"human_phenotype/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"human_phenotype/full_text/#properties","title":"Properties","text":""},{"location":"human_phenotype/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/full_text/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"human_phenotype/human_phenotype-template/","title":"human_phenotype-template","text":"

A template for extracting human phenotypes to HPO terms

URI: http://w3id.org/ontogpt/human_phenotype

"},{"location":"human_phenotype/id/","title":"Slot: id","text":"

URI: human_phenotype:id

"},{"location":"human_phenotype/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot HumanPhenotypeSet no HumanPhenotype no NamedEntity no RelationshipType no Publication no"},{"location":"human_phenotype/id/#properties","title":"Properties","text":""},{"location":"human_phenotype/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"human_phenotype/input_id/","title":"Slot: input_id","text":"

URI: human_phenotype:input_id

"},{"location":"human_phenotype/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/input_id/#properties","title":"Properties","text":""},{"location":"human_phenotype/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/input_id/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"human_phenotype/input_text/","title":"Slot: input_text","text":"

URI: human_phenotype:input_text

"},{"location":"human_phenotype/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/input_text/#properties","title":"Properties","text":""},{"location":"human_phenotype/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/input_text/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"human_phenotype/input_title/","title":"Slot: input_title","text":"

URI: human_phenotype:input_title

"},{"location":"human_phenotype/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/input_title/#properties","title":"Properties","text":""},{"location":"human_phenotype/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/input_title/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"human_phenotype/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"human_phenotype/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot HumanPhenotypeSet no HumanPhenotype no NamedEntity no RelationshipType no"},{"location":"human_phenotype/label/#properties","title":"Properties","text":""},{"location":"human_phenotype/label/#aliases","title":"Aliases","text":""},{"location":"human_phenotype/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"human_phenotype/label/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"human_phenotype/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: human_phenotype:named_entities

"},{"location":"human_phenotype/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/named_entities/#properties","title":"Properties","text":""},{"location":"human_phenotype/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"human_phenotype/object/","title":"Slot: object","text":"

URI: human_phenotype:object

"},{"location":"human_phenotype/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/object/#properties","title":"Properties","text":""},{"location":"human_phenotype/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/object/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"human_phenotype/object_id/","title":"Slot: object_id","text":"

URI: human_phenotype:object_id

"},{"location":"human_phenotype/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"human_phenotype/object_id/#properties","title":"Properties","text":""},{"location":"human_phenotype/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/object_id/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"human_phenotype/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: human_phenotype:object_qualifier

"},{"location":"human_phenotype/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/object_qualifier/#properties","title":"Properties","text":""},{"location":"human_phenotype/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"human_phenotype/object_text/","title":"Slot: object_text","text":"

URI: human_phenotype:object_text

"},{"location":"human_phenotype/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"human_phenotype/object_text/#properties","title":"Properties","text":""},{"location":"human_phenotype/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/object_text/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"human_phenotype/phenotypes/","title":"Slot: phenotypes","text":"

A semicolon-separated list of human phenotypes, including symptoms of disease. It must be semicolon-separated. Labels containing the word 'with' should be split into multiple phenotypes.

URI: human_phenotype:phenotypes

"},{"location":"human_phenotype/phenotypes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot HumanPhenotypeSet no"},{"location":"human_phenotype/phenotypes/#properties","title":"Properties","text":""},{"location":"human_phenotype/phenotypes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/phenotypes/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/phenotypes/#linkml-source","title":"LinkML Source","text":"
name: phenotypes\ndescription: A semicolon-separated list of human phenotypes, including symptoms of\n  disease. It must be semicolon-separated. Labels containing the word 'with' should\n  be split into multiple phenotypes.\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nmultivalued: true\nalias: phenotypes\nowner: HumanPhenotypeSet\ndomain_of:\n- HumanPhenotypeSet\nrange: HumanPhenotype\n\n
"},{"location":"human_phenotype/predicate/","title":"Slot: predicate","text":"

URI: human_phenotype:predicate

"},{"location":"human_phenotype/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/predicate/#properties","title":"Properties","text":""},{"location":"human_phenotype/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/predicate/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"human_phenotype/prompt/","title":"Slot: prompt","text":"

URI: human_phenotype:prompt

"},{"location":"human_phenotype/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/prompt/#properties","title":"Properties","text":""},{"location":"human_phenotype/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/prompt/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"human_phenotype/publication/","title":"Slot: publication","text":"

URI: human_phenotype:publication

"},{"location":"human_phenotype/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"human_phenotype/publication/#properties","title":"Properties","text":""},{"location":"human_phenotype/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"human_phenotype/publication/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"human_phenotype/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: human_phenotype:qualifier

"},{"location":"human_phenotype/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/qualifier/#properties","title":"Properties","text":""},{"location":"human_phenotype/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"human_phenotype/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: human_phenotype:raw_completion_output

"},{"location":"human_phenotype/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"human_phenotype/raw_completion_output/#properties","title":"Properties","text":""},{"location":"human_phenotype/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"human_phenotype/subject/","title":"Slot: subject","text":"

URI: human_phenotype:subject

"},{"location":"human_phenotype/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/subject/#properties","title":"Properties","text":""},{"location":"human_phenotype/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/subject/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"human_phenotype/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: human_phenotype:subject_qualifier

"},{"location":"human_phenotype/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"human_phenotype/subject_qualifier/#properties","title":"Properties","text":""},{"location":"human_phenotype/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"human_phenotype/subject_text/","title":"Slot: subject_text","text":"

URI: human_phenotype:subject_text

"},{"location":"human_phenotype/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"human_phenotype/subject_text/#properties","title":"Properties","text":""},{"location":"human_phenotype/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"human_phenotype/title/","title":"Slot: title","text":"

The title of the publication

URI: human_phenotype:title

"},{"location":"human_phenotype/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"human_phenotype/title/#properties","title":"Properties","text":""},{"location":"human_phenotype/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/title/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"human_phenotype/triples/","title":"Slot: triples","text":"

URI: human_phenotype:triples

"},{"location":"human_phenotype/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"human_phenotype/triples/#properties","title":"Properties","text":""},{"location":"human_phenotype/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"human_phenotype/triples/#schema-source","title":"Schema Source","text":""},{"location":"human_phenotype/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/human_phenotype\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ibd/","title":"GO-CAM Template","text":"

A template for GO-CAMs

URI: http://w3id.org/ontogpt/gocam

Name: gocam-template

"},{"location":"ibd/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nIBDAnnotations {\n\n}\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nGeneGeneInteraction {\n\n}\nPathway {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\n\nIBDAnnotations ||--}o Gene : \"genes\"\nIBDAnnotations ||--}o Organism : \"organisms\"\nIBDAnnotations ||--}o GeneOrganismRelationship : \"gene_organisms\"\nIBDAnnotations ||--}o MolecularActivity : \"activities\"\nIBDAnnotations ||--}o GeneMolecularActivityRelationship : \"gene_functions\"\nIBDAnnotations ||--}o CellularProcess : \"cellular_processes\"\nIBDAnnotations ||--}o Pathway : \"pathways\"\nIBDAnnotations ||--}o GeneGeneInteraction : \"gene_gene_interactions\"\nIBDAnnotations ||--}o GeneSubcellularLocalizationRelationship : \"gene_localizations\"\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"ibd/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None GeneGeneInteraction None GeneMolecularActivityRelationship None GeneMolecularActivityRelationship2 None GeneOrganismRelationship None GeneSubcellularLocalizationRelationship None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text IBDAnnotations None NamedEntity None CellularProcess None Gene None GeneLocation None MolecularActivity None Molecule None Organism None Pathway None RelationshipType None Publication None TextWithTriples None"},{"location":"ibd/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication activities semicolon-separated list of molecular activities cellular_processes semicolon-separated list of cellular processes combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication gene gene1 gene2 gene_functions semicolon-separated list of gene to molecular activity relationships gene_gene_interactions semicolon-separated list of gene to gene interactions gene_localizations semicolon-separated list of genes plus their location in the cell; for exampl... gene_organisms genes semicolon-separated list of genes id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing location molecular_activity named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text organism organisms semicolon-separated list of organism taxons pathways semicolon-separated list of pathways predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text target title The title of the publication triples"},{"location":"ibd/#enumerations","title":"Enumerations","text":"Enumeration Description CellType GeneLocationEnum GOCellComponentType NullDataOptions"},{"location":"ibd/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"ibd/#subsets","title":"Subsets","text":"Subset Description"},{"location":"ibd/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: gocam:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"ibd/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"ibd/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"ibd/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:AnnotatorResult native gocam:AnnotatorResult"},{"location":"ibd/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n\n
"},{"location":"ibd/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"ibd/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"ibd/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ibd/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"ibd/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Any/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native gocam:Any"},{"location":"ibd/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/gocam\nclass_uri: linkml:Any\n\n
"},{"location":"ibd/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/gocam\nclass_uri: linkml:Any\n\n
"},{"location":"ibd/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"ibd/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"ibd/CellType/","title":"Enum: CellType","text":"

URI: CellType

This is a dynamic enum

"},{"location":"ibd/CellType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/CellType/#schema-source","title":"Schema Source","text":""},{"location":"ibd/CellType/#linkml-source","title":"LinkML Source","text":"
name: CellType\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nreachable_from:\n  source_ontology: obo:cl\n  source_nodes:\n  - CL:0000000\n\n
"},{"location":"ibd/CellularProcess/","title":"Class: CellularProcess","text":"

URI: gocam:CellularProcess

erDiagram\nCellularProcess {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/CellularProcess/#inheritance","title":"Inheritance","text":""},{"location":"ibd/CellularProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/CellularProcess/#usages","title":"Usages","text":"used by used in type used IBDAnnotations cellular_processes range CellularProcess"},{"location":"ibd/CellularProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/CellularProcess/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/CellularProcess/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"ibd/CellularProcess/#schema-source","title":"Schema Source","text":""},{"location":"ibd/CellularProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:CellularProcess native gocam:CellularProcess"},{"location":"ibd/CellularProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/CellularProcess/#direct","title":"Direct","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/CellularProcess/#induced","title":"Induced","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: gocam:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"ibd/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"ibd/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ibd/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"ibd/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:CompoundExpression native gocam:CompoundExpression"},{"location":"ibd/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\n\n
"},{"location":"ibd/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\n\n
"},{"location":"ibd/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"ibd/Curie/#comments","title":"Comments","text":""},{"location":"ibd/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Curie/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"ibd/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Date/#schema-source","title":"Schema Source","text":""},{"location":"ibd/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"ibd/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"ibd/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"ibd/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"ibd/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Double/#schema-source","title":"Schema Source","text":""},{"location":"ibd/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: gocam:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"ibd/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"ibd/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"ibd/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:ExtractionResult native gocam:ExtractionResult"},{"location":"ibd/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"ibd/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Float/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GOCellComponentType/","title":"Enum: GOCellComponentType","text":"

URI: GOCellComponentType

This is a dynamic enum

"},{"location":"ibd/GOCellComponentType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GOCellComponentType/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GOCellComponentType/#linkml-source","title":"LinkML Source","text":"
name: GOCellComponentType\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nreachable_from:\n  source_ontology: obo:go\n  source_nodes:\n  - GO:0005575\n\n
"},{"location":"ibd/Gene/","title":"Class: Gene","text":"

URI: gocam:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/Gene/#inheritance","title":"Inheritance","text":""},{"location":"ibd/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/Gene/#usages","title":"Usages","text":"used by used in type used IBDAnnotations genes range Gene GeneOrganismRelationship gene range Gene GeneMolecularActivityRelationship gene range Gene GeneMolecularActivityRelationship2 gene range Gene GeneSubcellularLocalizationRelationship gene range Gene GeneGeneInteraction gene1 range Gene GeneGeneInteraction gene2 range Gene"},{"location":"ibd/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, bioportal:hgnc-nr"},{"location":"ibd/Gene/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Gene native gocam:Gene"},{"location":"ibd/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\n- PR\n- UniProtKB\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/GeneGeneInteraction/","title":"Class: GeneGeneInteraction","text":"

URI: gocam:GeneGeneInteraction

erDiagram\nGeneGeneInteraction {\n\n}\nGene {\n    string id  \n    string label  \n}\n\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\n\n
"},{"location":"ibd/GeneGeneInteraction/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneGeneInteraction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene1 0..1 Gene direct gene2 0..1 Gene direct"},{"location":"ibd/GeneGeneInteraction/#usages","title":"Usages","text":"used by used in type used IBDAnnotations gene_gene_interactions range GeneGeneInteraction"},{"location":"ibd/GeneGeneInteraction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneGeneInteraction/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneGeneInteraction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneGeneInteraction native gocam:GeneGeneInteraction"},{"location":"ibd/GeneGeneInteraction/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneGeneInteraction/#direct","title":"Direct","text":"
name: GeneGeneInteraction\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene1:\n    name: gene1\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n  gene2:\n    name: gene2\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n\n
"},{"location":"ibd/GeneGeneInteraction/#induced","title":"Induced","text":"
name: GeneGeneInteraction\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene1:\n    name: gene1\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene1\n    owner: GeneGeneInteraction\n    domain_of:\n    - GeneGeneInteraction\n    range: Gene\n  gene2:\n    name: gene2\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene2\n    owner: GeneGeneInteraction\n    domain_of:\n    - GeneGeneInteraction\n    range: Gene\n\n
"},{"location":"ibd/GeneLocation/","title":"Class: GeneLocation","text":"

URI: gocam:GeneLocation

erDiagram\nGeneLocation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/GeneLocation/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneLocation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/GeneLocation/#usages","title":"Usages","text":"used by used in type used GeneSubcellularLocalizationRelationship location range GeneLocation"},{"location":"ibd/GeneLocation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneLocation/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/GeneLocation/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:cl"},{"location":"ibd/GeneLocation/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneLocation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneLocation native gocam:GeneLocation"},{"location":"ibd/GeneLocation/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneLocation/#direct","title":"Direct","text":"
name: GeneLocation\nid_prefixes:\n- GO\n- CL\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - GOCellComponentType\n    - CellType\n    domain_of:\n    - NamedEntity\n    - Publication\n\n
"},{"location":"ibd/GeneLocation/#induced","title":"Induced","text":"
name: GeneLocation\nid_prefixes:\n- GO\n- CL\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:cl\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nslot_usage:\n  id:\n    name: id\n    values_from:\n    - GOCellComponentType\n    - CellType\n    domain_of:\n    - NamedEntity\n    - Publication\nattributes:\n  id:\n    name: id\n    description: A unique identifier for the named entity\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    values_from:\n    - GOCellComponentType\n    - CellType\n    identifier: true\n    alias: id\n    owner: GeneLocation\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: GeneLocation\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/GeneLocationEnum/","title":"Enum: GeneLocationEnum","text":"

URI: GeneLocationEnum

This is a dynamic enum

"},{"location":"ibd/GeneLocationEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneLocationEnum/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneLocationEnum/#linkml-source","title":"LinkML Source","text":"
name: GeneLocationEnum\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\ninherits:\n- GOCellComponent\n- CellType\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship/","title":"Class: GeneMolecularActivityRelationship","text":"

URI: gocam:GeneMolecularActivityRelationship

erDiagram\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneMolecularActivityRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct molecular_activity 0..1 MolecularActivity direct"},{"location":"ibd/GeneMolecularActivityRelationship/#usages","title":"Usages","text":"used by used in type used IBDAnnotations gene_functions range GeneMolecularActivityRelationship"},{"location":"ibd/GeneMolecularActivityRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneMolecularActivityRelationship/#annotations","title":"Annotations","text":"property value prompt.example TODO

gene: HGNC:1234 molecular_activity: GO:0003674 |

"},{"location":"ibd/GeneMolecularActivityRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneMolecularActivityRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneMolecularActivityRelationship native gocam:GeneMolecularActivityRelationship"},{"location":"ibd/GeneMolecularActivityRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneMolecularActivityRelationship/#direct","title":"Direct","text":"
name: GeneMolecularActivityRelationship\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: 'TODO\n\n\n      gene: HGNC:1234\n\n      molecular_activity: GO:0003674'\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene in the pair. This comes first.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular function in the pair. This comes second.\n          May be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: MolecularActivity\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship/#induced","title":"Induced","text":"
name: GeneMolecularActivityRelationship\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: 'TODO\n\n\n      gene: HGNC:1234\n\n      molecular_activity: GO:0003674'\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene in the pair. This comes first.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular function in the pair. This comes second.\n          May be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: molecular_activity\n    owner: GeneMolecularActivityRelationship\n    domain_of:\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    range: MolecularActivity\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship2/","title":"Class: GeneMolecularActivityRelationship2","text":"

URI: gocam:GeneMolecularActivityRelationship2

erDiagram\nGeneMolecularActivityRelationship2 {\n\n}\nMolecule {\n    string id  \n    string label  \n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneMolecularActivityRelationship2 ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship2 ||--|o MolecularActivity : \"molecular_activity\"\nGeneMolecularActivityRelationship2 ||--|o Molecule : \"target\"\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship2/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneMolecularActivityRelationship2/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct molecular_activity 0..1 MolecularActivity direct target 0..1 Molecule direct"},{"location":"ibd/GeneMolecularActivityRelationship2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneMolecularActivityRelationship2/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneMolecularActivityRelationship2/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneMolecularActivityRelationship2 native gocam:GeneMolecularActivityRelationship2"},{"location":"ibd/GeneMolecularActivityRelationship2/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneMolecularActivityRelationship2/#direct","title":"Direct","text":"
name: GeneMolecularActivityRelationship2\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular activity, for example, ubiquitination. May\n          be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: MolecularActivity\n  target:\n    name: target\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular entity that is the target of the molecular\n          activity.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Molecule\n\n
"},{"location":"ibd/GeneMolecularActivityRelationship2/#induced","title":"Induced","text":"
name: GeneMolecularActivityRelationship2\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the gene.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  molecular_activity:\n    name: molecular_activity\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular activity, for example, ubiquitination. May\n          be a GO term.\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: molecular_activity\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    range: MolecularActivity\n  target:\n    name: target\n    annotations:\n      prompt:\n        tag: prompt\n        value: the name of the molecular entity that is the target of the molecular\n          activity.\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: target\n    owner: GeneMolecularActivityRelationship2\n    domain_of:\n    - GeneMolecularActivityRelationship2\n    range: Molecule\n\n
"},{"location":"ibd/GeneOrganismRelationship/","title":"Class: GeneOrganismRelationship","text":"

URI: gocam:GeneOrganismRelationship

erDiagram\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"ibd/GeneOrganismRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneOrganismRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct organism 0..1 Organism direct"},{"location":"ibd/GeneOrganismRelationship/#usages","title":"Usages","text":"used by used in type used IBDAnnotations gene_organisms range GeneOrganismRelationship"},{"location":"ibd/GeneOrganismRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneOrganismRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneOrganismRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneOrganismRelationship native gocam:GeneOrganismRelationship"},{"location":"ibd/GeneOrganismRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneOrganismRelationship/#direct","title":"Direct","text":"
name: GeneOrganismRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Gene\n  organism:\n    name: organism\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Organism\n\n
"},{"location":"ibd/GeneOrganismRelationship/#induced","title":"Induced","text":"
name: GeneOrganismRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: gene\n    owner: GeneOrganismRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  organism:\n    name: organism\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: organism\n    owner: GeneOrganismRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    range: Organism\n\n
"},{"location":"ibd/GeneSubcellularLocalizationRelationship/","title":"Class: GeneSubcellularLocalizationRelationship","text":"

URI: gocam:GeneSubcellularLocalizationRelationship

erDiagram\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\n\n
"},{"location":"ibd/GeneSubcellularLocalizationRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ibd/GeneSubcellularLocalizationRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene direct location 0..1 GeneLocation direct"},{"location":"ibd/GeneSubcellularLocalizationRelationship/#usages","title":"Usages","text":"used by used in type used IBDAnnotations gene_localizations range GeneSubcellularLocalizationRelationship"},{"location":"ibd/GeneSubcellularLocalizationRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/GeneSubcellularLocalizationRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ibd/GeneSubcellularLocalizationRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:GeneSubcellularLocalizationRelationship native gocam:GeneSubcellularLocalizationRelationship"},{"location":"ibd/GeneSubcellularLocalizationRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/GeneSubcellularLocalizationRelationship/#direct","title":"Direct","text":"
name: GeneSubcellularLocalizationRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    range: Gene\n  location:\n    name: location\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: GeneLocation\n\n
"},{"location":"ibd/GeneSubcellularLocalizationRelationship/#induced","title":"Induced","text":"
name: GeneSubcellularLocalizationRelationship\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: gene\n    owner: GeneSubcellularLocalizationRelationship\n    domain_of:\n    - GeneOrganismRelationship\n    - GeneMolecularActivityRelationship\n    - GeneMolecularActivityRelationship2\n    - GeneSubcellularLocalizationRelationship\n    range: Gene\n  location:\n    name: location\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: location\n    owner: GeneSubcellularLocalizationRelationship\n    domain_of:\n    - GeneSubcellularLocalizationRelationship\n    range: GeneLocation\n\n
"},{"location":"ibd/IBDAnnotations/","title":"Class: IBDAnnotations","text":"

URI: gocam:IBDAnnotations

erDiagram\nIBDAnnotations {\n\n}\nGeneSubcellularLocalizationRelationship {\n\n}\nGeneLocation {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nGeneGeneInteraction {\n\n}\nPathway {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nGeneMolecularActivityRelationship {\n\n}\nMolecularActivity {\n    string id  \n    string label  \n}\nGeneOrganismRelationship {\n\n}\nOrganism {\n    string id  \n    string label  \n}\n\nIBDAnnotations ||--}o Gene : \"genes\"\nIBDAnnotations ||--}o Organism : \"organisms\"\nIBDAnnotations ||--}o GeneOrganismRelationship : \"gene_organisms\"\nIBDAnnotations ||--}o MolecularActivity : \"activities\"\nIBDAnnotations ||--}o GeneMolecularActivityRelationship : \"gene_functions\"\nIBDAnnotations ||--}o CellularProcess : \"cellular_processes\"\nIBDAnnotations ||--}o Pathway : \"pathways\"\nIBDAnnotations ||--}o GeneGeneInteraction : \"gene_gene_interactions\"\nIBDAnnotations ||--}o GeneSubcellularLocalizationRelationship : \"gene_localizations\"\nGeneSubcellularLocalizationRelationship ||--|o Gene : \"gene\"\nGeneSubcellularLocalizationRelationship ||--|o GeneLocation : \"location\"\nGeneGeneInteraction ||--|o Gene : \"gene1\"\nGeneGeneInteraction ||--|o Gene : \"gene2\"\nGeneMolecularActivityRelationship ||--|o Gene : \"gene\"\nGeneMolecularActivityRelationship ||--|o MolecularActivity : \"molecular_activity\"\nGeneOrganismRelationship ||--|o Gene : \"gene\"\nGeneOrganismRelationship ||--|o Organism : \"organism\"\n\n
"},{"location":"ibd/IBDAnnotations/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance genes 0..* Gene semicolon-separated list of genes direct organisms 0..* Organism semicolon-separated list of organism taxons direct gene_organisms 0..* GeneOrganismRelationship direct activities 0..* MolecularActivity semicolon-separated list of molecular activities direct gene_functions 0..* GeneMolecularActivityRelationship semicolon-separated list of gene to molecular activity relationships direct cellular_processes 0..* CellularProcess semicolon-separated list of cellular processes direct pathways 0..* Pathway semicolon-separated list of pathways direct gene_gene_interactions 0..* GeneGeneInteraction semicolon-separated list of gene to gene interactions direct gene_localizations 0..* GeneSubcellularLocalizationRelationship semicolon-separated list of genes plus their location in the cell; for exampl... direct"},{"location":"ibd/IBDAnnotations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/IBDAnnotations/#schema-source","title":"Schema Source","text":""},{"location":"ibd/IBDAnnotations/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:IBDAnnotations native gocam:IBDAnnotations"},{"location":"ibd/IBDAnnotations/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/IBDAnnotations/#direct","title":"Direct","text":"
name: IBDAnnotations\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Gene\n  organisms:\n    name: organisms\n    description: semicolon-separated list of organism taxons\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Organism\n  gene_organisms:\n    name: gene_organisms\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of asterisk separated gene to organism relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneOrganismRelationship\n  activities:\n    name: activities\n    description: semicolon-separated list of molecular activities\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: MolecularActivity\n  gene_functions:\n    name: gene_functions\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneMolecularActivityRelationship\n  cellular_processes:\n    name: cellular_processes\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: CellularProcess\n  pathways:\n    name: pathways\n    description: semicolon-separated list of pathways\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Pathway\n  gene_gene_interactions:\n    name: gene_gene_interactions\n    description: semicolon-separated list of gene to gene interactions\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneGeneInteraction\n  gene_localizations:\n    name: gene_localizations\n    description: semicolon-separated list of genes plus their location in the cell;\n      for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: GeneSubcellularLocalizationRelationship\ntree_root: true\n\n
"},{"location":"ibd/IBDAnnotations/#induced","title":"Induced","text":"
name: IBDAnnotations\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: Gene\n  organisms:\n    name: organisms\n    description: semicolon-separated list of organism taxons\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: organisms\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: Organism\n  gene_organisms:\n    name: gene_organisms\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of asterisk separated gene to organism relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_organisms\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: GeneOrganismRelationship\n  activities:\n    name: activities\n    description: semicolon-separated list of molecular activities\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: activities\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: MolecularActivity\n  gene_functions:\n    name: gene_functions\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_functions\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: GeneMolecularActivityRelationship\n  cellular_processes:\n    name: cellular_processes\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: cellular_processes\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: CellularProcess\n  pathways:\n    name: pathways\n    description: semicolon-separated list of pathways\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: pathways\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: Pathway\n  gene_gene_interactions:\n    name: gene_gene_interactions\n    description: semicolon-separated list of gene to gene interactions\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_gene_interactions\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: GeneGeneInteraction\n  gene_localizations:\n    name: gene_localizations\n    description: semicolon-separated list of genes plus their location in the cell;\n      for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: gene_localizations\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: GeneSubcellularLocalizationRelationship\ntree_root: true\n\n
"},{"location":"ibd/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"ibd/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Integer/#schema-source","title":"Schema Source","text":""},{"location":"ibd/MolecularActivity/","title":"Class: MolecularActivity","text":"

URI: gocam:MolecularActivity

erDiagram\nMolecularActivity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/MolecularActivity/#inheritance","title":"Inheritance","text":""},{"location":"ibd/MolecularActivity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/MolecularActivity/#usages","title":"Usages","text":"used by used in type used IBDAnnotations activities range MolecularActivity GeneMolecularActivityRelationship molecular_activity range MolecularActivity GeneMolecularActivityRelationship2 molecular_activity range MolecularActivity"},{"location":"ibd/MolecularActivity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/MolecularActivity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/MolecularActivity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"ibd/MolecularActivity/#schema-source","title":"Schema Source","text":""},{"location":"ibd/MolecularActivity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:MolecularActivity native gocam:MolecularActivity"},{"location":"ibd/MolecularActivity/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/MolecularActivity/#direct","title":"Direct","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/MolecularActivity/#induced","title":"Induced","text":"
name: MolecularActivity\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MolecularActivity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: MolecularActivity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/Molecule/","title":"Class: Molecule","text":"

URI: gocam:Molecule

erDiagram\nMolecule {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/Molecule/#inheritance","title":"Inheritance","text":""},{"location":"ibd/Molecule/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/Molecule/#usages","title":"Usages","text":"used by used in type used GeneMolecularActivityRelationship2 target range Molecule"},{"location":"ibd/Molecule/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Molecule/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/Molecule/#annotations","title":"Annotations","text":"property value annotators gilda:, sqlite:obo:chebi"},{"location":"ibd/Molecule/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Molecule/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Molecule native gocam:Molecule"},{"location":"ibd/Molecule/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Molecule/#direct","title":"Direct","text":"
name: Molecule\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/Molecule/#induced","title":"Induced","text":"
name: Molecule\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Molecule\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Molecule\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/NamedEntity/","title":"Class: NamedEntity","text":"

URI: gocam:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"ibd/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"ibd/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"ibd/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"ibd/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:NamedEntity native gocam:NamedEntity"},{"location":"ibd/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"ibd/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/gocam\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"ibd/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"ibd/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"ibd/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"ibd/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"ibd/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"ibd/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"ibd/Objectidentifier/#comments","title":"Comments","text":""},{"location":"ibd/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Organism/","title":"Class: Organism","text":"

URI: gocam:Organism

erDiagram\nOrganism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/Organism/#inheritance","title":"Inheritance","text":""},{"location":"ibd/Organism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/Organism/#usages","title":"Usages","text":"used by used in type used IBDAnnotations organisms range Organism GeneOrganismRelationship organism range Organism"},{"location":"ibd/Organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Organism/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/Organism/#annotations","title":"Annotations","text":"property value annotators gilda:, sqlite:obo:ncbitaxon"},{"location":"ibd/Organism/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Organism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Organism native gocam:Organism"},{"location":"ibd/Organism/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Organism/#direct","title":"Direct","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/Organism/#induced","title":"Induced","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/Pathway/","title":"Class: Pathway","text":"

URI: gocam:Pathway

erDiagram\nPathway {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/Pathway/#inheritance","title":"Inheritance","text":""},{"location":"ibd/Pathway/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/Pathway/#usages","title":"Usages","text":"used by used in type used IBDAnnotations pathways range Pathway"},{"location":"ibd/Pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Pathway/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/Pathway/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:pw"},{"location":"ibd/Pathway/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Pathway/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Pathway native gocam:Pathway"},{"location":"ibd/Pathway/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Pathway/#direct","title":"Direct","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/Pathway/#induced","title":"Induced","text":"
name: Pathway\nid_prefixes:\n- GO\n- PW\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:pw\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Pathway\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Pathway\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/Publication/","title":"Class: Publication","text":"

URI: gocam:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"ibd/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"ibd/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"ibd/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Publication/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Publication native gocam:Publication"},{"location":"ibd/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/gocam\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n\n
"},{"location":"ibd/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/gocam\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"ibd/RelationshipType/","title":"Class: RelationshipType","text":"

URI: gocam:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"ibd/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"ibd/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"ibd/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:RelationshipType native gocam:RelationshipType"},{"location":"ibd/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\n\n
"},{"location":"ibd/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/gocam\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"ibd/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/String/#schema-source","title":"Schema Source","text":""},{"location":"ibd/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: gocam:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"ibd/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"ibd/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:TextWithTriples native gocam:TextWithTriples"},{"location":"ibd/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/gocam\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"ibd/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Time/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: gocam:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd/Triple/#inheritance","title":"Inheritance","text":""},{"location":"ibd/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"ibd/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"ibd/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Triple/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self gocam:Triple native gocam:Triple"},{"location":"ibd/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"ibd/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/gocam\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/gocam\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ibd/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"ibd/Uri/#comments","title":"Comments","text":""},{"location":"ibd/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Uri/#schema-source","title":"Schema Source","text":""},{"location":"ibd/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"ibd/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"ibd/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: gocam:abstract

"},{"location":"ibd/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd/abstract/#properties","title":"Properties","text":""},{"location":"ibd/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/abstract/#schema-source","title":"Schema Source","text":""},{"location":"ibd/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd/activities/","title":"Slot: activities","text":"

semicolon-separated list of molecular activities

URI: gocam:activities

"},{"location":"ibd/activities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/activities/#properties","title":"Properties","text":""},{"location":"ibd/activities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/activities/#schema-source","title":"Schema Source","text":""},{"location":"ibd/activities/#linkml-source","title":"LinkML Source","text":"
name: activities\ndescription: semicolon-separated list of molecular activities\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: activities\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: MolecularActivity\n\n
"},{"location":"ibd/cellular_processes/","title":"Slot: cellular_processes","text":"

semicolon-separated list of cellular processes

URI: gocam:cellular_processes

"},{"location":"ibd/cellular_processes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/cellular_processes/#properties","title":"Properties","text":""},{"location":"ibd/cellular_processes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/cellular_processes/#schema-source","title":"Schema Source","text":""},{"location":"ibd/cellular_processes/#linkml-source","title":"LinkML Source","text":"
name: cellular_processes\ndescription: semicolon-separated list of cellular processes\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: cellular_processes\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: CellularProcess\n\n
"},{"location":"ibd/combined_text/","title":"Slot: combined_text","text":"

URI: gocam:combined_text

"},{"location":"ibd/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd/combined_text/#properties","title":"Properties","text":""},{"location":"ibd/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: gocam:extracted_object

"},{"location":"ibd/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/extracted_object/#properties","title":"Properties","text":""},{"location":"ibd/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"ibd/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"ibd/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: gocam:full_text

"},{"location":"ibd/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd/full_text/#properties","title":"Properties","text":""},{"location":"ibd/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/full_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd/gene/","title":"Slot: gene","text":"

URI: gocam:gene

"},{"location":"ibd/gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneOrganismRelationship no GeneMolecularActivityRelationship no GeneMolecularActivityRelationship2 no GeneSubcellularLocalizationRelationship no"},{"location":"ibd/gene/#properties","title":"Properties","text":""},{"location":"ibd/gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene/#linkml-source","title":"LinkML Source","text":"
name: gene\nalias: gene\ndomain_of:\n- GeneOrganismRelationship\n- GeneMolecularActivityRelationship\n- GeneMolecularActivityRelationship2\n- GeneSubcellularLocalizationRelationship\nrange: string\n\n
"},{"location":"ibd/gene1/","title":"Slot: gene1","text":"

URI: gocam:gene1

"},{"location":"ibd/gene1/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneGeneInteraction no"},{"location":"ibd/gene1/#properties","title":"Properties","text":""},{"location":"ibd/gene1/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene1/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene1/#linkml-source","title":"LinkML Source","text":"
name: gene1\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: gene1\nowner: GeneGeneInteraction\ndomain_of:\n- GeneGeneInteraction\nrange: Gene\n\n
"},{"location":"ibd/gene2/","title":"Slot: gene2","text":"

URI: gocam:gene2

"},{"location":"ibd/gene2/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneGeneInteraction no"},{"location":"ibd/gene2/#properties","title":"Properties","text":""},{"location":"ibd/gene2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene2/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene2/#linkml-source","title":"LinkML Source","text":"
name: gene2\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: gene2\nowner: GeneGeneInteraction\ndomain_of:\n- GeneGeneInteraction\nrange: Gene\n\n
"},{"location":"ibd/gene_functions/","title":"Slot: gene_functions","text":"

semicolon-separated list of gene to molecular activity relationships

URI: gocam:gene_functions

"},{"location":"ibd/gene_functions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/gene_functions/#properties","title":"Properties","text":""},{"location":"ibd/gene_functions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene_functions/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene_functions/#linkml-source","title":"LinkML Source","text":"
name: gene_functions\ndescription: semicolon-separated list of gene to molecular activity relationships\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_functions\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: GeneMolecularActivityRelationship\n\n
"},{"location":"ibd/gene_gene_interactions/","title":"Slot: gene_gene_interactions","text":"

semicolon-separated list of gene to gene interactions

URI: gocam:gene_gene_interactions

"},{"location":"ibd/gene_gene_interactions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/gene_gene_interactions/#properties","title":"Properties","text":""},{"location":"ibd/gene_gene_interactions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene_gene_interactions/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene_gene_interactions/#linkml-source","title":"LinkML Source","text":"
name: gene_gene_interactions\ndescription: semicolon-separated list of gene to gene interactions\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_gene_interactions\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: GeneGeneInteraction\n\n
"},{"location":"ibd/gene_localizations/","title":"Slot: gene_localizations","text":"

semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"

URI: gocam:gene_localizations

"},{"location":"ibd/gene_localizations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/gene_localizations/#properties","title":"Properties","text":""},{"location":"ibd/gene_localizations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene_localizations/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene_localizations/#linkml-source","title":"LinkML Source","text":"
name: gene_localizations\ndescription: semicolon-separated list of genes plus their location in the cell; for\n  example, \"gene1 / cytoplasm; gene2 / mitochondrion\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_localizations\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: GeneSubcellularLocalizationRelationship\n\n
"},{"location":"ibd/gene_organisms/","title":"Slot: gene_organisms","text":"

URI: gocam:gene_organisms

"},{"location":"ibd/gene_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/gene_organisms/#properties","title":"Properties","text":""},{"location":"ibd/gene_organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/gene_organisms/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of asterisk separated gene to organism relationships"},{"location":"ibd/gene_organisms/#schema-source","title":"Schema Source","text":""},{"location":"ibd/gene_organisms/#linkml-source","title":"LinkML Source","text":"
name: gene_organisms\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of asterisk separated gene to organism relationships\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: gene_organisms\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: GeneOrganismRelationship\n\n
"},{"location":"ibd/genes/","title":"Slot: genes","text":"

semicolon-separated list of genes

URI: gocam:genes

"},{"location":"ibd/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/genes/#properties","title":"Properties","text":""},{"location":"ibd/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/genes/#schema-source","title":"Schema Source","text":""},{"location":"ibd/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\ndescription: semicolon-separated list of genes\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: genes\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: Gene\n\n
"},{"location":"ibd/gocam-template/","title":"gocam-template","text":"

A template for GO-CAMs

URI: http://w3id.org/ontogpt/gocam

"},{"location":"ibd/id/","title":"Slot: id","text":"

URI: gocam:id

"},{"location":"ibd/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Pathway no CellularProcess no MolecularActivity no GeneLocation yes Organism no Molecule no NamedEntity no RelationshipType no Publication no"},{"location":"ibd/id/#properties","title":"Properties","text":""},{"location":"ibd/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"ibd/input_id/","title":"Slot: input_id","text":"

URI: gocam:input_id

"},{"location":"ibd/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/input_id/#properties","title":"Properties","text":""},{"location":"ibd/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/input_id/#schema-source","title":"Schema Source","text":""},{"location":"ibd/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd/input_text/","title":"Slot: input_text","text":"

URI: gocam:input_text

"},{"location":"ibd/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/input_text/#properties","title":"Properties","text":""},{"location":"ibd/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/input_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd/input_title/","title":"Slot: input_title","text":"

URI: gocam:input_title

"},{"location":"ibd/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/input_title/#properties","title":"Properties","text":""},{"location":"ibd/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/input_title/#schema-source","title":"Schema Source","text":""},{"location":"ibd/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"ibd/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Pathway no CellularProcess no MolecularActivity no GeneLocation no Organism no Molecule no NamedEntity no RelationshipType no"},{"location":"ibd/label/#properties","title":"Properties","text":""},{"location":"ibd/label/#aliases","title":"Aliases","text":""},{"location":"ibd/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"ibd/label/#schema-source","title":"Schema Source","text":""},{"location":"ibd/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/gocam\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"ibd/location/","title":"Slot: location","text":"

URI: gocam:location

"},{"location":"ibd/location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneSubcellularLocalizationRelationship no"},{"location":"ibd/location/#properties","title":"Properties","text":""},{"location":"ibd/location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/location/#schema-source","title":"Schema Source","text":""},{"location":"ibd/location/#linkml-source","title":"LinkML Source","text":"
name: location\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: location\nowner: GeneSubcellularLocalizationRelationship\ndomain_of:\n- GeneSubcellularLocalizationRelationship\nrange: GeneLocation\n\n
"},{"location":"ibd/molecular_activity/","title":"Slot: molecular_activity","text":"

URI: gocam:molecular_activity

"},{"location":"ibd/molecular_activity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship no GeneMolecularActivityRelationship2 no"},{"location":"ibd/molecular_activity/#properties","title":"Properties","text":""},{"location":"ibd/molecular_activity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/molecular_activity/#linkml-source","title":"LinkML Source","text":"
name: molecular_activity\nalias: molecular_activity\ndomain_of:\n- GeneMolecularActivityRelationship\n- GeneMolecularActivityRelationship2\nrange: string\n\n
"},{"location":"ibd/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: gocam:named_entities

"},{"location":"ibd/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/named_entities/#properties","title":"Properties","text":""},{"location":"ibd/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"ibd/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ibd/object/","title":"Slot: object","text":"

URI: gocam:object

"},{"location":"ibd/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/object/#properties","title":"Properties","text":""},{"location":"ibd/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/object/#schema-source","title":"Schema Source","text":""},{"location":"ibd/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ibd/object_id/","title":"Slot: object_id","text":"

URI: gocam:object_id

"},{"location":"ibd/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd/object_id/#properties","title":"Properties","text":""},{"location":"ibd/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/object_id/#schema-source","title":"Schema Source","text":""},{"location":"ibd/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: gocam:object_qualifier

"},{"location":"ibd/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/object_qualifier/#properties","title":"Properties","text":""},{"location":"ibd/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ibd/object_text/","title":"Slot: object_text","text":"

URI: gocam:object_text

"},{"location":"ibd/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd/object_text/#properties","title":"Properties","text":""},{"location":"ibd/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/object_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd/organism/","title":"Slot: organism","text":"

URI: gocam:organism

"},{"location":"ibd/organism/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneOrganismRelationship no"},{"location":"ibd/organism/#properties","title":"Properties","text":""},{"location":"ibd/organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/organism/#schema-source","title":"Schema Source","text":""},{"location":"ibd/organism/#linkml-source","title":"LinkML Source","text":"
name: organism\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: organism\nowner: GeneOrganismRelationship\ndomain_of:\n- GeneOrganismRelationship\nrange: Organism\n\n
"},{"location":"ibd/organisms/","title":"Slot: organisms","text":"

semicolon-separated list of organism taxons

URI: gocam:organisms

"},{"location":"ibd/organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/organisms/#properties","title":"Properties","text":""},{"location":"ibd/organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/organisms/#schema-source","title":"Schema Source","text":""},{"location":"ibd/organisms/#linkml-source","title":"LinkML Source","text":"
name: organisms\ndescription: semicolon-separated list of organism taxons\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: organisms\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: Organism\n\n
"},{"location":"ibd/pathways/","title":"Slot: pathways","text":"

semicolon-separated list of pathways

URI: gocam:pathways

"},{"location":"ibd/pathways/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd/pathways/#properties","title":"Properties","text":""},{"location":"ibd/pathways/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/pathways/#schema-source","title":"Schema Source","text":""},{"location":"ibd/pathways/#linkml-source","title":"LinkML Source","text":"
name: pathways\ndescription: semicolon-separated list of pathways\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: pathways\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: Pathway\n\n
"},{"location":"ibd/predicate/","title":"Slot: predicate","text":"

URI: gocam:predicate

"},{"location":"ibd/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/predicate/#properties","title":"Properties","text":""},{"location":"ibd/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/predicate/#schema-source","title":"Schema Source","text":""},{"location":"ibd/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"ibd/prompt/","title":"Slot: prompt","text":"

URI: gocam:prompt

"},{"location":"ibd/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/prompt/#properties","title":"Properties","text":""},{"location":"ibd/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/prompt/#schema-source","title":"Schema Source","text":""},{"location":"ibd/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd/publication/","title":"Slot: publication","text":"

URI: gocam:publication

"},{"location":"ibd/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ibd/publication/#properties","title":"Properties","text":""},{"location":"ibd/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"ibd/publication/#schema-source","title":"Schema Source","text":""},{"location":"ibd/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"ibd/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: gocam:qualifier

"},{"location":"ibd/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/qualifier/#properties","title":"Properties","text":""},{"location":"ibd/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"ibd/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: gocam:raw_completion_output

"},{"location":"ibd/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd/raw_completion_output/#properties","title":"Properties","text":""},{"location":"ibd/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"ibd/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd/subject/","title":"Slot: subject","text":"

URI: gocam:subject

"},{"location":"ibd/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/subject/#properties","title":"Properties","text":""},{"location":"ibd/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/subject/#schema-source","title":"Schema Source","text":""},{"location":"ibd/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ibd/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: gocam:subject_qualifier

"},{"location":"ibd/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd/subject_qualifier/#properties","title":"Properties","text":""},{"location":"ibd/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ibd/subject_text/","title":"Slot: subject_text","text":"

URI: gocam:subject_text

"},{"location":"ibd/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd/subject_text/#properties","title":"Properties","text":""},{"location":"ibd/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd/target/","title":"Slot: target","text":"

URI: gocam:target

"},{"location":"ibd/target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneMolecularActivityRelationship2 no"},{"location":"ibd/target/#properties","title":"Properties","text":""},{"location":"ibd/target/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/target/#annotations","title":"Annotations","text":"property value prompt the name of the molecular entity that is the target of the molecular activity."},{"location":"ibd/target/#schema-source","title":"Schema Source","text":""},{"location":"ibd/target/#linkml-source","title":"LinkML Source","text":"
name: target\nannotations:\n  prompt:\n    tag: prompt\n    value: the name of the molecular entity that is the target of the molecular activity.\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: target\nowner: GeneMolecularActivityRelationship2\ndomain_of:\n- GeneMolecularActivityRelationship2\nrange: Molecule\n\n
"},{"location":"ibd/title/","title":"Slot: title","text":"

The title of the publication

URI: gocam:title

"},{"location":"ibd/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd/title/#properties","title":"Properties","text":""},{"location":"ibd/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/title/#schema-source","title":"Schema Source","text":""},{"location":"ibd/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd/triples/","title":"Slot: triples","text":"

URI: gocam:triples

"},{"location":"ibd/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ibd/triples/#properties","title":"Properties","text":""},{"location":"ibd/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd/triples/#schema-source","title":"Schema Source","text":""},{"location":"ibd/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/gocam\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ibd_literature/","title":"IBD Literature Template","text":"

A template for extracting information from IBD literature

URI: http://w3id.org/ontogpt/ibd_literature

Name: ibd-literature-template

"},{"location":"ibd_literature/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nIBDAnnotations {\n\n}\nDiseaseCellularProcessRelationship {\n\n}\nNamedEntity {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nDiseaseToCellularProcessPredicate {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGeneExposureRelationship {\n\n}\nGene {\n    string id  \n    string label  \n}\nChemicalExposureToGenePredicate {\n    string id  \n    string label  \n}\nChemicalExposure {\n    string id  \n    string label  \n}\n\nIBDAnnotations ||--}o Gene : \"genes\"\nIBDAnnotations ||--}o ChemicalExposure : \"exposures\"\nIBDAnnotations ||--}o GeneExposureRelationship : \"gene_exposures_relationships\"\nIBDAnnotations ||--}o Disease : \"diseases\"\nIBDAnnotations ||--}o CellularProcess : \"cellular_process\"\nIBDAnnotations ||--}o DiseaseCellularProcessRelationship : \"disease_cellular_process_relationships\"\nDiseaseCellularProcessRelationship ||--|o Disease : \"subject\"\nDiseaseCellularProcessRelationship ||--|o DiseaseToCellularProcessPredicate : \"predicate\"\nDiseaseCellularProcessRelationship ||--|o CellularProcess : \"object\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"subject_qualifier\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"object_qualifier\"\nGeneExposureRelationship ||--|o ChemicalExposure : \"subject\"\nGeneExposureRelationship ||--|o ChemicalExposureToGenePredicate : \"predicate\"\nGeneExposureRelationship ||--|o Gene : \"object\"\nGeneExposureRelationship ||--|o NamedEntity : \"subject_qualifier\"\nGeneExposureRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None DiseaseCellularProcessRelationship None GeneExposureRelationship None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text IBDAnnotations None NamedEntity None CellularProcess None ChemicalExposure None ChemicalExposureToGenePredicate None Disease None DiseaseToCellularProcessPredicate None Gene None RelationshipType None Publication None TextWithTriples None"},{"location":"ibd_literature/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication cellular_process semicolon-separated list of cellular processes combined_text disease_cellular_process_relationships semicolon-separated list of disease to cellular process relationships diseases semicolon-separated list of diseases exposures semicolon-separated list of exposures extracted_object The complex objects extracted from the text full_text The full text of the publication gene_exposures_relationships semicolon-separated list of gene to molecular activity relationships genes semicolon-separated list of genes id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object The name of the gene in the pair object_id object_qualifier An optional qualifier or modifier for the gene object_text predicate The name of the type of relationship between a chemical exposure and a gene prompt publication qualifier A qualifier for the statements, e raw_completion_output subject The name of the exposure, such as a exposure to a chemical toxin subject_qualifier An optional qualifier or modifier for the chemical exposure subject_text title The title of the publication triples"},{"location":"ibd_literature/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"ibd_literature/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"ibd_literature/#subsets","title":"Subsets","text":"Subset Description"},{"location":"ibd_literature/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: ibdlit:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"ibd_literature/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"ibd_literature/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:AnnotatorResult native ibdlit:AnnotatorResult"},{"location":"ibd_literature/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n\n
"},{"location":"ibd_literature/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"ibd_literature/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"ibd_literature/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ibd_literature/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"ibd_literature/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Any/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native ibdlit:Any"},{"location":"ibd_literature/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nclass_uri: linkml:Any\n\n
"},{"location":"ibd_literature/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nclass_uri: linkml:Any\n\n
"},{"location":"ibd_literature/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"ibd_literature/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/CellularProcess/","title":"Class: CellularProcess","text":"

URI: ibdlit:CellularProcess

erDiagram\nCellularProcess {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/CellularProcess/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/CellularProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/CellularProcess/#usages","title":"Usages","text":"used by used in type used IBDAnnotations cellular_process range CellularProcess DiseaseCellularProcessRelationship object range CellularProcess"},{"location":"ibd_literature/CellularProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/CellularProcess/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/CellularProcess/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"ibd_literature/CellularProcess/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/CellularProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:CellularProcess native ibdlit:CellularProcess"},{"location":"ibd_literature/CellularProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/CellularProcess/#direct","title":"Direct","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\n  prompt:\n    tag: prompt\n    value: the name of the cellular process\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/CellularProcess/#induced","title":"Induced","text":"
name: CellularProcess\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\n  prompt:\n    tag: prompt\n    value: the name of the cellular process\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: CellularProcess\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/ChemicalExposure/","title":"Class: ChemicalExposure","text":"

URI: ibdlit:ChemicalExposure

erDiagram\nChemicalExposure {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/ChemicalExposure/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/ChemicalExposure/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/ChemicalExposure/#usages","title":"Usages","text":"used by used in type used IBDAnnotations exposures range ChemicalExposure GeneExposureRelationship subject range ChemicalExposure"},{"location":"ibd_literature/ChemicalExposure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/ChemicalExposure/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/ChemicalExposure/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ecto, sqlite:obo:chebi"},{"location":"ibd_literature/ChemicalExposure/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/ChemicalExposure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:ChemicalExposure native ibdlit:ChemicalExposure"},{"location":"ibd_literature/ChemicalExposure/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/ChemicalExposure/#direct","title":"Direct","text":"
name: ChemicalExposure\nid_prefixes:\n- CHEBI\n- ECTO\n- ExO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ecto, sqlite:obo:chebi\n  prompt:\n    tag: prompt\n    value: the name of the exposure, such as a exposure to a chemical toxin. For example,\n      CHEBI:17968 butyrate.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/ChemicalExposure/#induced","title":"Induced","text":"
name: ChemicalExposure\nid_prefixes:\n- CHEBI\n- ECTO\n- ExO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ecto, sqlite:obo:chebi\n  prompt:\n    tag: prompt\n    value: the name of the exposure, such as a exposure to a chemical toxin. For example,\n      CHEBI:17968 butyrate.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalExposure\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalExposure\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/","title":"Class: ChemicalExposureToGenePredicate","text":"

URI: ibdlit:ChemicalExposureToGenePredicate

erDiagram\nChemicalExposureToGenePredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#usages","title":"Usages","text":"used by used in type used GeneExposureRelationship predicate range ChemicalExposureToGenePredicate"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ro"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:ChemicalExposureToGenePredicate native ibdlit:ChemicalExposureToGenePredicate"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#direct","title":"Direct","text":"
name: ChemicalExposureToGenePredicate\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\n  prompt:\n    tag: prompt\n    value: the name of the type of relationship between a chemical exposure and a\n      gene.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/ChemicalExposureToGenePredicate/#induced","title":"Induced","text":"
name: ChemicalExposureToGenePredicate\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\n  prompt:\n    tag: prompt\n    value: the name of the type of relationship between a chemical exposure and a\n      gene.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalExposureToGenePredicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalExposureToGenePredicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: ibdlit:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"ibd_literature/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ibd_literature/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:CompoundExpression native ibdlit:CompoundExpression"},{"location":"ibd_literature/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nabstract: true\n\n
"},{"location":"ibd_literature/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nabstract: true\n\n
"},{"location":"ibd_literature/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"ibd_literature/Curie/#comments","title":"Comments","text":""},{"location":"ibd_literature/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Curie/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"ibd_literature/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Date/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"ibd_literature/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"ibd_literature/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"ibd_literature/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Disease/","title":"Class: Disease","text":"

URI: ibdlit:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/Disease/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/Disease/#usages","title":"Usages","text":"used by used in type used IBDAnnotations diseases range Disease DiseaseCellularProcessRelationship subject range Disease"},{"location":"ibd_literature/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Disease/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo"},{"location":"ibd_literature/Disease/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:Disease native ibdlit:Disease"},{"location":"ibd_literature/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/Disease/#direct","title":"Direct","text":"
name: Disease\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\n  prompt:\n    tag: prompt\n    value: the name of the disease\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/Disease/#induced","title":"Induced","text":"
name: Disease\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\n  prompt:\n    tag: prompt\n    value: the name of the disease\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/","title":"Class: DiseaseCellularProcessRelationship","text":"

URI: ibdlit:DiseaseCellularProcessRelationship

erDiagram\nDiseaseCellularProcessRelationship {\n\n}\nNamedEntity {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nDiseaseToCellularProcessPredicate {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nDiseaseCellularProcessRelationship ||--|o Disease : \"subject\"\nDiseaseCellularProcessRelationship ||--|o DiseaseToCellularProcessPredicate : \"predicate\"\nDiseaseCellularProcessRelationship ||--|o CellularProcess : \"object\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"subject_qualifier\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 Disease The name of the disease direct predicate 0..1 DiseaseToCellularProcessPredicate The name of the type of relationship between a disease and a cellular process direct object 0..1 CellularProcess The name of the cellular process direct subject_qualifier 0..1 NamedEntity direct object_qualifier 0..1 NamedEntity direct"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#usages","title":"Usages","text":"used by used in type used IBDAnnotations disease_cellular_process_relationships range DiseaseCellularProcessRelationship"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:DiseaseCellularProcessRelationship native ibdlit:DiseaseCellularProcessRelationship"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#direct","title":"Direct","text":"
name: DiseaseCellularProcessRelationship\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    description: The name of the disease.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: Disease\n  predicate:\n    name: predicate\n    description: The name of the type of relationship between a disease and a cellular\n      process.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: DiseaseToCellularProcessPredicate\n  object:\n    name: object\n    description: The name of the cellular process.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: CellularProcess\n  subject_qualifier:\n    name: subject_qualifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/DiseaseCellularProcessRelationship/#induced","title":"Induced","text":"
name: DiseaseCellularProcessRelationship\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    description: The name of the disease.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: subject\n    owner: DiseaseCellularProcessRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: Disease\n  predicate:\n    name: predicate\n    description: The name of the type of relationship between a disease and a cellular\n      process.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: predicate\n    owner: DiseaseCellularProcessRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: DiseaseToCellularProcessPredicate\n  object:\n    name: object\n    description: The name of the cellular process.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: object\n    owner: DiseaseCellularProcessRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: CellularProcess\n  subject_qualifier:\n    name: subject_qualifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: subject_qualifier\n    owner: DiseaseCellularProcessRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: object_qualifier\n    owner: DiseaseCellularProcessRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/","title":"Class: DiseaseToCellularProcessPredicate","text":"

URI: ibdlit:DiseaseToCellularProcessPredicate

erDiagram\nDiseaseToCellularProcessPredicate {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#usages","title":"Usages","text":"used by used in type used DiseaseCellularProcessRelationship predicate range DiseaseToCellularProcessPredicate"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ro"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:DiseaseToCellularProcessPredicate native ibdlit:DiseaseToCellularProcessPredicate"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#direct","title":"Direct","text":"
name: DiseaseToCellularProcessPredicate\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\n  prompt:\n    tag: prompt\n    value: the name of the type of relationship between a disease and a cellular process.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/DiseaseToCellularProcessPredicate/#induced","title":"Induced","text":"
name: DiseaseToCellularProcessPredicate\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\n  prompt:\n    tag: prompt\n    value: the name of the type of relationship between a disease and a cellular process.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DiseaseToCellularProcessPredicate\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: DiseaseToCellularProcessPredicate\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"ibd_literature/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Double/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: ibdlit:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"ibd_literature/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"ibd_literature/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:ExtractionResult native ibdlit:ExtractionResult"},{"location":"ibd_literature/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd_literature/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd_literature/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"ibd_literature/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Float/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Gene/","title":"Class: Gene","text":"

URI: ibdlit:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/Gene/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/Gene/#usages","title":"Usages","text":"used by used in type used IBDAnnotations genes range Gene GeneExposureRelationship object range Gene"},{"location":"ibd_literature/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/Gene/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hgnc, sqlite:obo:pr"},{"location":"ibd_literature/Gene/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:Gene native ibdlit:Gene"},{"location":"ibd_literature/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, sqlite:obo:pr\n  prompt:\n    tag: prompt\n    value: the name of the gene in the pair. This comes second in the pair.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hgnc, sqlite:obo:pr\n  prompt:\n    tag: prompt\n    value: the name of the gene in the pair. This comes second in the pair.\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/GeneExposureRelationship/","title":"Class: GeneExposureRelationship","text":"

URI: ibdlit:GeneExposureRelationship

erDiagram\nGeneExposureRelationship {\n\n}\nNamedEntity {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nChemicalExposureToGenePredicate {\n    string id  \n    string label  \n}\nChemicalExposure {\n    string id  \n    string label  \n}\n\nGeneExposureRelationship ||--|o ChemicalExposure : \"subject\"\nGeneExposureRelationship ||--|o ChemicalExposureToGenePredicate : \"predicate\"\nGeneExposureRelationship ||--|o Gene : \"object\"\nGeneExposureRelationship ||--|o NamedEntity : \"subject_qualifier\"\nGeneExposureRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/GeneExposureRelationship/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/GeneExposureRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 ChemicalExposure The name of the exposure, such as a exposure to a chemical toxin direct predicate 0..1 ChemicalExposureToGenePredicate The name of the type of relationship between a chemical exposure and a gene direct object 0..1 Gene The name of the gene in the pair direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the chemical exposure direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the gene direct"},{"location":"ibd_literature/GeneExposureRelationship/#usages","title":"Usages","text":"used by used in type used IBDAnnotations gene_exposures_relationships range GeneExposureRelationship"},{"location":"ibd_literature/GeneExposureRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/GeneExposureRelationship/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/GeneExposureRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:GeneExposureRelationship native ibdlit:GeneExposureRelationship"},{"location":"ibd_literature/GeneExposureRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/GeneExposureRelationship/#direct","title":"Direct","text":"
name: GeneExposureRelationship\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    description: The name of the exposure, such as a exposure to a chemical toxin.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: ChemicalExposure\n  predicate:\n    name: predicate\n    description: The name of the type of relationship between a chemical exposure\n      and a gene.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: ChemicalExposureToGenePredicate\n  object:\n    name: object\n    description: The name of the gene in the pair. This comes second in the pair.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: Gene\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the chemical exposure.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the gene.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/GeneExposureRelationship/#induced","title":"Induced","text":"
name: GeneExposureRelationship\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nattributes:\n  subject:\n    name: subject\n    description: The name of the exposure, such as a exposure to a chemical toxin.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: subject\n    owner: GeneExposureRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: ChemicalExposure\n  predicate:\n    name: predicate\n    description: The name of the type of relationship between a chemical exposure\n      and a gene.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: predicate\n    owner: GeneExposureRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: ChemicalExposureToGenePredicate\n  object:\n    name: object\n    description: The name of the gene in the pair. This comes second in the pair.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: object\n    owner: GeneExposureRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: Gene\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the chemical exposure.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: subject_qualifier\n    owner: GeneExposureRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the gene.\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: object_qualifier\n    owner: GeneExposureRelationship\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/IBDAnnotations/","title":"Class: IBDAnnotations","text":"

URI: ibdlit:IBDAnnotations

erDiagram\nIBDAnnotations {\n\n}\nDiseaseCellularProcessRelationship {\n\n}\nNamedEntity {\n    string id  \n    string label  \n}\nCellularProcess {\n    string id  \n    string label  \n}\nDiseaseToCellularProcessPredicate {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nGeneExposureRelationship {\n\n}\nGene {\n    string id  \n    string label  \n}\nChemicalExposureToGenePredicate {\n    string id  \n    string label  \n}\nChemicalExposure {\n    string id  \n    string label  \n}\n\nIBDAnnotations ||--}o Gene : \"genes\"\nIBDAnnotations ||--}o ChemicalExposure : \"exposures\"\nIBDAnnotations ||--}o GeneExposureRelationship : \"gene_exposures_relationships\"\nIBDAnnotations ||--}o Disease : \"diseases\"\nIBDAnnotations ||--}o CellularProcess : \"cellular_process\"\nIBDAnnotations ||--}o DiseaseCellularProcessRelationship : \"disease_cellular_process_relationships\"\nDiseaseCellularProcessRelationship ||--|o Disease : \"subject\"\nDiseaseCellularProcessRelationship ||--|o DiseaseToCellularProcessPredicate : \"predicate\"\nDiseaseCellularProcessRelationship ||--|o CellularProcess : \"object\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"subject_qualifier\"\nDiseaseCellularProcessRelationship ||--|o NamedEntity : \"object_qualifier\"\nGeneExposureRelationship ||--|o ChemicalExposure : \"subject\"\nGeneExposureRelationship ||--|o ChemicalExposureToGenePredicate : \"predicate\"\nGeneExposureRelationship ||--|o Gene : \"object\"\nGeneExposureRelationship ||--|o NamedEntity : \"subject_qualifier\"\nGeneExposureRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/IBDAnnotations/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance genes 0..* Gene semicolon-separated list of genes direct exposures 0..* ChemicalExposure semicolon-separated list of exposures direct gene_exposures_relationships 0..* GeneExposureRelationship semicolon-separated list of gene to molecular activity relationships direct diseases 0..* Disease semicolon-separated list of diseases direct cellular_process 0..* CellularProcess semicolon-separated list of cellular processes direct disease_cellular_process_relationships 0..* DiseaseCellularProcessRelationship semicolon-separated list of disease to cellular process relationships direct"},{"location":"ibd_literature/IBDAnnotations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/IBDAnnotations/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/IBDAnnotations/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:IBDAnnotations native ibdlit:IBDAnnotations"},{"location":"ibd_literature/IBDAnnotations/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/IBDAnnotations/#direct","title":"Direct","text":"
name: IBDAnnotations\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: Gene\n  exposures:\n    name: exposures\n    annotations:\n      prompt:\n        tag: prompt\n        value: a chemical or molecule whose direct or indirect effects cause one or\n          more entities to experience biological change\n    description: semicolon-separated list of exposures\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: ChemicalExposure\n  gene_exposures_relationships:\n    name: gene_exposures_relationships\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: GeneExposureRelationship\n  diseases:\n    name: diseases\n    description: semicolon-separated list of diseases\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: Disease\n  cellular_process:\n    name: cellular_process\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: CellularProcess\n  disease_cellular_process_relationships:\n    name: disease_cellular_process_relationships\n    description: semicolon-separated list of disease to cellular process relationships\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: DiseaseCellularProcessRelationship\ntree_root: true\n\n
"},{"location":"ibd_literature/IBDAnnotations/#induced","title":"Induced","text":"
name: IBDAnnotations\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  genes:\n    name: genes\n    description: semicolon-separated list of genes\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: Gene\n  exposures:\n    name: exposures\n    annotations:\n      prompt:\n        tag: prompt\n        value: a chemical or molecule whose direct or indirect effects cause one or\n          more entities to experience biological change\n    description: semicolon-separated list of exposures\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: exposures\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: ChemicalExposure\n  gene_exposures_relationships:\n    name: gene_exposures_relationships\n    description: semicolon-separated list of gene to molecular activity relationships\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: gene_exposures_relationships\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: GeneExposureRelationship\n  diseases:\n    name: diseases\n    description: semicolon-separated list of diseases\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: diseases\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: Disease\n  cellular_process:\n    name: cellular_process\n    description: semicolon-separated list of cellular processes\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: cellular_process\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: CellularProcess\n  disease_cellular_process_relationships:\n    name: disease_cellular_process_relationships\n    description: semicolon-separated list of disease to cellular process relationships\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: disease_cellular_process_relationships\n    owner: IBDAnnotations\n    domain_of:\n    - IBDAnnotations\n    range: DiseaseCellularProcessRelationship\ntree_root: true\n\n
"},{"location":"ibd_literature/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"ibd_literature/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Integer/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/NamedEntity/","title":"Class: NamedEntity","text":"

URI: ibdlit:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"ibd_literature/NamedEntity/#usages","title":"Usages","text":"used by used in type used GeneExposureRelationship subject_qualifier range NamedEntity GeneExposureRelationship object_qualifier range NamedEntity DiseaseCellularProcessRelationship subject_qualifier range NamedEntity DiseaseCellularProcessRelationship object_qualifier range NamedEntity Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"ibd_literature/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:NamedEntity native ibdlit:NamedEntity"},{"location":"ibd_literature/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"ibd_literature/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"ibd_literature/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"ibd_literature/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"ibd_literature/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"ibd_literature/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"ibd_literature/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"ibd_literature/Objectidentifier/#comments","title":"Comments","text":""},{"location":"ibd_literature/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Publication/","title":"Class: Publication","text":"

URI: ibdlit:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"ibd_literature/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"ibd_literature/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"ibd_literature/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Publication/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:Publication native ibdlit:Publication"},{"location":"ibd_literature/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n\n
"},{"location":"ibd_literature/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"ibd_literature/RelationshipType/","title":"Class: RelationshipType","text":"

URI: ibdlit:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ibd_literature/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ibd_literature/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"ibd_literature/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ibd_literature/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:RelationshipType native ibdlit:RelationshipType"},{"location":"ibd_literature/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\n\n
"},{"location":"ibd_literature/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ibd_literature/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"ibd_literature/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/String/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: ibdlit:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"ibd_literature/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:TextWithTriples native ibdlit:TextWithTriples"},{"location":"ibd_literature/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd_literature/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ibd_literature/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"ibd_literature/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Time/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: ibdlit:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ibd_literature/Triple/#inheritance","title":"Inheritance","text":""},{"location":"ibd_literature/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"ibd_literature/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"ibd_literature/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Triple/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self ibdlit:Triple native ibdlit:Triple"},{"location":"ibd_literature/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"ibd_literature/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: subject\n    owner: Triple\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: object\n    owner: Triple\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/ibd_literature\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - GeneExposureRelationship\n    - DiseaseCellularProcessRelationship\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ibd_literature/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"ibd_literature/Uri/#comments","title":"Comments","text":""},{"location":"ibd_literature/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Uri/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"ibd_literature/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: ibdlit:abstract

"},{"location":"ibd_literature/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd_literature/abstract/#properties","title":"Properties","text":""},{"location":"ibd_literature/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/abstract/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd_literature/cellular_process/","title":"Slot: cellular_process","text":"

semicolon-separated list of cellular processes

URI: ibdlit:cellular_process

"},{"location":"ibd_literature/cellular_process/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/cellular_process/#properties","title":"Properties","text":""},{"location":"ibd_literature/cellular_process/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/cellular_process/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/cellular_process/#linkml-source","title":"LinkML Source","text":"
name: cellular_process\ndescription: semicolon-separated list of cellular processes\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: cellular_process\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: CellularProcess\n\n
"},{"location":"ibd_literature/combined_text/","title":"Slot: combined_text","text":"

URI: ibdlit:combined_text

"},{"location":"ibd_literature/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd_literature/combined_text/#properties","title":"Properties","text":""},{"location":"ibd_literature/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd_literature/disease_cellular_process_relationships/","title":"Slot: disease_cellular_process_relationships","text":"

semicolon-separated list of disease to cellular process relationships

URI: ibdlit:disease_cellular_process_relationships

"},{"location":"ibd_literature/disease_cellular_process_relationships/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/disease_cellular_process_relationships/#properties","title":"Properties","text":""},{"location":"ibd_literature/disease_cellular_process_relationships/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/disease_cellular_process_relationships/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/disease_cellular_process_relationships/#linkml-source","title":"LinkML Source","text":"
name: disease_cellular_process_relationships\ndescription: semicolon-separated list of disease to cellular process relationships\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: disease_cellular_process_relationships\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: DiseaseCellularProcessRelationship\n\n
"},{"location":"ibd_literature/diseases/","title":"Slot: diseases","text":"

semicolon-separated list of diseases

URI: ibdlit:diseases

"},{"location":"ibd_literature/diseases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/diseases/#properties","title":"Properties","text":""},{"location":"ibd_literature/diseases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/diseases/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/diseases/#linkml-source","title":"LinkML Source","text":"
name: diseases\ndescription: semicolon-separated list of diseases\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: diseases\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: Disease\n\n
"},{"location":"ibd_literature/exposures/","title":"Slot: exposures","text":"

semicolon-separated list of exposures

URI: ibdlit:exposures

"},{"location":"ibd_literature/exposures/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/exposures/#properties","title":"Properties","text":""},{"location":"ibd_literature/exposures/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/exposures/#annotations","title":"Annotations","text":"property value prompt a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change"},{"location":"ibd_literature/exposures/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/exposures/#linkml-source","title":"LinkML Source","text":"
name: exposures\nannotations:\n  prompt:\n    tag: prompt\n    value: a chemical or molecule whose direct or indirect effects cause one or more\n      entities to experience biological change\ndescription: semicolon-separated list of exposures\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: exposures\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: ChemicalExposure\n\n
"},{"location":"ibd_literature/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: ibdlit:extracted_object

"},{"location":"ibd_literature/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/extracted_object/#properties","title":"Properties","text":""},{"location":"ibd_literature/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"ibd_literature/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: ibdlit:full_text

"},{"location":"ibd_literature/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd_literature/full_text/#properties","title":"Properties","text":""},{"location":"ibd_literature/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/full_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd_literature/gene_exposures_relationships/","title":"Slot: gene_exposures_relationships","text":"

semicolon-separated list of gene to molecular activity relationships

URI: ibdlit:gene_exposures_relationships

"},{"location":"ibd_literature/gene_exposures_relationships/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/gene_exposures_relationships/#properties","title":"Properties","text":""},{"location":"ibd_literature/gene_exposures_relationships/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/gene_exposures_relationships/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/gene_exposures_relationships/#linkml-source","title":"LinkML Source","text":"
name: gene_exposures_relationships\ndescription: semicolon-separated list of gene to molecular activity relationships\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: gene_exposures_relationships\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: GeneExposureRelationship\n\n
"},{"location":"ibd_literature/genes/","title":"Slot: genes","text":"

semicolon-separated list of genes

URI: ibdlit:genes

"},{"location":"ibd_literature/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot IBDAnnotations no"},{"location":"ibd_literature/genes/#properties","title":"Properties","text":""},{"location":"ibd_literature/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/genes/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\ndescription: semicolon-separated list of genes\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: genes\nowner: IBDAnnotations\ndomain_of:\n- IBDAnnotations\nrange: Gene\n\n
"},{"location":"ibd_literature/ibd-literature-template/","title":"ibd-literature-template","text":"

A template for extracting information from IBD literature

URI: http://w3id.org/ontogpt/ibd_literature

"},{"location":"ibd_literature/id/","title":"Slot: id","text":"

URI: ibdlit:id

"},{"location":"ibd_literature/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no ChemicalExposure no ChemicalExposureToGenePredicate no Disease no CellularProcess no DiseaseToCellularProcessPredicate no NamedEntity no RelationshipType no Publication no"},{"location":"ibd_literature/id/#properties","title":"Properties","text":""},{"location":"ibd_literature/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"ibd_literature/input_id/","title":"Slot: input_id","text":"

URI: ibdlit:input_id

"},{"location":"ibd_literature/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/input_id/#properties","title":"Properties","text":""},{"location":"ibd_literature/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/input_id/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd_literature/input_text/","title":"Slot: input_text","text":"

URI: ibdlit:input_text

"},{"location":"ibd_literature/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/input_text/#properties","title":"Properties","text":""},{"location":"ibd_literature/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/input_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd_literature/input_title/","title":"Slot: input_title","text":"

URI: ibdlit:input_title

"},{"location":"ibd_literature/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/input_title/#properties","title":"Properties","text":""},{"location":"ibd_literature/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/input_title/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd_literature/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"ibd_literature/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no ChemicalExposure no ChemicalExposureToGenePredicate no Disease no CellularProcess no DiseaseToCellularProcessPredicate no NamedEntity no RelationshipType no"},{"location":"ibd_literature/label/#properties","title":"Properties","text":""},{"location":"ibd_literature/label/#aliases","title":"Aliases","text":""},{"location":"ibd_literature/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"ibd_literature/label/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"ibd_literature/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: ibdlit:named_entities

"},{"location":"ibd_literature/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/named_entities/#properties","title":"Properties","text":""},{"location":"ibd_literature/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ibd_literature/object/","title":"Slot: object","text":"

URI: ibdlit:object

"},{"location":"ibd_literature/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneExposureRelationship no DiseaseCellularProcessRelationship no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/object/#properties","title":"Properties","text":""},{"location":"ibd_literature/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/object/#linkml-source","title":"LinkML Source","text":"
name: object\nalias: object\ndomain_of:\n- GeneExposureRelationship\n- DiseaseCellularProcessRelationship\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/object_id/","title":"Slot: object_id","text":"

URI: ibdlit:object_id

"},{"location":"ibd_literature/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd_literature/object_id/#properties","title":"Properties","text":""},{"location":"ibd_literature/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/object_id/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd_literature/object_qualifier/","title":"Slot: object_qualifier","text":"

URI: ibdlit:object_qualifier

"},{"location":"ibd_literature/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneExposureRelationship no DiseaseCellularProcessRelationship no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/object_qualifier/#properties","title":"Properties","text":""},{"location":"ibd_literature/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\nalias: object_qualifier\ndomain_of:\n- GeneExposureRelationship\n- DiseaseCellularProcessRelationship\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/object_text/","title":"Slot: object_text","text":"

URI: ibdlit:object_text

"},{"location":"ibd_literature/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd_literature/object_text/#properties","title":"Properties","text":""},{"location":"ibd_literature/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/object_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd_literature/predicate/","title":"Slot: predicate","text":"

URI: ibdlit:predicate

"},{"location":"ibd_literature/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneExposureRelationship no DiseaseCellularProcessRelationship no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/predicate/#properties","title":"Properties","text":""},{"location":"ibd_literature/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nalias: predicate\ndomain_of:\n- GeneExposureRelationship\n- DiseaseCellularProcessRelationship\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/prompt/","title":"Slot: prompt","text":"

URI: ibdlit:prompt

"},{"location":"ibd_literature/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/prompt/#properties","title":"Properties","text":""},{"location":"ibd_literature/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/prompt/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd_literature/publication/","title":"Slot: publication","text":"

URI: ibdlit:publication

"},{"location":"ibd_literature/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ibd_literature/publication/#properties","title":"Properties","text":""},{"location":"ibd_literature/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"ibd_literature/publication/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"ibd_literature/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: ibdlit:qualifier

"},{"location":"ibd_literature/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/qualifier/#properties","title":"Properties","text":""},{"location":"ibd_literature/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: ibdlit:raw_completion_output

"},{"location":"ibd_literature/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ibd_literature/raw_completion_output/#properties","title":"Properties","text":""},{"location":"ibd_literature/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ibd_literature/subject/","title":"Slot: subject","text":"

URI: ibdlit:subject

"},{"location":"ibd_literature/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneExposureRelationship no DiseaseCellularProcessRelationship no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/subject/#properties","title":"Properties","text":""},{"location":"ibd_literature/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nalias: subject\ndomain_of:\n- GeneExposureRelationship\n- DiseaseCellularProcessRelationship\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/subject_qualifier/","title":"Slot: subject_qualifier","text":"

URI: ibdlit:subject_qualifier

"},{"location":"ibd_literature/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneExposureRelationship no DiseaseCellularProcessRelationship no Triple Abstract parent for Relation Extraction tasks no"},{"location":"ibd_literature/subject_qualifier/#properties","title":"Properties","text":""},{"location":"ibd_literature/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\nalias: subject_qualifier\ndomain_of:\n- GeneExposureRelationship\n- DiseaseCellularProcessRelationship\n- Triple\nrange: string\n\n
"},{"location":"ibd_literature/subject_text/","title":"Slot: subject_text","text":"

URI: ibdlit:subject_text

"},{"location":"ibd_literature/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ibd_literature/subject_text/#properties","title":"Properties","text":""},{"location":"ibd_literature/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ibd_literature/title/","title":"Slot: title","text":"

The title of the publication

URI: ibdlit:title

"},{"location":"ibd_literature/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ibd_literature/title/#properties","title":"Properties","text":""},{"location":"ibd_literature/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/title/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ibd_literature/triples/","title":"Slot: triples","text":"

URI: ibdlit:triples

"},{"location":"ibd_literature/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ibd_literature/triples/#properties","title":"Properties","text":""},{"location":"ibd_literature/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ibd_literature/triples/#schema-source","title":"Schema Source","text":""},{"location":"ibd_literature/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/ibd_literature\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"maxo/","title":"Template for Medical Action Extraction","text":"

A template for extracting relationships relevant to the MAXO medical action ontology.

URI: http://w3id.org/ontogpt/maxo

Name: maxo

"},{"location":"maxo/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nMaxoAnnotations {\n\n}\nActionToSymptomRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nSymptom {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\nActionToDiseaseRelationship {\n    string qualifier  \n}\nDisease {\n    string id  \n    string label  \n}\n\nMaxoAnnotations ||--}o Action : \"action\"\nMaxoAnnotations ||--}o Disease : \"disease\"\nMaxoAnnotations ||--}o Symptom : \"symptom\"\nMaxoAnnotations ||--}o ActionToDiseaseRelationship : \"action_to_disease\"\nMaxoAnnotations ||--}o ActionToSymptomRelationship : \"action_to_symptom\"\nActionToSymptomRelationship ||--|o Action : \"subject\"\nActionToSymptomRelationship ||--|o NamedEntity : \"predicate\"\nActionToSymptomRelationship ||--}o Symptom : \"object\"\nActionToSymptomRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToSymptomRelationship ||--|o NamedEntity : \"object_qualifier\"\nActionToDiseaseRelationship ||--|o Action : \"subject\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"predicate\"\nActionToDiseaseRelationship ||--}o Disease : \"object\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a disease, for example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis. ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a symptom, for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion. ExtractionResult A result of extracting knowledge on text MaxoAnnotations None NamedEntity None Action A clinically prescribed procedure, therapy, intervention, or recommendation. Disease A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. RelationshipType None Symptom A condition or phenotype resulting from an abnormal health state. Publication None TextWithTriples None"},{"location":"maxo/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication action Semicolon-separated list of medical actions action_to_disease action_to_symptom combined_text disease Semicolon-separated list of diseases extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text symptom Semicolon-separated list of symptoms title The title of the publication triples"},{"location":"maxo/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"maxo/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"maxo/#subsets","title":"Subsets","text":"Subset Description"},{"location":"maxo/Action/","title":"Class: Action","text":"

A clinically prescribed procedure, therapy, intervention, or recommendation.

URI: maxo_extract:Action

erDiagram\nAction {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"maxo/Action/#inheritance","title":"Inheritance","text":""},{"location":"maxo/Action/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"maxo/Action/#usages","title":"Usages","text":"used by used in type used MaxoAnnotations action range Action ActionToDiseaseRelationship subject range Action ActionToSymptomRelationship subject range Action"},{"location":"maxo/Action/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Action/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"maxo/Action/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:maxo, sqlite:obo:ogms, sqlite:obo:ncit"},{"location":"maxo/Action/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Action/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:Action native maxo_extract:Action"},{"location":"maxo/Action/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Action/#direct","title":"Direct","text":"
name: Action\nid_prefixes:\n- MAXO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ogms, sqlite:obo:ncit\ndescription: A clinically prescribed procedure, therapy, intervention, or recommendation.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\n\n
"},{"location":"maxo/Action/#induced","title":"Induced","text":"
name: Action\nid_prefixes:\n- MAXO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ogms, sqlite:obo:ncit\ndescription: A clinically prescribed procedure, therapy, intervention, or recommendation.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Action\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Action\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"maxo/ActionToDiseaseRelationship/","title":"Class: ActionToDiseaseRelationship","text":"

A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a disease, for example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis.

URI: maxo_extract:ActionToDiseaseRelationship

erDiagram\nActionToDiseaseRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\n\nActionToDiseaseRelationship ||--|o Action : \"subject\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"predicate\"\nActionToDiseaseRelationship ||--}o Disease : \"object\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/ActionToDiseaseRelationship/#inheritance","title":"Inheritance","text":""},{"location":"maxo/ActionToDiseaseRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 Action Triple predicate 0..1 NamedEntity The relationship type, usually TREATS or IS USED TO DIAGNOSE Triple object 0..* Disease Triple qualifier 0..1 String A qualifier for the statements, e Triple subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the medical action Triple object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the disease Triple"},{"location":"maxo/ActionToDiseaseRelationship/#usages","title":"Usages","text":"used by used in type used MaxoAnnotations action_to_disease range ActionToDiseaseRelationship"},{"location":"maxo/ActionToDiseaseRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/ActionToDiseaseRelationship/#schema-source","title":"Schema Source","text":""},{"location":"maxo/ActionToDiseaseRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:ActionToDiseaseRelationship native maxo_extract:ActionToDiseaseRelationship"},{"location":"maxo/ActionToDiseaseRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/ActionToDiseaseRelationship/#direct","title":"Direct","text":"
name: ActionToDiseaseRelationship\ndescription: A triple representing a relationship between a medical action  (A clinically\n  prescribed procedure, therapy, intervention, or recommendation) and a disease, for\n  example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    domain_of:\n    - Triple\n    range: Action\n  object:\n    name: object\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Disease\n  predicate:\n    name: predicate\n    description: The relationship type, usually TREATS or IS USED TO DIAGNOSE\n    domain_of:\n    - Triple\n    range: NamedEntity\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease.\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"maxo/ActionToDiseaseRelationship/#induced","title":"Induced","text":"
name: ActionToDiseaseRelationship\ndescription: A triple representing a relationship between a medical action  (A clinically\n  prescribed procedure, therapy, intervention, or recommendation) and a disease, for\n  example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    domain_of:\n    - Triple\n    range: Action\n  object:\n    name: object\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Disease\n  predicate:\n    name: predicate\n    description: The relationship type, usually TREATS or IS USED TO DIAGNOSE\n    domain_of:\n    - Triple\n    range: NamedEntity\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease.\n    domain_of:\n    - Triple\n    range: NamedEntity\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: Action\n  predicate:\n    name: predicate\n    description: The relationship type, usually TREATS or IS USED TO DIAGNOSE\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: predicate\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: object\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: Disease\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: qualifier\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject_qualifier\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the disease.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object_qualifier\n    owner: ActionToDiseaseRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"maxo/ActionToSymptomRelationship/","title":"Class: ActionToSymptomRelationship","text":"

A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a symptom, for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.

URI: maxo_extract:ActionToSymptomRelationship

erDiagram\nActionToSymptomRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nSymptom {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\n\nActionToSymptomRelationship ||--|o Action : \"subject\"\nActionToSymptomRelationship ||--|o NamedEntity : \"predicate\"\nActionToSymptomRelationship ||--}o Symptom : \"object\"\nActionToSymptomRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToSymptomRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/ActionToSymptomRelationship/#inheritance","title":"Inheritance","text":""},{"location":"maxo/ActionToSymptomRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 Action Triple predicate 0..1 NamedEntity The relationship type, usually IS USED TO DIAGNOSE Triple object 0..* Symptom Triple qualifier 0..1 String A qualifier for the statements, e Triple subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the medical action Triple object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the symptom Triple"},{"location":"maxo/ActionToSymptomRelationship/#usages","title":"Usages","text":"used by used in type used MaxoAnnotations action_to_symptom range ActionToSymptomRelationship"},{"location":"maxo/ActionToSymptomRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/ActionToSymptomRelationship/#schema-source","title":"Schema Source","text":""},{"location":"maxo/ActionToSymptomRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:ActionToSymptomRelationship native maxo_extract:ActionToSymptomRelationship"},{"location":"maxo/ActionToSymptomRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/ActionToSymptomRelationship/#direct","title":"Direct","text":"
name: ActionToSymptomRelationship\ndescription: A triple representing a relationship between a medical action  (A clinically\n  prescribed procedure, therapy, intervention, or recommendation) and a symptom, for\n  example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    domain_of:\n    - Triple\n    range: Action\n  object:\n    name: object\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Symptom\n  predicate:\n    name: predicate\n    description: The relationship type, usually IS USED TO DIAGNOSE\n    domain_of:\n    - Triple\n    range: NamedEntity\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the symptom.\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"maxo/ActionToSymptomRelationship/#induced","title":"Induced","text":"
name: ActionToSymptomRelationship\ndescription: A triple representing a relationship between a medical action  (A clinically\n  prescribed procedure, therapy, intervention, or recommendation) and a symptom, for\n  example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: Triple\nslot_usage:\n  subject:\n    name: subject\n    domain_of:\n    - Triple\n    range: Action\n  object:\n    name: object\n    multivalued: true\n    domain_of:\n    - Triple\n    range: Symptom\n  predicate:\n    name: predicate\n    description: The relationship type, usually IS USED TO DIAGNOSE\n    domain_of:\n    - Triple\n    range: NamedEntity\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the symptom.\n    domain_of:\n    - Triple\n    range: NamedEntity\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: Action\n  predicate:\n    name: predicate\n    description: The relationship type, usually IS USED TO DIAGNOSE\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: predicate\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: object\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: Symptom\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: qualifier\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the medical action.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject_qualifier\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the symptom.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object_qualifier\n    owner: ActionToSymptomRelationship\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"maxo/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: maxo_extract:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"maxo/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"maxo/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"maxo/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:AnnotatorResult native maxo_extract:AnnotatorResult"},{"location":"maxo/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n\n
"},{"location":"maxo/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"maxo/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"maxo/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"maxo/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"maxo/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Any/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native maxo_extract:Any"},{"location":"maxo/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/maxo\nclass_uri: linkml:Any\n\n
"},{"location":"maxo/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/maxo\nclass_uri: linkml:Any\n\n
"},{"location":"maxo/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"maxo/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"maxo/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: maxo_extract:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"maxo/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"maxo/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"maxo/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"maxo/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:CompoundExpression native maxo_extract:CompoundExpression"},{"location":"maxo/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/maxo\nabstract: true\n\n
"},{"location":"maxo/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/maxo\nabstract: true\n\n
"},{"location":"maxo/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"maxo/Curie/#comments","title":"Comments","text":""},{"location":"maxo/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Curie/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"maxo/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Date/#schema-source","title":"Schema Source","text":""},{"location":"maxo/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"maxo/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"maxo/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"maxo/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Disease/","title":"Class: Disease","text":"

A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.

URI: maxo_extract:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"maxo/Disease/#inheritance","title":"Inheritance","text":""},{"location":"maxo/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"maxo/Disease/#usages","title":"Usages","text":"used by used in type used MaxoAnnotations disease range Disease ActionToDiseaseRelationship object range Disease"},{"location":"maxo/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Disease/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"maxo/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo"},{"location":"maxo/Disease/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:Disease native maxo_extract:Disease"},{"location":"maxo/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Disease/#direct","title":"Direct","text":"
name: Disease\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\ndescription: A disposition to undergo pathological processes that exists in an organism\n  because of one or more disorders in that organism.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\n\n
"},{"location":"maxo/Disease/#induced","title":"Induced","text":"
name: Disease\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\ndescription: A disposition to undergo pathological processes that exists in an organism\n  because of one or more disorders in that organism.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"maxo/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"maxo/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Double/#schema-source","title":"Schema Source","text":""},{"location":"maxo/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: maxo_extract:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"maxo/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"maxo/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"maxo/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:ExtractionResult native maxo_extract:ExtractionResult"},{"location":"maxo/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"maxo/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"maxo/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"maxo/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Float/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"maxo/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Integer/#schema-source","title":"Schema Source","text":""},{"location":"maxo/MaxoAnnotations/","title":"Class: MaxoAnnotations","text":"

URI: maxo_extract:MaxoAnnotations

erDiagram\nMaxoAnnotations {\n\n}\nActionToSymptomRelationship {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nSymptom {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\nActionToDiseaseRelationship {\n    string qualifier  \n}\nDisease {\n    string id  \n    string label  \n}\n\nMaxoAnnotations ||--}o Action : \"action\"\nMaxoAnnotations ||--}o Disease : \"disease\"\nMaxoAnnotations ||--}o Symptom : \"symptom\"\nMaxoAnnotations ||--}o ActionToDiseaseRelationship : \"action_to_disease\"\nMaxoAnnotations ||--}o ActionToSymptomRelationship : \"action_to_symptom\"\nActionToSymptomRelationship ||--|o Action : \"subject\"\nActionToSymptomRelationship ||--|o NamedEntity : \"predicate\"\nActionToSymptomRelationship ||--}o Symptom : \"object\"\nActionToSymptomRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToSymptomRelationship ||--|o NamedEntity : \"object_qualifier\"\nActionToDiseaseRelationship ||--|o Action : \"subject\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"predicate\"\nActionToDiseaseRelationship ||--}o Disease : \"object\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"subject_qualifier\"\nActionToDiseaseRelationship ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/MaxoAnnotations/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance action 0..* Action Semicolon-separated list of medical actions direct disease 0..* Disease Semicolon-separated list of diseases direct symptom 0..* Symptom Semicolon-separated list of symptoms direct action_to_disease 0..* ActionToDiseaseRelationship direct action_to_symptom 0..* ActionToSymptomRelationship direct"},{"location":"maxo/MaxoAnnotations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/MaxoAnnotations/#schema-source","title":"Schema Source","text":""},{"location":"maxo/MaxoAnnotations/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:MaxoAnnotations native maxo_extract:MaxoAnnotations"},{"location":"maxo/MaxoAnnotations/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/MaxoAnnotations/#direct","title":"Direct","text":"
name: MaxoAnnotations\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  action:\n    name: action\n    annotations:\n      prompt:\n        tag: prompt\n        value: Semicolon-separated list of medical actions, where each is a clinically\n          prescribed procedure, therapy, intervention, or recommendation.\n    description: Semicolon-separated list of medical actions.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: Action\n  disease:\n    name: disease\n    description: Semicolon-separated list of diseases.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: Disease\n  symptom:\n    name: symptom\n    description: Semicolon-separated list of symptoms.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: Symptom\n  action_to_disease:\n    name: action_to_disease\n    annotations:\n      prompt:\n        tag: prompt\n        value: Semicolon-separated list of medical action to disease relationships,\n          where each is a triple representing a relationship between a medical action  and\n          a disease, for example, radiation therapy TREATS cancer, or PET scan IS\n          USED TO DIAGNOSE myocarditis.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: ActionToDiseaseRelationship\n  action_to_symptom:\n    name: action_to_symptom\n    annotations:\n      prompt:\n        tag: prompt\n        value: A triple representing a relationship between a medical action  (A clinically\n          prescribed procedure, therapy, intervention, or recommendation) and a symptom,\n          for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: ActionToSymptomRelationship\ntree_root: true\n\n
"},{"location":"maxo/MaxoAnnotations/#induced","title":"Induced","text":"
name: MaxoAnnotations\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  action:\n    name: action\n    annotations:\n      prompt:\n        tag: prompt\n        value: Semicolon-separated list of medical actions, where each is a clinically\n          prescribed procedure, therapy, intervention, or recommendation.\n    description: Semicolon-separated list of medical actions.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: action\n    owner: MaxoAnnotations\n    domain_of:\n    - MaxoAnnotations\n    range: Action\n  disease:\n    name: disease\n    description: Semicolon-separated list of diseases.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: disease\n    owner: MaxoAnnotations\n    domain_of:\n    - MaxoAnnotations\n    range: Disease\n  symptom:\n    name: symptom\n    description: Semicolon-separated list of symptoms.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: symptom\n    owner: MaxoAnnotations\n    domain_of:\n    - MaxoAnnotations\n    range: Symptom\n  action_to_disease:\n    name: action_to_disease\n    annotations:\n      prompt:\n        tag: prompt\n        value: Semicolon-separated list of medical action to disease relationships,\n          where each is a triple representing a relationship between a medical action  and\n          a disease, for example, radiation therapy TREATS cancer, or PET scan IS\n          USED TO DIAGNOSE myocarditis.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: action_to_disease\n    owner: MaxoAnnotations\n    domain_of:\n    - MaxoAnnotations\n    range: ActionToDiseaseRelationship\n  action_to_symptom:\n    name: action_to_symptom\n    annotations:\n      prompt:\n        tag: prompt\n        value: A triple representing a relationship between a medical action  (A clinically\n          prescribed procedure, therapy, intervention, or recommendation) and a symptom,\n          for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: action_to_symptom\n    owner: MaxoAnnotations\n    domain_of:\n    - MaxoAnnotations\n    range: ActionToSymptomRelationship\ntree_root: true\n\n
"},{"location":"maxo/NamedEntity/","title":"Class: NamedEntity","text":"

URI: maxo_extract:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"maxo/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"maxo/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"maxo/NamedEntity/#usages","title":"Usages","text":"used by used in type used ActionToDiseaseRelationship predicate range NamedEntity ActionToDiseaseRelationship subject_qualifier range NamedEntity ActionToDiseaseRelationship object_qualifier range NamedEntity ActionToSymptomRelationship predicate range NamedEntity ActionToSymptomRelationship subject_qualifier range NamedEntity ActionToSymptomRelationship object_qualifier range NamedEntity Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"maxo/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"maxo/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:NamedEntity native maxo_extract:NamedEntity"},{"location":"maxo/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/maxo\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"maxo/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/maxo\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"maxo/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"maxo/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"maxo/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"maxo/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"maxo/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"maxo/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"maxo/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"maxo/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"maxo/Objectidentifier/#comments","title":"Comments","text":""},{"location":"maxo/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Publication/","title":"Class: Publication","text":"

URI: maxo_extract:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"maxo/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"maxo/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"maxo/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Publication/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:Publication native maxo_extract:Publication"},{"location":"maxo/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/maxo\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n\n
"},{"location":"maxo/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/maxo\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"maxo/RelationshipType/","title":"Class: RelationshipType","text":"

URI: maxo_extract:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"maxo/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"maxo/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"maxo/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"maxo/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"maxo/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"maxo/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:RelationshipType native maxo_extract:RelationshipType"},{"location":"maxo/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\n\n
"},{"location":"maxo/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"maxo/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"maxo/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/String/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Symptom/","title":"Class: Symptom","text":"

A condition or phenotype resulting from an abnormal health state.

URI: maxo_extract:Symptom

erDiagram\nSymptom {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"maxo/Symptom/#inheritance","title":"Inheritance","text":""},{"location":"maxo/Symptom/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"maxo/Symptom/#usages","title":"Usages","text":"used by used in type used MaxoAnnotations symptom range Symptom ActionToSymptomRelationship object range Symptom"},{"location":"maxo/Symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Symptom/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"maxo/Symptom/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp"},{"location":"maxo/Symptom/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Symptom/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:Symptom native maxo_extract:Symptom"},{"location":"maxo/Symptom/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Symptom/#direct","title":"Direct","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\ndescription: A condition or phenotype resulting from an abnormal health state.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\n\n
"},{"location":"maxo/Symptom/#induced","title":"Induced","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\ndescription: A condition or phenotype resulting from an abnormal health state.\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/maxo\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"maxo/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: maxo_extract:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"maxo/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"maxo/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:TextWithTriples native maxo_extract:TextWithTriples"},{"location":"maxo/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"maxo/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/maxo\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"maxo/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"maxo/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Time/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: maxo_extract:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"maxo/Triple/#inheritance","title":"Inheritance","text":""},{"location":"maxo/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"maxo/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"maxo/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Triple/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self maxo_extract:Triple native maxo_extract:Triple"},{"location":"maxo/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"maxo/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"maxo/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/maxo\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/maxo\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"maxo/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"maxo/Uri/#comments","title":"Comments","text":""},{"location":"maxo/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Uri/#schema-source","title":"Schema Source","text":""},{"location":"maxo/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"maxo/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"maxo/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: maxo_extract:abstract

"},{"location":"maxo/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"maxo/abstract/#properties","title":"Properties","text":""},{"location":"maxo/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/abstract/#schema-source","title":"Schema Source","text":""},{"location":"maxo/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"maxo/action/","title":"Slot: action","text":"

Semicolon-separated list of medical actions.

URI: maxo_extract:action

"},{"location":"maxo/action/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaxoAnnotations no"},{"location":"maxo/action/#properties","title":"Properties","text":""},{"location":"maxo/action/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/action/#annotations","title":"Annotations","text":"property value prompt Semicolon-separated list of medical actions, where each is a clinically prescribed procedure, therapy, intervention, or recommendation."},{"location":"maxo/action/#schema-source","title":"Schema Source","text":""},{"location":"maxo/action/#linkml-source","title":"LinkML Source","text":"
name: action\nannotations:\n  prompt:\n    tag: prompt\n    value: Semicolon-separated list of medical actions, where each is a clinically\n      prescribed procedure, therapy, intervention, or recommendation.\ndescription: Semicolon-separated list of medical actions.\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: action\nowner: MaxoAnnotations\ndomain_of:\n- MaxoAnnotations\nrange: Action\n\n
"},{"location":"maxo/action_to_disease/","title":"Slot: action_to_disease","text":"

URI: maxo_extract:action_to_disease

"},{"location":"maxo/action_to_disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaxoAnnotations no"},{"location":"maxo/action_to_disease/#properties","title":"Properties","text":""},{"location":"maxo/action_to_disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/action_to_disease/#annotations","title":"Annotations","text":"property value prompt Semicolon-separated list of medical action to disease relationships, where each is a triple representing a relationship between a medical action and a disease, for example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis."},{"location":"maxo/action_to_disease/#schema-source","title":"Schema Source","text":""},{"location":"maxo/action_to_disease/#linkml-source","title":"LinkML Source","text":"
name: action_to_disease\nannotations:\n  prompt:\n    tag: prompt\n    value: Semicolon-separated list of medical action to disease relationships, where\n      each is a triple representing a relationship between a medical action  and a\n      disease, for example, radiation therapy TREATS cancer, or PET scan IS USED TO\n      DIAGNOSE myocarditis.\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: action_to_disease\nowner: MaxoAnnotations\ndomain_of:\n- MaxoAnnotations\nrange: ActionToDiseaseRelationship\n\n
"},{"location":"maxo/action_to_symptom/","title":"Slot: action_to_symptom","text":"

URI: maxo_extract:action_to_symptom

"},{"location":"maxo/action_to_symptom/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaxoAnnotations no"},{"location":"maxo/action_to_symptom/#properties","title":"Properties","text":""},{"location":"maxo/action_to_symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/action_to_symptom/#annotations","title":"Annotations","text":"property value prompt A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a symptom, for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion."},{"location":"maxo/action_to_symptom/#schema-source","title":"Schema Source","text":""},{"location":"maxo/action_to_symptom/#linkml-source","title":"LinkML Source","text":"
name: action_to_symptom\nannotations:\n  prompt:\n    tag: prompt\n    value: A triple representing a relationship between a medical action  (A clinically\n      prescribed procedure, therapy, intervention, or recommendation) and a symptom,\n      for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: action_to_symptom\nowner: MaxoAnnotations\ndomain_of:\n- MaxoAnnotations\nrange: ActionToSymptomRelationship\n\n
"},{"location":"maxo/combined_text/","title":"Slot: combined_text","text":"

URI: maxo_extract:combined_text

"},{"location":"maxo/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"maxo/combined_text/#properties","title":"Properties","text":""},{"location":"maxo/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"maxo/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"maxo/disease/","title":"Slot: disease","text":"

Semicolon-separated list of diseases.

URI: maxo_extract:disease

"},{"location":"maxo/disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaxoAnnotations no"},{"location":"maxo/disease/#properties","title":"Properties","text":""},{"location":"maxo/disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/disease/#schema-source","title":"Schema Source","text":""},{"location":"maxo/disease/#linkml-source","title":"LinkML Source","text":"
name: disease\ndescription: Semicolon-separated list of diseases.\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: disease\nowner: MaxoAnnotations\ndomain_of:\n- MaxoAnnotations\nrange: Disease\n\n
"},{"location":"maxo/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: maxo_extract:extracted_object

"},{"location":"maxo/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/extracted_object/#properties","title":"Properties","text":""},{"location":"maxo/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"maxo/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"maxo/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: maxo_extract:full_text

"},{"location":"maxo/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"maxo/full_text/#properties","title":"Properties","text":""},{"location":"maxo/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/full_text/#schema-source","title":"Schema Source","text":""},{"location":"maxo/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"maxo/id/","title":"Slot: id","text":"

URI: maxo_extract:id

"},{"location":"maxo/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Action A clinically prescribed procedure, therapy, intervention, or recommendation no Disease A disposition to undergo pathological processes that exists in an organism be... no Symptom A condition or phenotype resulting from an abnormal health state no NamedEntity no RelationshipType no Publication no"},{"location":"maxo/id/#properties","title":"Properties","text":""},{"location":"maxo/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"maxo/input_id/","title":"Slot: input_id","text":"

URI: maxo_extract:input_id

"},{"location":"maxo/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/input_id/#properties","title":"Properties","text":""},{"location":"maxo/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/input_id/#schema-source","title":"Schema Source","text":""},{"location":"maxo/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"maxo/input_text/","title":"Slot: input_text","text":"

URI: maxo_extract:input_text

"},{"location":"maxo/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/input_text/#properties","title":"Properties","text":""},{"location":"maxo/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/input_text/#schema-source","title":"Schema Source","text":""},{"location":"maxo/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"maxo/input_title/","title":"Slot: input_title","text":"

URI: maxo_extract:input_title

"},{"location":"maxo/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/input_title/#properties","title":"Properties","text":""},{"location":"maxo/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/input_title/#schema-source","title":"Schema Source","text":""},{"location":"maxo/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"maxo/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"maxo/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Action A clinically prescribed procedure, therapy, intervention, or recommendation no Disease A disposition to undergo pathological processes that exists in an organism be... no Symptom A condition or phenotype resulting from an abnormal health state no NamedEntity no RelationshipType no"},{"location":"maxo/label/#properties","title":"Properties","text":""},{"location":"maxo/label/#aliases","title":"Aliases","text":""},{"location":"maxo/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"maxo/label/#schema-source","title":"Schema Source","text":""},{"location":"maxo/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/maxo\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"maxo/maxo/","title":"maxo","text":"

A template for extracting relationships relevant to the MAXO medical action ontology.

URI: http://w3id.org/ontogpt/maxo

"},{"location":"maxo/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: maxo_extract:named_entities

"},{"location":"maxo/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/named_entities/#properties","title":"Properties","text":""},{"location":"maxo/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"maxo/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"maxo/object/","title":"Slot: object","text":"

URI: maxo_extract:object

"},{"location":"maxo/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... yes ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/object/#properties","title":"Properties","text":""},{"location":"maxo/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/object/#schema-source","title":"Schema Source","text":""},{"location":"maxo/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"maxo/object_id/","title":"Slot: object_id","text":"

URI: maxo_extract:object_id

"},{"location":"maxo/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"maxo/object_id/#properties","title":"Properties","text":""},{"location":"maxo/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/object_id/#schema-source","title":"Schema Source","text":""},{"location":"maxo/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"maxo/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: maxo_extract:object_qualifier

"},{"location":"maxo/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... yes ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/object_qualifier/#properties","title":"Properties","text":""},{"location":"maxo/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"maxo/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"maxo/object_text/","title":"Slot: object_text","text":"

URI: maxo_extract:object_text

"},{"location":"maxo/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"maxo/object_text/#properties","title":"Properties","text":""},{"location":"maxo/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/object_text/#schema-source","title":"Schema Source","text":""},{"location":"maxo/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"maxo/predicate/","title":"Slot: predicate","text":"

URI: maxo_extract:predicate

"},{"location":"maxo/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... yes ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/predicate/#properties","title":"Properties","text":""},{"location":"maxo/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/predicate/#schema-source","title":"Schema Source","text":""},{"location":"maxo/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"maxo/prompt/","title":"Slot: prompt","text":"

URI: maxo_extract:prompt

"},{"location":"maxo/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/prompt/#properties","title":"Properties","text":""},{"location":"maxo/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/prompt/#schema-source","title":"Schema Source","text":""},{"location":"maxo/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"maxo/publication/","title":"Slot: publication","text":"

URI: maxo_extract:publication

"},{"location":"maxo/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"maxo/publication/#properties","title":"Properties","text":""},{"location":"maxo/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"maxo/publication/#schema-source","title":"Schema Source","text":""},{"location":"maxo/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"maxo/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: maxo_extract:qualifier

"},{"location":"maxo/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... no ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... no Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/qualifier/#properties","title":"Properties","text":""},{"location":"maxo/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"maxo/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"maxo/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: maxo_extract:raw_completion_output

"},{"location":"maxo/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"maxo/raw_completion_output/#properties","title":"Properties","text":""},{"location":"maxo/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"maxo/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"maxo/subject/","title":"Slot: subject","text":"

URI: maxo_extract:subject

"},{"location":"maxo/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... yes ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/subject/#properties","title":"Properties","text":""},{"location":"maxo/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/subject/#schema-source","title":"Schema Source","text":""},{"location":"maxo/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"maxo/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: maxo_extract:subject_qualifier

"},{"location":"maxo/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ActionToDiseaseRelationship A triple representing a relationship between a medical action (A clinically ... yes ActionToSymptomRelationship A triple representing a relationship between a medical action (A clinically ... yes Triple Abstract parent for Relation Extraction tasks no"},{"location":"maxo/subject_qualifier/#properties","title":"Properties","text":""},{"location":"maxo/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"maxo/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"maxo/subject_text/","title":"Slot: subject_text","text":"

URI: maxo_extract:subject_text

"},{"location":"maxo/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"maxo/subject_text/#properties","title":"Properties","text":""},{"location":"maxo/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"maxo/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"maxo/symptom/","title":"Slot: symptom","text":"

Semicolon-separated list of symptoms.

URI: maxo_extract:symptom

"},{"location":"maxo/symptom/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaxoAnnotations no"},{"location":"maxo/symptom/#properties","title":"Properties","text":""},{"location":"maxo/symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/symptom/#schema-source","title":"Schema Source","text":""},{"location":"maxo/symptom/#linkml-source","title":"LinkML Source","text":"
name: symptom\ndescription: Semicolon-separated list of symptoms.\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: symptom\nowner: MaxoAnnotations\ndomain_of:\n- MaxoAnnotations\nrange: Symptom\n\n
"},{"location":"maxo/title/","title":"Slot: title","text":"

The title of the publication

URI: maxo_extract:title

"},{"location":"maxo/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"maxo/title/#properties","title":"Properties","text":""},{"location":"maxo/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/title/#schema-source","title":"Schema Source","text":""},{"location":"maxo/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"maxo/triples/","title":"Slot: triples","text":"

URI: maxo_extract:triples

"},{"location":"maxo/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"maxo/triples/#properties","title":"Properties","text":""},{"location":"maxo/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"maxo/triples/#schema-source","title":"Schema Source","text":""},{"location":"maxo/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/maxo\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"mendelian_disease/","title":"GO-CAM Template","text":"

A template for GO-CAMs

URI: http://w3id.org/ontogpt/mendelian_disease

Name: mendelian_disease-template

"},{"location":"mendelian_disease/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nMendelianDisease {\n    string name  \n    string description  \n    stringList synonyms  \n    string id  \n    string label  \n}\nDiseaseCategory {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nSymptom {\n    string characteristic  \n    string affects  \n    string severity  \n    string id  \n    string label  \n}\nOnset {\n    string years_old  \n    stringList decades  \n    string juvenile_or_adult  \n    string id  \n    string label  \n}\nInheritance {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nMendelianDisease ||--}o DiseaseCategory : \"subclass_of\"\nMendelianDisease ||--}o Symptom : \"symptoms\"\nMendelianDisease ||--|o Inheritance : \"inheritance\"\nMendelianDisease ||--}o Gene : \"genes\"\nMendelianDisease ||--}o Onset : \"disease_onsets\"\nMendelianDisease ||--}o Publication : \"publications\"\nSymptom ||--|o Onset : \"onset_of_symptom\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"mendelian_disease/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None DiseaseCategory None Gene None Inheritance None MendelianDisease None Onset None RelationshipType None Symptom None Publication None TextWithTriples None"},{"location":"mendelian_disease/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication affects characteristic combined_text decades description a description of the disease disease_onsets extracted_object The complex objects extracted from the text full_text The full text of the publication genes id A unique identifier for the named entity inheritance input_id input_text input_title juvenile_or_adult label The label (name) of the named thing name the name of the disease named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text onset_of_symptom predicate prompt publication publications qualifier A qualifier for the statements, e raw_completion_output severity subclass_of subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text symptoms synonyms title The title of the publication triples years_old"},{"location":"mendelian_disease/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"mendelian_disease/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"mendelian_disease/#subsets","title":"Subsets","text":"Subset Description"},{"location":"mendelian_disease/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: mendelian_disease:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"mendelian_disease/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"mendelian_disease/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:AnnotatorResult native mendelian_disease:AnnotatorResult"},{"location":"mendelian_disease/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n\n
"},{"location":"mendelian_disease/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"mendelian_disease/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"mendelian_disease/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"mendelian_disease/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"mendelian_disease/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Any/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native mendelian_disease:Any"},{"location":"mendelian_disease/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nclass_uri: linkml:Any\n\n
"},{"location":"mendelian_disease/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nclass_uri: linkml:Any\n\n
"},{"location":"mendelian_disease/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"mendelian_disease/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: mendelian_disease:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"mendelian_disease/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"mendelian_disease/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:CompoundExpression native mendelian_disease:CompoundExpression"},{"location":"mendelian_disease/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nabstract: true\n\n
"},{"location":"mendelian_disease/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nabstract: true\n\n
"},{"location":"mendelian_disease/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"mendelian_disease/Curie/#comments","title":"Comments","text":""},{"location":"mendelian_disease/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Curie/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"mendelian_disease/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Date/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"mendelian_disease/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"mendelian_disease/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"mendelian_disease/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/DiseaseCategory/","title":"Class: DiseaseCategory","text":"

URI: mendelian_disease:DiseaseCategory

erDiagram\nDiseaseCategory {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/DiseaseCategory/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/DiseaseCategory/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/DiseaseCategory/#usages","title":"Usages","text":"used by used in type used MendelianDisease subclass_of range DiseaseCategory"},{"location":"mendelian_disease/DiseaseCategory/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/DiseaseCategory/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"mendelian_disease/DiseaseCategory/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo"},{"location":"mendelian_disease/DiseaseCategory/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/DiseaseCategory/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:DiseaseCategory native mendelian_disease:DiseaseCategory"},{"location":"mendelian_disease/DiseaseCategory/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/DiseaseCategory/#direct","title":"Direct","text":"
name: DiseaseCategory\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\n\n
"},{"location":"mendelian_disease/DiseaseCategory/#induced","title":"Induced","text":"
name: DiseaseCategory\nid_prefixes:\n- MONDO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DiseaseCategory\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: DiseaseCategory\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"mendelian_disease/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Double/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: mendelian_disease:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"mendelian_disease/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"mendelian_disease/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:ExtractionResult native mendelian_disease:ExtractionResult"},{"location":"mendelian_disease/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"mendelian_disease/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"mendelian_disease/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"mendelian_disease/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Float/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Gene/","title":"Class: Gene","text":"

URI: mendelian_disease:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/Gene/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/Gene/#usages","title":"Usages","text":"used by used in type used MendelianDisease genes range Gene"},{"location":"mendelian_disease/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"mendelian_disease/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, bioportal:hgnc-nr, sqlite:obo:pr"},{"location":"mendelian_disease/Gene/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Gene native mendelian_disease:Gene"},{"location":"mendelian_disease/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr, sqlite:obo:pr\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\n\n
"},{"location":"mendelian_disease/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr, sqlite:obo:pr\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/Inheritance/","title":"Class: Inheritance","text":"

URI: mendelian_disease:Inheritance

erDiagram\nInheritance {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/Inheritance/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/Inheritance/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/Inheritance/#usages","title":"Usages","text":"used by used in type used MendelianDisease inheritance range Inheritance"},{"location":"mendelian_disease/Inheritance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Inheritance/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:geno"},{"location":"mendelian_disease/Inheritance/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Inheritance/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Inheritance native mendelian_disease:Inheritance"},{"location":"mendelian_disease/Inheritance/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Inheritance/#direct","title":"Direct","text":"
name: Inheritance\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:geno\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\n\n
"},{"location":"mendelian_disease/Inheritance/#induced","title":"Induced","text":"
name: Inheritance\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:geno\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Inheritance\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Inheritance\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"mendelian_disease/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Integer/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/MendelianDisease/","title":"Class: MendelianDisease","text":"

URI: mendelian_disease:MendelianDisease

erDiagram\nMendelianDisease {\n    string name  \n    string description  \n    stringList synonyms  \n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nOnset {\n    string years_old  \n    stringList decades  \n    string juvenile_or_adult  \n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nInheritance {\n    string id  \n    string label  \n}\nSymptom {\n    string characteristic  \n    string affects  \n    string severity  \n    string id  \n    string label  \n}\nDiseaseCategory {\n    string id  \n    string label  \n}\n\nMendelianDisease ||--}o DiseaseCategory : \"subclass_of\"\nMendelianDisease ||--}o Symptom : \"symptoms\"\nMendelianDisease ||--|o Inheritance : \"inheritance\"\nMendelianDisease ||--}o Gene : \"genes\"\nMendelianDisease ||--}o Onset : \"disease_onsets\"\nMendelianDisease ||--}o Publication : \"publications\"\nSymptom ||--|o Onset : \"onset_of_symptom\"\n\n
"},{"location":"mendelian_disease/MendelianDisease/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/MendelianDisease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance name 0..1 String the name of the disease direct description 0..1 String a description of the disease direct synonyms 0..* String direct subclass_of 0..* DiseaseCategory direct symptoms 0..* Symptom direct inheritance 0..1 Inheritance direct genes 0..* Gene direct disease_onsets 0..* Onset direct publications 0..* Publication direct id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/MendelianDisease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/MendelianDisease/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/MendelianDisease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:MendelianDisease native mendelian_disease:MendelianDisease"},{"location":"mendelian_disease/MendelianDisease/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/MendelianDisease/#direct","title":"Direct","text":"
name: MendelianDisease\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  name:\n    name: name\n    description: the name of the disease\n    examples:\n    - value: peroxisome biogenesis disorder\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  description:\n    name: description\n    description: a description of the disease\n    examples:\n    - value: Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS)\n        is a group of autosomal recessive disorders affecting the formation of functional\n        peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal\n        degeneration, multiple organ dysfunction and psychomotor impairment\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  synonyms:\n    name: synonyms\n    examples:\n    - value: Zellweger syndrome spectrum\n    - value: PBD-ZSS\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n  subclass_of:\n    name: subclass_of\n    examples:\n    - value: lysosomal disease\n    - value: autosomal recessive disorder\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: DiseaseCategory\n  symptoms:\n    name: symptoms\n    examples:\n    - value: sensorineural hearing loss\n    - value: pigmentary retinal degeneration\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Symptom\n  inheritance:\n    name: inheritance\n    examples:\n    - value: autosomal recessive\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: Inheritance\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'semicolon separated list of gene symbols; for example: PEX1; PEX2;\n          PEX3'\n    examples:\n    - value: PEX1\n    - value: PEX2\n    - value: PEX3\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Gene\n  disease_onsets:\n    name: disease_onsets\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'semi-colon separated list of onsets at which the disease occurs, for\n          example: adult; juvenile; first decade'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Onset\n  publications:\n    name: publications\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Publication\n\n
"},{"location":"mendelian_disease/MendelianDisease/#induced","title":"Induced","text":"
name: MendelianDisease\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  name:\n    name: name\n    description: the name of the disease\n    examples:\n    - value: peroxisome biogenesis disorder\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: name\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: string\n  description:\n    name: description\n    description: a description of the disease\n    examples:\n    - value: Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS)\n        is a group of autosomal recessive disorders affecting the formation of functional\n        peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal\n        degeneration, multiple organ dysfunction and psychomotor impairment\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: description\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: string\n  synonyms:\n    name: synonyms\n    examples:\n    - value: Zellweger syndrome spectrum\n    - value: PBD-ZSS\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: string\n  subclass_of:\n    name: subclass_of\n    examples:\n    - value: lysosomal disease\n    - value: autosomal recessive disorder\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: subclass_of\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: DiseaseCategory\n  symptoms:\n    name: symptoms\n    examples:\n    - value: sensorineural hearing loss\n    - value: pigmentary retinal degeneration\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: symptoms\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: Symptom\n  inheritance:\n    name: inheritance\n    examples:\n    - value: autosomal recessive\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: inheritance\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: Inheritance\n  genes:\n    name: genes\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'semicolon separated list of gene symbols; for example: PEX1; PEX2;\n          PEX3'\n    examples:\n    - value: PEX1\n    - value: PEX2\n    - value: PEX3\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: Gene\n  disease_onsets:\n    name: disease_onsets\n    annotations:\n      prompt:\n        tag: prompt\n        value: 'semi-colon separated list of onsets at which the disease occurs, for\n          example: adult; juvenile; first decade'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: disease_onsets\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: Onset\n  publications:\n    name: publications\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: publications\n    owner: MendelianDisease\n    domain_of:\n    - MendelianDisease\n    range: Publication\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MendelianDisease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: MendelianDisease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/NamedEntity/","title":"Class: NamedEntity","text":"

URI: mendelian_disease:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"mendelian_disease/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"mendelian_disease/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:NamedEntity native mendelian_disease:NamedEntity"},{"location":"mendelian_disease/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"mendelian_disease/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"mendelian_disease/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"mendelian_disease/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"mendelian_disease/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"mendelian_disease/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"mendelian_disease/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"mendelian_disease/Objectidentifier/#comments","title":"Comments","text":""},{"location":"mendelian_disease/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Onset/","title":"Class: Onset","text":"

URI: mendelian_disease:Onset

erDiagram\nOnset {\n    string years_old  \n    stringList decades  \n    string juvenile_or_adult  \n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/Onset/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/Onset/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance years_old 0..1 String direct decades 0..* String direct juvenile_or_adult 0..1 String direct id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/Onset/#usages","title":"Usages","text":"used by used in type used MendelianDisease disease_onsets range Onset Symptom onset_of_symptom range Onset"},{"location":"mendelian_disease/Onset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Onset/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"mendelian_disease/Onset/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:hsapdv"},{"location":"mendelian_disease/Onset/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Onset/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Onset native mendelian_disease:Onset"},{"location":"mendelian_disease/Onset/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Onset/#direct","title":"Direct","text":"
name: Onset\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:hsapdv\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  years_old:\n    name: years_old\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  decades:\n    name: decades\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n  juvenile_or_adult:\n    name: juvenile_or_adult\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n\n
"},{"location":"mendelian_disease/Onset/#induced","title":"Induced","text":"
name: Onset\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:hsapdv\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  years_old:\n    name: years_old\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: years_old\n    owner: Onset\n    domain_of:\n    - Onset\n    range: string\n  decades:\n    name: decades\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: decades\n    owner: Onset\n    domain_of:\n    - Onset\n    range: string\n  juvenile_or_adult:\n    name: juvenile_or_adult\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: juvenile_or_adult\n    owner: Onset\n    domain_of:\n    - Onset\n    range: string\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Onset\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Onset\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/Publication/","title":"Class: Publication","text":"

URI: mendelian_disease:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"mendelian_disease/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"mendelian_disease/Publication/#usages","title":"Usages","text":"used by used in type used MendelianDisease publications range Publication TextWithTriples publication range Publication"},{"location":"mendelian_disease/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Publication/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Publication native mendelian_disease:Publication"},{"location":"mendelian_disease/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n\n
"},{"location":"mendelian_disease/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"mendelian_disease/RelationshipType/","title":"Class: RelationshipType","text":"

URI: mendelian_disease:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"mendelian_disease/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"mendelian_disease/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"mendelian_disease/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:RelationshipType native mendelian_disease:RelationshipType"},{"location":"mendelian_disease/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\n\n
"},{"location":"mendelian_disease/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"mendelian_disease/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/String/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Symptom/","title":"Class: Symptom","text":"

URI: mendelian_disease:Symptom

erDiagram\nSymptom {\n    string characteristic  \n    string affects  \n    string severity  \n    string id  \n    string label  \n}\nOnset {\n    string years_old  \n    stringList decades  \n    string juvenile_or_adult  \n    string id  \n    string label  \n}\n\nSymptom ||--|o Onset : \"onset_of_symptom\"\n\n
"},{"location":"mendelian_disease/Symptom/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/Symptom/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance characteristic 0..1 String direct affects 0..1 String direct severity 0..1 String direct onset_of_symptom 0..1 Onset direct id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"mendelian_disease/Symptom/#usages","title":"Usages","text":"used by used in type used MendelianDisease symptoms range Symptom"},{"location":"mendelian_disease/Symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Symptom/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"mendelian_disease/Symptom/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:mondo"},{"location":"mendelian_disease/Symptom/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Symptom/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Symptom native mendelian_disease:Symptom"},{"location":"mendelian_disease/Symptom/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Symptom/#direct","title":"Direct","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  characteristic:\n    name: characteristic\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  affects:\n    name: affects\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  severity:\n    name: severity\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n  onset_of_symptom:\n    name: onset_of_symptom\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: Onset\n\n
"},{"location":"mendelian_disease/Symptom/#induced","title":"Induced","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: NamedEntity\nattributes:\n  characteristic:\n    name: characteristic\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: characteristic\n    owner: Symptom\n    domain_of:\n    - Symptom\n    range: string\n  affects:\n    name: affects\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: affects\n    owner: Symptom\n    domain_of:\n    - Symptom\n    range: string\n  severity:\n    name: severity\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: severity\n    owner: Symptom\n    domain_of:\n    - Symptom\n    range: string\n  onset_of_symptom:\n    name: onset_of_symptom\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: onset_of_symptom\n    owner: Symptom\n    domain_of:\n    - Symptom\n    range: Onset\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"mendelian_disease/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: mendelian_disease:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"mendelian_disease/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"mendelian_disease/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:TextWithTriples native mendelian_disease:TextWithTriples"},{"location":"mendelian_disease/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"mendelian_disease/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"mendelian_disease/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"mendelian_disease/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Time/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: mendelian_disease:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"mendelian_disease/Triple/#inheritance","title":"Inheritance","text":""},{"location":"mendelian_disease/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"mendelian_disease/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"mendelian_disease/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Triple/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self mendelian_disease:Triple native mendelian_disease:Triple"},{"location":"mendelian_disease/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"mendelian_disease/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"mendelian_disease/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/mendelian_disease\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"mendelian_disease/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"mendelian_disease/Uri/#comments","title":"Comments","text":""},{"location":"mendelian_disease/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Uri/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"mendelian_disease/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: mendelian_disease:abstract

"},{"location":"mendelian_disease/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"mendelian_disease/abstract/#properties","title":"Properties","text":""},{"location":"mendelian_disease/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/abstract/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"mendelian_disease/affects/","title":"Slot: affects","text":"

URI: mendelian_disease:affects

"},{"location":"mendelian_disease/affects/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Symptom no"},{"location":"mendelian_disease/affects/#properties","title":"Properties","text":""},{"location":"mendelian_disease/affects/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/affects/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/affects/#linkml-source","title":"LinkML Source","text":"
name: affects\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: affects\nowner: Symptom\ndomain_of:\n- Symptom\nrange: string\n\n
"},{"location":"mendelian_disease/characteristic/","title":"Slot: characteristic","text":"

URI: mendelian_disease:characteristic

"},{"location":"mendelian_disease/characteristic/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Symptom no"},{"location":"mendelian_disease/characteristic/#properties","title":"Properties","text":""},{"location":"mendelian_disease/characteristic/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/characteristic/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/characteristic/#linkml-source","title":"LinkML Source","text":"
name: characteristic\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: characteristic\nowner: Symptom\ndomain_of:\n- Symptom\nrange: string\n\n
"},{"location":"mendelian_disease/combined_text/","title":"Slot: combined_text","text":"

URI: mendelian_disease:combined_text

"},{"location":"mendelian_disease/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"mendelian_disease/combined_text/#properties","title":"Properties","text":""},{"location":"mendelian_disease/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"mendelian_disease/decades/","title":"Slot: decades","text":"

URI: mendelian_disease:decades

"},{"location":"mendelian_disease/decades/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Onset no"},{"location":"mendelian_disease/decades/#properties","title":"Properties","text":""},{"location":"mendelian_disease/decades/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/decades/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/decades/#linkml-source","title":"LinkML Source","text":"
name: decades\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: decades\nowner: Onset\ndomain_of:\n- Onset\nrange: string\n\n
"},{"location":"mendelian_disease/description/","title":"Slot: description","text":"

a description of the disease

URI: mendelian_disease:description

"},{"location":"mendelian_disease/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/description/#properties","title":"Properties","text":""},{"location":"mendelian_disease/description/#examples","title":"Examples","text":"Value Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment"},{"location":"mendelian_disease/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/description/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a description of the disease\nexamples:\n- value: Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is\n    a group of autosomal recessive disorders affecting the formation of functional\n    peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration,\n    multiple organ dysfunction and psychomotor impairment\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: description\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: string\n\n
"},{"location":"mendelian_disease/disease_onsets/","title":"Slot: disease_onsets","text":"

URI: mendelian_disease:disease_onsets

"},{"location":"mendelian_disease/disease_onsets/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/disease_onsets/#properties","title":"Properties","text":""},{"location":"mendelian_disease/disease_onsets/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/disease_onsets/#annotations","title":"Annotations","text":"property value prompt semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade"},{"location":"mendelian_disease/disease_onsets/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/disease_onsets/#linkml-source","title":"LinkML Source","text":"
name: disease_onsets\nannotations:\n  prompt:\n    tag: prompt\n    value: 'semi-colon separated list of onsets at which the disease occurs, for example:\n      adult; juvenile; first decade'\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: disease_onsets\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: Onset\n\n
"},{"location":"mendelian_disease/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: mendelian_disease:extracted_object

"},{"location":"mendelian_disease/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"mendelian_disease/extracted_object/#properties","title":"Properties","text":""},{"location":"mendelian_disease/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"mendelian_disease/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: mendelian_disease:full_text

"},{"location":"mendelian_disease/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"mendelian_disease/full_text/#properties","title":"Properties","text":""},{"location":"mendelian_disease/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/full_text/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"mendelian_disease/genes/","title":"Slot: genes","text":"

URI: mendelian_disease:genes

"},{"location":"mendelian_disease/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/genes/#properties","title":"Properties","text":""},{"location":"mendelian_disease/genes/#examples","title":"Examples","text":"Value PEX1 PEX2 PEX3"},{"location":"mendelian_disease/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/genes/#annotations","title":"Annotations","text":"property value prompt semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3"},{"location":"mendelian_disease/genes/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\nannotations:\n  prompt:\n    tag: prompt\n    value: 'semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3'\nexamples:\n- value: PEX1\n- value: PEX2\n- value: PEX3\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: genes\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: Gene\n\n
"},{"location":"mendelian_disease/id/","title":"Slot: id","text":"

URI: mendelian_disease:id

"},{"location":"mendelian_disease/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no DiseaseCategory no Gene no Symptom no Onset no Inheritance no NamedEntity no RelationshipType no Publication no"},{"location":"mendelian_disease/id/#properties","title":"Properties","text":""},{"location":"mendelian_disease/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"mendelian_disease/inheritance/","title":"Slot: inheritance","text":"

URI: mendelian_disease:inheritance

"},{"location":"mendelian_disease/inheritance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/inheritance/#properties","title":"Properties","text":""},{"location":"mendelian_disease/inheritance/#examples","title":"Examples","text":"Value autosomal recessive"},{"location":"mendelian_disease/inheritance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/inheritance/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/inheritance/#linkml-source","title":"LinkML Source","text":"
name: inheritance\nexamples:\n- value: autosomal recessive\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: inheritance\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: Inheritance\n\n
"},{"location":"mendelian_disease/input_id/","title":"Slot: input_id","text":"

URI: mendelian_disease:input_id

"},{"location":"mendelian_disease/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"mendelian_disease/input_id/#properties","title":"Properties","text":""},{"location":"mendelian_disease/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/input_id/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"mendelian_disease/input_text/","title":"Slot: input_text","text":"

URI: mendelian_disease:input_text

"},{"location":"mendelian_disease/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"mendelian_disease/input_text/#properties","title":"Properties","text":""},{"location":"mendelian_disease/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/input_text/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
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URI: mendelian_disease:input_title

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name: input_title\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"mendelian_disease/juvenile_or_adult/","title":"Slot: juvenile_or_adult","text":"

URI: mendelian_disease:juvenile_or_adult

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name: juvenile_or_adult\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: juvenile_or_adult\nowner: Onset\ndomain_of:\n- Onset\nrange: string\n\n
"},{"location":"mendelian_disease/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

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"},{"location":"mendelian_disease/mendelian_disease-template/","title":"mendelian_disease-template","text":"

A template for GO-CAMs

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the name of the disease

URI: mendelian_disease:name

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name: name\ndescription: the name of the disease\nexamples:\n- value: peroxisome biogenesis disorder\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: name\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: string\n\n
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Named entities extracted from the text

URI: mendelian_disease:named_entities

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name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"mendelian_disease/object/","title":"Slot: object","text":"

URI: mendelian_disease:object

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name: object\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
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URI: mendelian_disease:object_id

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name: object_id\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"mendelian_disease/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: mendelian_disease:object_qualifier

"},{"location":"mendelian_disease/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"mendelian_disease/object_qualifier/#properties","title":"Properties","text":""},{"location":"mendelian_disease/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"mendelian_disease/object_text/","title":"Slot: object_text","text":"

URI: mendelian_disease:object_text

"},{"location":"mendelian_disease/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"mendelian_disease/object_text/#properties","title":"Properties","text":""},{"location":"mendelian_disease/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/object_text/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"mendelian_disease/onset_of_symptom/","title":"Slot: onset_of_symptom","text":"

URI: mendelian_disease:onset_of_symptom

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name: onset_of_symptom\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: onset_of_symptom\nowner: Symptom\ndomain_of:\n- Symptom\nrange: Onset\n\n
"},{"location":"mendelian_disease/predicate/","title":"Slot: predicate","text":"

URI: mendelian_disease:predicate

"},{"location":"mendelian_disease/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"mendelian_disease/predicate/#properties","title":"Properties","text":""},{"location":"mendelian_disease/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/predicate/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"mendelian_disease/prompt/","title":"Slot: prompt","text":"

URI: mendelian_disease:prompt

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name: prompt\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"mendelian_disease/publication/","title":"Slot: publication","text":"

URI: mendelian_disease:publication

"},{"location":"mendelian_disease/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"mendelian_disease/publication/#properties","title":"Properties","text":""},{"location":"mendelian_disease/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"mendelian_disease/publication/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"mendelian_disease/publications/","title":"Slot: publications","text":"

URI: mendelian_disease:publications

"},{"location":"mendelian_disease/publications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/publications/#properties","title":"Properties","text":""},{"location":"mendelian_disease/publications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/publications/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"mendelian_disease/publications/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/publications/#linkml-source","title":"LinkML Source","text":"
name: publications\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: publications\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: Publication\n\n
"},{"location":"mendelian_disease/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: mendelian_disease:qualifier

"},{"location":"mendelian_disease/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"mendelian_disease/qualifier/#properties","title":"Properties","text":""},{"location":"mendelian_disease/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"mendelian_disease/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: mendelian_disease:raw_completion_output

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name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"mendelian_disease/severity/","title":"Slot: severity","text":"

URI: mendelian_disease:severity

"},{"location":"mendelian_disease/severity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Symptom no"},{"location":"mendelian_disease/severity/#properties","title":"Properties","text":""},{"location":"mendelian_disease/severity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/severity/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/severity/#linkml-source","title":"LinkML Source","text":"
name: severity\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: severity\nowner: Symptom\ndomain_of:\n- Symptom\nrange: string\n\n
"},{"location":"mendelian_disease/subclass_of/","title":"Slot: subclass_of","text":"

URI: mendelian_disease:subclass_of

"},{"location":"mendelian_disease/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/subclass_of/#properties","title":"Properties","text":""},{"location":"mendelian_disease/subclass_of/#examples","title":"Examples","text":"Value lysosomal disease autosomal recessive disorder"},{"location":"mendelian_disease/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\nexamples:\n- value: lysosomal disease\n- value: autosomal recessive disorder\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: subclass_of\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: DiseaseCategory\n\n
"},{"location":"mendelian_disease/subject/","title":"Slot: subject","text":"

URI: mendelian_disease:subject

"},{"location":"mendelian_disease/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"mendelian_disease/subject/#properties","title":"Properties","text":""},{"location":"mendelian_disease/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/subject/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"mendelian_disease/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: mendelian_disease:subject_qualifier

"},{"location":"mendelian_disease/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"mendelian_disease/subject_qualifier/#properties","title":"Properties","text":""},{"location":"mendelian_disease/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"mendelian_disease/subject_text/","title":"Slot: subject_text","text":"

URI: mendelian_disease:subject_text

"},{"location":"mendelian_disease/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"mendelian_disease/subject_text/#properties","title":"Properties","text":""},{"location":"mendelian_disease/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"mendelian_disease/symptoms/","title":"Slot: symptoms","text":"

URI: mendelian_disease:symptoms

"},{"location":"mendelian_disease/symptoms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/symptoms/#properties","title":"Properties","text":""},{"location":"mendelian_disease/symptoms/#examples","title":"Examples","text":"Value sensorineural hearing loss pigmentary retinal degeneration"},{"location":"mendelian_disease/symptoms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/symptoms/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/symptoms/#linkml-source","title":"LinkML Source","text":"
name: symptoms\nexamples:\n- value: sensorineural hearing loss\n- value: pigmentary retinal degeneration\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: symptoms\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: Symptom\n\n
"},{"location":"mendelian_disease/synonyms/","title":"Slot: synonyms","text":"

URI: mendelian_disease:synonyms

"},{"location":"mendelian_disease/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MendelianDisease no"},{"location":"mendelian_disease/synonyms/#properties","title":"Properties","text":""},{"location":"mendelian_disease/synonyms/#examples","title":"Examples","text":"Value Zellweger syndrome spectrum PBD-ZSS"},{"location":"mendelian_disease/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\nexamples:\n- value: Zellweger syndrome spectrum\n- value: PBD-ZSS\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: MendelianDisease\ndomain_of:\n- MendelianDisease\nrange: string\n\n
"},{"location":"mendelian_disease/title/","title":"Slot: title","text":"

The title of the publication

URI: mendelian_disease:title

"},{"location":"mendelian_disease/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"mendelian_disease/title/#properties","title":"Properties","text":""},{"location":"mendelian_disease/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/title/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"mendelian_disease/triples/","title":"Slot: triples","text":"

URI: mendelian_disease:triples

"},{"location":"mendelian_disease/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"mendelian_disease/triples/#properties","title":"Properties","text":""},{"location":"mendelian_disease/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/triples/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"mendelian_disease/years_old/","title":"Slot: years_old","text":"

URI: mendelian_disease:years_old

"},{"location":"mendelian_disease/years_old/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Onset no"},{"location":"mendelian_disease/years_old/#properties","title":"Properties","text":""},{"location":"mendelian_disease/years_old/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mendelian_disease/years_old/#schema-source","title":"Schema Source","text":""},{"location":"mendelian_disease/years_old/#linkml-source","title":"LinkML Source","text":"
name: years_old\nfrom_schema: http://w3id.org/ontogpt/mendelian_disease\nrank: 1000\nalias: years_old\nowner: Onset\ndomain_of:\n- Onset\nrange: string\n\n
"},{"location":"metabolic_process/","title":"metabolic Process Template","text":"

A template for GO-CAMs

URI: https://w3id.org/ontogpt/metabolic_process

Name: metabolic-process-template

"},{"location":"metabolic_process/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nMetabolicProcess {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nMetabolicProcessCategory {\n    string id  \n    string label  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nMetabolicProcess ||--}o MetabolicProcessCategory : \"subclass_of\"\nMetabolicProcess ||--|o MetabolicProcessCategory : \"category\"\nMetabolicProcess ||--}o ChemicalEntity : \"inputs\"\nMetabolicProcess ||--}o ChemicalEntity : \"outputs\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"metabolic_process/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None ChemicalEntity None MetabolicProcess None MetabolicProcessCategory None RelationshipType None Publication None TextWithTriples None"},{"location":"metabolic_process/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication category the category of metabolic process, e combined_text description a textual description of the metabolic process extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title inputs the inputs of the metabolic process label the name of the metabolic process named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text outputs the outputs of the metabolic process predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subclass_of a semicolon separated list of broader metabolic processes which this is a sub... subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text synonyms alternative names of the metabolic process title The title of the publication triples"},{"location":"metabolic_process/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"metabolic_process/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"metabolic_process/#subsets","title":"Subsets","text":"Subset Description"},{"location":"metabolic_process/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: bp:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"metabolic_process/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"metabolic_process/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:AnnotatorResult native bp:AnnotatorResult"},{"location":"metabolic_process/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n\n
"},{"location":"metabolic_process/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"metabolic_process/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"metabolic_process/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"metabolic_process/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"metabolic_process/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Any/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native bp:Any"},{"location":"metabolic_process/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nclass_uri: linkml:Any\n\n
"},{"location":"metabolic_process/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nclass_uri: linkml:Any\n\n
"},{"location":"metabolic_process/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"metabolic_process/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/ChemicalEntity/","title":"Class: ChemicalEntity","text":"

URI: bp:ChemicalEntity

erDiagram\nChemicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metabolic_process/ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metabolic_process/ChemicalEntity/#usages","title":"Usages","text":"used by used in type used MetabolicProcess inputs range ChemicalEntity MetabolicProcess outputs range ChemicalEntity"},{"location":"metabolic_process/ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metabolic_process/ChemicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"metabolic_process/ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ChemicalEntity native bp:ChemicalEntity"},{"location":"metabolic_process/ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\n\n
"},{"location":"metabolic_process/ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalEntity\n    domain_of:\n    - MetabolicProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"metabolic_process/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: bp:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"metabolic_process/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"metabolic_process/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:CompoundExpression native bp:CompoundExpression"},{"location":"metabolic_process/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nabstract: true\n\n
"},{"location":"metabolic_process/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nabstract: true\n\n
"},{"location":"metabolic_process/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"metabolic_process/Curie/#comments","title":"Comments","text":""},{"location":"metabolic_process/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Curie/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"metabolic_process/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Date/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"metabolic_process/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"metabolic_process/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"metabolic_process/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"metabolic_process/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Double/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: bp:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"metabolic_process/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"metabolic_process/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:ExtractionResult native bp:ExtractionResult"},{"location":"metabolic_process/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metabolic_process/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metabolic_process/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"metabolic_process/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Float/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"metabolic_process/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Integer/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/MetabolicProcess/","title":"Class: MetabolicProcess","text":"

URI: bp:MetabolicProcess

erDiagram\nMetabolicProcess {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nMetabolicProcessCategory {\n    string id  \n    string label  \n}\n\nMetabolicProcess ||--}o MetabolicProcessCategory : \"subclass_of\"\nMetabolicProcess ||--|o MetabolicProcessCategory : \"category\"\nMetabolicProcess ||--}o ChemicalEntity : \"inputs\"\nMetabolicProcess ||--}o ChemicalEntity : \"outputs\"\n\n
"},{"location":"metabolic_process/MetabolicProcess/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/MetabolicProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 0..1 String the name of the metabolic process direct description 0..1 String a textual description of the metabolic process direct synonyms 0..* String alternative names of the metabolic process direct subclass_of 0..* MetabolicProcessCategory a semicolon separated list of broader metabolic processes which this is a sub... direct category 0..1 MetabolicProcessCategory the category of metabolic process, e direct inputs 0..* ChemicalEntity the inputs of the metabolic process direct outputs 0..* ChemicalEntity the outputs of the metabolic process direct id 1..1 String A unique identifier for the named entity NamedEntity"},{"location":"metabolic_process/MetabolicProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/MetabolicProcess/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/MetabolicProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:MetabolicProcess native bp:MetabolicProcess"},{"location":"metabolic_process/MetabolicProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/MetabolicProcess/#direct","title":"Direct","text":"
name: MetabolicProcess\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  description:\n    name: description\n    description: a textual description of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  synonyms:\n    name: synonyms\n    description: alternative names of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n  subclass_of:\n    name: subclass_of\n    description: a semicolon separated list of broader metabolic processes which this\n      is a subclass of\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    range: MetabolicProcessCategory\n  category:\n    name: category\n    description: the category of metabolic process, e.g metabolic process, catabolic\n      process, biosynthetic process, small molecule sensor activity\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: MetabolicProcessCategory\n  inputs:\n    name: inputs\n    description: the inputs of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n  outputs:\n    name: outputs\n    description: the outputs of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n\n
"},{"location":"metabolic_process/MetabolicProcess/#induced","title":"Induced","text":"
name: MetabolicProcess\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: label\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    - NamedEntity\n    range: string\n  description:\n    name: description\n    description: a textual description of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: description\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: string\n  synonyms:\n    name: synonyms\n    description: alternative names of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: string\n  subclass_of:\n    name: subclass_of\n    description: a semicolon separated list of broader metabolic processes which this\n      is a subclass of\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: subclass_of\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: MetabolicProcessCategory\n  category:\n    name: category\n    description: the category of metabolic process, e.g metabolic process, catabolic\n      process, biosynthetic process, small molecule sensor activity\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: category\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: MetabolicProcessCategory\n  inputs:\n    name: inputs\n    description: the inputs of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: inputs\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: ChemicalEntity\n  outputs:\n    name: outputs\n    description: the outputs of the metabolic process\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: outputs\n    owner: MetabolicProcess\n    domain_of:\n    - MetabolicProcess\n    range: ChemicalEntity\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetabolicProcess\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n\n
"},{"location":"metabolic_process/MetabolicProcessCategory/","title":"Class: MetabolicProcessCategory","text":"

URI: bp:MetabolicProcessCategory

erDiagram\nMetabolicProcessCategory {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metabolic_process/MetabolicProcessCategory/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/MetabolicProcessCategory/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metabolic_process/MetabolicProcessCategory/#usages","title":"Usages","text":"used by used in type used MetabolicProcess subclass_of range MetabolicProcessCategory MetabolicProcess category range MetabolicProcessCategory"},{"location":"metabolic_process/MetabolicProcessCategory/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/MetabolicProcessCategory/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metabolic_process/MetabolicProcessCategory/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"metabolic_process/MetabolicProcessCategory/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/MetabolicProcessCategory/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:MetabolicProcessCategory native bp:MetabolicProcessCategory"},{"location":"metabolic_process/MetabolicProcessCategory/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/MetabolicProcessCategory/#direct","title":"Direct","text":"
name: MetabolicProcessCategory\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\n\n
"},{"location":"metabolic_process/MetabolicProcessCategory/#induced","title":"Induced","text":"
name: MetabolicProcessCategory\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetabolicProcessCategory\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: MetabolicProcessCategory\n    domain_of:\n    - MetabolicProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"metabolic_process/NamedEntity/","title":"Class: NamedEntity","text":"

URI: bp:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metabolic_process/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"metabolic_process/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"metabolic_process/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:NamedEntity native bp:NamedEntity"},{"location":"metabolic_process/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"metabolic_process/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - MetabolicProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"metabolic_process/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"metabolic_process/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"metabolic_process/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"metabolic_process/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"metabolic_process/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"metabolic_process/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"metabolic_process/Objectidentifier/#comments","title":"Comments","text":""},{"location":"metabolic_process/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Publication/","title":"Class: Publication","text":"

URI: bp:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"metabolic_process/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"metabolic_process/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"metabolic_process/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Publication/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Publication native bp:Publication"},{"location":"metabolic_process/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n\n
"},{"location":"metabolic_process/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"metabolic_process/RelationshipType/","title":"Class: RelationshipType","text":"

URI: bp:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metabolic_process/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metabolic_process/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"metabolic_process/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metabolic_process/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:RelationshipType native bp:RelationshipType"},{"location":"metabolic_process/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\n\n
"},{"location":"metabolic_process/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - MetabolicProcess\n    - NamedEntity\n    range: string\n\n
"},{"location":"metabolic_process/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"metabolic_process/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/String/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: bp:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"metabolic_process/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"metabolic_process/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:TextWithTriples native bp:TextWithTriples"},{"location":"metabolic_process/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metabolic_process/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metabolic_process/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"metabolic_process/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Time/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: bp:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"metabolic_process/Triple/#inheritance","title":"Inheritance","text":""},{"location":"metabolic_process/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"metabolic_process/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"metabolic_process/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Triple/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self bp:Triple native bp:Triple"},{"location":"metabolic_process/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"metabolic_process/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"metabolic_process/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/metabolic_process\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"metabolic_process/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"metabolic_process/Uri/#comments","title":"Comments","text":""},{"location":"metabolic_process/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Uri/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"metabolic_process/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: bp:abstract

"},{"location":"metabolic_process/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metabolic_process/abstract/#properties","title":"Properties","text":""},{"location":"metabolic_process/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/abstract/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metabolic_process/category/","title":"Slot: category","text":"

the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity

URI: bp:category

"},{"location":"metabolic_process/category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/category/#properties","title":"Properties","text":""},{"location":"metabolic_process/category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/category/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/category/#linkml-source","title":"LinkML Source","text":"
name: category\ndescription: the category of metabolic process, e.g metabolic process, catabolic process,\n  biosynthetic process, small molecule sensor activity\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: category\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: MetabolicProcessCategory\n\n
"},{"location":"metabolic_process/combined_text/","title":"Slot: combined_text","text":"

URI: bp:combined_text

"},{"location":"metabolic_process/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metabolic_process/combined_text/#properties","title":"Properties","text":""},{"location":"metabolic_process/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metabolic_process/description/","title":"Slot: description","text":"

a textual description of the metabolic process

URI: bp:description

"},{"location":"metabolic_process/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/description/#properties","title":"Properties","text":""},{"location":"metabolic_process/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/description/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a textual description of the metabolic process\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: description\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: string\n\n
"},{"location":"metabolic_process/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: bp:extracted_object

"},{"location":"metabolic_process/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/extracted_object/#properties","title":"Properties","text":""},{"location":"metabolic_process/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"metabolic_process/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: bp:full_text

"},{"location":"metabolic_process/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metabolic_process/full_text/#properties","title":"Properties","text":""},{"location":"metabolic_process/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/full_text/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metabolic_process/id/","title":"Slot: id","text":"

URI: bp:id

"},{"location":"metabolic_process/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no MetabolicProcessCategory no ChemicalEntity no NamedEntity no RelationshipType no Publication no"},{"location":"metabolic_process/id/#properties","title":"Properties","text":""},{"location":"metabolic_process/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"metabolic_process/input_id/","title":"Slot: input_id","text":"

URI: bp:input_id

"},{"location":"metabolic_process/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/input_id/#properties","title":"Properties","text":""},{"location":"metabolic_process/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/input_id/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metabolic_process/input_text/","title":"Slot: input_text","text":"

URI: bp:input_text

"},{"location":"metabolic_process/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/input_text/#properties","title":"Properties","text":""},{"location":"metabolic_process/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/input_text/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metabolic_process/input_title/","title":"Slot: input_title","text":"

URI: bp:input_title

"},{"location":"metabolic_process/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/input_title/#properties","title":"Properties","text":""},{"location":"metabolic_process/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/input_title/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metabolic_process/inputs/","title":"Slot: inputs","text":"

the inputs of the metabolic process

URI: bp:inputs

"},{"location":"metabolic_process/inputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/inputs/#properties","title":"Properties","text":""},{"location":"metabolic_process/inputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/inputs/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/inputs/#linkml-source","title":"LinkML Source","text":"
name: inputs\ndescription: the inputs of the metabolic process\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: inputs\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: ChemicalEntity\n\n
"},{"location":"metabolic_process/label/","title":"Slot: label","text":"

URI: bp:label

"},{"location":"metabolic_process/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no MetabolicProcessCategory no ChemicalEntity no NamedEntity no RelationshipType no"},{"location":"metabolic_process/label/#properties","title":"Properties","text":""},{"location":"metabolic_process/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- MetabolicProcess\n- NamedEntity\nrange: string\n\n
"},{"location":"metabolic_process/metabolic-process-template/","title":"metabolic-process-template","text":"

A template for GO-CAMs

URI: https://w3id.org/ontogpt/metabolic_process

"},{"location":"metabolic_process/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: bp:named_entities

"},{"location":"metabolic_process/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/named_entities/#properties","title":"Properties","text":""},{"location":"metabolic_process/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"metabolic_process/object/","title":"Slot: object","text":"

URI: bp:object

"},{"location":"metabolic_process/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/object/#properties","title":"Properties","text":""},{"location":"metabolic_process/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/object/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metabolic_process/object_id/","title":"Slot: object_id","text":"

URI: bp:object_id

"},{"location":"metabolic_process/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metabolic_process/object_id/#properties","title":"Properties","text":""},{"location":"metabolic_process/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/object_id/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metabolic_process/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: bp:object_qualifier

"},{"location":"metabolic_process/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/object_qualifier/#properties","title":"Properties","text":""},{"location":"metabolic_process/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metabolic_process/object_text/","title":"Slot: object_text","text":"

URI: bp:object_text

"},{"location":"metabolic_process/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metabolic_process/object_text/#properties","title":"Properties","text":""},{"location":"metabolic_process/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/object_text/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metabolic_process/outputs/","title":"Slot: outputs","text":"

the outputs of the metabolic process

URI: bp:outputs

"},{"location":"metabolic_process/outputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/outputs/#properties","title":"Properties","text":""},{"location":"metabolic_process/outputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/outputs/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/outputs/#linkml-source","title":"LinkML Source","text":"
name: outputs\ndescription: the outputs of the metabolic process\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: outputs\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: ChemicalEntity\n\n
"},{"location":"metabolic_process/predicate/","title":"Slot: predicate","text":"

URI: bp:predicate

"},{"location":"metabolic_process/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/predicate/#properties","title":"Properties","text":""},{"location":"metabolic_process/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/predicate/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"metabolic_process/prompt/","title":"Slot: prompt","text":"

URI: bp:prompt

"},{"location":"metabolic_process/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/prompt/#properties","title":"Properties","text":""},{"location":"metabolic_process/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/prompt/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metabolic_process/publication/","title":"Slot: publication","text":"

URI: bp:publication

"},{"location":"metabolic_process/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"metabolic_process/publication/#properties","title":"Properties","text":""},{"location":"metabolic_process/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"metabolic_process/publication/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"metabolic_process/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: bp:qualifier

"},{"location":"metabolic_process/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/qualifier/#properties","title":"Properties","text":""},{"location":"metabolic_process/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"metabolic_process/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: bp:raw_completion_output

"},{"location":"metabolic_process/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metabolic_process/raw_completion_output/#properties","title":"Properties","text":""},{"location":"metabolic_process/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metabolic_process/subclass_of/","title":"Slot: subclass_of","text":"

a semicolon separated list of broader metabolic processes which this is a subclass of

URI: bp:subclass_of

"},{"location":"metabolic_process/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/subclass_of/#properties","title":"Properties","text":""},{"location":"metabolic_process/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\ndescription: a semicolon separated list of broader metabolic processes which this\n  is a subclass of\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: subclass_of\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: MetabolicProcessCategory\n\n
"},{"location":"metabolic_process/subject/","title":"Slot: subject","text":"

URI: bp:subject

"},{"location":"metabolic_process/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/subject/#properties","title":"Properties","text":""},{"location":"metabolic_process/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/subject/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metabolic_process/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: bp:subject_qualifier

"},{"location":"metabolic_process/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metabolic_process/subject_qualifier/#properties","title":"Properties","text":""},{"location":"metabolic_process/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metabolic_process/subject_text/","title":"Slot: subject_text","text":"

URI: bp:subject_text

"},{"location":"metabolic_process/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metabolic_process/subject_text/#properties","title":"Properties","text":""},{"location":"metabolic_process/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metabolic_process/synonyms/","title":"Slot: synonyms","text":"

alternative names of the metabolic process

URI: bp:synonyms

"},{"location":"metabolic_process/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolicProcess no"},{"location":"metabolic_process/synonyms/#properties","title":"Properties","text":""},{"location":"metabolic_process/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\ndescription: alternative names of the metabolic process\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: MetabolicProcess\ndomain_of:\n- MetabolicProcess\nrange: string\n\n
"},{"location":"metabolic_process/title/","title":"Slot: title","text":"

The title of the publication

URI: bp:title

"},{"location":"metabolic_process/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metabolic_process/title/#properties","title":"Properties","text":""},{"location":"metabolic_process/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/title/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metabolic_process/triples/","title":"Slot: triples","text":"

URI: bp:triples

"},{"location":"metabolic_process/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"metabolic_process/triples/#properties","title":"Properties","text":""},{"location":"metabolic_process/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolic_process/triples/#schema-source","title":"Schema Source","text":""},{"location":"metabolic_process/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/metabolic_process\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"metagenome_study/","title":"Environmental Metagenome Template","text":"

A template for Environmental Metagenome Studies

URI: http://w3id.org/ontogpt/metagenome

Name: environmental-metagenome

"},{"location":"metagenome_study/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nStudy {\n\n}\nLocation {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nEnvironment {\n    string id  \n    string label  \n}\nVariable {\n    string id  \n    string label  \n}\nUnit {\n    string id  \n    string label  \n}\nMeasurement {\n    string value  \n}\nCausalRelationship {\n\n}\nSequencingTechnology {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nOrganism {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nStudy ||--}o Environment : \"environments\"\nStudy ||--}o CausalRelationship : \"causal_relationships\"\nStudy ||--}o Variable : \"variables\"\nStudy ||--}o Treatment : \"treatments\"\nStudy ||--}o Measurement : \"measurements\"\nStudy ||--}o Location : \"location\"\nStudy ||--}o EnvironmentalMaterial : \"environmental_material\"\nStudy ||--|o SequencingTechnology : \"sequencing_technologies\"\nStudy ||--}o Organism : \"organisms\"\nMeasurement ||--|o Unit : \"unit\"\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"metagenome_study/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None CausalRelationship None Measurement None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None Environment None EnvironmentalMaterial None Location None Organism None RelationshipType None SequencingTechnology None Treatment None Unit None Variable None Publication None Study None TextWithTriples None"},{"location":"metagenome_study/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication causal_relationships cause the variable that is the cause of the effect combined_text effect the things that is affected environmental_material the environmental material that was sampled environments extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing location the sites at which the study was conducted measurements named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text organisms semicolon-separated list of all studied organism taxons predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output sequencing_technologies subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication treatments triples unit the unit of the measurement value the value of the measurement variables"},{"location":"metagenome_study/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"metagenome_study/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"metagenome_study/#subsets","title":"Subsets","text":"Subset Description"},{"location":"metagenome_study/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: eg:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"metagenome_study/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"metagenome_study/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:AnnotatorResult native eg:AnnotatorResult"},{"location":"metagenome_study/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n\n
"},{"location":"metagenome_study/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"metagenome_study/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"metagenome_study/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"metagenome_study/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"metagenome_study/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Any/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native eg:Any"},{"location":"metagenome_study/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/metagenome\nclass_uri: linkml:Any\n\n
"},{"location":"metagenome_study/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/metagenome\nclass_uri: linkml:Any\n\n
"},{"location":"metagenome_study/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"metagenome_study/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/CausalRelationship/","title":"Class: CausalRelationship","text":"

URI: eg:CausalRelationship

erDiagram\nCausalRelationship {\n\n}\nVariable {\n    string id  \n    string label  \n}\n\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\n\n
"},{"location":"metagenome_study/CausalRelationship/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/CausalRelationship/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance cause 0..1 Variable the variable that is the cause of the effect direct effect 0..1 Variable the things that is affected direct"},{"location":"metagenome_study/CausalRelationship/#usages","title":"Usages","text":"used by used in type used Study causal_relationships range CausalRelationship"},{"location":"metagenome_study/CausalRelationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/CausalRelationship/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/CausalRelationship/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:CausalRelationship native eg:CausalRelationship"},{"location":"metagenome_study/CausalRelationship/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/CausalRelationship/#direct","title":"Direct","text":"
name: CausalRelationship\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nattributes:\n  cause:\n    name: cause\n    description: the variable that is the cause of the effect\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: Variable\n  effect:\n    name: effect\n    description: the things that is affected\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: Variable\n\n
"},{"location":"metagenome_study/CausalRelationship/#induced","title":"Induced","text":"
name: CausalRelationship\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nattributes:\n  cause:\n    name: cause\n    description: the variable that is the cause of the effect\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: cause\n    owner: CausalRelationship\n    domain_of:\n    - CausalRelationship\n    range: Variable\n  effect:\n    name: effect\n    description: the things that is affected\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: effect\n    owner: CausalRelationship\n    domain_of:\n    - CausalRelationship\n    range: Variable\n\n
"},{"location":"metagenome_study/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: eg:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"metagenome_study/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"metagenome_study/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:CompoundExpression native eg:CompoundExpression"},{"location":"metagenome_study/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/metagenome\nabstract: true\n\n
"},{"location":"metagenome_study/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/metagenome\nabstract: true\n\n
"},{"location":"metagenome_study/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"metagenome_study/Curie/#comments","title":"Comments","text":""},{"location":"metagenome_study/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Curie/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"metagenome_study/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Date/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"metagenome_study/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"metagenome_study/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"metagenome_study/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"metagenome_study/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Double/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Environment/","title":"Class: Environment","text":"

URI: eg:Environment

erDiagram\nEnvironment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Environment/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Environment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Environment/#usages","title":"Usages","text":"used by used in type used Study environments range Environment"},{"location":"metagenome_study/Environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Environment/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Environment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo"},{"location":"metagenome_study/Environment/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Environment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Environment native eg:Environment"},{"location":"metagenome_study/Environment/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Environment/#direct","title":"Direct","text":"
name: Environment\nid_prefixes:\n- ENVO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Environment/#induced","title":"Induced","text":"
name: Environment\nid_prefixes:\n- ENVO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Environment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/EnvironmentalMaterial/","title":"Class: EnvironmentalMaterial","text":"

URI: eg:EnvironmentalMaterial

erDiagram\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/EnvironmentalMaterial/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/EnvironmentalMaterial/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/EnvironmentalMaterial/#usages","title":"Usages","text":"used by used in type used Study environmental_material range EnvironmentalMaterial"},{"location":"metagenome_study/EnvironmentalMaterial/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/EnvironmentalMaterial/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/EnvironmentalMaterial/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo"},{"location":"metagenome_study/EnvironmentalMaterial/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/EnvironmentalMaterial/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:EnvironmentalMaterial native eg:EnvironmentalMaterial"},{"location":"metagenome_study/EnvironmentalMaterial/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/EnvironmentalMaterial/#direct","title":"Direct","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/EnvironmentalMaterial/#induced","title":"Induced","text":"
name: EnvironmentalMaterial\nid_prefixes:\n- ENVO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: EnvironmentalMaterial\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: eg:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"metagenome_study/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"metagenome_study/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:ExtractionResult native eg:ExtractionResult"},{"location":"metagenome_study/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metagenome_study/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metagenome_study/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"metagenome_study/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Float/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"metagenome_study/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Integer/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Location/","title":"Class: Location","text":"

URI: eg:Location

erDiagram\nLocation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Location/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Location/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Location/#usages","title":"Usages","text":"used by used in type used Study location range Location"},{"location":"metagenome_study/Location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Location/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Location/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:gaz"},{"location":"metagenome_study/Location/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Location/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Location native eg:Location"},{"location":"metagenome_study/Location/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Location/#direct","title":"Direct","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:gaz\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Location/#induced","title":"Induced","text":"
name: Location\nid_prefixes:\n- ENVO\n- GAZ\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:gaz\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Location\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Location\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/Measurement/","title":"Class: Measurement","text":"

URI: eg:Measurement

erDiagram\nMeasurement {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\n\nMeasurement ||--|o Unit : \"unit\"\n\n
"},{"location":"metagenome_study/Measurement/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Measurement/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance value 0..1 String the value of the measurement direct unit 0..1 Unit the unit of the measurement direct"},{"location":"metagenome_study/Measurement/#usages","title":"Usages","text":"used by used in type used Study measurements range Measurement"},{"location":"metagenome_study/Measurement/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Measurement/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Measurement/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Measurement native eg:Measurement"},{"location":"metagenome_study/Measurement/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Measurement/#direct","title":"Direct","text":"
name: Measurement\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    description: the value of the measurement\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  unit:\n    name: unit\n    description: the unit of the measurement\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: Unit\n\n
"},{"location":"metagenome_study/Measurement/#induced","title":"Induced","text":"
name: Measurement\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    description: the value of the measurement\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: value\n    owner: Measurement\n    domain_of:\n    - Measurement\n    range: string\n  unit:\n    name: unit\n    description: the unit of the measurement\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: unit\n    owner: Measurement\n    domain_of:\n    - Measurement\n    range: Unit\n\n
"},{"location":"metagenome_study/NamedEntity/","title":"Class: NamedEntity","text":"

URI: eg:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"metagenome_study/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"metagenome_study/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:NamedEntity native eg:NamedEntity"},{"location":"metagenome_study/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/metagenome\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"metagenome_study/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/metagenome\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"metagenome_study/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"metagenome_study/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"metagenome_study/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"metagenome_study/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"metagenome_study/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"metagenome_study/Objectidentifier/#comments","title":"Comments","text":""},{"location":"metagenome_study/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Organism/","title":"Class: Organism","text":"

URI: eg:Organism

erDiagram\nOrganism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Organism/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Organism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Organism/#usages","title":"Usages","text":"used by used in type used Study organisms range Organism"},{"location":"metagenome_study/Organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Organism/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Organism/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ncbitaxon, gilda:"},{"location":"metagenome_study/Organism/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Organism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Organism native eg:Organism"},{"location":"metagenome_study/Organism/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Organism/#direct","title":"Direct","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\nannotations:\n  annotators:\n    tag: annotators\n    value: 'sqlite:obo:ncbitaxon, gilda:'\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Organism/#induced","title":"Induced","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\nannotations:\n  annotators:\n    tag: annotators\n    value: 'sqlite:obo:ncbitaxon, gilda:'\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/Publication/","title":"Class: Publication","text":"

URI: eg:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"metagenome_study/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"metagenome_study/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"metagenome_study/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Publication/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Publication native eg:Publication"},{"location":"metagenome_study/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/metagenome\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n\n
"},{"location":"metagenome_study/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/metagenome\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"metagenome_study/RelationshipType/","title":"Class: RelationshipType","text":"

URI: eg:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"metagenome_study/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:RelationshipType native eg:RelationshipType"},{"location":"metagenome_study/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/SequencingTechnology/","title":"Class: SequencingTechnology","text":"

URI: eg:SequencingTechnology

erDiagram\nSequencingTechnology {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/SequencingTechnology/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/SequencingTechnology/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/SequencingTechnology/#usages","title":"Usages","text":"used by used in type used Study sequencing_technologies range SequencingTechnology"},{"location":"metagenome_study/SequencingTechnology/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/SequencingTechnology/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/SequencingTechnology/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:obi, sqlite:obo:efo, bioportal:bero"},{"location":"metagenome_study/SequencingTechnology/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/SequencingTechnology/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:SequencingTechnology native eg:SequencingTechnology"},{"location":"metagenome_study/SequencingTechnology/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/SequencingTechnology/#direct","title":"Direct","text":"
name: SequencingTechnology\nid_prefixes:\n- IDO\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:obi, sqlite:obo:efo, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/SequencingTechnology/#induced","title":"Induced","text":"
name: SequencingTechnology\nid_prefixes:\n- IDO\n- EFO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:obi, sqlite:obo:efo, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: SequencingTechnology\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: SequencingTechnology\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"metagenome_study/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/String/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Study/","title":"Class: Study","text":"

URI: eg:Study

erDiagram\nStudy {\n\n}\nOrganism {\n    string id  \n    string label  \n}\nSequencingTechnology {\n    string id  \n    string label  \n}\nEnvironmentalMaterial {\n    string id  \n    string label  \n}\nLocation {\n    string id  \n    string label  \n}\nMeasurement {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nVariable {\n    string id  \n    string label  \n}\nCausalRelationship {\n\n}\nEnvironment {\n    string id  \n    string label  \n}\n\nStudy ||--}o Environment : \"environments\"\nStudy ||--}o CausalRelationship : \"causal_relationships\"\nStudy ||--}o Variable : \"variables\"\nStudy ||--}o Treatment : \"treatments\"\nStudy ||--}o Measurement : \"measurements\"\nStudy ||--}o Location : \"location\"\nStudy ||--}o EnvironmentalMaterial : \"environmental_material\"\nStudy ||--|o SequencingTechnology : \"sequencing_technologies\"\nStudy ||--}o Organism : \"organisms\"\nMeasurement ||--|o Unit : \"unit\"\nCausalRelationship ||--|o Variable : \"cause\"\nCausalRelationship ||--|o Variable : \"effect\"\n\n
"},{"location":"metagenome_study/Study/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance environments 0..* Environment direct causal_relationships 0..* CausalRelationship direct variables 0..* Variable direct treatments 0..* Treatment direct measurements 0..* Measurement direct location 0..* Location the sites at which the study was conducted direct environmental_material 0..* EnvironmentalMaterial the environmental material that was sampled direct sequencing_technologies 0..1 SequencingTechnology direct organisms 0..* Organism semicolon-separated list of all studied organism taxons direct"},{"location":"metagenome_study/Study/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Study/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Study/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Study native eg:Study"},{"location":"metagenome_study/Study/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Study/#direct","title":"Direct","text":"
name: Study\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental systems or biomes in which\n          the study was conducted\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Environment\n  causal_relationships:\n    name: causal_relationships\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of cause-effect pairs, for example, effect\n          of temperature on growth\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: CausalRelationship\n  variables:\n    name: variables\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental variables which are studies.\n          E.g. temperature, pH, salinity\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Variable\n  treatments:\n    name: treatments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of treatments that are applied\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Treatment\n  measurements:\n    name: measurements\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of value-measurement pairs\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Measurement\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of sites at which the study was conducted\n    description: the sites at which the study was conducted\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: EnvironmentalMaterial\n  sequencing_technologies:\n    name: sequencing_technologies\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of  sequencing technologies used in the project\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: SequencingTechnology\n  organisms:\n    name: organisms\n    description: semicolon-separated list of all studied organism taxons\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Organism\n\n
"},{"location":"metagenome_study/Study/#induced","title":"Induced","text":"
name: Study\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  environments:\n    name: environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental systems or biomes in which\n          the study was conducted\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: environments\n    owner: Study\n    domain_of:\n    - Study\n    range: Environment\n  causal_relationships:\n    name: causal_relationships\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of cause-effect pairs, for example, effect\n          of temperature on growth\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: causal_relationships\n    owner: Study\n    domain_of:\n    - Study\n    range: CausalRelationship\n  variables:\n    name: variables\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental variables which are studies.\n          E.g. temperature, pH, salinity\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: variables\n    owner: Study\n    domain_of:\n    - Study\n    range: Variable\n  treatments:\n    name: treatments\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of treatments that are applied\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: treatments\n    owner: Study\n    domain_of:\n    - Study\n    range: Treatment\n  measurements:\n    name: measurements\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of value-measurement pairs\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: measurements\n    owner: Study\n    domain_of:\n    - Study\n    range: Measurement\n  location:\n    name: location\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of sites at which the study was conducted\n    description: the sites at which the study was conducted\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: location\n    owner: Study\n    domain_of:\n    - Study\n    range: Location\n  environmental_material:\n    name: environmental_material\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of environmental materials\n    description: the environmental material that was sampled\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: environmental_material\n    owner: Study\n    domain_of:\n    - Study\n    range: EnvironmentalMaterial\n  sequencing_technologies:\n    name: sequencing_technologies\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of  sequencing technologies used in the project\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: sequencing_technologies\n    owner: Study\n    domain_of:\n    - Study\n    range: SequencingTechnology\n  organisms:\n    name: organisms\n    description: semicolon-separated list of all studied organism taxons\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: organisms\n    owner: Study\n    domain_of:\n    - Study\n    range: Organism\n\n
"},{"location":"metagenome_study/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: eg:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"metagenome_study/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"metagenome_study/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:TextWithTriples native eg:TextWithTriples"},{"location":"metagenome_study/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metagenome_study/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/metagenome\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"metagenome_study/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"metagenome_study/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Time/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Treatment/","title":"Class: Treatment","text":"

URI: eg:Treatment

erDiagram\nTreatment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Treatment/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Treatment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Treatment/#usages","title":"Usages","text":"used by used in type used Study treatments range Treatment"},{"location":"metagenome_study/Treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Treatment/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Treatment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:peco, sqlite:obo:obi, bioportal:bero"},{"location":"metagenome_study/Treatment/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Treatment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Treatment native eg:Treatment"},{"location":"metagenome_study/Treatment/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Treatment/#direct","title":"Direct","text":"
name: Treatment\nid_prefixes:\n- PECO\n- OBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:peco, sqlite:obo:obi, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Treatment/#induced","title":"Induced","text":"
name: Treatment\nid_prefixes:\n- PECO\n- OBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:peco, sqlite:obo:obi, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: eg:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"metagenome_study/Triple/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"metagenome_study/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"metagenome_study/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Triple/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Triple native eg:Triple"},{"location":"metagenome_study/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"metagenome_study/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"metagenome_study/Unit/","title":"Class: Unit","text":"

URI: eg:Unit

erDiagram\nUnit {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Unit/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Unit/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Unit/#usages","title":"Usages","text":"used by used in type used Measurement unit range Unit"},{"location":"metagenome_study/Unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Unit/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Unit/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uo, bioportal:ncit"},{"location":"metagenome_study/Unit/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Unit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Unit native eg:Unit"},{"location":"metagenome_study/Unit/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Unit/#direct","title":"Direct","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, bioportal:ncit\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Unit/#induced","title":"Induced","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, bioportal:ncit\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"metagenome_study/Uri/#comments","title":"Comments","text":""},{"location":"metagenome_study/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Uri/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"metagenome_study/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Variable/","title":"Class: Variable","text":"

URI: eg:Variable

erDiagram\nVariable {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"metagenome_study/Variable/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_study/Variable/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"metagenome_study/Variable/#usages","title":"Usages","text":"used by used in type used Study variables range Variable CausalRelationship cause range Variable CausalRelationship effect range Variable"},{"location":"metagenome_study/Variable/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/Variable/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"metagenome_study/Variable/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:envo, bioportal:bero"},{"location":"metagenome_study/Variable/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/Variable/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self eg:Variable native eg:Variable"},{"location":"metagenome_study/Variable/#linkml-source","title":"LinkML Source","text":""},{"location":"metagenome_study/Variable/#direct","title":"Direct","text":"
name: Variable\nid_prefixes:\n- ENVO\n- MIXS\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\n\n
"},{"location":"metagenome_study/Variable/#induced","title":"Induced","text":"
name: Variable\nid_prefixes:\n- ENVO\n- MIXS\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:envo, bioportal:bero\nfrom_schema: http://w3id.org/ontogpt/metagenome\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/metagenome\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Variable\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/metagenome\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Variable\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"metagenome_study/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: eg:abstract

"},{"location":"metagenome_study/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metagenome_study/abstract/#properties","title":"Properties","text":""},{"location":"metagenome_study/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/abstract/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metagenome_study/causal_relationships/","title":"Slot: causal_relationships","text":"

URI: eg:causal_relationships

"},{"location":"metagenome_study/causal_relationships/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/causal_relationships/#properties","title":"Properties","text":""},{"location":"metagenome_study/causal_relationships/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/causal_relationships/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth"},{"location":"metagenome_study/causal_relationships/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/causal_relationships/#linkml-source","title":"LinkML Source","text":"
name: causal_relationships\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of cause-effect pairs, for example, effect of\n      temperature on growth\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: causal_relationships\nowner: Study\ndomain_of:\n- Study\nrange: CausalRelationship\n\n
"},{"location":"metagenome_study/cause/","title":"Slot: cause","text":"

the variable that is the cause of the effect

URI: eg:cause

"},{"location":"metagenome_study/cause/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CausalRelationship no"},{"location":"metagenome_study/cause/#properties","title":"Properties","text":""},{"location":"metagenome_study/cause/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/cause/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/cause/#linkml-source","title":"LinkML Source","text":"
name: cause\ndescription: the variable that is the cause of the effect\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: cause\nowner: CausalRelationship\ndomain_of:\n- CausalRelationship\nrange: Variable\n\n
"},{"location":"metagenome_study/combined_text/","title":"Slot: combined_text","text":"

URI: eg:combined_text

"},{"location":"metagenome_study/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metagenome_study/combined_text/#properties","title":"Properties","text":""},{"location":"metagenome_study/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metagenome_study/effect/","title":"Slot: effect","text":"

the things that is affected

URI: eg:effect

"},{"location":"metagenome_study/effect/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CausalRelationship no"},{"location":"metagenome_study/effect/#properties","title":"Properties","text":""},{"location":"metagenome_study/effect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/effect/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/effect/#linkml-source","title":"LinkML Source","text":"
name: effect\ndescription: the things that is affected\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: effect\nowner: CausalRelationship\ndomain_of:\n- CausalRelationship\nrange: Variable\n\n
"},{"location":"metagenome_study/environmental-metagenome/","title":"environmental-metagenome","text":"

A template for Environmental Metagenome Studies

URI: http://w3id.org/ontogpt/metagenome

"},{"location":"metagenome_study/environmental_material/","title":"Slot: environmental_material","text":"

the environmental material that was sampled

URI: eg:environmental_material

"},{"location":"metagenome_study/environmental_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/environmental_material/#properties","title":"Properties","text":""},{"location":"metagenome_study/environmental_material/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/environmental_material/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental materials"},{"location":"metagenome_study/environmental_material/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/environmental_material/#linkml-source","title":"LinkML Source","text":"
name: environmental_material\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental materials\ndescription: the environmental material that was sampled\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: environmental_material\nowner: Study\ndomain_of:\n- Study\nrange: EnvironmentalMaterial\n\n
"},{"location":"metagenome_study/environments/","title":"Slot: environments","text":"

URI: eg:environments

"},{"location":"metagenome_study/environments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/environments/#properties","title":"Properties","text":""},{"location":"metagenome_study/environments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/environments/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental systems or biomes in which the study was conducted"},{"location":"metagenome_study/environments/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/environments/#linkml-source","title":"LinkML Source","text":"
name: environments\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental systems or biomes in which the\n      study was conducted\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: environments\nowner: Study\ndomain_of:\n- Study\nrange: Environment\n\n
"},{"location":"metagenome_study/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: eg:extracted_object

"},{"location":"metagenome_study/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/extracted_object/#properties","title":"Properties","text":""},{"location":"metagenome_study/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"metagenome_study/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: eg:full_text

"},{"location":"metagenome_study/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metagenome_study/full_text/#properties","title":"Properties","text":""},{"location":"metagenome_study/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/full_text/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metagenome_study/id/","title":"Slot: id","text":"

URI: eg:id

"},{"location":"metagenome_study/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Location no EnvironmentalMaterial no Environment no Variable no Unit no SequencingTechnology no Treatment no Organism no NamedEntity no RelationshipType no Publication no"},{"location":"metagenome_study/id/#properties","title":"Properties","text":""},{"location":"metagenome_study/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"metagenome_study/input_id/","title":"Slot: input_id","text":"

URI: eg:input_id

"},{"location":"metagenome_study/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/input_id/#properties","title":"Properties","text":""},{"location":"metagenome_study/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/input_id/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metagenome_study/input_text/","title":"Slot: input_text","text":"

URI: eg:input_text

"},{"location":"metagenome_study/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/input_text/#properties","title":"Properties","text":""},{"location":"metagenome_study/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/input_text/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metagenome_study/input_title/","title":"Slot: input_title","text":"

URI: eg:input_title

"},{"location":"metagenome_study/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/input_title/#properties","title":"Properties","text":""},{"location":"metagenome_study/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/input_title/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metagenome_study/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"metagenome_study/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Location no EnvironmentalMaterial no Environment no Variable no Unit no SequencingTechnology no Treatment no Organism no NamedEntity no RelationshipType no"},{"location":"metagenome_study/label/#properties","title":"Properties","text":""},{"location":"metagenome_study/label/#aliases","title":"Aliases","text":""},{"location":"metagenome_study/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"metagenome_study/label/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/metagenome\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"metagenome_study/location/","title":"Slot: location","text":"

the sites at which the study was conducted

URI: eg:location

"},{"location":"metagenome_study/location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/location/#properties","title":"Properties","text":""},{"location":"metagenome_study/location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/location/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of sites at which the study was conducted"},{"location":"metagenome_study/location/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/location/#linkml-source","title":"LinkML Source","text":"
name: location\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of sites at which the study was conducted\ndescription: the sites at which the study was conducted\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: location\nowner: Study\ndomain_of:\n- Study\nrange: Location\n\n
"},{"location":"metagenome_study/measurements/","title":"Slot: measurements","text":"

URI: eg:measurements

"},{"location":"metagenome_study/measurements/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/measurements/#properties","title":"Properties","text":""},{"location":"metagenome_study/measurements/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/measurements/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of value-measurement pairs"},{"location":"metagenome_study/measurements/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/measurements/#linkml-source","title":"LinkML Source","text":"
name: measurements\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of value-measurement pairs\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: measurements\nowner: Study\ndomain_of:\n- Study\nrange: Measurement\n\n
"},{"location":"metagenome_study/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: eg:named_entities

"},{"location":"metagenome_study/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/named_entities/#properties","title":"Properties","text":""},{"location":"metagenome_study/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"metagenome_study/object/","title":"Slot: object","text":"

URI: eg:object

"},{"location":"metagenome_study/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/object/#properties","title":"Properties","text":""},{"location":"metagenome_study/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/object/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metagenome_study/object_id/","title":"Slot: object_id","text":"

URI: eg:object_id

"},{"location":"metagenome_study/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metagenome_study/object_id/#properties","title":"Properties","text":""},{"location":"metagenome_study/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/object_id/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metagenome_study/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: eg:object_qualifier

"},{"location":"metagenome_study/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/object_qualifier/#properties","title":"Properties","text":""},{"location":"metagenome_study/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metagenome_study/object_text/","title":"Slot: object_text","text":"

URI: eg:object_text

"},{"location":"metagenome_study/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metagenome_study/object_text/#properties","title":"Properties","text":""},{"location":"metagenome_study/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/object_text/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metagenome_study/organisms/","title":"Slot: organisms","text":"

semicolon-separated list of all studied organism taxons

URI: eg:organisms

"},{"location":"metagenome_study/organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/organisms/#properties","title":"Properties","text":""},{"location":"metagenome_study/organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/organisms/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/organisms/#linkml-source","title":"LinkML Source","text":"
name: organisms\ndescription: semicolon-separated list of all studied organism taxons\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: organisms\nowner: Study\ndomain_of:\n- Study\nrange: Organism\n\n
"},{"location":"metagenome_study/predicate/","title":"Slot: predicate","text":"

URI: eg:predicate

"},{"location":"metagenome_study/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/predicate/#properties","title":"Properties","text":""},{"location":"metagenome_study/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/predicate/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"metagenome_study/prompt/","title":"Slot: prompt","text":"

URI: eg:prompt

"},{"location":"metagenome_study/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/prompt/#properties","title":"Properties","text":""},{"location":"metagenome_study/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/prompt/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metagenome_study/publication/","title":"Slot: publication","text":"

URI: eg:publication

"},{"location":"metagenome_study/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"metagenome_study/publication/#properties","title":"Properties","text":""},{"location":"metagenome_study/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"metagenome_study/publication/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"metagenome_study/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: eg:qualifier

"},{"location":"metagenome_study/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/qualifier/#properties","title":"Properties","text":""},{"location":"metagenome_study/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"metagenome_study/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: eg:raw_completion_output

"},{"location":"metagenome_study/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"metagenome_study/raw_completion_output/#properties","title":"Properties","text":""},{"location":"metagenome_study/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"metagenome_study/sequencing_technologies/","title":"Slot: sequencing_technologies","text":"

URI: eg:sequencing_technologies

"},{"location":"metagenome_study/sequencing_technologies/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/sequencing_technologies/#properties","title":"Properties","text":""},{"location":"metagenome_study/sequencing_technologies/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/sequencing_technologies/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of sequencing technologies used in the project"},{"location":"metagenome_study/sequencing_technologies/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/sequencing_technologies/#linkml-source","title":"LinkML Source","text":"
name: sequencing_technologies\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of  sequencing technologies used in the project\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: sequencing_technologies\nowner: Study\ndomain_of:\n- Study\nrange: SequencingTechnology\n\n
"},{"location":"metagenome_study/subject/","title":"Slot: subject","text":"

URI: eg:subject

"},{"location":"metagenome_study/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/subject/#properties","title":"Properties","text":""},{"location":"metagenome_study/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/subject/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metagenome_study/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: eg:subject_qualifier

"},{"location":"metagenome_study/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"metagenome_study/subject_qualifier/#properties","title":"Properties","text":""},{"location":"metagenome_study/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"metagenome_study/subject_text/","title":"Slot: subject_text","text":"

URI: eg:subject_text

"},{"location":"metagenome_study/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"metagenome_study/subject_text/#properties","title":"Properties","text":""},{"location":"metagenome_study/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"metagenome_study/title/","title":"Slot: title","text":"

The title of the publication

URI: eg:title

"},{"location":"metagenome_study/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"metagenome_study/title/#properties","title":"Properties","text":""},{"location":"metagenome_study/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/title/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"metagenome_study/treatments/","title":"Slot: treatments","text":"

URI: eg:treatments

"},{"location":"metagenome_study/treatments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/treatments/#properties","title":"Properties","text":""},{"location":"metagenome_study/treatments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/treatments/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of treatments that are applied"},{"location":"metagenome_study/treatments/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/treatments/#linkml-source","title":"LinkML Source","text":"
name: treatments\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of treatments that are applied\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: treatments\nowner: Study\ndomain_of:\n- Study\nrange: Treatment\n\n
"},{"location":"metagenome_study/triples/","title":"Slot: triples","text":"

URI: eg:triples

"},{"location":"metagenome_study/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"metagenome_study/triples/#properties","title":"Properties","text":""},{"location":"metagenome_study/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/triples/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"metagenome_study/unit/","title":"Slot: unit","text":"

the unit of the measurement

URI: eg:unit

"},{"location":"metagenome_study/unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Measurement no"},{"location":"metagenome_study/unit/#properties","title":"Properties","text":""},{"location":"metagenome_study/unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/unit/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/unit/#linkml-source","title":"LinkML Source","text":"
name: unit\ndescription: the unit of the measurement\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: unit\nowner: Measurement\ndomain_of:\n- Measurement\nrange: Unit\n\n
"},{"location":"metagenome_study/value/","title":"Slot: value","text":"

the value of the measurement

URI: eg:value

"},{"location":"metagenome_study/value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Measurement no"},{"location":"metagenome_study/value/#properties","title":"Properties","text":""},{"location":"metagenome_study/value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/value/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/value/#linkml-source","title":"LinkML Source","text":"
name: value\ndescription: the value of the measurement\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nalias: value\nowner: Measurement\ndomain_of:\n- Measurement\nrange: string\n\n
"},{"location":"metagenome_study/variables/","title":"Slot: variables","text":"

URI: eg:variables

"},{"location":"metagenome_study/variables/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study no"},{"location":"metagenome_study/variables/#properties","title":"Properties","text":""},{"location":"metagenome_study/variables/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_study/variables/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity"},{"location":"metagenome_study/variables/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_study/variables/#linkml-source","title":"LinkML Source","text":"
name: variables\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of environmental variables which are studies.\n      E.g. temperature, pH, salinity\nfrom_schema: http://w3id.org/ontogpt/metagenome\nrank: 1000\nmultivalued: true\nalias: variables\nowner: Study\ndomain_of:\n- Study\nrange: Variable\n\n
"},{"location":"ontology_class/","title":"Ontology Class Template","text":"

A template for Ontology Classes

URI: https://w3id.org/ontogpt/ontology_class

Name: ontology-class

"},{"location":"ontology_class/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nOntologyClass {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nLogicalDefinition {\n\n}\nRelation {\n    string id  \n    string label  \n}\n\nOntologyClass ||--}o OntologyClass : \"categories\"\nOntologyClass ||--}o OntologyClass : \"subclass_of\"\nOntologyClass ||--|o LogicalDefinition : \"logical_definition\"\nLogicalDefinition ||--}o OntologyClass : \"genus\"\nLogicalDefinition ||--|o Relation : \"differentiating_characteristic_relationship\"\nLogicalDefinition ||--}o OntologyClass : \"differentiating_characteristic_parents\"\n\n
"},{"location":"ontology_class/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text LogicalDefinition None NamedEntity None OntologyClass None Relation None RelationshipType None Publication None TextWithTriples None"},{"location":"ontology_class/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication categories the categories to which this entity belongs combined_text description a textual description of the entity differentiating_characteristic_parents differentiating_characteristic_relationship extracted_object The complex objects extracted from the text full_text The full text of the publication genus id A unique identifier for the named entity input_id input_text input_title label the name of the main entity being defined logical_definition the necessary and sufficient conditions for this entity to be an instance of ... named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subclass_of subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text synonyms alternative names of the entity title The title of the publication triples"},{"location":"ontology_class/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"ontology_class/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"ontology_class/#subsets","title":"Subsets","text":"Subset Description"},{"location":"ontology_class/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: oc:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"ontology_class/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"ontology_class/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:AnnotatorResult native oc:AnnotatorResult"},{"location":"ontology_class/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n\n
"},{"location":"ontology_class/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"ontology_class/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"ontology_class/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ontology_class/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"ontology_class/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Any/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native oc:Any"},{"location":"ontology_class/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nclass_uri: linkml:Any\n\n
"},{"location":"ontology_class/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nclass_uri: linkml:Any\n\n
"},{"location":"ontology_class/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"ontology_class/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: oc:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"ontology_class/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ontology_class/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:CompoundExpression native oc:CompoundExpression"},{"location":"ontology_class/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nabstract: true\n\n
"},{"location":"ontology_class/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nabstract: true\n\n
"},{"location":"ontology_class/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"ontology_class/Curie/#comments","title":"Comments","text":""},{"location":"ontology_class/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Curie/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"ontology_class/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Date/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"ontology_class/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"ontology_class/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"ontology_class/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"ontology_class/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Double/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: oc:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"ontology_class/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"ontology_class/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:ExtractionResult native oc:ExtractionResult"},{"location":"ontology_class/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_class/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_class/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"ontology_class/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Float/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"ontology_class/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Integer/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/LogicalDefinition/","title":"Class: LogicalDefinition","text":"

URI: oc:LogicalDefinition

erDiagram\nLogicalDefinition {\n\n}\nOntologyClass {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nRelation {\n    string id  \n    string label  \n}\n\nLogicalDefinition ||--}o OntologyClass : \"genus\"\nLogicalDefinition ||--|o Relation : \"differentiating_characteristic_relationship\"\nLogicalDefinition ||--}o OntologyClass : \"differentiating_characteristic_parents\"\nOntologyClass ||--}o OntologyClass : \"categories\"\nOntologyClass ||--}o OntologyClass : \"subclass_of\"\nOntologyClass ||--|o LogicalDefinition : \"logical_definition\"\n\n
"},{"location":"ontology_class/LogicalDefinition/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance genus 0..* OntologyClass direct differentiating_characteristic_relationship 0..1 Relation direct differentiating_characteristic_parents 0..* OntologyClass direct"},{"location":"ontology_class/LogicalDefinition/#usages","title":"Usages","text":"used by used in type used OntologyClass logical_definition range LogicalDefinition"},{"location":"ontology_class/LogicalDefinition/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/LogicalDefinition/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/LogicalDefinition/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:LogicalDefinition native oc:LogicalDefinition"},{"location":"ontology_class/LogicalDefinition/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/LogicalDefinition/#direct","title":"Direct","text":"
name: LogicalDefinition\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  genus:\n    name: genus\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this is the parent (genus) class,\n          e.g. bone\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n  differentiating_characteristic_relationship:\n    name: differentiating_characteristic_relationship\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this is the parent (differentiating\n          characteristic) relationship type, e.g. part of\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: Relation\n  differentiating_characteristic_parents:\n    name: differentiating_characteristic_parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this the parent (differentiating\n          characteristic) class, e.g. hand\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n\n
"},{"location":"ontology_class/LogicalDefinition/#induced","title":"Induced","text":"
name: LogicalDefinition\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  genus:\n    name: genus\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this is the parent (genus) class,\n          e.g. bone\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: genus\n    owner: LogicalDefinition\n    domain_of:\n    - LogicalDefinition\n    range: OntologyClass\n  differentiating_characteristic_relationship:\n    name: differentiating_characteristic_relationship\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this is the parent (differentiating\n          characteristic) relationship type, e.g. part of\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: differentiating_characteristic_relationship\n    owner: LogicalDefinition\n    domain_of:\n    - LogicalDefinition\n    range: Relation\n  differentiating_characteristic_parents:\n    name: differentiating_characteristic_parents\n    annotations:\n      prompt:\n        tag: prompt\n        value: in a logical definition expression, this the parent (differentiating\n          characteristic) class, e.g. hand\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: differentiating_characteristic_parents\n    owner: LogicalDefinition\n    domain_of:\n    - LogicalDefinition\n    range: OntologyClass\n\n
"},{"location":"ontology_class/NamedEntity/","title":"Class: NamedEntity","text":"

URI: oc:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_class/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"ontology_class/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"ontology_class/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:NamedEntity native oc:NamedEntity"},{"location":"ontology_class/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"ontology_class/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - OntologyClass\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_class/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"ontology_class/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"ontology_class/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"ontology_class/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"ontology_class/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"ontology_class/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"ontology_class/Objectidentifier/#comments","title":"Comments","text":""},{"location":"ontology_class/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/OntologyClass/","title":"Class: OntologyClass","text":"

URI: oc:OntologyClass

erDiagram\nOntologyClass {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nLogicalDefinition {\n\n}\nRelation {\n    string id  \n    string label  \n}\n\nOntologyClass ||--}o OntologyClass : \"categories\"\nOntologyClass ||--}o OntologyClass : \"subclass_of\"\nOntologyClass ||--|o LogicalDefinition : \"logical_definition\"\nLogicalDefinition ||--}o OntologyClass : \"genus\"\nLogicalDefinition ||--|o Relation : \"differentiating_characteristic_relationship\"\nLogicalDefinition ||--}o OntologyClass : \"differentiating_characteristic_parents\"\n\n
"},{"location":"ontology_class/OntologyClass/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/OntologyClass/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 0..1 String the name of the main entity being defined direct description 0..1 String a textual description of the entity direct synonyms 0..* String alternative names of the entity direct categories 0..* OntologyClass the categories to which this entity belongs direct subclass_of 0..* OntologyClass direct logical_definition 0..1 LogicalDefinition the necessary and sufficient conditions for this entity to be an instance of ... direct id 1..1 String A unique identifier for the named entity NamedEntity"},{"location":"ontology_class/OntologyClass/#usages","title":"Usages","text":"used by used in type used OntologyClass categories range OntologyClass OntologyClass subclass_of range OntologyClass LogicalDefinition genus range OntologyClass LogicalDefinition differentiating_characteristic_parents range OntologyClass"},{"location":"ontology_class/OntologyClass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/OntologyClass/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/OntologyClass/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyClass native oc:OntologyClass"},{"location":"ontology_class/OntologyClass/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/OntologyClass/#direct","title":"Direct","text":"
name: OntologyClass\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the main entity being defined\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  description:\n    name: description\n    description: a textual description of the entity\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  synonyms:\n    name: synonyms\n    description: alternative names of the entity\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n  categories:\n    name: categories\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of categories to which the entity belongs.\n          These may be taken from an upper level ontology such as COB, BioLink, or\n          UMLS semantic types.\n    description: the categories to which this entity belongs.\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n  subclass_of:\n    name: subclass_of\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent classes, indicating broader concepts.\n          E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n  logical_definition:\n    name: logical_definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: the necessary and sufficient conditions for this entity to be an instance\n          of this class, written in OWL manchester syntax, e.g. bone and (part_of\n          some 'hand')\n    description: the necessary and sufficient conditions for this entity to be an\n      instance of this class\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: LogicalDefinition\ntree_root: true\n\n
"},{"location":"ontology_class/OntologyClass/#induced","title":"Induced","text":"
name: OntologyClass\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the main entity being defined\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: label\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    - NamedEntity\n    range: string\n  description:\n    name: description\n    description: a textual description of the entity\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: description\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    range: string\n  synonyms:\n    name: synonyms\n    description: alternative names of the entity\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    range: string\n  categories:\n    name: categories\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of categories to which the entity belongs.\n          These may be taken from an upper level ontology such as COB, BioLink, or\n          UMLS semantic types.\n    description: the categories to which this entity belongs.\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: categories\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    range: OntologyClass\n  subclass_of:\n    name: subclass_of\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of parent classes, indicating broader concepts.\n          E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: subclass_of\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    range: OntologyClass\n  logical_definition:\n    name: logical_definition\n    annotations:\n      prompt:\n        tag: prompt\n        value: the necessary and sufficient conditions for this entity to be an instance\n          of this class, written in OWL manchester syntax, e.g. bone and (part_of\n          some 'hand')\n    description: the necessary and sufficient conditions for this entity to be an\n      instance of this class\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: logical_definition\n    owner: OntologyClass\n    domain_of:\n    - OntologyClass\n    range: LogicalDefinition\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: OntologyClass\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\ntree_root: true\n\n
"},{"location":"ontology_class/Publication/","title":"Class: Publication","text":"

URI: oc:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"ontology_class/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"ontology_class/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"ontology_class/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Publication/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Publication native oc:Publication"},{"location":"ontology_class/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/ontology_class\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n\n
"},{"location":"ontology_class/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"ontology_class/Relation/","title":"Class: Relation","text":"

URI: oc:Relation

erDiagram\nRelation {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_class/Relation/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/Relation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ontology_class/Relation/#usages","title":"Usages","text":"used by used in type used LogicalDefinition differentiating_characteristic_relationship range Relation"},{"location":"ontology_class/Relation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Relation/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ontology_class/Relation/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ro"},{"location":"ontology_class/Relation/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Relation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Relation native oc:Relation"},{"location":"ontology_class/Relation/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/Relation/#direct","title":"Direct","text":"
name: Relation\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\n\n
"},{"location":"ontology_class/Relation/#induced","title":"Induced","text":"
name: Relation\nid_prefixes:\n- RO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ro\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Relation\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Relation\n    domain_of:\n    - OntologyClass\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_class/RelationshipType/","title":"Class: RelationshipType","text":"

URI: oc:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_class/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ontology_class/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"ontology_class/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ontology_class/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:RelationshipType native oc:RelationshipType"},{"location":"ontology_class/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\n\n
"},{"location":"ontology_class/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - OntologyClass\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_class/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"ontology_class/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/String/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: oc:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ontology_class/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"ontology_class/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:TextWithTriples native oc:TextWithTriples"},{"location":"ontology_class/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_class/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_class/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"ontology_class/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Time/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: oc:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ontology_class/Triple/#inheritance","title":"Inheritance","text":""},{"location":"ontology_class/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"ontology_class/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"ontology_class/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Triple/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Triple native oc:Triple"},{"location":"ontology_class/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_class/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"ontology_class/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/ontology_class\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ontology_class/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"ontology_class/Uri/#comments","title":"Comments","text":""},{"location":"ontology_class/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Uri/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"ontology_class/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: oc:abstract

"},{"location":"ontology_class/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_class/abstract/#properties","title":"Properties","text":""},{"location":"ontology_class/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/abstract/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_class/categories/","title":"Slot: categories","text":"

the categories to which this entity belongs.

URI: oc:categories

"},{"location":"ontology_class/categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no"},{"location":"ontology_class/categories/#properties","title":"Properties","text":""},{"location":"ontology_class/categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/categories/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types."},{"location":"ontology_class/categories/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/categories/#linkml-source","title":"LinkML Source","text":"
name: categories\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of categories to which the entity belongs. These\n      may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic\n      types.\ndescription: the categories to which this entity belongs.\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: categories\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: OntologyClass\n\n
"},{"location":"ontology_class/combined_text/","title":"Slot: combined_text","text":"

URI: oc:combined_text

"},{"location":"ontology_class/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_class/combined_text/#properties","title":"Properties","text":""},{"location":"ontology_class/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_class/description/","title":"Slot: description","text":"

a textual description of the entity

URI: oc:description

"},{"location":"ontology_class/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no"},{"location":"ontology_class/description/#properties","title":"Properties","text":""},{"location":"ontology_class/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/description/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a textual description of the entity\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: description\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: string\n\n
"},{"location":"ontology_class/differentiating_characteristic_parents/","title":"Slot: differentiating_characteristic_parents","text":"

URI: oc:differentiating_characteristic_parents

"},{"location":"ontology_class/differentiating_characteristic_parents/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LogicalDefinition no"},{"location":"ontology_class/differentiating_characteristic_parents/#properties","title":"Properties","text":""},{"location":"ontology_class/differentiating_characteristic_parents/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/differentiating_characteristic_parents/#annotations","title":"Annotations","text":"property value prompt in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand"},{"location":"ontology_class/differentiating_characteristic_parents/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/differentiating_characteristic_parents/#linkml-source","title":"LinkML Source","text":"
name: differentiating_characteristic_parents\nannotations:\n  prompt:\n    tag: prompt\n    value: in a logical definition expression, this the parent (differentiating characteristic)\n      class, e.g. hand\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: differentiating_characteristic_parents\nowner: LogicalDefinition\ndomain_of:\n- LogicalDefinition\nrange: OntologyClass\n\n
"},{"location":"ontology_class/differentiating_characteristic_relationship/","title":"Slot: differentiating_characteristic_relationship","text":"

URI: oc:differentiating_characteristic_relationship

"},{"location":"ontology_class/differentiating_characteristic_relationship/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LogicalDefinition no"},{"location":"ontology_class/differentiating_characteristic_relationship/#properties","title":"Properties","text":""},{"location":"ontology_class/differentiating_characteristic_relationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/differentiating_characteristic_relationship/#annotations","title":"Annotations","text":"property value prompt in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of"},{"location":"ontology_class/differentiating_characteristic_relationship/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/differentiating_characteristic_relationship/#linkml-source","title":"LinkML Source","text":"
name: differentiating_characteristic_relationship\nannotations:\n  prompt:\n    tag: prompt\n    value: in a logical definition expression, this is the parent (differentiating\n      characteristic) relationship type, e.g. part of\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: differentiating_characteristic_relationship\nowner: LogicalDefinition\ndomain_of:\n- LogicalDefinition\nrange: Relation\n\n
"},{"location":"ontology_class/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: oc:extracted_object

"},{"location":"ontology_class/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/extracted_object/#properties","title":"Properties","text":""},{"location":"ontology_class/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"ontology_class/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: oc:full_text

"},{"location":"ontology_class/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_class/full_text/#properties","title":"Properties","text":""},{"location":"ontology_class/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/full_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_class/genus/","title":"Slot: genus","text":"

URI: oc:genus

"},{"location":"ontology_class/genus/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LogicalDefinition no"},{"location":"ontology_class/genus/#properties","title":"Properties","text":""},{"location":"ontology_class/genus/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/genus/#annotations","title":"Annotations","text":"property value prompt in a logical definition expression, this is the parent (genus) class, e.g. bone"},{"location":"ontology_class/genus/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/genus/#linkml-source","title":"LinkML Source","text":"
name: genus\nannotations:\n  prompt:\n    tag: prompt\n    value: in a logical definition expression, this is the parent (genus) class, e.g.\n      bone\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: genus\nowner: LogicalDefinition\ndomain_of:\n- LogicalDefinition\nrange: OntologyClass\n\n
"},{"location":"ontology_class/id/","title":"Slot: id","text":"

URI: oc:id

"},{"location":"ontology_class/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no Relation no NamedEntity no RelationshipType no Publication no"},{"location":"ontology_class/id/#properties","title":"Properties","text":""},{"location":"ontology_class/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"ontology_class/input_id/","title":"Slot: input_id","text":"

URI: oc:input_id

"},{"location":"ontology_class/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/input_id/#properties","title":"Properties","text":""},{"location":"ontology_class/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/input_id/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_class/input_text/","title":"Slot: input_text","text":"

URI: oc:input_text

"},{"location":"ontology_class/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/input_text/#properties","title":"Properties","text":""},{"location":"ontology_class/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/input_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_class/input_title/","title":"Slot: input_title","text":"

URI: oc:input_title

"},{"location":"ontology_class/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/input_title/#properties","title":"Properties","text":""},{"location":"ontology_class/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/input_title/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_class/label/","title":"Slot: label","text":"

URI: oc:label

"},{"location":"ontology_class/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no Relation no NamedEntity no RelationshipType no"},{"location":"ontology_class/label/#properties","title":"Properties","text":""},{"location":"ontology_class/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- OntologyClass\n- NamedEntity\nrange: string\n\n
"},{"location":"ontology_class/logical_definition/","title":"Slot: logical_definition","text":"

the necessary and sufficient conditions for this entity to be an instance of this class

URI: oc:logical_definition

"},{"location":"ontology_class/logical_definition/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no"},{"location":"ontology_class/logical_definition/#properties","title":"Properties","text":""},{"location":"ontology_class/logical_definition/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/logical_definition/#annotations","title":"Annotations","text":"property value prompt the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')"},{"location":"ontology_class/logical_definition/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/logical_definition/#linkml-source","title":"LinkML Source","text":"
name: logical_definition\nannotations:\n  prompt:\n    tag: prompt\n    value: the necessary and sufficient conditions for this entity to be an instance\n      of this class, written in OWL manchester syntax, e.g. bone and (part_of some\n      'hand')\ndescription: the necessary and sufficient conditions for this entity to be an instance\n  of this class\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: logical_definition\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: LogicalDefinition\n\n
"},{"location":"ontology_class/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: oc:named_entities

"},{"location":"ontology_class/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/named_entities/#properties","title":"Properties","text":""},{"location":"ontology_class/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ontology_class/object/","title":"Slot: object","text":"

URI: oc:object

"},{"location":"ontology_class/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/object/#properties","title":"Properties","text":""},{"location":"ontology_class/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/object/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_class/object_id/","title":"Slot: object_id","text":"

URI: oc:object_id

"},{"location":"ontology_class/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_class/object_id/#properties","title":"Properties","text":""},{"location":"ontology_class/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/object_id/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_class/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: oc:object_qualifier

"},{"location":"ontology_class/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/object_qualifier/#properties","title":"Properties","text":""},{"location":"ontology_class/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_class/object_text/","title":"Slot: object_text","text":"

URI: oc:object_text

"},{"location":"ontology_class/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_class/object_text/#properties","title":"Properties","text":""},{"location":"ontology_class/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/object_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_class/ontology-class/","title":"ontology-class","text":"

A template for Ontology Classes

URI: https://w3id.org/ontogpt/ontology_class

"},{"location":"ontology_class/predicate/","title":"Slot: predicate","text":"

URI: oc:predicate

"},{"location":"ontology_class/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/predicate/#properties","title":"Properties","text":""},{"location":"ontology_class/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/predicate/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"ontology_class/prompt/","title":"Slot: prompt","text":"

URI: oc:prompt

"},{"location":"ontology_class/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/prompt/#properties","title":"Properties","text":""},{"location":"ontology_class/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/prompt/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_class/publication/","title":"Slot: publication","text":"

URI: oc:publication

"},{"location":"ontology_class/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ontology_class/publication/#properties","title":"Properties","text":""},{"location":"ontology_class/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"ontology_class/publication/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"ontology_class/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: oc:qualifier

"},{"location":"ontology_class/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/qualifier/#properties","title":"Properties","text":""},{"location":"ontology_class/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"ontology_class/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: oc:raw_completion_output

"},{"location":"ontology_class/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_class/raw_completion_output/#properties","title":"Properties","text":""},{"location":"ontology_class/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_class/subclass_of/","title":"Slot: subclass_of","text":"

URI: oc:subclass_of

"},{"location":"ontology_class/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no"},{"location":"ontology_class/subclass_of/#properties","title":"Properties","text":""},{"location":"ontology_class/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/subclass_of/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\""},{"location":"ontology_class/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of parent classes, indicating broader concepts.\n      E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: subclass_of\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: OntologyClass\n\n
"},{"location":"ontology_class/subject/","title":"Slot: subject","text":"

URI: oc:subject

"},{"location":"ontology_class/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/subject/#properties","title":"Properties","text":""},{"location":"ontology_class/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/subject/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_class/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: oc:subject_qualifier

"},{"location":"ontology_class/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_class/subject_qualifier/#properties","title":"Properties","text":""},{"location":"ontology_class/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_class/subject_text/","title":"Slot: subject_text","text":"

URI: oc:subject_text

"},{"location":"ontology_class/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_class/subject_text/#properties","title":"Properties","text":""},{"location":"ontology_class/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_class/synonyms/","title":"Slot: synonyms","text":"

alternative names of the entity

URI: oc:synonyms

"},{"location":"ontology_class/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no"},{"location":"ontology_class/synonyms/#properties","title":"Properties","text":""},{"location":"ontology_class/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\ndescription: alternative names of the entity\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: string\n\n
"},{"location":"ontology_class/title/","title":"Slot: title","text":"

The title of the publication

URI: oc:title

"},{"location":"ontology_class/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_class/title/#properties","title":"Properties","text":""},{"location":"ontology_class/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/title/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_class/triples/","title":"Slot: triples","text":"

URI: oc:triples

"},{"location":"ontology_class/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ontology_class/triples/#properties","title":"Properties","text":""},{"location":"ontology_class/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_class/triples/#schema-source","title":"Schema Source","text":""},{"location":"ontology_class/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/ontology_class\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ontology_issue/","title":"Ontology Issue Data Model","text":"

A data model for representing the contents of a GitHub issue on an ontology tracker

URI: https://w3id.org/ontogpt/ontology_issue

Name: ontology-issue

"},{"location":"ontology_issue/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nOntologyIssue {\n    string title  \n    string summary  \n    string status  \n}\nOntologyChange {\n    string description  \n    ChangeType category  \n}\nOntologyClass {\n    string id  \n    string label  \n}\nOntologyProblem {\n    string description  \n    string severity  \n    ProblemType category  \n}\n\nOntologyIssue ||--}o OntologyClass : \"domains\"\nOntologyIssue ||--}o OntologyProblem : \"problem_list\"\nOntologyIssue ||--}o OntologyChange : \"proposed_changes\"\nOntologyChange ||--}o OntologyClass : \"about\"\nOntologyProblem ||--}o OntologyClass : \"about\"\n\n
"},{"location":"ontology_issue/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None OntologyChange None OntologyProblem None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None OntologyClass None RelationshipType None OntologyIssue None Publication None TextWithTriples None"},{"location":"ontology_issue/#slots","title":"Slots","text":"Slot Description about What terms in the ontology is this problem about? abstract The abstract of the publication category What category does this problem fall into? combined_text description A succinct description of the problem domains What part of the ontology does this pertain to extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate problem_list A list of problems stated at a high level prompt proposed_changes What part of the ontology does this pertain to publication qualifier A qualifier for the statements, e raw_completion_output severity How severe is this problem? status subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text summary a high level summary title the title of the issue triples"},{"location":"ontology_issue/#enumerations","title":"Enumerations","text":"Enumeration Description ChangeType NullDataOptions ProblemType"},{"location":"ontology_issue/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"ontology_issue/#subsets","title":"Subsets","text":"Subset Description"},{"location":"ontology_issue/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: oc:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"ontology_issue/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"ontology_issue/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:AnnotatorResult native oc:AnnotatorResult"},{"location":"ontology_issue/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n\n
"},{"location":"ontology_issue/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"ontology_issue/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"ontology_issue/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ontology_issue/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"ontology_issue/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Any/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native oc:Any"},{"location":"ontology_issue/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nclass_uri: linkml:Any\n\n
"},{"location":"ontology_issue/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nclass_uri: linkml:Any\n\n
"},{"location":"ontology_issue/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"ontology_issue/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/ChangeType/","title":"Enum: ChangeType","text":"

URI: ChangeType

"},{"location":"ontology_issue/ChangeType/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNKNOWN None CHANGE_DEFINITION None CHANGE_LABEL None CHANGE_XREF None MOVE_TERM None"},{"location":"ontology_issue/ChangeType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/ChangeType/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/ChangeType/#linkml-source","title":"LinkML Source","text":"
name: ChangeType\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\npermissible_values:\n  UNKNOWN:\n    text: UNKNOWN\n  CHANGE_DEFINITION:\n    text: CHANGE_DEFINITION\n  CHANGE_LABEL:\n    text: CHANGE_LABEL\n  CHANGE_XREF:\n    text: CHANGE_XREF\n  MOVE_TERM:\n    text: MOVE_TERM\n\n
"},{"location":"ontology_issue/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: oc:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"ontology_issue/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"ontology_issue/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:CompoundExpression native oc:CompoundExpression"},{"location":"ontology_issue/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nabstract: true\n\n
"},{"location":"ontology_issue/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nabstract: true\n\n
"},{"location":"ontology_issue/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"ontology_issue/Curie/#comments","title":"Comments","text":""},{"location":"ontology_issue/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Curie/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"ontology_issue/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Date/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"ontology_issue/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"ontology_issue/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"ontology_issue/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"ontology_issue/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Double/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: oc:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"ontology_issue/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"ontology_issue/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:ExtractionResult native oc:ExtractionResult"},{"location":"ontology_issue/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_issue/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_issue/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"ontology_issue/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Float/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"ontology_issue/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Integer/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/NamedEntity/","title":"Class: NamedEntity","text":"

URI: oc:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_issue/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"ontology_issue/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"ontology_issue/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:NamedEntity native oc:NamedEntity"},{"location":"ontology_issue/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"ontology_issue/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_issue/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"ontology_issue/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"ontology_issue/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"ontology_issue/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"ontology_issue/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"ontology_issue/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"ontology_issue/Objectidentifier/#comments","title":"Comments","text":""},{"location":"ontology_issue/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/OntologyChange/","title":"Class: OntologyChange","text":"

URI: oc:OntologyChange

erDiagram\nOntologyChange {\n    string description  \n    ChangeType category  \n}\nOntologyClass {\n    string id  \n    string label  \n}\n\nOntologyChange ||--}o OntologyClass : \"about\"\n\n
"},{"location":"ontology_issue/OntologyChange/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/OntologyChange/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance description 0..1 String A succinct description of the proposed change direct category 0..1 ChangeType What kind of change? direct about 0..* OntologyClass What terms in the ontology will this change affect? direct"},{"location":"ontology_issue/OntologyChange/#usages","title":"Usages","text":"used by used in type used OntologyIssue proposed_changes range OntologyChange"},{"location":"ontology_issue/OntologyChange/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/OntologyChange/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/OntologyChange/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyChange native oc:OntologyChange"},{"location":"ontology_issue/OntologyChange/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/OntologyChange/#direct","title":"Direct","text":"
name: OntologyChange\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nattributes:\n  description:\n    name: description\n    description: A succinct description of the proposed change\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n  category:\n    name: category\n    description: What kind of change?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    range: ChangeType\n  about:\n    name: about\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of specific terms in the ontology which will\n          be affected by the change.\n    description: What terms in the ontology will this change affect?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    multivalued: true\n    range: OntologyClass\n\n
"},{"location":"ontology_issue/OntologyChange/#induced","title":"Induced","text":"
name: OntologyChange\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nattributes:\n  description:\n    name: description\n    description: A succinct description of the proposed change\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    alias: description\n    owner: OntologyChange\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: string\n  category:\n    name: category\n    description: What kind of change?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    alias: category\n    owner: OntologyChange\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: ChangeType\n  about:\n    name: about\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of specific terms in the ontology which will\n          be affected by the change.\n    description: What terms in the ontology will this change affect?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    multivalued: true\n    alias: about\n    owner: OntologyChange\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: OntologyClass\n\n
"},{"location":"ontology_issue/OntologyClass/","title":"Class: OntologyClass","text":"

URI: oc:OntologyClass

erDiagram\nOntologyClass {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_issue/OntologyClass/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/OntologyClass/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ontology_issue/OntologyClass/#usages","title":"Usages","text":"used by used in type used OntologyIssue domains range OntologyClass OntologyProblem about range OntologyClass OntologyChange about range OntologyClass"},{"location":"ontology_issue/OntologyClass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/OntologyClass/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"ontology_issue/OntologyClass/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/OntologyClass/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyClass native oc:OntologyClass"},{"location":"ontology_issue/OntologyClass/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/OntologyClass/#direct","title":"Direct","text":"
name: OntologyClass\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: NamedEntity\n\n
"},{"location":"ontology_issue/OntologyClass/#induced","title":"Induced","text":"
name: OntologyClass\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: OntologyClass\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: OntologyClass\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_issue/OntologyIssue/","title":"Class: OntologyIssue","text":"

URI: oc:OntologyIssue

erDiagram\nOntologyIssue {\n    string title  \n    string summary  \n    string status  \n}\nOntologyChange {\n    string description  \n    ChangeType category  \n}\nOntologyClass {\n    string id  \n    string label  \n}\nOntologyProblem {\n    string description  \n    string severity  \n    ProblemType category  \n}\n\nOntologyIssue ||--}o OntologyClass : \"domains\"\nOntologyIssue ||--}o OntologyProblem : \"problem_list\"\nOntologyIssue ||--}o OntologyChange : \"proposed_changes\"\nOntologyChange ||--}o OntologyClass : \"about\"\nOntologyProblem ||--}o OntologyClass : \"about\"\n\n
"},{"location":"ontology_issue/OntologyIssue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance title 0..1 String the title of the issue direct summary 0..1 String a high level summary direct status 0..1 String direct domains 0..* OntologyClass What part of the ontology does this pertain to direct problem_list 0..* OntologyProblem A list of problems stated at a high level direct proposed_changes 0..* OntologyChange What part of the ontology does this pertain to direct"},{"location":"ontology_issue/OntologyIssue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/OntologyIssue/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/OntologyIssue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyIssue native oc:OntologyIssue"},{"location":"ontology_issue/OntologyIssue/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/OntologyIssue/#direct","title":"Direct","text":"
name: OntologyIssue\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  title:\n    name: title\n    description: the title of the issue\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  summary:\n    name: summary\n    annotations:\n      prompt:\n        tag: prompt\n        value: a high level one or two line summary of the issue, e.g. \"the definition\n          of the class 'bone' is too vague\"\n    description: a high level summary\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  status:\n    name: status\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  domains:\n    name: domains\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of grouping terms in the ontology.\n    description: What part of the ontology does this pertain to.\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n  problem_list:\n    name: problem_list\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of problems each written as a simple statement.\n          For example \"T cell is classified in the wrong place\"\n    description: A list of problems stated at a high level\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: OntologyProblem\n  proposed_changes:\n    name: proposed_changes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of grouping terms in the ontology. Example\n          terms will be high level terms in the relevant ontology, e.g. \"skeletal\n          system\" for an anatomy ontology.\n    description: What part of the ontology does this pertain to.\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: OntologyChange\ntree_root: true\n\n
"},{"location":"ontology_issue/OntologyIssue/#induced","title":"Induced","text":"
name: OntologyIssue\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  title:\n    name: title\n    description: the title of the issue\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: title\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    - Publication\n    range: string\n  summary:\n    name: summary\n    annotations:\n      prompt:\n        tag: prompt\n        value: a high level one or two line summary of the issue, e.g. \"the definition\n          of the class 'bone' is too vague\"\n    description: a high level summary\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: summary\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    range: string\n  status:\n    name: status\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: status\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    range: string\n  domains:\n    name: domains\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of grouping terms in the ontology.\n    description: What part of the ontology does this pertain to.\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: domains\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    range: OntologyClass\n  problem_list:\n    name: problem_list\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of problems each written as a simple statement.\n          For example \"T cell is classified in the wrong place\"\n    description: A list of problems stated at a high level\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: problem_list\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    range: OntologyProblem\n  proposed_changes:\n    name: proposed_changes\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of grouping terms in the ontology. Example\n          terms will be high level terms in the relevant ontology, e.g. \"skeletal\n          system\" for an anatomy ontology.\n    description: What part of the ontology does this pertain to.\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: proposed_changes\n    owner: OntologyIssue\n    domain_of:\n    - OntologyIssue\n    range: OntologyChange\ntree_root: true\n\n
"},{"location":"ontology_issue/OntologyProblem/","title":"Class: OntologyProblem","text":"

URI: oc:OntologyProblem

erDiagram\nOntologyProblem {\n    string description  \n    string severity  \n    ProblemType category  \n}\nOntologyClass {\n    string id  \n    string label  \n}\n\nOntologyProblem ||--}o OntologyClass : \"about\"\n\n
"},{"location":"ontology_issue/OntologyProblem/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/OntologyProblem/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance description 0..1 String A succinct description of the problem direct severity 0..1 String How severe is this problem? direct category 0..1 ProblemType What category does this problem fall into? direct about 0..* OntologyClass What terms in the ontology is this problem about? direct"},{"location":"ontology_issue/OntologyProblem/#usages","title":"Usages","text":"used by used in type used OntologyIssue problem_list range OntologyProblem"},{"location":"ontology_issue/OntologyProblem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/OntologyProblem/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/OntologyProblem/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:OntologyProblem native oc:OntologyProblem"},{"location":"ontology_issue/OntologyProblem/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/OntologyProblem/#direct","title":"Direct","text":"
name: OntologyProblem\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nattributes:\n  description:\n    name: description\n    description: A succinct description of the problem\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  severity:\n    name: severity\n    description: How severe is this problem?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  category:\n    name: category\n    description: What category does this problem fall into?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: ProblemType\n  about:\n    name: about\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of terms in the ontology that are problematic.\n    description: What terms in the ontology is this problem about?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: OntologyClass\n\n
"},{"location":"ontology_issue/OntologyProblem/#induced","title":"Induced","text":"
name: OntologyProblem\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nattributes:\n  description:\n    name: description\n    description: A succinct description of the problem\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: description\n    owner: OntologyProblem\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: string\n  severity:\n    name: severity\n    description: How severe is this problem?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: severity\n    owner: OntologyProblem\n    domain_of:\n    - OntologyProblem\n    range: string\n  category:\n    name: category\n    description: What category does this problem fall into?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: category\n    owner: OntologyProblem\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: ProblemType\n  about:\n    name: about\n    annotations:\n      prompt:\n        tag: prompt\n        value: semicolon-separated list of terms in the ontology that are problematic.\n    description: What terms in the ontology is this problem about?\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: about\n    owner: OntologyProblem\n    domain_of:\n    - OntologyProblem\n    - OntologyChange\n    range: OntologyClass\n\n
"},{"location":"ontology_issue/ProblemType/","title":"Enum: ProblemType","text":"

URI: ProblemType

"},{"location":"ontology_issue/ProblemType/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNKNOWN None TYPO None BAD_XREF None MISSING_DEFINITION None MISSING_PARENT None BAD_RELATIONSHIP None OTHER None"},{"location":"ontology_issue/ProblemType/#slots","title":"Slots","text":"Name Description category What category does this problem fall into?"},{"location":"ontology_issue/ProblemType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/ProblemType/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/ProblemType/#linkml-source","title":"LinkML Source","text":"
name: ProblemType\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\npermissible_values:\n  UNKNOWN:\n    text: UNKNOWN\n  TYPO:\n    text: TYPO\n  BAD_XREF:\n    text: BAD_XREF\n  MISSING_DEFINITION:\n    text: MISSING_DEFINITION\n  MISSING_PARENT:\n    text: MISSING_PARENT\n  BAD_RELATIONSHIP:\n    text: BAD_RELATIONSHIP\n  OTHER:\n    text: OTHER\n\n
"},{"location":"ontology_issue/Publication/","title":"Class: Publication","text":"

URI: oc:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"ontology_issue/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"ontology_issue/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"ontology_issue/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Publication/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Publication native oc:Publication"},{"location":"ontology_issue/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n\n
"},{"location":"ontology_issue/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    alias: title\n    owner: Publication\n    domain_of:\n    - OntologyIssue\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"ontology_issue/RelationshipType/","title":"Class: RelationshipType","text":"

URI: oc:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"ontology_issue/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"ontology_issue/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"ontology_issue/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ontology_issue/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:RelationshipType native oc:RelationshipType"},{"location":"ontology_issue/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: NamedEntity\n\n
"},{"location":"ontology_issue/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"ontology_issue/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"ontology_issue/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/String/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: oc:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ontology_issue/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"ontology_issue/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:TextWithTriples native oc:TextWithTriples"},{"location":"ontology_issue/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_issue/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"ontology_issue/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"ontology_issue/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Time/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: oc:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"ontology_issue/Triple/#inheritance","title":"Inheritance","text":""},{"location":"ontology_issue/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"ontology_issue/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"ontology_issue/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Triple/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self oc:Triple native oc:Triple"},{"location":"ontology_issue/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"ontology_issue/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"ontology_issue/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/ontology_issue\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"ontology_issue/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"ontology_issue/Uri/#comments","title":"Comments","text":""},{"location":"ontology_issue/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Uri/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"ontology_issue/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/about/","title":"Slot: about","text":"

URI: oc:about

"},{"location":"ontology_issue/about/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyProblem no OntologyChange no"},{"location":"ontology_issue/about/#properties","title":"Properties","text":""},{"location":"ontology_issue/about/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/about/#linkml-source","title":"LinkML Source","text":"
name: about\nalias: about\ndomain_of:\n- OntologyProblem\n- OntologyChange\nrange: string\n\n
"},{"location":"ontology_issue/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: oc:abstract

"},{"location":"ontology_issue/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_issue/abstract/#properties","title":"Properties","text":""},{"location":"ontology_issue/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/abstract/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_issue/category/","title":"Slot: category","text":"

URI: oc:category

"},{"location":"ontology_issue/category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyProblem no OntologyChange no"},{"location":"ontology_issue/category/#properties","title":"Properties","text":""},{"location":"ontology_issue/category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/category/#linkml-source","title":"LinkML Source","text":"
name: category\nalias: category\ndomain_of:\n- OntologyProblem\n- OntologyChange\nrange: string\n\n
"},{"location":"ontology_issue/combined_text/","title":"Slot: combined_text","text":"

URI: oc:combined_text

"},{"location":"ontology_issue/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_issue/combined_text/#properties","title":"Properties","text":""},{"location":"ontology_issue/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_issue/description/","title":"Slot: description","text":"

URI: oc:description

"},{"location":"ontology_issue/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyProblem no OntologyChange no"},{"location":"ontology_issue/description/#properties","title":"Properties","text":""},{"location":"ontology_issue/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/description/#linkml-source","title":"LinkML Source","text":"
name: description\nalias: description\ndomain_of:\n- OntologyProblem\n- OntologyChange\nrange: string\n\n
"},{"location":"ontology_issue/domains/","title":"Slot: domains","text":"

What part of the ontology does this pertain to.

URI: oc:domains

"},{"location":"ontology_issue/domains/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no"},{"location":"ontology_issue/domains/#properties","title":"Properties","text":""},{"location":"ontology_issue/domains/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/domains/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of grouping terms in the ontology."},{"location":"ontology_issue/domains/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/domains/#linkml-source","title":"LinkML Source","text":"
name: domains\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of grouping terms in the ontology.\ndescription: What part of the ontology does this pertain to.\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nmultivalued: true\nalias: domains\nowner: OntologyIssue\ndomain_of:\n- OntologyIssue\nrange: OntologyClass\n\n
"},{"location":"ontology_issue/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: oc:extracted_object

"},{"location":"ontology_issue/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/extracted_object/#properties","title":"Properties","text":""},{"location":"ontology_issue/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"ontology_issue/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: oc:full_text

"},{"location":"ontology_issue/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"ontology_issue/full_text/#properties","title":"Properties","text":""},{"location":"ontology_issue/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/full_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"ontology_issue/id/","title":"Slot: id","text":"

URI: oc:id

"},{"location":"ontology_issue/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no NamedEntity no RelationshipType no Publication no"},{"location":"ontology_issue/id/#properties","title":"Properties","text":""},{"location":"ontology_issue/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"ontology_issue/input_id/","title":"Slot: input_id","text":"

URI: oc:input_id

"},{"location":"ontology_issue/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/input_id/#properties","title":"Properties","text":""},{"location":"ontology_issue/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/input_id/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_issue/input_text/","title":"Slot: input_text","text":"

URI: oc:input_text

"},{"location":"ontology_issue/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/input_text/#properties","title":"Properties","text":""},{"location":"ontology_issue/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/input_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_issue/input_title/","title":"Slot: input_title","text":"

URI: oc:input_title

"},{"location":"ontology_issue/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/input_title/#properties","title":"Properties","text":""},{"location":"ontology_issue/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/input_title/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_issue/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"ontology_issue/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyClass no NamedEntity no RelationshipType no"},{"location":"ontology_issue/label/#properties","title":"Properties","text":""},{"location":"ontology_issue/label/#aliases","title":"Aliases","text":""},{"location":"ontology_issue/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"ontology_issue/label/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"ontology_issue/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: oc:named_entities

"},{"location":"ontology_issue/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/named_entities/#properties","title":"Properties","text":""},{"location":"ontology_issue/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"ontology_issue/object/","title":"Slot: object","text":"

URI: oc:object

"},{"location":"ontology_issue/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/object/#properties","title":"Properties","text":""},{"location":"ontology_issue/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/object/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_issue/object_id/","title":"Slot: object_id","text":"

URI: oc:object_id

"},{"location":"ontology_issue/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_issue/object_id/#properties","title":"Properties","text":""},{"location":"ontology_issue/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/object_id/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_issue/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: oc:object_qualifier

"},{"location":"ontology_issue/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/object_qualifier/#properties","title":"Properties","text":""},{"location":"ontology_issue/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_issue/object_text/","title":"Slot: object_text","text":"

URI: oc:object_text

"},{"location":"ontology_issue/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_issue/object_text/#properties","title":"Properties","text":""},{"location":"ontology_issue/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/object_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_issue/ontology-issue/","title":"ontology-issue","text":"

A data model for representing the contents of a GitHub issue on an ontology tracker

URI: https://w3id.org/ontogpt/ontology_issue

"},{"location":"ontology_issue/predicate/","title":"Slot: predicate","text":"

URI: oc:predicate

"},{"location":"ontology_issue/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/predicate/#properties","title":"Properties","text":""},{"location":"ontology_issue/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/predicate/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"ontology_issue/problem_list/","title":"Slot: problem_list","text":"

A list of problems stated at a high level

URI: oc:problem_list

"},{"location":"ontology_issue/problem_list/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no"},{"location":"ontology_issue/problem_list/#properties","title":"Properties","text":""},{"location":"ontology_issue/problem_list/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/problem_list/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\""},{"location":"ontology_issue/problem_list/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/problem_list/#linkml-source","title":"LinkML Source","text":"
name: problem_list\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of problems each written as a simple statement.\n      For example \"T cell is classified in the wrong place\"\ndescription: A list of problems stated at a high level\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nmultivalued: true\nalias: problem_list\nowner: OntologyIssue\ndomain_of:\n- OntologyIssue\nrange: OntologyProblem\n\n
"},{"location":"ontology_issue/prompt/","title":"Slot: prompt","text":"

URI: oc:prompt

"},{"location":"ontology_issue/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/prompt/#properties","title":"Properties","text":""},{"location":"ontology_issue/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/prompt/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_issue/proposed_changes/","title":"Slot: proposed_changes","text":"

What part of the ontology does this pertain to.

URI: oc:proposed_changes

"},{"location":"ontology_issue/proposed_changes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no"},{"location":"ontology_issue/proposed_changes/#properties","title":"Properties","text":""},{"location":"ontology_issue/proposed_changes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/proposed_changes/#annotations","title":"Annotations","text":"property value prompt semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology."},{"location":"ontology_issue/proposed_changes/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/proposed_changes/#linkml-source","title":"LinkML Source","text":"
name: proposed_changes\nannotations:\n  prompt:\n    tag: prompt\n    value: semicolon-separated list of grouping terms in the ontology. Example terms\n      will be high level terms in the relevant ontology, e.g. \"skeletal system\" for\n      an anatomy ontology.\ndescription: What part of the ontology does this pertain to.\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nmultivalued: true\nalias: proposed_changes\nowner: OntologyIssue\ndomain_of:\n- OntologyIssue\nrange: OntologyChange\n\n
"},{"location":"ontology_issue/publication/","title":"Slot: publication","text":"

URI: oc:publication

"},{"location":"ontology_issue/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ontology_issue/publication/#properties","title":"Properties","text":""},{"location":"ontology_issue/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"ontology_issue/publication/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"ontology_issue/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: oc:qualifier

"},{"location":"ontology_issue/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/qualifier/#properties","title":"Properties","text":""},{"location":"ontology_issue/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"ontology_issue/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: oc:raw_completion_output

"},{"location":"ontology_issue/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"ontology_issue/raw_completion_output/#properties","title":"Properties","text":""},{"location":"ontology_issue/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"ontology_issue/severity/","title":"Slot: severity","text":"

How severe is this problem?

URI: oc:severity

"},{"location":"ontology_issue/severity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyProblem no"},{"location":"ontology_issue/severity/#properties","title":"Properties","text":""},{"location":"ontology_issue/severity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/severity/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/severity/#linkml-source","title":"LinkML Source","text":"
name: severity\ndescription: How severe is this problem?\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: severity\nowner: OntologyProblem\ndomain_of:\n- OntologyProblem\nrange: string\n\n
"},{"location":"ontology_issue/status/","title":"Slot: status","text":"

URI: oc:status

"},{"location":"ontology_issue/status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no"},{"location":"ontology_issue/status/#properties","title":"Properties","text":""},{"location":"ontology_issue/status/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/status/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/status/#linkml-source","title":"LinkML Source","text":"
name: status\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: status\nowner: OntologyIssue\ndomain_of:\n- OntologyIssue\nrange: string\n\n
"},{"location":"ontology_issue/subject/","title":"Slot: subject","text":"

URI: oc:subject

"},{"location":"ontology_issue/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/subject/#properties","title":"Properties","text":""},{"location":"ontology_issue/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/subject/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_issue/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: oc:subject_qualifier

"},{"location":"ontology_issue/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"ontology_issue/subject_qualifier/#properties","title":"Properties","text":""},{"location":"ontology_issue/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"ontology_issue/subject_text/","title":"Slot: subject_text","text":"

URI: oc:subject_text

"},{"location":"ontology_issue/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"ontology_issue/subject_text/#properties","title":"Properties","text":""},{"location":"ontology_issue/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"ontology_issue/summary/","title":"Slot: summary","text":"

a high level summary

URI: oc:summary

"},{"location":"ontology_issue/summary/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no"},{"location":"ontology_issue/summary/#properties","title":"Properties","text":""},{"location":"ontology_issue/summary/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/summary/#annotations","title":"Annotations","text":"property value prompt a high level one or two line summary of the issue, e.g. \"the definition of the class 'bone' is too vague\""},{"location":"ontology_issue/summary/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/summary/#linkml-source","title":"LinkML Source","text":"
name: summary\nannotations:\n  prompt:\n    tag: prompt\n    value: a high level one or two line summary of the issue, e.g. \"the definition\n      of the class 'bone' is too vague\"\ndescription: a high level summary\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nalias: summary\nowner: OntologyIssue\ndomain_of:\n- OntologyIssue\nrange: string\n\n
"},{"location":"ontology_issue/title/","title":"Slot: title","text":"

URI: oc:title

"},{"location":"ontology_issue/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyIssue no Publication no"},{"location":"ontology_issue/title/#properties","title":"Properties","text":""},{"location":"ontology_issue/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/title/#linkml-source","title":"LinkML Source","text":"
name: title\nalias: title\ndomain_of:\n- OntologyIssue\n- Publication\nrange: string\n\n
"},{"location":"ontology_issue/triples/","title":"Slot: triples","text":"

URI: oc:triples

"},{"location":"ontology_issue/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"ontology_issue/triples/#properties","title":"Properties","text":""},{"location":"ontology_issue/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ontology_issue/triples/#schema-source","title":"Schema Source","text":""},{"location":"ontology_issue/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/ontology_issue\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"phenotype/","title":"EQ Template","text":"

A template for Computational Phenotypes

URI: http://w3id.org/ontogpt/eq

Name: eq-template

"},{"location":"phenotype/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nTrait {\n\n}\nChemicalEntity {\n    string id  \n    string label  \n}\nAnatomicalEntity {\n    string id  \n    string label  \n}\nQuality {\n    string id  \n    string label  \n}\n\nTrait ||--|o Quality : \"quality\"\nTrait ||--|o AnatomicalEntity : \"anatomical_entity\"\nTrait ||--|o ChemicalEntity : \"chemical_entity\"\n\n
"},{"location":"phenotype/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None AnatomicalEntity None ChemicalEntity None Quality None RelationshipType None Publication None TextWithTriples None Trait None"},{"location":"phenotype/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication anatomical_entity The anatomical location that the chemical entity is measured in chemical_entity The chemical entity that is being measured combined_text extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e quality The property being measured, or changes in this property, for example, amount... raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples"},{"location":"phenotype/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"phenotype/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"phenotype/#subsets","title":"Subsets","text":"Subset Description"},{"location":"phenotype/AnatomicalEntity/","title":"Class: AnatomicalEntity","text":"

URI: phenotype:AnatomicalEntity

erDiagram\nAnatomicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"phenotype/AnatomicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/AnatomicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"phenotype/AnatomicalEntity/#usages","title":"Usages","text":"used by used in type used Trait anatomical_entity range AnatomicalEntity"},{"location":"phenotype/AnatomicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/AnatomicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"phenotype/AnatomicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uberon"},{"location":"phenotype/AnatomicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/AnatomicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:AnatomicalEntity native phenotype:AnatomicalEntity"},{"location":"phenotype/AnatomicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/AnatomicalEntity/#direct","title":"Direct","text":"
name: AnatomicalEntity\nid_prefixes:\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\n\n
"},{"location":"phenotype/AnatomicalEntity/#induced","title":"Induced","text":"
name: AnatomicalEntity\nid_prefixes:\n- UBERON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uberon\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: AnatomicalEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: AnatomicalEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"phenotype/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: phenotype:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"phenotype/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"phenotype/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:AnnotatorResult native phenotype:AnnotatorResult"},{"location":"phenotype/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n\n
"},{"location":"phenotype/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"phenotype/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"phenotype/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"phenotype/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"phenotype/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Any/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native phenotype:Any"},{"location":"phenotype/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/eq\nclass_uri: linkml:Any\n\n
"},{"location":"phenotype/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/eq\nclass_uri: linkml:Any\n\n
"},{"location":"phenotype/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"phenotype/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/ChemicalEntity/","title":"Class: ChemicalEntity","text":"

URI: phenotype:ChemicalEntity

erDiagram\nChemicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"phenotype/ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"phenotype/ChemicalEntity/#usages","title":"Usages","text":"used by used in type used Trait chemical_entity range ChemicalEntity"},{"location":"phenotype/ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"phenotype/ChemicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"phenotype/ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:ChemicalEntity native phenotype:ChemicalEntity"},{"location":"phenotype/ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\n\n
"},{"location":"phenotype/ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\n- PR\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"phenotype/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: phenotype:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"phenotype/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"phenotype/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:CompoundExpression native phenotype:CompoundExpression"},{"location":"phenotype/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/eq\nabstract: true\n\n
"},{"location":"phenotype/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/eq\nabstract: true\n\n
"},{"location":"phenotype/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"phenotype/Curie/#comments","title":"Comments","text":""},{"location":"phenotype/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Curie/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"phenotype/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Date/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"phenotype/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"phenotype/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"phenotype/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"phenotype/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Double/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: phenotype:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"phenotype/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"phenotype/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:ExtractionResult native phenotype:ExtractionResult"},{"location":"phenotype/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"phenotype/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"phenotype/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"phenotype/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Float/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"phenotype/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Integer/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/NamedEntity/","title":"Class: NamedEntity","text":"

URI: phenotype:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"phenotype/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"phenotype/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"phenotype/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:NamedEntity native phenotype:NamedEntity"},{"location":"phenotype/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/eq\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"phenotype/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/eq\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"phenotype/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"phenotype/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"phenotype/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"phenotype/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"phenotype/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"phenotype/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"phenotype/Objectidentifier/#comments","title":"Comments","text":""},{"location":"phenotype/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Publication/","title":"Class: Publication","text":"

URI: phenotype:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"phenotype/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"phenotype/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"phenotype/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Publication/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:Publication native phenotype:Publication"},{"location":"phenotype/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/eq\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n\n
"},{"location":"phenotype/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/eq\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"phenotype/Quality/","title":"Class: Quality","text":"

URI: phenotype:Quality

erDiagram\nQuality {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"phenotype/Quality/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/Quality/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"phenotype/Quality/#usages","title":"Usages","text":"used by used in type used Trait quality range Quality"},{"location":"phenotype/Quality/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Quality/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"phenotype/Quality/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:pato"},{"location":"phenotype/Quality/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Quality/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:Quality native phenotype:Quality"},{"location":"phenotype/Quality/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/Quality/#direct","title":"Direct","text":"
name: Quality\nid_prefixes:\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:pato\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\n\n
"},{"location":"phenotype/Quality/#induced","title":"Induced","text":"
name: Quality\nid_prefixes:\n- PATO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:pato\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Quality\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Quality\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"phenotype/RelationshipType/","title":"Class: RelationshipType","text":"

URI: phenotype:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"phenotype/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"phenotype/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"phenotype/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"phenotype/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:RelationshipType native phenotype:RelationshipType"},{"location":"phenotype/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\n\n
"},{"location":"phenotype/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/eq\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"phenotype/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"phenotype/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/String/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: phenotype:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"phenotype/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"phenotype/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:TextWithTriples native phenotype:TextWithTriples"},{"location":"phenotype/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"phenotype/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"phenotype/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"phenotype/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Time/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Trait/","title":"Class: Trait","text":"

URI: phenotype:Trait

erDiagram\nTrait {\n\n}\nChemicalEntity {\n    string id  \n    string label  \n}\nAnatomicalEntity {\n    string id  \n    string label  \n}\nQuality {\n    string id  \n    string label  \n}\n\nTrait ||--|o Quality : \"quality\"\nTrait ||--|o AnatomicalEntity : \"anatomical_entity\"\nTrait ||--|o ChemicalEntity : \"chemical_entity\"\n\n
"},{"location":"phenotype/Trait/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance quality 0..1 Quality The property being measured, or changes in this property, for example, amount... direct anatomical_entity 0..1 AnatomicalEntity The anatomical location that the chemical entity is measured in direct chemical_entity 0..1 ChemicalEntity The chemical entity that is being measured direct"},{"location":"phenotype/Trait/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Trait/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Trait/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:Trait native phenotype:Trait"},{"location":"phenotype/Trait/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/Trait/#direct","title":"Direct","text":"
name: Trait\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  quality:\n    name: quality\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: amount, level, increased amount, decreased concentration\n    description: The property being measured, or changes in this property, for example,\n      amount, level, increased amount, decreased concentration\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: Quality\n  anatomical_entity:\n    name: anatomical_entity\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: liver, heart, brain, finger\n    description: The anatomical location that the chemical entity is measured in\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: AnatomicalEntity\n  chemical_entity:\n    name: chemical_entity\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: lysine, metabolite\n    description: The chemical entity that is being measured\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: ChemicalEntity\ntree_root: true\n\n
"},{"location":"phenotype/Trait/#induced","title":"Induced","text":"
name: Trait\nfrom_schema: http://w3id.org/ontogpt/eq\nattributes:\n  quality:\n    name: quality\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: amount, level, increased amount, decreased concentration\n    description: The property being measured, or changes in this property, for example,\n      amount, level, increased amount, decreased concentration\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: quality\n    owner: Trait\n    domain_of:\n    - Trait\n    range: Quality\n  anatomical_entity:\n    name: anatomical_entity\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: liver, heart, brain, finger\n    description: The anatomical location that the chemical entity is measured in\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: anatomical_entity\n    owner: Trait\n    domain_of:\n    - Trait\n    range: AnatomicalEntity\n  chemical_entity:\n    name: chemical_entity\n    annotations:\n      prompt.example:\n        tag: prompt.example\n        value: lysine, metabolite\n    description: The chemical entity that is being measured\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: chemical_entity\n    owner: Trait\n    domain_of:\n    - Trait\n    range: ChemicalEntity\ntree_root: true\n\n
"},{"location":"phenotype/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: phenotype:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"phenotype/Triple/#inheritance","title":"Inheritance","text":""},{"location":"phenotype/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"phenotype/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"phenotype/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Triple/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self phenotype:Triple native phenotype:Triple"},{"location":"phenotype/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"phenotype/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"phenotype/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/eq\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/eq\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"phenotype/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"phenotype/Uri/#comments","title":"Comments","text":""},{"location":"phenotype/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Uri/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"phenotype/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: phenotype:abstract

"},{"location":"phenotype/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"phenotype/abstract/#properties","title":"Properties","text":""},{"location":"phenotype/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/abstract/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"phenotype/anatomical_entity/","title":"Slot: anatomical_entity","text":"

The anatomical location that the chemical entity is measured in

URI: phenotype:anatomical_entity

"},{"location":"phenotype/anatomical_entity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Trait no"},{"location":"phenotype/anatomical_entity/#properties","title":"Properties","text":""},{"location":"phenotype/anatomical_entity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/anatomical_entity/#annotations","title":"Annotations","text":"property value prompt.example liver, heart, brain, finger"},{"location":"phenotype/anatomical_entity/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/anatomical_entity/#linkml-source","title":"LinkML Source","text":"
name: anatomical_entity\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: liver, heart, brain, finger\ndescription: The anatomical location that the chemical entity is measured in\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: anatomical_entity\nowner: Trait\ndomain_of:\n- Trait\nrange: AnatomicalEntity\n\n
"},{"location":"phenotype/chemical_entity/","title":"Slot: chemical_entity","text":"

The chemical entity that is being measured

URI: phenotype:chemical_entity

"},{"location":"phenotype/chemical_entity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Trait no"},{"location":"phenotype/chemical_entity/#properties","title":"Properties","text":""},{"location":"phenotype/chemical_entity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/chemical_entity/#annotations","title":"Annotations","text":"property value prompt.example lysine, metabolite"},{"location":"phenotype/chemical_entity/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/chemical_entity/#linkml-source","title":"LinkML Source","text":"
name: chemical_entity\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: lysine, metabolite\ndescription: The chemical entity that is being measured\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: chemical_entity\nowner: Trait\ndomain_of:\n- Trait\nrange: ChemicalEntity\n\n
"},{"location":"phenotype/combined_text/","title":"Slot: combined_text","text":"

URI: phenotype:combined_text

"},{"location":"phenotype/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"phenotype/combined_text/#properties","title":"Properties","text":""},{"location":"phenotype/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"phenotype/eq-template/","title":"eq-template","text":"

A template for Computational Phenotypes

URI: http://w3id.org/ontogpt/eq

"},{"location":"phenotype/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: phenotype:extracted_object

"},{"location":"phenotype/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/extracted_object/#properties","title":"Properties","text":""},{"location":"phenotype/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"phenotype/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: phenotype:full_text

"},{"location":"phenotype/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"phenotype/full_text/#properties","title":"Properties","text":""},{"location":"phenotype/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/full_text/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"phenotype/id/","title":"Slot: id","text":"

URI: phenotype:id

"},{"location":"phenotype/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Quality no ChemicalEntity no AnatomicalEntity no NamedEntity no RelationshipType no Publication no"},{"location":"phenotype/id/#properties","title":"Properties","text":""},{"location":"phenotype/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"phenotype/input_id/","title":"Slot: input_id","text":"

URI: phenotype:input_id

"},{"location":"phenotype/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/input_id/#properties","title":"Properties","text":""},{"location":"phenotype/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/input_id/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"phenotype/input_text/","title":"Slot: input_text","text":"

URI: phenotype:input_text

"},{"location":"phenotype/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/input_text/#properties","title":"Properties","text":""},{"location":"phenotype/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/input_text/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"phenotype/input_title/","title":"Slot: input_title","text":"

URI: phenotype:input_title

"},{"location":"phenotype/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/input_title/#properties","title":"Properties","text":""},{"location":"phenotype/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/input_title/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"phenotype/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"phenotype/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Quality no ChemicalEntity no AnatomicalEntity no NamedEntity no RelationshipType no"},{"location":"phenotype/label/#properties","title":"Properties","text":""},{"location":"phenotype/label/#aliases","title":"Aliases","text":""},{"location":"phenotype/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"phenotype/label/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/eq\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"phenotype/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: phenotype:named_entities

"},{"location":"phenotype/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/named_entities/#properties","title":"Properties","text":""},{"location":"phenotype/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"phenotype/object/","title":"Slot: object","text":"

URI: phenotype:object

"},{"location":"phenotype/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/object/#properties","title":"Properties","text":""},{"location":"phenotype/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/object/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"phenotype/object_id/","title":"Slot: object_id","text":"

URI: phenotype:object_id

"},{"location":"phenotype/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"phenotype/object_id/#properties","title":"Properties","text":""},{"location":"phenotype/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/object_id/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"phenotype/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: phenotype:object_qualifier

"},{"location":"phenotype/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/object_qualifier/#properties","title":"Properties","text":""},{"location":"phenotype/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"phenotype/object_text/","title":"Slot: object_text","text":"

URI: phenotype:object_text

"},{"location":"phenotype/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"phenotype/object_text/#properties","title":"Properties","text":""},{"location":"phenotype/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/object_text/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"phenotype/predicate/","title":"Slot: predicate","text":"

URI: phenotype:predicate

"},{"location":"phenotype/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/predicate/#properties","title":"Properties","text":""},{"location":"phenotype/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/predicate/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"phenotype/prompt/","title":"Slot: prompt","text":"

URI: phenotype:prompt

"},{"location":"phenotype/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/prompt/#properties","title":"Properties","text":""},{"location":"phenotype/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/prompt/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"phenotype/publication/","title":"Slot: publication","text":"

URI: phenotype:publication

"},{"location":"phenotype/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"phenotype/publication/#properties","title":"Properties","text":""},{"location":"phenotype/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"phenotype/publication/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"phenotype/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: phenotype:qualifier

"},{"location":"phenotype/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/qualifier/#properties","title":"Properties","text":""},{"location":"phenotype/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"phenotype/quality/","title":"Slot: quality","text":"

The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration

URI: phenotype:quality

"},{"location":"phenotype/quality/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Trait no"},{"location":"phenotype/quality/#properties","title":"Properties","text":""},{"location":"phenotype/quality/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/quality/#annotations","title":"Annotations","text":"property value prompt.example amount, level, increased amount, decreased concentration"},{"location":"phenotype/quality/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/quality/#linkml-source","title":"LinkML Source","text":"
name: quality\nannotations:\n  prompt.example:\n    tag: prompt.example\n    value: amount, level, increased amount, decreased concentration\ndescription: The property being measured, or changes in this property, for example,\n  amount, level, increased amount, decreased concentration\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: quality\nowner: Trait\ndomain_of:\n- Trait\nrange: Quality\n\n
"},{"location":"phenotype/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: phenotype:raw_completion_output

"},{"location":"phenotype/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"phenotype/raw_completion_output/#properties","title":"Properties","text":""},{"location":"phenotype/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"phenotype/subject/","title":"Slot: subject","text":"

URI: phenotype:subject

"},{"location":"phenotype/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/subject/#properties","title":"Properties","text":""},{"location":"phenotype/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/subject/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"phenotype/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: phenotype:subject_qualifier

"},{"location":"phenotype/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"phenotype/subject_qualifier/#properties","title":"Properties","text":""},{"location":"phenotype/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"phenotype/subject_text/","title":"Slot: subject_text","text":"

URI: phenotype:subject_text

"},{"location":"phenotype/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"phenotype/subject_text/#properties","title":"Properties","text":""},{"location":"phenotype/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"phenotype/title/","title":"Slot: title","text":"

The title of the publication

URI: phenotype:title

"},{"location":"phenotype/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"phenotype/title/#properties","title":"Properties","text":""},{"location":"phenotype/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/title/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"phenotype/triples/","title":"Slot: triples","text":"

URI: phenotype:triples

"},{"location":"phenotype/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"phenotype/triples/#properties","title":"Properties","text":""},{"location":"phenotype/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phenotype/triples/#schema-source","title":"Schema Source","text":""},{"location":"phenotype/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/eq\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"reaction/","title":"reaction Template","text":"

A template for reactions

URI: https://w3id.org/ontogpt/reaction

Name: reaction-template

"},{"location":"reaction/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nReaction {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nGeneToReaction {\n\n}\nReactionDocument {\n\n}\nGeneReactionPairing {\n\n}\nReactionGrouping {\n    string id  \n    string label  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nEvidence {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\nOrganism {\n    string id  \n    string label  \n}\nAny {\n\n}\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nCompoundExpression {\n\n}\nTriple {\n    string qualifier  \n}\nTextWithTriples {\n\n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\nReaction ||--|o ReactionGrouping : \"subclass_of\"\nReaction ||--}o ChemicalEntity : \"left_side\"\nReaction ||--}o ChemicalEntity : \"right_side\"\nGeneToReaction ||--|o Gene : \"gene\"\nGeneToReaction ||--}o Reaction : \"reactions\"\nGeneToReaction ||--|o Organism : \"organism\"\nReactionDocument ||--}o Gene : \"genes\"\nReactionDocument ||--}o Reaction : \"reactions\"\nReactionDocument ||--}o GeneReactionPairing : \"gene_reaction_pairings\"\nReactionDocument ||--|o Organism : \"organism\"\nReactionDocument ||--}o Evidence : \"has_evidence\"\nGeneReactionPairing ||--|o Gene : \"gene\"\nGeneReactionPairing ||--|o Reaction : \"reaction\"\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\n\n
"},{"location":"reaction/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None GeneReactionPairing None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text GeneToReaction None NamedEntity None ChemicalEntity None Evidence None Gene None Organism None Reaction None ReactionGrouping None RelationshipType None Publication None ReactionDocument None TextWithTriples None"},{"location":"reaction/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication combined_text description a textual description of the reaction extracted_object The complex objects extracted from the text full_text The full text of the publication gene name of the gene that catalyzes the reaction gene_reaction_pairings semicolon separated list of gene to reaction pairings genes semicolon separated list of genes that catalyzes the mentioned reactions has_evidence evidence for the reaction id A unique identifier for the named entity input_id input_text input_title label the name of the reaction left_side semicolon separated list of chemical entities on the left side named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text organism predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output reaction equation describing the reaction (e reactions semicolon separated list of reaction equations (e right_side semicolon separated list of chemical entities on the right side subclass_of the category to which this biological process belongs subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text synonyms alternative names of the reaction title The title of the publication triples"},{"location":"reaction/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"reaction/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"reaction/#subsets","title":"Subsets","text":"Subset Description"},{"location":"reaction/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: reaction:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"reaction/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"reaction/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"reaction/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:AnnotatorResult native reaction:AnnotatorResult"},{"location":"reaction/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n\n
"},{"location":"reaction/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"reaction/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"reaction/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"reaction/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"reaction/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Any/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native reaction:Any"},{"location":"reaction/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/reaction\nclass_uri: linkml:Any\n\n
"},{"location":"reaction/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/reaction\nclass_uri: linkml:Any\n\n
"},{"location":"reaction/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"reaction/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"reaction/ChemicalEntity/","title":"Class: ChemicalEntity","text":"

URI: reaction:ChemicalEntity

erDiagram\nChemicalEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"reaction/ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/ChemicalEntity/#usages","title":"Usages","text":"used by used in type used Reaction left_side range ChemicalEntity Reaction right_side range ChemicalEntity"},{"location":"reaction/ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/ChemicalEntity/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi"},{"location":"reaction/ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"reaction/ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:ChemicalEntity native reaction:ChemicalEntity"},{"location":"reaction/ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- CHEBI\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ChemicalEntity\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: reaction:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"reaction/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"reaction/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"reaction/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"reaction/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:CompoundExpression native reaction:CompoundExpression"},{"location":"reaction/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/reaction\nabstract: true\n\n
"},{"location":"reaction/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/reaction\nabstract: true\n\n
"},{"location":"reaction/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"reaction/Curie/#comments","title":"Comments","text":""},{"location":"reaction/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Curie/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"reaction/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Date/#schema-source","title":"Schema Source","text":""},{"location":"reaction/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"reaction/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"reaction/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"reaction/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"reaction/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Double/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Evidence/","title":"Class: Evidence","text":"

URI: reaction:Evidence

erDiagram\nEvidence {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/Evidence/#inheritance","title":"Inheritance","text":""},{"location":"reaction/Evidence/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/Evidence/#usages","title":"Usages","text":"used by used in type used ReactionDocument has_evidence range Evidence"},{"location":"reaction/Evidence/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Evidence/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/Evidence/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms"},{"location":"reaction/Evidence/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Evidence/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Evidence native reaction:Evidence"},{"location":"reaction/Evidence/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Evidence/#direct","title":"Direct","text":"
name: Evidence\nid_prefixes:\n- OBI\n- ECO\n- MS\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/Evidence/#induced","title":"Induced","text":"
name: Evidence\nid_prefixes:\n- OBI\n- ECO\n- MS\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Evidence\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Evidence\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: reaction:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"reaction/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"reaction/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"reaction/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:ExtractionResult native reaction:ExtractionResult"},{"location":"reaction/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"reaction/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"reaction/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"reaction/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Float/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Gene/","title":"Class: Gene","text":"

URI: reaction:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/Gene/#inheritance","title":"Inheritance","text":""},{"location":"reaction/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/Gene/#usages","title":"Usages","text":"used by used in type used GeneToReaction gene range Gene ReactionDocument genes range Gene GeneReactionPairing gene range Gene"},{"location":"reaction/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, bioportal:hgnc-nr, bioportal:pr"},{"location":"reaction/Gene/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Gene native reaction:Gene"},{"location":"reaction/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr, bioportal:pr\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, bioportal:hgnc-nr, bioportal:pr\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/GeneReactionPairing/","title":"Class: GeneReactionPairing","text":"

URI: reaction:GeneReactionPairing

erDiagram\nGeneReactionPairing {\n\n}\nReaction {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nReactionGrouping {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneReactionPairing ||--|o Gene : \"gene\"\nGeneReactionPairing ||--|o Reaction : \"reaction\"\nReaction ||--|o ReactionGrouping : \"subclass_of\"\nReaction ||--}o ChemicalEntity : \"left_side\"\nReaction ||--}o ChemicalEntity : \"right_side\"\n\n
"},{"location":"reaction/GeneReactionPairing/#inheritance","title":"Inheritance","text":""},{"location":"reaction/GeneReactionPairing/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene name of the gene that catalyzes the reaction direct reaction 0..1 Reaction equation describing the reaction (e direct"},{"location":"reaction/GeneReactionPairing/#usages","title":"Usages","text":"used by used in type used ReactionDocument gene_reaction_pairings range GeneReactionPairing"},{"location":"reaction/GeneReactionPairing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/GeneReactionPairing/#schema-source","title":"Schema Source","text":""},{"location":"reaction/GeneReactionPairing/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:GeneReactionPairing native reaction:GeneReactionPairing"},{"location":"reaction/GeneReactionPairing/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/GeneReactionPairing/#direct","title":"Direct","text":"
name: GeneReactionPairing\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    description: name of the gene that catalyzes the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    range: Gene\n  reaction:\n    name: reaction\n    description: equation describing the reaction (e.g. A+B = C+D) catalyzed by the\n      gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: Reaction\n\n
"},{"location":"reaction/GeneReactionPairing/#induced","title":"Induced","text":"
name: GeneReactionPairing\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: CompoundExpression\nattributes:\n  gene:\n    name: gene\n    description: name of the gene that catalyzes the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    alias: gene\n    owner: GeneReactionPairing\n    domain_of:\n    - GeneToReaction\n    - GeneReactionPairing\n    range: Gene\n  reaction:\n    name: reaction\n    description: equation describing the reaction (e.g. A+B = C+D) catalyzed by the\n      gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: reaction\n    owner: GeneReactionPairing\n    domain_of:\n    - GeneReactionPairing\n    range: Reaction\n\n
"},{"location":"reaction/GeneToReaction/","title":"Class: GeneToReaction","text":"

URI: reaction:GeneToReaction

erDiagram\nGeneToReaction {\n\n}\nOrganism {\n    string id  \n    string label  \n}\nReaction {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nReactionGrouping {\n    string id  \n    string label  \n}\nGene {\n    string id  \n    string label  \n}\n\nGeneToReaction ||--|o Gene : \"gene\"\nGeneToReaction ||--}o Reaction : \"reactions\"\nGeneToReaction ||--|o Organism : \"organism\"\nReaction ||--|o ReactionGrouping : \"subclass_of\"\nReaction ||--}o ChemicalEntity : \"left_side\"\nReaction ||--}o ChemicalEntity : \"right_side\"\n\n
"},{"location":"reaction/GeneToReaction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gene 0..1 Gene name of the gene that catalyzes the reaction direct reactions 0..* Reaction semicolon separated list of reaction equations (e direct organism 0..1 Organism direct"},{"location":"reaction/GeneToReaction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/GeneToReaction/#schema-source","title":"Schema Source","text":""},{"location":"reaction/GeneToReaction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:GeneToReaction native reaction:GeneToReaction"},{"location":"reaction/GeneToReaction/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/GeneToReaction/#direct","title":"Direct","text":"
name: GeneToReaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  gene:\n    name: gene\n    description: name of the gene that catalyzes the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: Gene\n  reactions:\n    name: reactions\n    description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed\n      by the gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: Reaction\n    inlined: true\n  organism:\n    name: organism\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: Organism\n\n
"},{"location":"reaction/GeneToReaction/#induced","title":"Induced","text":"
name: GeneToReaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  gene:\n    name: gene\n    description: name of the gene that catalyzes the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: gene\n    owner: GeneToReaction\n    domain_of:\n    - GeneToReaction\n    - GeneReactionPairing\n    range: Gene\n  reactions:\n    name: reactions\n    description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed\n      by the gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: reactions\n    owner: GeneToReaction\n    domain_of:\n    - GeneToReaction\n    - ReactionDocument\n    range: Reaction\n    inlined: true\n  organism:\n    name: organism\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: organism\n    owner: GeneToReaction\n    domain_of:\n    - GeneToReaction\n    - ReactionDocument\n    range: Organism\n\n
"},{"location":"reaction/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"reaction/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Integer/#schema-source","title":"Schema Source","text":""},{"location":"reaction/NamedEntity/","title":"Class: NamedEntity","text":"

URI: reaction:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"reaction/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"reaction/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"reaction/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"reaction/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:NamedEntity native reaction:NamedEntity"},{"location":"reaction/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/reaction\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"reaction/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/reaction\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"reaction/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"reaction/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"reaction/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"reaction/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"reaction/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"reaction/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"reaction/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"reaction/Objectidentifier/#comments","title":"Comments","text":""},{"location":"reaction/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Organism/","title":"Class: Organism","text":"

URI: reaction:Organism

erDiagram\nOrganism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/Organism/#inheritance","title":"Inheritance","text":""},{"location":"reaction/Organism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/Organism/#usages","title":"Usages","text":"used by used in type used GeneToReaction organism range Organism ReactionDocument organism range Organism"},{"location":"reaction/Organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Organism/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/Organism/#annotations","title":"Annotations","text":"property value annotators gilda:, sqlite:obo:ncbitaxon"},{"location":"reaction/Organism/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Organism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Organism native reaction:Organism"},{"location":"reaction/Organism/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Organism/#direct","title":"Direct","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/Organism/#induced","title":"Induced","text":"
name: Organism\nid_prefixes:\n- NCBITaxon\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, sqlite:obo:ncbitaxon\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Organism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Organism\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/Publication/","title":"Class: Publication","text":"

URI: reaction:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"reaction/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"reaction/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"reaction/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Publication/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Publication native reaction:Publication"},{"location":"reaction/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/reaction\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n\n
"},{"location":"reaction/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/reaction\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"reaction/Reaction/","title":"Class: Reaction","text":"

URI: reaction:Reaction

erDiagram\nReaction {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nChemicalEntity {\n    string id  \n    string label  \n}\nReactionGrouping {\n    string id  \n    string label  \n}\n\nReaction ||--|o ReactionGrouping : \"subclass_of\"\nReaction ||--}o ChemicalEntity : \"left_side\"\nReaction ||--}o ChemicalEntity : \"right_side\"\n\n
"},{"location":"reaction/Reaction/#inheritance","title":"Inheritance","text":""},{"location":"reaction/Reaction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 0..1 String the name of the reaction direct description 0..1 String a textual description of the reaction direct synonyms 0..* String alternative names of the reaction direct subclass_of 0..1 ReactionGrouping the category to which this biological process belongs direct left_side 0..* ChemicalEntity semicolon separated list of chemical entities on the left side direct right_side 0..* ChemicalEntity semicolon separated list of chemical entities on the right side direct id 1..1 String A unique identifier for the named entity NamedEntity"},{"location":"reaction/Reaction/#usages","title":"Usages","text":"used by used in type used GeneToReaction reactions range Reaction ReactionDocument reactions range Reaction GeneReactionPairing reaction range Reaction"},{"location":"reaction/Reaction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Reaction/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Reaction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Reaction native reaction:Reaction"},{"location":"reaction/Reaction/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Reaction/#direct","title":"Direct","text":"
name: Reaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  description:\n    name: description\n    description: a textual description of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n  synonyms:\n    name: synonyms\n    description: alternative names of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n  subclass_of:\n    name: subclass_of\n    description: the category to which this biological process belongs\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: ReactionGrouping\n  left_side:\n    name: left_side\n    description: semicolon separated list of chemical entities on the left side\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n  right_side:\n    name: right_side\n    description: semicolon separated list of chemical entities on the right side\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: ChemicalEntity\n\n
"},{"location":"reaction/Reaction/#induced","title":"Induced","text":"
name: Reaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  label:\n    name: label\n    description: the name of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: label\n    owner: Reaction\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n  description:\n    name: description\n    description: a textual description of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: description\n    owner: Reaction\n    domain_of:\n    - Reaction\n    range: string\n  synonyms:\n    name: synonyms\n    description: alternative names of the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: synonyms\n    owner: Reaction\n    domain_of:\n    - Reaction\n    range: string\n  subclass_of:\n    name: subclass_of\n    description: the category to which this biological process belongs\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: subclass_of\n    owner: Reaction\n    domain_of:\n    - Reaction\n    range: ReactionGrouping\n  left_side:\n    name: left_side\n    description: semicolon separated list of chemical entities on the left side\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: left_side\n    owner: Reaction\n    domain_of:\n    - Reaction\n    range: ChemicalEntity\n  right_side:\n    name: right_side\n    description: semicolon separated list of chemical entities on the right side\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: right_side\n    owner: Reaction\n    domain_of:\n    - Reaction\n    range: ChemicalEntity\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Reaction\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n\n
"},{"location":"reaction/ReactionDocument/","title":"Class: ReactionDocument","text":"

URI: reaction:ReactionDocument

erDiagram\nReactionDocument {\n\n}\nEvidence {\n    string id  \n    string label  \n}\nOrganism {\n    string id  \n    string label  \n}\nGeneReactionPairing {\n\n}\nReaction {\n    string label  \n    string description  \n    stringList synonyms  \n    string id  \n}\nGene {\n    string id  \n    string label  \n}\n\nReactionDocument ||--}o Gene : \"genes\"\nReactionDocument ||--}o Reaction : \"reactions\"\nReactionDocument ||--}o GeneReactionPairing : \"gene_reaction_pairings\"\nReactionDocument ||--|o Organism : \"organism\"\nReactionDocument ||--}o Evidence : \"has_evidence\"\nGeneReactionPairing ||--|o Gene : \"gene\"\nGeneReactionPairing ||--|o Reaction : \"reaction\"\nReaction ||--|o ReactionGrouping : \"subclass_of\"\nReaction ||--}o ChemicalEntity : \"left_side\"\nReaction ||--}o ChemicalEntity : \"right_side\"\n\n
"},{"location":"reaction/ReactionDocument/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance genes 0..* Gene semicolon separated list of genes that catalyzes the mentioned reactions direct reactions 0..* Reaction semicolon separated list of reaction equations (e direct gene_reaction_pairings 0..* GeneReactionPairing semicolon separated list of gene to reaction pairings direct organism 0..1 Organism direct has_evidence 0..* Evidence evidence for the reaction direct"},{"location":"reaction/ReactionDocument/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/ReactionDocument/#schema-source","title":"Schema Source","text":""},{"location":"reaction/ReactionDocument/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:ReactionDocument native reaction:ReactionDocument"},{"location":"reaction/ReactionDocument/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/ReactionDocument/#direct","title":"Direct","text":"
name: ReactionDocument\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  genes:\n    name: genes\n    description: semicolon separated list of genes that catalyzes the mentioned reactions\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: Gene\n  reactions:\n    name: reactions\n    description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed\n      by the gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    multivalued: true\n    range: Reaction\n    inlined: true\n  gene_reaction_pairings:\n    name: gene_reaction_pairings\n    description: semicolon separated list of gene to reaction pairings\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: GeneReactionPairing\n    inlined: true\n  organism:\n    name: organism\n    from_schema: https://w3id.org/ontogpt/reaction\n    range: Organism\n  has_evidence:\n    name: has_evidence\n    description: evidence for the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: Evidence\n\n
"},{"location":"reaction/ReactionDocument/#induced","title":"Induced","text":"
name: ReactionDocument\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  genes:\n    name: genes\n    description: semicolon separated list of genes that catalyzes the mentioned reactions\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: genes\n    owner: ReactionDocument\n    domain_of:\n    - ReactionDocument\n    range: Gene\n  reactions:\n    name: reactions\n    description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed\n      by the gene\n    from_schema: https://w3id.org/ontogpt/reaction\n    multivalued: true\n    alias: reactions\n    owner: ReactionDocument\n    domain_of:\n    - GeneToReaction\n    - ReactionDocument\n    range: Reaction\n    inlined: true\n  gene_reaction_pairings:\n    name: gene_reaction_pairings\n    description: semicolon separated list of gene to reaction pairings\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: gene_reaction_pairings\n    owner: ReactionDocument\n    domain_of:\n    - ReactionDocument\n    range: GeneReactionPairing\n    inlined: true\n  organism:\n    name: organism\n    from_schema: https://w3id.org/ontogpt/reaction\n    alias: organism\n    owner: ReactionDocument\n    domain_of:\n    - GeneToReaction\n    - ReactionDocument\n    range: Organism\n  has_evidence:\n    name: has_evidence\n    description: evidence for the reaction\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: has_evidence\n    owner: ReactionDocument\n    domain_of:\n    - ReactionDocument\n    range: Evidence\n\n
"},{"location":"reaction/ReactionGrouping/","title":"Class: ReactionGrouping","text":"

URI: reaction:ReactionGrouping

erDiagram\nReactionGrouping {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/ReactionGrouping/#inheritance","title":"Inheritance","text":""},{"location":"reaction/ReactionGrouping/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/ReactionGrouping/#usages","title":"Usages","text":"used by used in type used Reaction subclass_of range ReactionGrouping"},{"location":"reaction/ReactionGrouping/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/ReactionGrouping/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/ReactionGrouping/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go"},{"location":"reaction/ReactionGrouping/#schema-source","title":"Schema Source","text":""},{"location":"reaction/ReactionGrouping/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:ReactionGrouping native reaction:ReactionGrouping"},{"location":"reaction/ReactionGrouping/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/ReactionGrouping/#direct","title":"Direct","text":"
name: ReactionGrouping\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/ReactionGrouping/#induced","title":"Induced","text":"
name: ReactionGrouping\nid_prefixes:\n- GO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ReactionGrouping\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: ReactionGrouping\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/RelationshipType/","title":"Class: RelationshipType","text":"

URI: reaction:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"reaction/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"reaction/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"reaction/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"reaction/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"reaction/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"reaction/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:RelationshipType native reaction:RelationshipType"},{"location":"reaction/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\n\n
"},{"location":"reaction/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/reaction\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - Reaction\n    - NamedEntity\n    range: string\n\n
"},{"location":"reaction/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"reaction/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/String/#schema-source","title":"Schema Source","text":""},{"location":"reaction/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: reaction:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"reaction/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"reaction/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"reaction/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:TextWithTriples native reaction:TextWithTriples"},{"location":"reaction/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"reaction/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/reaction\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"reaction/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"reaction/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Time/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: reaction:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"reaction/Triple/#inheritance","title":"Inheritance","text":""},{"location":"reaction/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"reaction/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"reaction/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Triple/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self reaction:Triple native reaction:Triple"},{"location":"reaction/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"reaction/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"reaction/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/reaction\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/reaction\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"reaction/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"reaction/Uri/#comments","title":"Comments","text":""},{"location":"reaction/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Uri/#schema-source","title":"Schema Source","text":""},{"location":"reaction/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"reaction/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"reaction/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: reaction:abstract

"},{"location":"reaction/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"reaction/abstract/#properties","title":"Properties","text":""},{"location":"reaction/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/abstract/#schema-source","title":"Schema Source","text":""},{"location":"reaction/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"reaction/combined_text/","title":"Slot: combined_text","text":"

URI: reaction:combined_text

"},{"location":"reaction/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"reaction/combined_text/#properties","title":"Properties","text":""},{"location":"reaction/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"reaction/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"reaction/description/","title":"Slot: description","text":"

a textual description of the reaction

URI: reaction:description

"},{"location":"reaction/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no"},{"location":"reaction/description/#properties","title":"Properties","text":""},{"location":"reaction/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/description/#schema-source","title":"Schema Source","text":""},{"location":"reaction/description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a textual description of the reaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: description\nowner: Reaction\ndomain_of:\n- Reaction\nrange: string\n\n
"},{"location":"reaction/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: reaction:extracted_object

"},{"location":"reaction/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/extracted_object/#properties","title":"Properties","text":""},{"location":"reaction/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"reaction/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"reaction/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: reaction:full_text

"},{"location":"reaction/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"reaction/full_text/#properties","title":"Properties","text":""},{"location":"reaction/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/full_text/#schema-source","title":"Schema Source","text":""},{"location":"reaction/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"reaction/gene/","title":"Slot: gene","text":"

URI: reaction:gene

"},{"location":"reaction/gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneToReaction no GeneReactionPairing no"},{"location":"reaction/gene/#properties","title":"Properties","text":""},{"location":"reaction/gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/gene/#linkml-source","title":"LinkML Source","text":"
name: gene\nalias: gene\ndomain_of:\n- GeneToReaction\n- GeneReactionPairing\nrange: string\n\n
"},{"location":"reaction/gene_reaction_pairings/","title":"Slot: gene_reaction_pairings","text":"

semicolon separated list of gene to reaction pairings

URI: reaction:gene_reaction_pairings

"},{"location":"reaction/gene_reaction_pairings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionDocument no"},{"location":"reaction/gene_reaction_pairings/#properties","title":"Properties","text":""},{"location":"reaction/gene_reaction_pairings/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/gene_reaction_pairings/#schema-source","title":"Schema Source","text":""},{"location":"reaction/gene_reaction_pairings/#linkml-source","title":"LinkML Source","text":"
name: gene_reaction_pairings\ndescription: semicolon separated list of gene to reaction pairings\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: gene_reaction_pairings\nowner: ReactionDocument\ndomain_of:\n- ReactionDocument\nrange: GeneReactionPairing\ninlined: true\n\n
"},{"location":"reaction/genes/","title":"Slot: genes","text":"

semicolon separated list of genes that catalyzes the mentioned reactions

URI: reaction:genes

"},{"location":"reaction/genes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionDocument no"},{"location":"reaction/genes/#properties","title":"Properties","text":""},{"location":"reaction/genes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/genes/#schema-source","title":"Schema Source","text":""},{"location":"reaction/genes/#linkml-source","title":"LinkML Source","text":"
name: genes\ndescription: semicolon separated list of genes that catalyzes the mentioned reactions\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: genes\nowner: ReactionDocument\ndomain_of:\n- ReactionDocument\nrange: Gene\n\n
"},{"location":"reaction/has_evidence/","title":"Slot: has_evidence","text":"

evidence for the reaction

URI: reaction:has_evidence

"},{"location":"reaction/has_evidence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionDocument no"},{"location":"reaction/has_evidence/#properties","title":"Properties","text":""},{"location":"reaction/has_evidence/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/has_evidence/#schema-source","title":"Schema Source","text":""},{"location":"reaction/has_evidence/#linkml-source","title":"LinkML Source","text":"
name: has_evidence\ndescription: evidence for the reaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: has_evidence\nowner: ReactionDocument\ndomain_of:\n- ReactionDocument\nrange: Evidence\n\n
"},{"location":"reaction/id/","title":"Slot: id","text":"

URI: reaction:id

"},{"location":"reaction/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no ReactionGrouping no ChemicalEntity no Evidence no Gene no Organism no NamedEntity no RelationshipType no Publication no"},{"location":"reaction/id/#properties","title":"Properties","text":""},{"location":"reaction/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"reaction/input_id/","title":"Slot: input_id","text":"

URI: reaction:input_id

"},{"location":"reaction/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/input_id/#properties","title":"Properties","text":""},{"location":"reaction/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/input_id/#schema-source","title":"Schema Source","text":""},{"location":"reaction/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"reaction/input_text/","title":"Slot: input_text","text":"

URI: reaction:input_text

"},{"location":"reaction/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/input_text/#properties","title":"Properties","text":""},{"location":"reaction/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/input_text/#schema-source","title":"Schema Source","text":""},{"location":"reaction/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"reaction/input_title/","title":"Slot: input_title","text":"

URI: reaction:input_title

"},{"location":"reaction/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/input_title/#properties","title":"Properties","text":""},{"location":"reaction/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/input_title/#schema-source","title":"Schema Source","text":""},{"location":"reaction/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"reaction/label/","title":"Slot: label","text":"

URI: reaction:label

"},{"location":"reaction/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no ReactionGrouping no ChemicalEntity no Evidence no Gene no Organism no NamedEntity no RelationshipType no"},{"location":"reaction/label/#properties","title":"Properties","text":""},{"location":"reaction/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- Reaction\n- NamedEntity\nrange: string\n\n
"},{"location":"reaction/left_side/","title":"Slot: left_side","text":"

semicolon separated list of chemical entities on the left side

URI: reaction:left_side

"},{"location":"reaction/left_side/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no"},{"location":"reaction/left_side/#properties","title":"Properties","text":""},{"location":"reaction/left_side/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/left_side/#schema-source","title":"Schema Source","text":""},{"location":"reaction/left_side/#linkml-source","title":"LinkML Source","text":"
name: left_side\ndescription: semicolon separated list of chemical entities on the left side\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: left_side\nowner: Reaction\ndomain_of:\n- Reaction\nrange: ChemicalEntity\n\n
"},{"location":"reaction/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: reaction:named_entities

"},{"location":"reaction/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/named_entities/#properties","title":"Properties","text":""},{"location":"reaction/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"reaction/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"reaction/object/","title":"Slot: object","text":"

URI: reaction:object

"},{"location":"reaction/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/object/#properties","title":"Properties","text":""},{"location":"reaction/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/object/#schema-source","title":"Schema Source","text":""},{"location":"reaction/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"reaction/object_id/","title":"Slot: object_id","text":"

URI: reaction:object_id

"},{"location":"reaction/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"reaction/object_id/#properties","title":"Properties","text":""},{"location":"reaction/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/object_id/#schema-source","title":"Schema Source","text":""},{"location":"reaction/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"reaction/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: reaction:object_qualifier

"},{"location":"reaction/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/object_qualifier/#properties","title":"Properties","text":""},{"location":"reaction/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"reaction/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"reaction/object_text/","title":"Slot: object_text","text":"

URI: reaction:object_text

"},{"location":"reaction/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"reaction/object_text/#properties","title":"Properties","text":""},{"location":"reaction/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/object_text/#schema-source","title":"Schema Source","text":""},{"location":"reaction/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"reaction/organism/","title":"Slot: organism","text":"

URI: reaction:organism

"},{"location":"reaction/organism/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneToReaction no ReactionDocument no"},{"location":"reaction/organism/#properties","title":"Properties","text":""},{"location":"reaction/organism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/organism/#linkml-source","title":"LinkML Source","text":"
name: organism\nalias: organism\ndomain_of:\n- GeneToReaction\n- ReactionDocument\nrange: string\n\n
"},{"location":"reaction/predicate/","title":"Slot: predicate","text":"

URI: reaction:predicate

"},{"location":"reaction/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/predicate/#properties","title":"Properties","text":""},{"location":"reaction/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/predicate/#schema-source","title":"Schema Source","text":""},{"location":"reaction/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"reaction/prompt/","title":"Slot: prompt","text":"

URI: reaction:prompt

"},{"location":"reaction/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/prompt/#properties","title":"Properties","text":""},{"location":"reaction/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/prompt/#schema-source","title":"Schema Source","text":""},{"location":"reaction/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"reaction/publication/","title":"Slot: publication","text":"

URI: reaction:publication

"},{"location":"reaction/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"reaction/publication/#properties","title":"Properties","text":""},{"location":"reaction/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"reaction/publication/#schema-source","title":"Schema Source","text":""},{"location":"reaction/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"reaction/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: reaction:qualifier

"},{"location":"reaction/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/qualifier/#properties","title":"Properties","text":""},{"location":"reaction/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"reaction/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"reaction/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: reaction:raw_completion_output

"},{"location":"reaction/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"reaction/raw_completion_output/#properties","title":"Properties","text":""},{"location":"reaction/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"reaction/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"reaction/reaction-template/","title":"reaction-template","text":"

A template for reactions

URI: https://w3id.org/ontogpt/reaction

"},{"location":"reaction/reaction/","title":"Slot: reaction","text":"

equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene

URI: reaction:reaction

"},{"location":"reaction/reaction/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneReactionPairing no"},{"location":"reaction/reaction/#properties","title":"Properties","text":""},{"location":"reaction/reaction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/reaction/#schema-source","title":"Schema Source","text":""},{"location":"reaction/reaction/#linkml-source","title":"LinkML Source","text":"
name: reaction\ndescription: equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: reaction\nowner: GeneReactionPairing\ndomain_of:\n- GeneReactionPairing\nrange: Reaction\n\n
"},{"location":"reaction/reactions/","title":"Slot: reactions","text":"

URI: reaction:reactions

"},{"location":"reaction/reactions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeneToReaction no ReactionDocument no"},{"location":"reaction/reactions/#properties","title":"Properties","text":""},{"location":"reaction/reactions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/reactions/#linkml-source","title":"LinkML Source","text":"
name: reactions\nalias: reactions\ndomain_of:\n- GeneToReaction\n- ReactionDocument\nrange: string\n\n
"},{"location":"reaction/right_side/","title":"Slot: right_side","text":"

semicolon separated list of chemical entities on the right side

URI: reaction:right_side

"},{"location":"reaction/right_side/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no"},{"location":"reaction/right_side/#properties","title":"Properties","text":""},{"location":"reaction/right_side/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/right_side/#schema-source","title":"Schema Source","text":""},{"location":"reaction/right_side/#linkml-source","title":"LinkML Source","text":"
name: right_side\ndescription: semicolon separated list of chemical entities on the right side\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: right_side\nowner: Reaction\ndomain_of:\n- Reaction\nrange: ChemicalEntity\n\n
"},{"location":"reaction/subclass_of/","title":"Slot: subclass_of","text":"

the category to which this biological process belongs

URI: reaction:subclass_of

"},{"location":"reaction/subclass_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no"},{"location":"reaction/subclass_of/#properties","title":"Properties","text":""},{"location":"reaction/subclass_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/subclass_of/#schema-source","title":"Schema Source","text":""},{"location":"reaction/subclass_of/#linkml-source","title":"LinkML Source","text":"
name: subclass_of\ndescription: the category to which this biological process belongs\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: subclass_of\nowner: Reaction\ndomain_of:\n- Reaction\nrange: ReactionGrouping\n\n
"},{"location":"reaction/subject/","title":"Slot: subject","text":"

URI: reaction:subject

"},{"location":"reaction/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/subject/#properties","title":"Properties","text":""},{"location":"reaction/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/subject/#schema-source","title":"Schema Source","text":""},{"location":"reaction/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"reaction/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: reaction:subject_qualifier

"},{"location":"reaction/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"reaction/subject_qualifier/#properties","title":"Properties","text":""},{"location":"reaction/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"reaction/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"reaction/subject_text/","title":"Slot: subject_text","text":"

URI: reaction:subject_text

"},{"location":"reaction/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"reaction/subject_text/#properties","title":"Properties","text":""},{"location":"reaction/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"reaction/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"reaction/synonyms/","title":"Slot: synonyms","text":"

alternative names of the reaction

URI: reaction:synonyms

"},{"location":"reaction/synonyms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction no"},{"location":"reaction/synonyms/#properties","title":"Properties","text":""},{"location":"reaction/synonyms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/synonyms/#schema-source","title":"Schema Source","text":""},{"location":"reaction/synonyms/#linkml-source","title":"LinkML Source","text":"
name: synonyms\ndescription: alternative names of the reaction\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: synonyms\nowner: Reaction\ndomain_of:\n- Reaction\nrange: string\n\n
"},{"location":"reaction/title/","title":"Slot: title","text":"

The title of the publication

URI: reaction:title

"},{"location":"reaction/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"reaction/title/#properties","title":"Properties","text":""},{"location":"reaction/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/title/#schema-source","title":"Schema Source","text":""},{"location":"reaction/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"reaction/triples/","title":"Slot: triples","text":"

URI: reaction:triples

"},{"location":"reaction/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"reaction/triples/#properties","title":"Properties","text":""},{"location":"reaction/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reaction/triples/#schema-source","title":"Schema Source","text":""},{"location":"reaction/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/reaction\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"recipe/","title":"Food Recipe Template","text":"

A template for food recipes

URI: https://w3id.org/ontogpt/recipe

Name: recipe-template

"},{"location":"recipe/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nRecipe {\n    uriorcurie url  \n    string label  \n    string description  \n}\nStep {\n\n}\nUtensilType {\n    string id  \n    string label  \n}\nFoodItem {\n    string state  \n}\nFoodType {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\nIngredient {\n\n}\nQuantity {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\nRecipeCategory {\n    string id  \n    string label  \n}\n\nRecipe ||--}o RecipeCategory : \"categories\"\nRecipe ||--}o Ingredient : \"ingredients\"\nRecipe ||--}o Step : \"steps\"\nStep ||--|o Action : \"action\"\nStep ||--}o FoodItem : \"inputs\"\nStep ||--}o FoodItem : \"outputs\"\nStep ||--}o UtensilType : \"utensils\"\nFoodItem ||--|o FoodType : \"food\"\nIngredient ||--|o FoodItem : \"food_item\"\nIngredient ||--|o Quantity : \"amount\"\nQuantity ||--|o Unit : \"unit\"\n\n
"},{"location":"recipe/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None FoodItem None Ingredient None Quantity None Step None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None Action None FoodType None RecipeCategory None RelationshipType None Unit None UtensilType None Publication None Recipe None TextWithTriples None"},{"location":"recipe/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication action the action taken in this step (e amount the quantity of the ingredient, e categories a semicolon separated list of the categories to which this recipe belongs combined_text description a brief textual description of the recipe extracted_object The complex objects extracted from the text food the food item food_item the food item full_text The full text of the publication id A unique identifier for the named entity ingredients a semicolon separated list of the ingredients plus quantities of the recipe input_id input_text input_title inputs a semicolon separated list of the inputs of this step label the name of the recipe named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text outputs a semicolon separated list of the outputs of this step predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output state the state of the food item (e steps a semicolon separated list of the individual steps involved in this recipe subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication triples unit the unit of the quantity, e url utensils the kitchen utensil used in this step (e value the value of the quantity"},{"location":"recipe/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"recipe/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"recipe/#subsets","title":"Subsets","text":"Subset Description"},{"location":"recipe/Action/","title":"Class: Action","text":"

URI: recipe:Action

erDiagram\nAction {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/Action/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Action/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/Action/#usages","title":"Usages","text":"used by used in type used Step action range Action"},{"location":"recipe/Action/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Action/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/Action/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:dbpediaont, sqlite:obo:foodon"},{"location":"recipe/Action/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Action/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Action native recipe:Action"},{"location":"recipe/Action/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Action/#direct","title":"Direct","text":"
name: Action\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/Action/#induced","title":"Induced","text":"
name: Action\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Action\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Action\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: recipe:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"recipe/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"recipe/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"recipe/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:AnnotatorResult native recipe:AnnotatorResult"},{"location":"recipe/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n\n
"},{"location":"recipe/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"recipe/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"recipe/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"recipe/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"recipe/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Any/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native recipe:Any"},{"location":"recipe/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/recipe\nclass_uri: linkml:Any\n\n
"},{"location":"recipe/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: https://w3id.org/ontogpt/recipe\nclass_uri: linkml:Any\n\n
"},{"location":"recipe/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"recipe/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"recipe/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: recipe:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"recipe/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"recipe/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"recipe/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"recipe/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:CompoundExpression native recipe:CompoundExpression"},{"location":"recipe/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/recipe\nabstract: true\n\n
"},{"location":"recipe/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: https://w3id.org/ontogpt/recipe\nabstract: true\n\n
"},{"location":"recipe/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"recipe/Curie/#comments","title":"Comments","text":""},{"location":"recipe/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Curie/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"recipe/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Date/#schema-source","title":"Schema Source","text":""},{"location":"recipe/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"recipe/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"recipe/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"recipe/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"recipe/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Double/#schema-source","title":"Schema Source","text":""},{"location":"recipe/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: recipe:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"recipe/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"recipe/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"recipe/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:ExtractionResult native recipe:ExtractionResult"},{"location":"recipe/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"recipe/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  input_id:\n    name: input_id\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"recipe/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"recipe/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Float/#schema-source","title":"Schema Source","text":""},{"location":"recipe/FoodItem/","title":"Class: FoodItem","text":"

URI: recipe:FoodItem

erDiagram\nFoodItem {\n    string state  \n}\nFoodType {\n    string id  \n    string label  \n}\n\nFoodItem ||--|o FoodType : \"food\"\n\n
"},{"location":"recipe/FoodItem/#inheritance","title":"Inheritance","text":""},{"location":"recipe/FoodItem/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance food 0..1 FoodType the food item direct state 0..1 String the state of the food item (e direct"},{"location":"recipe/FoodItem/#usages","title":"Usages","text":"used by used in type used Ingredient food_item range FoodItem Step inputs range FoodItem Step outputs range FoodItem"},{"location":"recipe/FoodItem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/FoodItem/#annotations","title":"Annotations","text":"property value owl IntersectionOf"},{"location":"recipe/FoodItem/#schema-source","title":"Schema Source","text":""},{"location":"recipe/FoodItem/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:FoodItem native recipe:FoodItem"},{"location":"recipe/FoodItem/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/FoodItem/#direct","title":"Direct","text":"
name: FoodItem\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  food:\n    name: food\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the food item\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: BFO:0000051\n    range: FoodType\n  state:\n    name: state\n    annotations:\n      owl:\n        tag: owl\n        value: DataProperty, DataHasValue\n    description: the state of the food item (e.g. chopped, diced)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n\n
"},{"location":"recipe/FoodItem/#induced","title":"Induced","text":"
name: FoodItem\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  food:\n    name: food\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the food item\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: BFO:0000051\n    alias: food\n    owner: FoodItem\n    domain_of:\n    - FoodItem\n    range: FoodType\n  state:\n    name: state\n    annotations:\n      owl:\n        tag: owl\n        value: DataProperty, DataHasValue\n    description: the state of the food item (e.g. chopped, diced)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: state\n    owner: FoodItem\n    domain_of:\n    - FoodItem\n    range: string\n\n
"},{"location":"recipe/FoodType/","title":"Class: FoodType","text":"

URI: recipe:FoodType

erDiagram\nFoodType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/FoodType/#inheritance","title":"Inheritance","text":""},{"location":"recipe/FoodType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/FoodType/#usages","title":"Usages","text":"used by used in type used FoodItem food range FoodType"},{"location":"recipe/FoodType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/FoodType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/FoodType/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:foodon, sqlite:obo:dbpediaont"},{"location":"recipe/FoodType/#schema-source","title":"Schema Source","text":""},{"location":"recipe/FoodType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:FoodType native recipe:FoodType"},{"location":"recipe/FoodType/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/FoodType/#direct","title":"Direct","text":"
name: FoodType\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon, sqlite:obo:dbpediaont\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/FoodType/#induced","title":"Induced","text":"
name: FoodType\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon, sqlite:obo:dbpediaont\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: FoodType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: FoodType\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/Ingredient/","title":"Class: Ingredient","text":"

URI: FOODON:00004085

erDiagram\nIngredient {\n\n}\nQuantity {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\nFoodItem {\n    string state  \n}\nFoodType {\n    string id  \n    string label  \n}\n\nIngredient ||--|o FoodItem : \"food_item\"\nIngredient ||--|o Quantity : \"amount\"\nQuantity ||--|o Unit : \"unit\"\nFoodItem ||--|o FoodType : \"food\"\n\n
"},{"location":"recipe/Ingredient/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Ingredient/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance food_item 0..1 FoodItem the food item direct amount 0..1 Quantity the quantity of the ingredient, e direct"},{"location":"recipe/Ingredient/#usages","title":"Usages","text":"used by used in type used Recipe ingredients range Ingredient"},{"location":"recipe/Ingredient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Ingredient/#annotations","title":"Annotations","text":"property value owl IntersectionOf"},{"location":"recipe/Ingredient/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Ingredient/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self FOODON:00004085 native recipe:Ingredient"},{"location":"recipe/Ingredient/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Ingredient/#direct","title":"Direct","text":"
name: Ingredient\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  food_item:\n    name: food_item\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the food item\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: FoodItem\n  amount:\n    name: amount\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the quantity of the ingredient, e.g. 2 lbs\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: Quantity\nclass_uri: FOODON:00004085\n\n
"},{"location":"recipe/Ingredient/#induced","title":"Induced","text":"
name: Ingredient\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  food_item:\n    name: food_item\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the food item\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: food_item\n    owner: Ingredient\n    domain_of:\n    - Ingredient\n    range: FoodItem\n  amount:\n    name: amount\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the quantity of the ingredient, e.g. 2 lbs\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: amount\n    owner: Ingredient\n    domain_of:\n    - Ingredient\n    range: Quantity\nclass_uri: FOODON:00004085\n\n
"},{"location":"recipe/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"recipe/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Integer/#schema-source","title":"Schema Source","text":""},{"location":"recipe/NamedEntity/","title":"Class: NamedEntity","text":"

URI: recipe:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"recipe/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"recipe/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"recipe/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"recipe/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:NamedEntity native recipe:NamedEntity"},{"location":"recipe/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/recipe\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"recipe/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: https://w3id.org/ontogpt/recipe\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"recipe/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"recipe/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"recipe/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"recipe/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"recipe/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"recipe/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"recipe/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"recipe/Objectidentifier/#comments","title":"Comments","text":""},{"location":"recipe/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Publication/","title":"Class: Publication","text":"

URI: recipe:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"recipe/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"recipe/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"recipe/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Publication/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Publication native recipe:Publication"},{"location":"recipe/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/recipe\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n\n
"},{"location":"recipe/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: https://w3id.org/ontogpt/recipe\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"recipe/Quantity/","title":"Class: Quantity","text":"

URI: recipe:Quantity

erDiagram\nQuantity {\n    string value  \n}\nUnit {\n    string id  \n    string label  \n}\n\nQuantity ||--|o Unit : \"unit\"\n\n
"},{"location":"recipe/Quantity/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Quantity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance value 0..1 String the value of the quantity direct unit 0..1 Unit the unit of the quantity, e direct"},{"location":"recipe/Quantity/#usages","title":"Usages","text":"used by used in type used Ingredient amount range Quantity"},{"location":"recipe/Quantity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Quantity/#annotations","title":"Annotations","text":"property value owl IntersectionOf"},{"location":"recipe/Quantity/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Quantity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Quantity native recipe:Quantity"},{"location":"recipe/Quantity/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Quantity/#direct","title":"Direct","text":"
name: Quantity\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    annotations:\n      owl:\n        tag: owl\n        value: DataProperty, DataHasValue\n    description: the value of the quantity\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n  unit:\n    name: unit\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the unit of the quantity, e.g. grams, cups, etc.\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: qudt:unit\n    range: Unit\n\n
"},{"location":"recipe/Quantity/#induced","title":"Induced","text":"
name: Quantity\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  value:\n    name: value\n    annotations:\n      owl:\n        tag: owl\n        value: DataProperty, DataHasValue\n    description: the value of the quantity\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: value\n    owner: Quantity\n    domain_of:\n    - Quantity\n    range: string\n  unit:\n    name: unit\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the unit of the quantity, e.g. grams, cups, etc.\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: qudt:unit\n    alias: unit\n    owner: Quantity\n    domain_of:\n    - Quantity\n    range: Unit\n\n
"},{"location":"recipe/Recipe/","title":"Class: Recipe","text":"

URI: recipe:Recipe

erDiagram\nRecipe {\n    uriorcurie url  \n    string label  \n    string description  \n}\nStep {\n\n}\nUtensilType {\n    string id  \n    string label  \n}\nFoodItem {\n    string state  \n}\nAction {\n    string id  \n    string label  \n}\nIngredient {\n\n}\nQuantity {\n    string value  \n}\nRecipeCategory {\n    string id  \n    string label  \n}\n\nRecipe ||--}o RecipeCategory : \"categories\"\nRecipe ||--}o Ingredient : \"ingredients\"\nRecipe ||--}o Step : \"steps\"\nStep ||--|o Action : \"action\"\nStep ||--}o FoodItem : \"inputs\"\nStep ||--}o FoodItem : \"outputs\"\nStep ||--}o UtensilType : \"utensils\"\nFoodItem ||--|o FoodType : \"food\"\nIngredient ||--|o FoodItem : \"food_item\"\nIngredient ||--|o Quantity : \"amount\"\nQuantity ||--|o Unit : \"unit\"\n\n
"},{"location":"recipe/Recipe/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance url 1..1 Uriorcurie direct label 0..1 String the name of the recipe direct description 0..1 String a brief textual description of the recipe direct categories 0..* RecipeCategory a semicolon separated list of the categories to which this recipe belongs direct ingredients 0..* Ingredient a semicolon separated list of the ingredients plus quantities of the recipe direct steps 0..* Step a semicolon separated list of the individual steps involved in this recipe direct"},{"location":"recipe/Recipe/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Recipe/#annotations","title":"Annotations","text":"property value owl Class {{url}} ObjectIntersectionOf( recipe:Recipe 
{% for step in steps %}\nObjectSomeValuesFrom(\n  recipe:steps\n  {{tr(step)}}\n)\n{% endfor %}\n{% for ingredient in ingredients %}\nObjectSomeValuesFrom(\n  FOODON:00002420\n  {{tr(ingredient)}}\n)\n{% endfor %}\n

) ) |

"},{"location":"recipe/Recipe/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Recipe/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Recipe native recipe:Recipe close FOODON:00004081"},{"location":"recipe/Recipe/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Recipe/#direct","title":"Direct","text":"
name: Recipe\nannotations:\n  owl:\n    tag: owl\n    value: Class\n  owl.template:\n    tag: owl.template\n    value: \"EquivalentClasses(\\n  {{url}}\\n  ObjectIntersectionOf(\\n    recipe:Recipe\\n\\\n      \\    \\n    {% for step in steps %}\\n    ObjectSomeValuesFrom(\\n      recipe:steps\\n\\\n      \\      {{tr(step)}}\\n    )\\n    {% endfor %}\\n    {% for ingredient in ingredients\\\n      \\ %}\\n    ObjectSomeValuesFrom(\\n      FOODON:00002420\\n      {{tr(ingredient)}}\\n\\\n      \\    )\\n    {% endfor %}\\n  )\\n)\\n\"\nfrom_schema: https://w3id.org/ontogpt/recipe\nclose_mappings:\n- FOODON:00004081\nattributes:\n  url:\n    name: url\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: the name of the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: rdfs:label\n  description:\n    name: description\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: a brief textual description of the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: dcterms:description\n  categories:\n    name: categories\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: a semicolon separated list of the categories to which this recipe\n      belongs\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: dcterms:subject\n    multivalued: true\n    range: RecipeCategory\n  ingredients:\n    name: ingredients\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the ingredients plus quantities of\n      the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: FOODON:00002420\n    multivalued: true\n    range: Ingredient\n  steps:\n    name: steps\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the individual steps involved in this\n      recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    range: Step\ntree_root: true\n\n
"},{"location":"recipe/Recipe/#induced","title":"Induced","text":"
name: Recipe\nannotations:\n  owl:\n    tag: owl\n    value: Class\n  owl.template:\n    tag: owl.template\n    value: \"EquivalentClasses(\\n  {{url}}\\n  ObjectIntersectionOf(\\n    recipe:Recipe\\n\\\n      \\    \\n    {% for step in steps %}\\n    ObjectSomeValuesFrom(\\n      recipe:steps\\n\\\n      \\      {{tr(step)}}\\n    )\\n    {% endfor %}\\n    {% for ingredient in ingredients\\\n      \\ %}\\n    ObjectSomeValuesFrom(\\n      FOODON:00002420\\n      {{tr(ingredient)}}\\n\\\n      \\    )\\n    {% endfor %}\\n  )\\n)\\n\"\nfrom_schema: https://w3id.org/ontogpt/recipe\nclose_mappings:\n- FOODON:00004081\nattributes:\n  url:\n    name: url\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'True'\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: rdf:Resource\n    identifier: true\n    alias: url\n    owner: Recipe\n    domain_of:\n    - Recipe\n    range: uriorcurie\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: the name of the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Recipe\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n  description:\n    name: description\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: a brief textual description of the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Recipe\n    domain_of:\n    - Recipe\n    range: string\n  categories:\n    name: categories\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationAssertion\n    description: a semicolon separated list of the categories to which this recipe\n      belongs\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: dcterms:subject\n    multivalued: true\n    alias: categories\n    owner: Recipe\n    domain_of:\n    - Recipe\n    range: RecipeCategory\n  ingredients:\n    name: ingredients\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the ingredients plus quantities of\n      the recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: FOODON:00002420\n    multivalued: true\n    alias: ingredients\n    owner: Recipe\n    domain_of:\n    - Recipe\n    range: Ingredient\n  steps:\n    name: steps\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the individual steps involved in this\n      recipe\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    alias: steps\n    owner: Recipe\n    domain_of:\n    - Recipe\n    range: Step\ntree_root: true\n\n
"},{"location":"recipe/RecipeCategory/","title":"Class: RecipeCategory","text":"

URI: recipe:RecipeCategory

erDiagram\nRecipeCategory {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/RecipeCategory/#inheritance","title":"Inheritance","text":""},{"location":"recipe/RecipeCategory/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/RecipeCategory/#usages","title":"Usages","text":"used by used in type used Recipe categories range RecipeCategory"},{"location":"recipe/RecipeCategory/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/RecipeCategory/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/RecipeCategory/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:foodon, sqlite:obo:dbpediaont"},{"location":"recipe/RecipeCategory/#schema-source","title":"Schema Source","text":""},{"location":"recipe/RecipeCategory/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:RecipeCategory native recipe:RecipeCategory"},{"location":"recipe/RecipeCategory/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/RecipeCategory/#direct","title":"Direct","text":"
name: RecipeCategory\nid_prefixes:\n- dbpediaont\n- FOODON\n- HANCESTRO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon, sqlite:obo:dbpediaont\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/RecipeCategory/#induced","title":"Induced","text":"
name: RecipeCategory\nid_prefixes:\n- dbpediaont\n- FOODON\n- HANCESTRO\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:foodon, sqlite:obo:dbpediaont\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RecipeCategory\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RecipeCategory\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/RelationshipType/","title":"Class: RelationshipType","text":"

URI: recipe:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"recipe/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"recipe/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"recipe/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:RelationshipType native recipe:RelationshipType"},{"location":"recipe/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/Step/","title":"Class: Step","text":"

URI: FOODON:00004087

erDiagram\nStep {\n\n}\nUtensilType {\n    string id  \n    string label  \n}\nFoodItem {\n    string state  \n}\nFoodType {\n    string id  \n    string label  \n}\nAction {\n    string id  \n    string label  \n}\n\nStep ||--|o Action : \"action\"\nStep ||--}o FoodItem : \"inputs\"\nStep ||--}o FoodItem : \"outputs\"\nStep ||--}o UtensilType : \"utensils\"\nFoodItem ||--|o FoodType : \"food\"\n\n
"},{"location":"recipe/Step/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Step/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance action 0..1 Action the action taken in this step (e direct inputs 0..* FoodItem a semicolon separated list of the inputs of this step direct outputs 0..* FoodItem a semicolon separated list of the outputs of this step direct utensils 0..* UtensilType the kitchen utensil used in this step (e direct"},{"location":"recipe/Step/#usages","title":"Usages","text":"used by used in type used Recipe steps range Step"},{"location":"recipe/Step/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Step/#annotations","title":"Annotations","text":"property value owl IntersectionOf"},{"location":"recipe/Step/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Step/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self FOODON:00004087 native recipe:Step"},{"location":"recipe/Step/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Step/#direct","title":"Direct","text":"
name: Step\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  action:\n    name: action\n    description: the action taken in this step (e.g. mix, add)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: Action\n  inputs:\n    name: inputs\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the inputs of this step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002233\n    multivalued: true\n    range: FoodItem\n  outputs:\n    name: outputs\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the outputs of this step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002234\n    multivalued: true\n    range: FoodItem\n  utensils:\n    name: utensils\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the kitchen utensil used in this step (e.g. pan, bowl)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002500\n    multivalued: true\n    range: UtensilType\nclass_uri: FOODON:00004087\n\n
"},{"location":"recipe/Step/#induced","title":"Induced","text":"
name: Step\nannotations:\n  owl:\n    tag: owl\n    value: IntersectionOf\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nattributes:\n  action:\n    name: action\n    description: the action taken in this step (e.g. mix, add)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: action\n    owner: Step\n    domain_of:\n    - Step\n    range: Action\n  inputs:\n    name: inputs\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the inputs of this step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002233\n    multivalued: true\n    alias: inputs\n    owner: Step\n    domain_of:\n    - Step\n    range: FoodItem\n  outputs:\n    name: outputs\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: a semicolon separated list of the outputs of this step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002234\n    multivalued: true\n    alias: outputs\n    owner: Step\n    domain_of:\n    - Step\n    range: FoodItem\n  utensils:\n    name: utensils\n    annotations:\n      owl:\n        tag: owl\n        value: ObjectProperty, ObjectSomeValuesFrom\n    description: the kitchen utensil used in this step (e.g. pan, bowl)\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    slot_uri: RO:0002500\n    multivalued: true\n    alias: utensils\n    owner: Step\n    domain_of:\n    - Step\n    range: UtensilType\nclass_uri: FOODON:00004087\n\n
"},{"location":"recipe/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"recipe/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/String/#schema-source","title":"Schema Source","text":""},{"location":"recipe/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: recipe:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"recipe/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"recipe/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"recipe/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:TextWithTriples native recipe:TextWithTriples"},{"location":"recipe/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"recipe/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: https://w3id.org/ontogpt/recipe\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"recipe/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"recipe/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Time/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: recipe:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"recipe/Triple/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"recipe/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"recipe/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Triple/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Triple native recipe:Triple"},{"location":"recipe/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"recipe/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"recipe/Unit/","title":"Class: Unit","text":"

URI: recipe:Unit

erDiagram\nUnit {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/Unit/#inheritance","title":"Inheritance","text":""},{"location":"recipe/Unit/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/Unit/#usages","title":"Usages","text":"used by used in type used Quantity unit range Unit"},{"location":"recipe/Unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Unit/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/Unit/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon"},{"location":"recipe/Unit/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Unit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:Unit native recipe:Unit"},{"location":"recipe/Unit/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/Unit/#direct","title":"Direct","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\n- dbpediaont\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/Unit/#induced","title":"Induced","text":"
name: Unit\nid_prefixes:\n- UO\n- NCIT\n- dbpediaont\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Unit\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: Unit\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"recipe/Uri/#comments","title":"Comments","text":""},{"location":"recipe/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Uri/#schema-source","title":"Schema Source","text":""},{"location":"recipe/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"recipe/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"recipe/UtensilType/","title":"Class: UtensilType","text":"

URI: recipe:UtensilType

erDiagram\nUtensilType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"recipe/UtensilType/#inheritance","title":"Inheritance","text":""},{"location":"recipe/UtensilType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"recipe/UtensilType/#usages","title":"Usages","text":"used by used in type used Step utensils range UtensilType"},{"location":"recipe/UtensilType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/UtensilType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"recipe/UtensilType/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:dbpediaont, sqlite:obo:foodon"},{"location":"recipe/UtensilType/#schema-source","title":"Schema Source","text":""},{"location":"recipe/UtensilType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self recipe:UtensilType native recipe:UtensilType"},{"location":"recipe/UtensilType/#linkml-source","title":"LinkML Source","text":""},{"location":"recipe/UtensilType/#direct","title":"Direct","text":"
name: UtensilType\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\n\n
"},{"location":"recipe/UtensilType/#induced","title":"Induced","text":"
name: UtensilType\nid_prefixes:\n- dbpediaont\n- FOODON\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:dbpediaont, sqlite:obo:foodon\nfrom_schema: https://w3id.org/ontogpt/recipe\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: https://w3id.org/ontogpt/recipe\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: UtensilType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: https://w3id.org/ontogpt/recipe\n    aliases:\n    - name\n    slot_uri: rdfs:label\n    alias: label\n    owner: UtensilType\n    domain_of:\n    - Recipe\n    - NamedEntity\n    range: string\n\n
"},{"location":"recipe/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: recipe:abstract

"},{"location":"recipe/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"recipe/abstract/#properties","title":"Properties","text":""},{"location":"recipe/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/abstract/#schema-source","title":"Schema Source","text":""},{"location":"recipe/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"recipe/action/","title":"Slot: action","text":"

the action taken in this step (e.g. mix, add)

URI: recipe:action

"},{"location":"recipe/action/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Step no"},{"location":"recipe/action/#properties","title":"Properties","text":""},{"location":"recipe/action/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/action/#schema-source","title":"Schema Source","text":""},{"location":"recipe/action/#linkml-source","title":"LinkML Source","text":"
name: action\ndescription: the action taken in this step (e.g. mix, add)\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: action\nowner: Step\ndomain_of:\n- Step\nrange: Action\n\n
"},{"location":"recipe/amount/","title":"Slot: amount","text":"

the quantity of the ingredient, e.g. 2 lbs

URI: recipe:amount

"},{"location":"recipe/amount/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Ingredient no"},{"location":"recipe/amount/#properties","title":"Properties","text":""},{"location":"recipe/amount/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/amount/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/amount/#schema-source","title":"Schema Source","text":""},{"location":"recipe/amount/#linkml-source","title":"LinkML Source","text":"
name: amount\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: the quantity of the ingredient, e.g. 2 lbs\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: amount\nowner: Ingredient\ndomain_of:\n- Ingredient\nrange: Quantity\n\n
"},{"location":"recipe/categories/","title":"Slot: categories","text":"

a semicolon separated list of the categories to which this recipe belongs

URI: dcterms:subject

"},{"location":"recipe/categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no"},{"location":"recipe/categories/#properties","title":"Properties","text":""},{"location":"recipe/categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/categories/#annotations","title":"Annotations","text":"property value owl AnnotationAssertion"},{"location":"recipe/categories/#schema-source","title":"Schema Source","text":""},{"location":"recipe/categories/#linkml-source","title":"LinkML Source","text":"
name: categories\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationAssertion\ndescription: a semicolon separated list of the categories to which this recipe belongs\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: dcterms:subject\nmultivalued: true\nalias: categories\nowner: Recipe\ndomain_of:\n- Recipe\nrange: RecipeCategory\n\n
"},{"location":"recipe/combined_text/","title":"Slot: combined_text","text":"

URI: recipe:combined_text

"},{"location":"recipe/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"recipe/combined_text/#properties","title":"Properties","text":""},{"location":"recipe/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"recipe/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"recipe/description/","title":"Slot: description","text":"

a brief textual description of the recipe

URI: dcterms:description

"},{"location":"recipe/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no"},{"location":"recipe/description/#properties","title":"Properties","text":""},{"location":"recipe/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/description/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"recipe/description/#schema-source","title":"Schema Source","text":""},{"location":"recipe/description/#linkml-source","title":"LinkML Source","text":"
name: description\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: a brief textual description of the recipe\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: dcterms:description\nalias: description\nowner: Recipe\ndomain_of:\n- Recipe\nrange: string\n\n
"},{"location":"recipe/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: recipe:extracted_object

"},{"location":"recipe/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/extracted_object/#properties","title":"Properties","text":""},{"location":"recipe/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"recipe/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"recipe/food/","title":"Slot: food","text":"

the food item

URI: BFO:0000051

"},{"location":"recipe/food/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FoodItem no"},{"location":"recipe/food/#properties","title":"Properties","text":""},{"location":"recipe/food/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/food/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/food/#schema-source","title":"Schema Source","text":""},{"location":"recipe/food/#linkml-source","title":"LinkML Source","text":"
name: food\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: the food item\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: BFO:0000051\nalias: food\nowner: FoodItem\ndomain_of:\n- FoodItem\nrange: FoodType\n\n
"},{"location":"recipe/food_item/","title":"Slot: food_item","text":"

the food item

URI: recipe:food_item

"},{"location":"recipe/food_item/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Ingredient no"},{"location":"recipe/food_item/#properties","title":"Properties","text":""},{"location":"recipe/food_item/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/food_item/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/food_item/#schema-source","title":"Schema Source","text":""},{"location":"recipe/food_item/#linkml-source","title":"LinkML Source","text":"
name: food_item\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: the food item\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: food_item\nowner: Ingredient\ndomain_of:\n- Ingredient\nrange: FoodItem\n\n
"},{"location":"recipe/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: recipe:full_text

"},{"location":"recipe/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"recipe/full_text/#properties","title":"Properties","text":""},{"location":"recipe/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/full_text/#schema-source","title":"Schema Source","text":""},{"location":"recipe/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"recipe/id/","title":"Slot: id","text":"

URI: recipe:id

"},{"location":"recipe/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FoodType no RecipeCategory no Action no UtensilType no Unit no NamedEntity no RelationshipType no Publication no"},{"location":"recipe/id/#properties","title":"Properties","text":""},{"location":"recipe/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"recipe/ingredients/","title":"Slot: ingredients","text":"

a semicolon separated list of the ingredients plus quantities of the recipe

URI: FOODON:00002420

"},{"location":"recipe/ingredients/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no"},{"location":"recipe/ingredients/#properties","title":"Properties","text":""},{"location":"recipe/ingredients/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/ingredients/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/ingredients/#schema-source","title":"Schema Source","text":""},{"location":"recipe/ingredients/#linkml-source","title":"LinkML Source","text":"
name: ingredients\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: a semicolon separated list of the ingredients plus quantities of the\n  recipe\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: FOODON:00002420\nmultivalued: true\nalias: ingredients\nowner: Recipe\ndomain_of:\n- Recipe\nrange: Ingredient\n\n
"},{"location":"recipe/input_id/","title":"Slot: input_id","text":"

URI: recipe:input_id

"},{"location":"recipe/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/input_id/#properties","title":"Properties","text":""},{"location":"recipe/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/input_id/#schema-source","title":"Schema Source","text":""},{"location":"recipe/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"recipe/input_text/","title":"Slot: input_text","text":"

URI: recipe:input_text

"},{"location":"recipe/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/input_text/#properties","title":"Properties","text":""},{"location":"recipe/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/input_text/#schema-source","title":"Schema Source","text":""},{"location":"recipe/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"recipe/input_title/","title":"Slot: input_title","text":"

URI: recipe:input_title

"},{"location":"recipe/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/input_title/#properties","title":"Properties","text":""},{"location":"recipe/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/input_title/#schema-source","title":"Schema Source","text":""},{"location":"recipe/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"recipe/inputs/","title":"Slot: inputs","text":"

a semicolon separated list of the inputs of this step

URI: RO:0002233

"},{"location":"recipe/inputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Step no"},{"location":"recipe/inputs/#properties","title":"Properties","text":""},{"location":"recipe/inputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/inputs/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/inputs/#schema-source","title":"Schema Source","text":""},{"location":"recipe/inputs/#linkml-source","title":"LinkML Source","text":"
name: inputs\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: a semicolon separated list of the inputs of this step\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: RO:0002233\nmultivalued: true\nalias: inputs\nowner: Step\ndomain_of:\n- Step\nrange: FoodItem\n\n
"},{"location":"recipe/label/","title":"Slot: label","text":"

URI: recipe:label

"},{"location":"recipe/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no FoodType no RecipeCategory no Action no UtensilType no Unit no NamedEntity no RelationshipType no"},{"location":"recipe/label/#properties","title":"Properties","text":""},{"location":"recipe/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/label/#linkml-source","title":"LinkML Source","text":"
name: label\nalias: label\ndomain_of:\n- Recipe\n- NamedEntity\nrange: string\n\n
"},{"location":"recipe/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: recipe:named_entities

"},{"location":"recipe/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/named_entities/#properties","title":"Properties","text":""},{"location":"recipe/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"recipe/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"recipe/object/","title":"Slot: object","text":"

URI: recipe:object

"},{"location":"recipe/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/object/#properties","title":"Properties","text":""},{"location":"recipe/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/object/#schema-source","title":"Schema Source","text":""},{"location":"recipe/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"recipe/object_id/","title":"Slot: object_id","text":"

URI: recipe:object_id

"},{"location":"recipe/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"recipe/object_id/#properties","title":"Properties","text":""},{"location":"recipe/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/object_id/#schema-source","title":"Schema Source","text":""},{"location":"recipe/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"recipe/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: recipe:object_qualifier

"},{"location":"recipe/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/object_qualifier/#properties","title":"Properties","text":""},{"location":"recipe/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"recipe/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"recipe/object_text/","title":"Slot: object_text","text":"

URI: recipe:object_text

"},{"location":"recipe/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"recipe/object_text/#properties","title":"Properties","text":""},{"location":"recipe/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/object_text/#schema-source","title":"Schema Source","text":""},{"location":"recipe/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"recipe/outputs/","title":"Slot: outputs","text":"

a semicolon separated list of the outputs of this step

URI: RO:0002234

"},{"location":"recipe/outputs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Step no"},{"location":"recipe/outputs/#properties","title":"Properties","text":""},{"location":"recipe/outputs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/outputs/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/outputs/#schema-source","title":"Schema Source","text":""},{"location":"recipe/outputs/#linkml-source","title":"LinkML Source","text":"
name: outputs\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: a semicolon separated list of the outputs of this step\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: RO:0002234\nmultivalued: true\nalias: outputs\nowner: Step\ndomain_of:\n- Step\nrange: FoodItem\n\n
"},{"location":"recipe/predicate/","title":"Slot: predicate","text":"

URI: recipe:predicate

"},{"location":"recipe/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/predicate/#properties","title":"Properties","text":""},{"location":"recipe/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/predicate/#schema-source","title":"Schema Source","text":""},{"location":"recipe/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"recipe/prompt/","title":"Slot: prompt","text":"

URI: recipe:prompt

"},{"location":"recipe/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/prompt/#properties","title":"Properties","text":""},{"location":"recipe/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/prompt/#schema-source","title":"Schema Source","text":""},{"location":"recipe/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"recipe/publication/","title":"Slot: publication","text":"

URI: recipe:publication

"},{"location":"recipe/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"recipe/publication/#properties","title":"Properties","text":""},{"location":"recipe/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"recipe/publication/#schema-source","title":"Schema Source","text":""},{"location":"recipe/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"recipe/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: recipe:qualifier

"},{"location":"recipe/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/qualifier/#properties","title":"Properties","text":""},{"location":"recipe/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"recipe/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"recipe/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: recipe:raw_completion_output

"},{"location":"recipe/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"recipe/raw_completion_output/#properties","title":"Properties","text":""},{"location":"recipe/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"recipe/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"recipe/recipe-template/","title":"recipe-template","text":"

A template for food recipes

URI: https://w3id.org/ontogpt/recipe

"},{"location":"recipe/state/","title":"Slot: state","text":"

the state of the food item (e.g. chopped, diced)

URI: recipe:state

"},{"location":"recipe/state/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FoodItem no"},{"location":"recipe/state/#properties","title":"Properties","text":""},{"location":"recipe/state/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/state/#annotations","title":"Annotations","text":"property value owl DataProperty, DataHasValue"},{"location":"recipe/state/#schema-source","title":"Schema Source","text":""},{"location":"recipe/state/#linkml-source","title":"LinkML Source","text":"
name: state\nannotations:\n  owl:\n    tag: owl\n    value: DataProperty, DataHasValue\ndescription: the state of the food item (e.g. chopped, diced)\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: state\nowner: FoodItem\ndomain_of:\n- FoodItem\nrange: string\n\n
"},{"location":"recipe/steps/","title":"Slot: steps","text":"

a semicolon separated list of the individual steps involved in this recipe

URI: recipe:steps

"},{"location":"recipe/steps/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no"},{"location":"recipe/steps/#properties","title":"Properties","text":""},{"location":"recipe/steps/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/steps/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/steps/#schema-source","title":"Schema Source","text":""},{"location":"recipe/steps/#linkml-source","title":"LinkML Source","text":"
name: steps\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: a semicolon separated list of the individual steps involved in this recipe\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nmultivalued: true\nalias: steps\nowner: Recipe\ndomain_of:\n- Recipe\nrange: Step\n\n
"},{"location":"recipe/subject/","title":"Slot: subject","text":"

URI: recipe:subject

"},{"location":"recipe/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/subject/#properties","title":"Properties","text":""},{"location":"recipe/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/subject/#schema-source","title":"Schema Source","text":""},{"location":"recipe/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"recipe/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: recipe:subject_qualifier

"},{"location":"recipe/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"recipe/subject_qualifier/#properties","title":"Properties","text":""},{"location":"recipe/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"recipe/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"recipe/subject_text/","title":"Slot: subject_text","text":"

URI: recipe:subject_text

"},{"location":"recipe/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"recipe/subject_text/#properties","title":"Properties","text":""},{"location":"recipe/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"recipe/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"recipe/title/","title":"Slot: title","text":"

The title of the publication

URI: recipe:title

"},{"location":"recipe/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"recipe/title/#properties","title":"Properties","text":""},{"location":"recipe/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/title/#schema-source","title":"Schema Source","text":""},{"location":"recipe/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"recipe/triples/","title":"Slot: triples","text":"

URI: recipe:triples

"},{"location":"recipe/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"recipe/triples/#properties","title":"Properties","text":""},{"location":"recipe/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/triples/#schema-source","title":"Schema Source","text":""},{"location":"recipe/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"recipe/unit/","title":"Slot: unit","text":"

the unit of the quantity, e.g. grams, cups, etc.

URI: qudt:unit

"},{"location":"recipe/unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Quantity no"},{"location":"recipe/unit/#properties","title":"Properties","text":""},{"location":"recipe/unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/unit/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/unit/#schema-source","title":"Schema Source","text":""},{"location":"recipe/unit/#linkml-source","title":"LinkML Source","text":"
name: unit\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: the unit of the quantity, e.g. grams, cups, etc.\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: qudt:unit\nalias: unit\nowner: Quantity\ndomain_of:\n- Quantity\nrange: Unit\n\n
"},{"location":"recipe/url/","title":"Slot: url","text":"

URI: rdf:Resource

"},{"location":"recipe/url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Recipe no"},{"location":"recipe/url/#properties","title":"Properties","text":""},{"location":"recipe/url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/url/#annotations","title":"Annotations","text":"property value prompt.skip True"},{"location":"recipe/url/#schema-source","title":"Schema Source","text":""},{"location":"recipe/url/#linkml-source","title":"LinkML Source","text":"
name: url\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'True'\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: rdf:Resource\nidentifier: true\nalias: url\nowner: Recipe\ndomain_of:\n- Recipe\nrange: uriorcurie\nrequired: true\n\n
"},{"location":"recipe/utensils/","title":"Slot: utensils","text":"

the kitchen utensil used in this step (e.g. pan, bowl)

URI: RO:0002500

"},{"location":"recipe/utensils/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Step no"},{"location":"recipe/utensils/#properties","title":"Properties","text":""},{"location":"recipe/utensils/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/utensils/#annotations","title":"Annotations","text":"property value owl ObjectProperty, ObjectSomeValuesFrom"},{"location":"recipe/utensils/#schema-source","title":"Schema Source","text":""},{"location":"recipe/utensils/#linkml-source","title":"LinkML Source","text":"
name: utensils\nannotations:\n  owl:\n    tag: owl\n    value: ObjectProperty, ObjectSomeValuesFrom\ndescription: the kitchen utensil used in this step (e.g. pan, bowl)\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nslot_uri: RO:0002500\nmultivalued: true\nalias: utensils\nowner: Step\ndomain_of:\n- Step\nrange: UtensilType\n\n
"},{"location":"recipe/value/","title":"Slot: value","text":"

the value of the quantity

URI: recipe:value

"},{"location":"recipe/value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Quantity no"},{"location":"recipe/value/#properties","title":"Properties","text":""},{"location":"recipe/value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"recipe/value/#annotations","title":"Annotations","text":"property value owl DataProperty, DataHasValue"},{"location":"recipe/value/#schema-source","title":"Schema Source","text":""},{"location":"recipe/value/#linkml-source","title":"LinkML Source","text":"
name: value\nannotations:\n  owl:\n    tag: owl\n    value: DataProperty, DataHasValue\ndescription: the value of the quantity\nfrom_schema: https://w3id.org/ontogpt/recipe\nrank: 1000\nalias: value\nowner: Quantity\ndomain_of:\n- Quantity\nrange: string\n\n
"},{"location":"traits/","title":"Traits Template","text":"

A template for Traits

URI: http://w3id.org/ontogpt/traits

Name: traits

"},{"location":"traits/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nTaxon {\n\n}\nTrait {\n    string id  \n    string label  \n}\n\nTaxon ||--}o Trait : \"metabolic_traits\"\nTaxon ||--}o Trait : \"morphological_traits\"\nTaxon ||--}o Trait : \"genetic_traits\"\nTaxon ||--}o Trait : \"cellular_traits\"\nTaxon ||--}o Trait : \"ecological_traits\"\nTaxon ||--}o Trait : \"reproductive_traits\"\nTaxon ||--}o Trait : \"survival_traits\"\nTaxon ||--}o Trait : \"phenotypic_plasticiticy_traits\"\nTaxon ||--}o Trait : \"preferred_environments\"\n\n
"},{"location":"traits/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None Triple Abstract parent for Relation Extraction tasks ExtractionResult A result of extracting knowledge on text NamedEntity None RelationshipType None Trait None Publication None Taxon None TextWithTriples None"},{"location":"traits/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication cellular_traits The cellular traits for the taxon combined_text ecological_traits The ecological traits for the taxon extracted_object The complex objects extracted from the text full_text The full text of the publication genetic_traits The genetic traits for the taxon id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing metabolic_traits The metabolic traits for the taxon morphological_traits The morphological traits for the taxon named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text phenotypic_plasticiticy_traits The phenotypic plasticiticy traits for the taxon predicate preferred_environments The preferred environments for the taxon prompt publication qualifier A qualifier for the statements, e raw_completion_output reproductive_traits The reproductive traits for the taxon subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text survival_traits The survival traits for the taxon title The title of the publication triples"},{"location":"traits/#enumerations","title":"Enumerations","text":"Enumeration Description NullDataOptions"},{"location":"traits/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"traits/#subsets","title":"Subsets","text":"Subset Description"},{"location":"traits/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: traits:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"traits/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"traits/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"traits/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:AnnotatorResult native traits:AnnotatorResult"},{"location":"traits/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n\n
"},{"location":"traits/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"traits/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"traits/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"traits/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"traits/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Any/#schema-source","title":"Schema Source","text":""},{"location":"traits/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native traits:Any"},{"location":"traits/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/traits\nclass_uri: linkml:Any\n\n
"},{"location":"traits/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/traits\nclass_uri: linkml:Any\n\n
"},{"location":"traits/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"traits/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"traits/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: traits:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"traits/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"traits/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"traits/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"traits/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:CompoundExpression native traits:CompoundExpression"},{"location":"traits/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/traits\nabstract: true\n\n
"},{"location":"traits/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/traits\nabstract: true\n\n
"},{"location":"traits/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"traits/Curie/#comments","title":"Comments","text":""},{"location":"traits/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Curie/#schema-source","title":"Schema Source","text":""},{"location":"traits/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"traits/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Date/#schema-source","title":"Schema Source","text":""},{"location":"traits/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"traits/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"traits/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"traits/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"traits/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"traits/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"traits/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"traits/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Double/#schema-source","title":"Schema Source","text":""},{"location":"traits/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: traits:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"traits/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"traits/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"traits/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:ExtractionResult native traits:ExtractionResult"},{"location":"traits/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"traits/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"traits/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"traits/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Float/#schema-source","title":"Schema Source","text":""},{"location":"traits/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"traits/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Integer/#schema-source","title":"Schema Source","text":""},{"location":"traits/NamedEntity/","title":"Class: NamedEntity","text":"

URI: traits:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"traits/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"traits/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"traits/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"traits/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"traits/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:NamedEntity native traits:NamedEntity"},{"location":"traits/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/traits\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/traits\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"traits/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/traits\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/traits\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"traits/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"traits/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"traits/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"traits/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"traits/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"traits/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"traits/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"traits/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"traits/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"traits/Objectidentifier/#comments","title":"Comments","text":""},{"location":"traits/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"traits/Publication/","title":"Class: Publication","text":"

URI: traits:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"traits/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"traits/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"traits/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Publication/#schema-source","title":"Schema Source","text":""},{"location":"traits/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:Publication native traits:Publication"},{"location":"traits/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/traits\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n\n
"},{"location":"traits/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/traits\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"traits/RelationshipType/","title":"Class: RelationshipType","text":"

URI: traits:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"traits/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"traits/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"traits/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"traits/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"traits/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"traits/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:RelationshipType native traits:RelationshipType"},{"location":"traits/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: NamedEntity\n\n
"},{"location":"traits/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/traits\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"traits/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"traits/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/String/#schema-source","title":"Schema Source","text":""},{"location":"traits/Taxon/","title":"Class: Taxon","text":"

URI: traits:Taxon

erDiagram\nTaxon {\n\n}\nTrait {\n    string id  \n    string label  \n}\n\nTaxon ||--}o Trait : \"metabolic_traits\"\nTaxon ||--}o Trait : \"morphological_traits\"\nTaxon ||--}o Trait : \"genetic_traits\"\nTaxon ||--}o Trait : \"cellular_traits\"\nTaxon ||--}o Trait : \"ecological_traits\"\nTaxon ||--}o Trait : \"reproductive_traits\"\nTaxon ||--}o Trait : \"survival_traits\"\nTaxon ||--}o Trait : \"phenotypic_plasticiticy_traits\"\nTaxon ||--}o Trait : \"preferred_environments\"\n\n
"},{"location":"traits/Taxon/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance metabolic_traits 0..* Trait The metabolic traits for the taxon direct morphological_traits 0..* Trait The morphological traits for the taxon direct genetic_traits 0..* Trait The genetic traits for the taxon direct cellular_traits 0..* Trait The cellular traits for the taxon direct ecological_traits 0..* Trait The ecological traits for the taxon direct reproductive_traits 0..* Trait The reproductive traits for the taxon direct survival_traits 0..* Trait The survival traits for the taxon direct phenotypic_plasticiticy_traits 0..* Trait The phenotypic plasticiticy traits for the taxon direct preferred_environments 0..* Trait The preferred environments for the taxon direct"},{"location":"traits/Taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Taxon/#schema-source","title":"Schema Source","text":""},{"location":"traits/Taxon/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:Taxon native traits:Taxon"},{"location":"traits/Taxon/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/Taxon/#direct","title":"Direct","text":"
name: Taxon\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  metabolic_traits:\n    name: metabolic_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism metabolic trait\n    description: The metabolic traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  morphological_traits:\n    name: morphological_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism morphological\n          trait\n    description: The morphological traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  genetic_traits:\n    name: genetic_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism genetic trait\n    description: The genetic traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  cellular_traits:\n    name: cellular_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism cellular trait\n    description: The cellular traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  ecological_traits:\n    name: ecological_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism ecological trait\n    description: The ecological traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  reproductive_traits:\n    name: reproductive_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism reproductive\n          trait\n    description: The reproductive traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  survival_traits:\n    name: survival_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism survival trait\n    description: The survival traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  phenotypic_plasticiticy_traits:\n    name: phenotypic_plasticiticy_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism phenotypic plasticiticy\n          trait\n    description: The phenotypic plasticiticy traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\n  preferred_environments:\n    name: preferred_environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of the environments the organism is typically\n          found in or isolated from\n    description: The preferred environments for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Trait\ntree_root: true\n\n
"},{"location":"traits/Taxon/#induced","title":"Induced","text":"
name: Taxon\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  metabolic_traits:\n    name: metabolic_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism metabolic trait\n    description: The metabolic traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: metabolic_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  morphological_traits:\n    name: morphological_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism morphological\n          trait\n    description: The morphological traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: morphological_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  genetic_traits:\n    name: genetic_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism genetic trait\n    description: The genetic traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: genetic_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  cellular_traits:\n    name: cellular_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism cellular trait\n    description: The cellular traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: cellular_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  ecological_traits:\n    name: ecological_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism ecological trait\n    description: The ecological traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: ecological_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  reproductive_traits:\n    name: reproductive_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism reproductive\n          trait\n    description: The reproductive traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: reproductive_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  survival_traits:\n    name: survival_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism survival trait\n    description: The survival traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: survival_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  phenotypic_plasticiticy_traits:\n    name: phenotypic_plasticiticy_traits\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of every specific organism phenotypic plasticiticy\n          trait\n    description: The phenotypic plasticiticy traits for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: phenotypic_plasticiticy_traits\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\n  preferred_environments:\n    name: preferred_environments\n    annotations:\n      prompt:\n        tag: prompt\n        value: a semicolon separated list of the environments the organism is typically\n          found in or isolated from\n    description: The preferred environments for the taxon.\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: preferred_environments\n    owner: Taxon\n    domain_of:\n    - Taxon\n    range: Trait\ntree_root: true\n\n
"},{"location":"traits/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: traits:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"traits/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"traits/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"traits/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:TextWithTriples native traits:TextWithTriples"},{"location":"traits/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"traits/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/traits\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"traits/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"traits/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Time/#schema-source","title":"Schema Source","text":""},{"location":"traits/Trait/","title":"Class: Trait","text":"

URI: traits:Trait

erDiagram\nTrait {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"traits/Trait/#inheritance","title":"Inheritance","text":""},{"location":"traits/Trait/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"traits/Trait/#usages","title":"Usages","text":"used by used in type used Taxon metabolic_traits range Trait Taxon morphological_traits range Trait Taxon genetic_traits range Trait Taxon cellular_traits range Trait Taxon ecological_traits range Trait Taxon reproductive_traits range Trait Taxon survival_traits range Trait Taxon phenotypic_plasticiticy_traits range Trait Taxon preferred_environments range Trait"},{"location":"traits/Trait/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Trait/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"traits/Trait/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes"},{"location":"traits/Trait/#schema-source","title":"Schema Source","text":""},{"location":"traits/Trait/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:Trait native traits:Trait"},{"location":"traits/Trait/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/Trait/#direct","title":"Direct","text":"
name: Trait\nid_prefixes:\n- ECOCORE\n- PATO\n- GO\n- OBA\n- BIODIVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: NamedEntity\n\n
"},{"location":"traits/Trait/#induced","title":"Induced","text":"
name: Trait\nid_prefixes:\n- ECOCORE\n- PATO\n- GO\n- OBA\n- BIODIVTHES\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Trait\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/traits\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Trait\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"traits/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: traits:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"traits/Triple/#inheritance","title":"Inheritance","text":""},{"location":"traits/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"traits/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"traits/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Triple/#schema-source","title":"Schema Source","text":""},{"location":"traits/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self traits:Triple native traits:Triple"},{"location":"traits/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"traits/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"traits/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/traits\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/traits\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"traits/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"traits/Uri/#comments","title":"Comments","text":""},{"location":"traits/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Uri/#schema-source","title":"Schema Source","text":""},{"location":"traits/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"traits/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"traits/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: traits:abstract

"},{"location":"traits/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"traits/abstract/#properties","title":"Properties","text":""},{"location":"traits/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/abstract/#schema-source","title":"Schema Source","text":""},{"location":"traits/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"traits/cellular_traits/","title":"Slot: cellular_traits","text":"

The cellular traits for the taxon.

URI: traits:cellular_traits

"},{"location":"traits/cellular_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/cellular_traits/#properties","title":"Properties","text":""},{"location":"traits/cellular_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/cellular_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism cellular trait"},{"location":"traits/cellular_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/cellular_traits/#linkml-source","title":"LinkML Source","text":"
name: cellular_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism cellular trait\ndescription: The cellular traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: cellular_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/combined_text/","title":"Slot: combined_text","text":"

URI: traits:combined_text

"},{"location":"traits/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"traits/combined_text/#properties","title":"Properties","text":""},{"location":"traits/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"traits/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"traits/ecological_traits/","title":"Slot: ecological_traits","text":"

The ecological traits for the taxon.

URI: traits:ecological_traits

"},{"location":"traits/ecological_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/ecological_traits/#properties","title":"Properties","text":""},{"location":"traits/ecological_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/ecological_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism ecological trait"},{"location":"traits/ecological_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/ecological_traits/#linkml-source","title":"LinkML Source","text":"
name: ecological_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism ecological trait\ndescription: The ecological traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: ecological_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: traits:extracted_object

"},{"location":"traits/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/extracted_object/#properties","title":"Properties","text":""},{"location":"traits/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"traits/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"traits/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: traits:full_text

"},{"location":"traits/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"traits/full_text/#properties","title":"Properties","text":""},{"location":"traits/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/full_text/#schema-source","title":"Schema Source","text":""},{"location":"traits/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"traits/genetic_traits/","title":"Slot: genetic_traits","text":"

The genetic traits for the taxon.

URI: traits:genetic_traits

"},{"location":"traits/genetic_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/genetic_traits/#properties","title":"Properties","text":""},{"location":"traits/genetic_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/genetic_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism genetic trait"},{"location":"traits/genetic_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/genetic_traits/#linkml-source","title":"LinkML Source","text":"
name: genetic_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism genetic trait\ndescription: The genetic traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: genetic_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/id/","title":"Slot: id","text":"

URI: traits:id

"},{"location":"traits/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Trait no NamedEntity no RelationshipType no Publication no"},{"location":"traits/id/#properties","title":"Properties","text":""},{"location":"traits/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"traits/input_id/","title":"Slot: input_id","text":"

URI: traits:input_id

"},{"location":"traits/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/input_id/#properties","title":"Properties","text":""},{"location":"traits/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/input_id/#schema-source","title":"Schema Source","text":""},{"location":"traits/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"traits/input_text/","title":"Slot: input_text","text":"

URI: traits:input_text

"},{"location":"traits/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/input_text/#properties","title":"Properties","text":""},{"location":"traits/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/input_text/#schema-source","title":"Schema Source","text":""},{"location":"traits/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"traits/input_title/","title":"Slot: input_title","text":"

URI: traits:input_title

"},{"location":"traits/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/input_title/#properties","title":"Properties","text":""},{"location":"traits/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/input_title/#schema-source","title":"Schema Source","text":""},{"location":"traits/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"traits/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"traits/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Trait no NamedEntity no RelationshipType no"},{"location":"traits/label/#properties","title":"Properties","text":""},{"location":"traits/label/#aliases","title":"Aliases","text":""},{"location":"traits/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"traits/label/#schema-source","title":"Schema Source","text":""},{"location":"traits/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/traits\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"traits/metabolic_traits/","title":"Slot: metabolic_traits","text":"

The metabolic traits for the taxon.

URI: traits:metabolic_traits

"},{"location":"traits/metabolic_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/metabolic_traits/#properties","title":"Properties","text":""},{"location":"traits/metabolic_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/metabolic_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism metabolic trait"},{"location":"traits/metabolic_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/metabolic_traits/#linkml-source","title":"LinkML Source","text":"
name: metabolic_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism metabolic trait\ndescription: The metabolic traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: metabolic_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/morphological_traits/","title":"Slot: morphological_traits","text":"

The morphological traits for the taxon.

URI: traits:morphological_traits

"},{"location":"traits/morphological_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/morphological_traits/#properties","title":"Properties","text":""},{"location":"traits/morphological_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/morphological_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism morphological trait"},{"location":"traits/morphological_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/morphological_traits/#linkml-source","title":"LinkML Source","text":"
name: morphological_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism morphological trait\ndescription: The morphological traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: morphological_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: traits:named_entities

"},{"location":"traits/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/named_entities/#properties","title":"Properties","text":""},{"location":"traits/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"traits/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"traits/object/","title":"Slot: object","text":"

URI: traits:object

"},{"location":"traits/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/object/#properties","title":"Properties","text":""},{"location":"traits/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/object/#schema-source","title":"Schema Source","text":""},{"location":"traits/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"traits/object_id/","title":"Slot: object_id","text":"

URI: traits:object_id

"},{"location":"traits/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"traits/object_id/#properties","title":"Properties","text":""},{"location":"traits/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/object_id/#schema-source","title":"Schema Source","text":""},{"location":"traits/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"traits/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: traits:object_qualifier

"},{"location":"traits/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/object_qualifier/#properties","title":"Properties","text":""},{"location":"traits/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"traits/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"traits/object_text/","title":"Slot: object_text","text":"

URI: traits:object_text

"},{"location":"traits/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"traits/object_text/#properties","title":"Properties","text":""},{"location":"traits/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/object_text/#schema-source","title":"Schema Source","text":""},{"location":"traits/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"traits/phenotypic_plasticiticy_traits/","title":"Slot: phenotypic_plasticiticy_traits","text":"

The phenotypic plasticiticy traits for the taxon.

URI: traits:phenotypic_plasticiticy_traits

"},{"location":"traits/phenotypic_plasticiticy_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/phenotypic_plasticiticy_traits/#properties","title":"Properties","text":""},{"location":"traits/phenotypic_plasticiticy_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/phenotypic_plasticiticy_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism phenotypic plasticiticy trait"},{"location":"traits/phenotypic_plasticiticy_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/phenotypic_plasticiticy_traits/#linkml-source","title":"LinkML Source","text":"
name: phenotypic_plasticiticy_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism phenotypic plasticiticy\n      trait\ndescription: The phenotypic plasticiticy traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: phenotypic_plasticiticy_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/predicate/","title":"Slot: predicate","text":"

URI: traits:predicate

"},{"location":"traits/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/predicate/#properties","title":"Properties","text":""},{"location":"traits/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/predicate/#schema-source","title":"Schema Source","text":""},{"location":"traits/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"traits/preferred_environments/","title":"Slot: preferred_environments","text":"

The preferred environments for the taxon.

URI: traits:preferred_environments

"},{"location":"traits/preferred_environments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/preferred_environments/#properties","title":"Properties","text":""},{"location":"traits/preferred_environments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/preferred_environments/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of the environments the organism is typically found in or isolated from"},{"location":"traits/preferred_environments/#schema-source","title":"Schema Source","text":""},{"location":"traits/preferred_environments/#linkml-source","title":"LinkML Source","text":"
name: preferred_environments\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of the environments the organism is typically\n      found in or isolated from\ndescription: The preferred environments for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: preferred_environments\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/prompt/","title":"Slot: prompt","text":"

URI: traits:prompt

"},{"location":"traits/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/prompt/#properties","title":"Properties","text":""},{"location":"traits/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/prompt/#schema-source","title":"Schema Source","text":""},{"location":"traits/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"traits/publication/","title":"Slot: publication","text":"

URI: traits:publication

"},{"location":"traits/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"traits/publication/#properties","title":"Properties","text":""},{"location":"traits/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"traits/publication/#schema-source","title":"Schema Source","text":""},{"location":"traits/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"traits/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: traits:qualifier

"},{"location":"traits/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/qualifier/#properties","title":"Properties","text":""},{"location":"traits/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"traits/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"traits/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: traits:raw_completion_output

"},{"location":"traits/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"traits/raw_completion_output/#properties","title":"Properties","text":""},{"location":"traits/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"traits/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"traits/reproductive_traits/","title":"Slot: reproductive_traits","text":"

The reproductive traits for the taxon.

URI: traits:reproductive_traits

"},{"location":"traits/reproductive_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/reproductive_traits/#properties","title":"Properties","text":""},{"location":"traits/reproductive_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/reproductive_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism reproductive trait"},{"location":"traits/reproductive_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/reproductive_traits/#linkml-source","title":"LinkML Source","text":"
name: reproductive_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism reproductive trait\ndescription: The reproductive traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: reproductive_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/subject/","title":"Slot: subject","text":"

URI: traits:subject

"},{"location":"traits/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/subject/#properties","title":"Properties","text":""},{"location":"traits/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/subject/#schema-source","title":"Schema Source","text":""},{"location":"traits/subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: subject\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"traits/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: traits:subject_qualifier

"},{"location":"traits/subject_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"traits/subject_qualifier/#properties","title":"Properties","text":""},{"location":"traits/subject_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/subject_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"traits/subject_qualifier/#linkml-source","title":"LinkML Source","text":"
name: subject_qualifier\ndescription: An optional qualifier or modifier for the subject of the statement, e.g.\n  \"high dose\" or \"intravenously administered\"\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: subject_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"traits/subject_text/","title":"Slot: subject_text","text":"

URI: traits:subject_text

"},{"location":"traits/subject_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"traits/subject_text/#properties","title":"Properties","text":""},{"location":"traits/subject_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/subject_text/#schema-source","title":"Schema Source","text":""},{"location":"traits/subject_text/#linkml-source","title":"LinkML Source","text":"
name: subject_text\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"traits/survival_traits/","title":"Slot: survival_traits","text":"

The survival traits for the taxon.

URI: traits:survival_traits

"},{"location":"traits/survival_traits/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Taxon no"},{"location":"traits/survival_traits/#properties","title":"Properties","text":""},{"location":"traits/survival_traits/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/survival_traits/#annotations","title":"Annotations","text":"property value prompt a semicolon separated list of every specific organism survival trait"},{"location":"traits/survival_traits/#schema-source","title":"Schema Source","text":""},{"location":"traits/survival_traits/#linkml-source","title":"LinkML Source","text":"
name: survival_traits\nannotations:\n  prompt:\n    tag: prompt\n    value: a semicolon separated list of every specific organism survival trait\ndescription: The survival traits for the taxon.\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: survival_traits\nowner: Taxon\ndomain_of:\n- Taxon\nrange: Trait\n\n
"},{"location":"traits/title/","title":"Slot: title","text":"

The title of the publication

URI: traits:title

"},{"location":"traits/title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"traits/title/#properties","title":"Properties","text":""},{"location":"traits/title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/title/#schema-source","title":"Schema Source","text":""},{"location":"traits/title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"traits/traits/","title":"traits","text":"

A template for Traits

URI: http://w3id.org/ontogpt/traits

"},{"location":"traits/triples/","title":"Slot: triples","text":"

URI: traits:triples

"},{"location":"traits/triples/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"traits/triples/#properties","title":"Properties","text":""},{"location":"traits/triples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"traits/triples/#schema-source","title":"Schema Source","text":""},{"location":"traits/triples/#linkml-source","title":"LinkML Source","text":"
name: triples\nfrom_schema: http://w3id.org/ontogpt/traits\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"treatment/","title":"MAXO treatment Template","text":"

A template for MAXO treatments

URI: http://w3id.org/ontogpt/treatment

Name: treatment-template

"},{"location":"treatment/#schema-diagram","title":"Schema Diagram","text":"
erDiagram\nDiseaseTreatmentSummary {\n\n}\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nDiseaseTreatmentSummary ||--|o Disease : \"disease\"\nDiseaseTreatmentSummary ||--}o Drug : \"drugs\"\nDiseaseTreatmentSummary ||--}o Treatment : \"treatments\"\nDiseaseTreatmentSummary ||--}o Treatment : \"contraindications\"\nDiseaseTreatmentSummary ||--}o TreatmentMechanism : \"treatment_mechanisms\"\nDiseaseTreatmentSummary ||--}o TreatmentEfficacy : \"treatment_efficacies\"\nDiseaseTreatmentSummary ||--}o TreatmentAdverseEffect : \"treatment_adverse_effects\"\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"treatment/#classes","title":"Classes","text":"Class Description AnnotatorResult None Any None CompoundExpression None TreatmentAdverseEffect None TreatmentEfficacy None TreatmentMechanism None Triple Abstract parent for Relation Extraction tasks DiseaseTreatmentSummary None ExtractionResult A result of extracting knowledge on text NamedEntity None AdverseEffect None Disease None Drug None Gene None Mechanism None RelationshipType None Symptom None Treatment None Publication None TextWithTriples None"},{"location":"treatment/#slots","title":"Slots","text":"Slot Description abstract The abstract of the publication adverse_effects combined_text contraindications semicolon-separated list of therapies and treatments that are contra-indicate... disease the name of the disease that is treated drugs semicolon-separated list of named small molecule drugs efficacy extracted_object The complex objects extracted from the text full_text The full text of the publication id A unique identifier for the named entity input_id input_text input_title label The label (name) of the named thing mechanism named_entities Named entities extracted from the text object object_id object_qualifier An optional qualifier or modifier for the object of the statement, e object_text predicate prompt publication qualifier A qualifier for the statements, e raw_completion_output subject subject_qualifier An optional qualifier or modifier for the subject of the statement, e subject_text title The title of the publication treatment treatment_adverse_effects semicolon-separated list of treatment to adverse effect associations, e treatment_efficacies semicolon-separated list of treatment to efficacy associations, e treatment_mechanisms semicolon-separated list of treatment to asterisk-separated mechanism associa... treatments semicolon-separated list of therapies and treatments are indicated for treati... triples"},{"location":"treatment/#enumerations","title":"Enumerations","text":"Enumeration Description CHEBIDrugType MAXOActionType MESHTherapeuticType NCITDrugType NCITTActivityType NCITTreatmentType NullDataOptions"},{"location":"treatment/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"treatment/#subsets","title":"Subsets","text":"Subset Description"},{"location":"treatment/AdverseEffect/","title":"Class: AdverseEffect","text":"

URI: treatment:AdverseEffect

erDiagram\nAdverseEffect {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/AdverseEffect/#inheritance","title":"Inheritance","text":""},{"location":"treatment/AdverseEffect/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/AdverseEffect/#usages","title":"Usages","text":"used by used in type used TreatmentAdverseEffect adverse_effects range AdverseEffect"},{"location":"treatment/AdverseEffect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/AdverseEffect/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp, sqlite:obo:ncit"},{"location":"treatment/AdverseEffect/#schema-source","title":"Schema Source","text":""},{"location":"treatment/AdverseEffect/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:AdverseEffect native treatment:AdverseEffect"},{"location":"treatment/AdverseEffect/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/AdverseEffect/#direct","title":"Direct","text":"
name: AdverseEffect\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/AdverseEffect/#induced","title":"Induced","text":"
name: AdverseEffect\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp, sqlite:obo:ncit\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: AdverseEffect\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: AdverseEffect\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/AnnotatorResult/","title":"Class: AnnotatorResult","text":"

URI: treatment:AnnotatorResult

erDiagram\nAnnotatorResult {\n    string subject_text  \n    string object_id  \n    string object_text  \n}\n\n\n\n
"},{"location":"treatment/AnnotatorResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_text 0..1 String direct object_id 0..1 String direct object_text 0..1 String direct"},{"location":"treatment/AnnotatorResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/AnnotatorResult/#schema-source","title":"Schema Source","text":""},{"location":"treatment/AnnotatorResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:AnnotatorResult native treatment:AnnotatorResult"},{"location":"treatment/AnnotatorResult/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/AnnotatorResult/#direct","title":"Direct","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n\n
"},{"location":"treatment/AnnotatorResult/#induced","title":"Induced","text":"
name: AnnotatorResult\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  subject_text:\n    name: subject_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: subject_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_id:\n    name: object_id\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: object_id\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n  object_text:\n    name: object_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: object_text\n    owner: AnnotatorResult\n    domain_of:\n    - AnnotatorResult\n    range: string\n\n
"},{"location":"treatment/Any/","title":"Class: Any","text":"

URI: linkml:Any

erDiagram\nAny {\n\n}\n\n\n\n
"},{"location":"treatment/Any/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"treatment/Any/#usages","title":"Usages","text":"used by used in type used ExtractionResult extracted_object range Any ExtractionResult named_entities range Any"},{"location":"treatment/Any/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Any/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Any/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:Any native treatment:Any"},{"location":"treatment/Any/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Any/#direct","title":"Direct","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/treatment\nclass_uri: linkml:Any\n\n
"},{"location":"treatment/Any/#induced","title":"Induced","text":"
name: Any\nfrom_schema: http://w3id.org/ontogpt/treatment\nclass_uri: linkml:Any\n\n
"},{"location":"treatment/Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"treatment/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Boolean/#schema-source","title":"Schema Source","text":""},{"location":"treatment/CHEBIDrugType/","title":"Enum: CHEBIDrugType","text":"

URI: CHEBIDrugType

This is a dynamic enum

"},{"location":"treatment/CHEBIDrugType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/CHEBIDrugType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/CHEBIDrugType/#linkml-source","title":"LinkML Source","text":"
name: CHEBIDrugType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:chebi\n  source_nodes:\n  - CHEBI:23888\n  relationship_types:\n  - rdfs:subClassOf\n  - RO:0000087\n\n
"},{"location":"treatment/CompoundExpression/","title":"Class: CompoundExpression","text":"

URI: treatment:CompoundExpression

erDiagram\nCompoundExpression {\n\n}\n\n\n\n
"},{"location":"treatment/CompoundExpression/#inheritance","title":"Inheritance","text":""},{"location":"treatment/CompoundExpression/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"treatment/CompoundExpression/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/CompoundExpression/#schema-source","title":"Schema Source","text":""},{"location":"treatment/CompoundExpression/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:CompoundExpression native treatment:CompoundExpression"},{"location":"treatment/CompoundExpression/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/CompoundExpression/#direct","title":"Direct","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/treatment\nabstract: true\n\n
"},{"location":"treatment/CompoundExpression/#induced","title":"Induced","text":"
name: CompoundExpression\nfrom_schema: http://w3id.org/ontogpt/treatment\nabstract: true\n\n
"},{"location":"treatment/Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"treatment/Curie/#comments","title":"Comments","text":""},{"location":"treatment/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Curie/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"treatment/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Date/#schema-source","title":"Schema Source","text":""},{"location":"treatment/DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"treatment/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"treatment/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Datetime/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"treatment/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Decimal/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Disease/","title":"Class: Disease","text":"

URI: treatment:Disease

erDiagram\nDisease {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Disease/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Disease/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Disease/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary disease range Disease"},{"location":"treatment/Disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Disease/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:mondo"},{"location":"treatment/Disease/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Disease native treatment:Disease"},{"location":"treatment/Disease/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Disease/#direct","title":"Direct","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/Disease/#induced","title":"Induced","text":"
name: Disease\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:mondo\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Disease\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/DiseaseTreatmentSummary/","title":"Class: DiseaseTreatmentSummary","text":"

URI: treatment:DiseaseTreatmentSummary

erDiagram\nDiseaseTreatmentSummary {\n\n}\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nDrug {\n    string id  \n    string label  \n}\nDisease {\n    string id  \n    string label  \n}\n\nDiseaseTreatmentSummary ||--|o Disease : \"disease\"\nDiseaseTreatmentSummary ||--}o Drug : \"drugs\"\nDiseaseTreatmentSummary ||--}o Treatment : \"treatments\"\nDiseaseTreatmentSummary ||--}o Treatment : \"contraindications\"\nDiseaseTreatmentSummary ||--}o TreatmentMechanism : \"treatment_mechanisms\"\nDiseaseTreatmentSummary ||--}o TreatmentEfficacy : \"treatment_efficacies\"\nDiseaseTreatmentSummary ||--}o TreatmentAdverseEffect : \"treatment_adverse_effects\"\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"treatment/DiseaseTreatmentSummary/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance disease 0..1 Disease the name of the disease that is treated direct drugs 0..* Drug semicolon-separated list of named small molecule drugs direct treatments 0..* Treatment semicolon-separated list of therapies and treatments are indicated for treati... direct contraindications 0..* Treatment semicolon-separated list of therapies and treatments that are contra-indicate... direct treatment_mechanisms 0..* TreatmentMechanism semicolon-separated list of treatment to asterisk-separated mechanism associa... direct treatment_efficacies 0..* TreatmentEfficacy semicolon-separated list of treatment to efficacy associations, e direct treatment_adverse_effects 0..* TreatmentAdverseEffect semicolon-separated list of treatment to adverse effect associations, e direct"},{"location":"treatment/DiseaseTreatmentSummary/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/DiseaseTreatmentSummary/#schema-source","title":"Schema Source","text":""},{"location":"treatment/DiseaseTreatmentSummary/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:DiseaseTreatmentSummary native treatment:DiseaseTreatmentSummary"},{"location":"treatment/DiseaseTreatmentSummary/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/DiseaseTreatmentSummary/#direct","title":"Direct","text":"
name: DiseaseTreatmentSummary\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  disease:\n    name: disease\n    description: the name of the disease that is treated.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: Disease\n  drugs:\n    name: drugs\n    description: semicolon-separated list of named small molecule drugs\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: Drug\n  treatments:\n    name: treatments\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Imatinib, exercise, surgery\n    description: semicolon-separated list of therapies and treatments are indicated\n      for treating the disease.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: Treatment\n  contraindications:\n    name: contraindications\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Beta-blockers, exercise, surgery\n    description: semicolon-separated list of therapies and treatments that are contra-indicated\n      for the disease, and should not be used, due to risk of adverse effects.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: Treatment\n  treatment_mechanisms:\n    name: treatment_mechanisms\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to asterisk-separated mechanism\n      associations\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: TreatmentMechanism\n  treatment_efficacies:\n    name: treatment_efficacies\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to efficacy associations, e.g.\n      Imatinib*effective\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: TreatmentEfficacy\n  treatment_adverse_effects:\n    name: treatment_adverse_effects\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to adverse effect associations,\n      e.g. Imatinib*nausea\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: TreatmentAdverseEffect\ntree_root: true\n\n
"},{"location":"treatment/DiseaseTreatmentSummary/#induced","title":"Induced","text":"
name: DiseaseTreatmentSummary\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  disease:\n    name: disease\n    description: the name of the disease that is treated.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: disease\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: Disease\n  drugs:\n    name: drugs\n    description: semicolon-separated list of named small molecule drugs\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: drugs\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: Drug\n  treatments:\n    name: treatments\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Imatinib, exercise, surgery\n    description: semicolon-separated list of therapies and treatments are indicated\n      for treating the disease.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: treatments\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: Treatment\n  contraindications:\n    name: contraindications\n    annotations:\n      prompt.examples:\n        tag: prompt.examples\n        value: Beta-blockers, exercise, surgery\n    description: semicolon-separated list of therapies and treatments that are contra-indicated\n      for the disease, and should not be used, due to risk of adverse effects.\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: contraindications\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: Treatment\n  treatment_mechanisms:\n    name: treatment_mechanisms\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to asterisk-separated mechanism\n      associations\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: treatment_mechanisms\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: TreatmentMechanism\n  treatment_efficacies:\n    name: treatment_efficacies\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to efficacy associations, e.g.\n      Imatinib*effective\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: treatment_efficacies\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: TreatmentEfficacy\n  treatment_adverse_effects:\n    name: treatment_adverse_effects\n    annotations:\n      prompt.separator:\n        tag: prompt.separator\n        value: '*'\n    description: semicolon-separated list of treatment to adverse effect associations,\n      e.g. Imatinib*nausea\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: treatment_adverse_effects\n    owner: DiseaseTreatmentSummary\n    domain_of:\n    - DiseaseTreatmentSummary\n    range: TreatmentAdverseEffect\ntree_root: true\n\n
"},{"location":"treatment/Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"treatment/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Double/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Drug/","title":"Class: Drug","text":"

URI: treatment:Drug

erDiagram\nDrug {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Drug/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Drug/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Drug/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary drugs range Drug"},{"location":"treatment/Drug/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Drug/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:chebi, sqlite:obo:drugbank"},{"location":"treatment/Drug/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Drug/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Drug native treatment:Drug"},{"location":"treatment/Drug/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Drug/#direct","title":"Direct","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/Drug/#induced","title":"Induced","text":"
name: Drug\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:chebi, sqlite:obo:drugbank\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Drug\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/ExtractionResult/","title":"Class: ExtractionResult","text":"

A result of extracting knowledge on text

URI: treatment:ExtractionResult

erDiagram\nExtractionResult {\n    string input_id  \n    string input_title  \n    string input_text  \n    string raw_completion_output  \n    string prompt  \n}\nAny {\n\n}\n\nExtractionResult ||--|o Any : \"extracted_object\"\nExtractionResult ||--}o Any : \"named_entities\"\n\n
"},{"location":"treatment/ExtractionResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_id 0..1 String direct input_title 0..1 String direct input_text 0..1 String direct raw_completion_output 0..1 String direct prompt 0..1 String direct extracted_object 0..1 Any The complex objects extracted from the text direct named_entities 0..* Any Named entities extracted from the text direct"},{"location":"treatment/ExtractionResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/ExtractionResult/#schema-source","title":"Schema Source","text":""},{"location":"treatment/ExtractionResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:ExtractionResult native treatment:ExtractionResult"},{"location":"treatment/ExtractionResult/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/ExtractionResult/#direct","title":"Direct","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"treatment/ExtractionResult/#induced","title":"Induced","text":"
name: ExtractionResult\ndescription: A result of extracting knowledge on text\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  input_id:\n    name: input_id\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: input_id\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_title:\n    name: input_title\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: input_title\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  input_text:\n    name: input_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: input_text\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  raw_completion_output:\n    name: raw_completion_output\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: raw_completion_output\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  prompt:\n    name: prompt\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: prompt\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: string\n  extracted_object:\n    name: extracted_object\n    description: The complex objects extracted from the text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: extracted_object\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n  named_entities:\n    name: named_entities\n    description: Named entities extracted from the text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: named_entities\n    owner: ExtractionResult\n    domain_of:\n    - ExtractionResult\n    range: Any\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"treatment/Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"treatment/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Float/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Gene/","title":"Class: Gene","text":"

URI: treatment:Gene

erDiagram\nGene {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Gene/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Gene/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Gene/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"treatment/Gene/#annotations","title":"Annotations","text":"property value annotators gilda:, obo:sql:hgnc, bioportal:hgnc-nr"},{"location":"treatment/Gene/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Gene native treatment:Gene"},{"location":"treatment/Gene/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Gene/#direct","title":"Direct","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, obo:sql:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/Gene/#induced","title":"Induced","text":"
name: Gene\nid_prefixes:\n- HGNC\nannotations:\n  annotators:\n    tag: annotators\n    value: gilda:, obo:sql:hgnc, bioportal:hgnc-nr\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Gene\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"treatment/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Integer/#schema-source","title":"Schema Source","text":""},{"location":"treatment/MAXOActionType/","title":"Enum: MAXOActionType","text":"

URI: MAXOActionType

This is a dynamic enum

"},{"location":"treatment/MAXOActionType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/MAXOActionType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/MAXOActionType/#linkml-source","title":"LinkML Source","text":"
name: MAXOActionType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:maxo\n  source_nodes:\n  - MAXO:0000001\n\n
"},{"location":"treatment/MESHTherapeuticType/","title":"Enum: MESHTherapeuticType","text":"

URI: MESHTherapeuticType

This is a dynamic enum

"},{"location":"treatment/MESHTherapeuticType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/MESHTherapeuticType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/MESHTherapeuticType/#linkml-source","title":"LinkML Source","text":"
name: MESHTherapeuticType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:mesh\n  source_nodes:\n  - MESH:D013812\n\n
"},{"location":"treatment/Mechanism/","title":"Class: Mechanism","text":"

URI: treatment:Mechanism

erDiagram\nMechanism {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Mechanism/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Mechanism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Mechanism/#usages","title":"Usages","text":"used by used in type used TreatmentMechanism mechanism range Mechanism"},{"location":"treatment/Mechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Mechanism/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh"},{"location":"treatment/Mechanism/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Mechanism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Mechanism native treatment:Mechanism"},{"location":"treatment/Mechanism/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Mechanism/#direct","title":"Direct","text":"
name: Mechanism\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/Mechanism/#induced","title":"Induced","text":"
name: Mechanism\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Mechanism\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Mechanism\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/NCITDrugType/","title":"Enum: NCITDrugType","text":"

URI: NCITDrugType

This is a dynamic enum

"},{"location":"treatment/NCITDrugType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/NCITDrugType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NCITDrugType/#linkml-source","title":"LinkML Source","text":"
name: NCITDrugType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C1908\n\n
"},{"location":"treatment/NCITTActivityType/","title":"Enum: NCITTActivityType","text":"

URI: NCITTActivityType

This is a dynamic enum

"},{"location":"treatment/NCITTActivityType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/NCITTActivityType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NCITTActivityType/#linkml-source","title":"LinkML Source","text":"
name: NCITTActivityType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C43431\n\n
"},{"location":"treatment/NCITTreatmentType/","title":"Enum: NCITTreatmentType","text":"

URI: NCITTreatmentType

This is a dynamic enum

"},{"location":"treatment/NCITTreatmentType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/NCITTreatmentType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NCITTreatmentType/#linkml-source","title":"LinkML Source","text":"
name: NCITTreatmentType\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nreachable_from:\n  source_ontology: obo:ncit\n  source_nodes:\n  - NCIT:C25218\n\n
"},{"location":"treatment/NamedEntity/","title":"Class: NamedEntity","text":"

URI: treatment:NamedEntity

erDiagram\nNamedEntity {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/NamedEntity/#inheritance","title":"Inheritance","text":""},{"location":"treatment/NamedEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity direct label 0..1 String The label (name) of the named thing direct"},{"location":"treatment/NamedEntity/#usages","title":"Usages","text":"used by used in type used Triple subject range NamedEntity Triple object range NamedEntity Triple subject_qualifier range NamedEntity Triple object_qualifier range NamedEntity"},{"location":"treatment/NamedEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/NamedEntity/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NamedEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:NamedEntity native treatment:NamedEntity"},{"location":"treatment/NamedEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/NamedEntity/#direct","title":"Direct","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/treatment\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    range: string\n\n
"},{"location":"treatment/NamedEntity/#induced","title":"Induced","text":"
name: NamedEntity\nfrom_schema: http://w3id.org/ontogpt/treatment\nabstract: true\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: NamedEntity\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"treatment/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Ncname/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"treatment/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NullDataOptions/","title":"Enum: NullDataOptions","text":"

URI: NullDataOptions

"},{"location":"treatment/NullDataOptions/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UNSPECIFIED_METHOD_OF_ADMINISTRATION NCIT:C149701 NOT_APPLICABLE NCIT:C18902 NOT_MENTIONED None"},{"location":"treatment/NullDataOptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/NullDataOptions/#schema-source","title":"Schema Source","text":""},{"location":"treatment/NullDataOptions/#linkml-source","title":"LinkML Source","text":"
name: NullDataOptions\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\npermissible_values:\n  UNSPECIFIED_METHOD_OF_ADMINISTRATION:\n    text: UNSPECIFIED_METHOD_OF_ADMINISTRATION\n    meaning: NCIT:C149701\n  NOT_APPLICABLE:\n    text: NOT_APPLICABLE\n    meaning: NCIT:C18902\n    aliases:\n    - not applicable\n    - N/A\n  NOT_MENTIONED:\n    text: NOT_MENTIONED\n\n
"},{"location":"treatment/Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"treatment/Objectidentifier/#comments","title":"Comments","text":""},{"location":"treatment/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Publication/","title":"Class: Publication","text":"

URI: treatment:Publication

erDiagram\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\n\n\n
"},{"location":"treatment/Publication/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String The publication identifier direct title 0..1 String The title of the publication direct abstract 0..1 String The abstract of the publication direct combined_text 0..1 String direct full_text 0..1 String The full text of the publication direct"},{"location":"treatment/Publication/#usages","title":"Usages","text":"used by used in type used TextWithTriples publication range Publication"},{"location":"treatment/Publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Publication/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Publication/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Publication native treatment:Publication"},{"location":"treatment/Publication/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Publication/#direct","title":"Direct","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/treatment\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n\n
"},{"location":"treatment/Publication/#induced","title":"Induced","text":"
name: Publication\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  id:\n    name: id\n    description: The publication identifier\n    from_schema: http://w3id.org/ontogpt/treatment\n    alias: id\n    owner: Publication\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n  title:\n    name: title\n    description: The title of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: title\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  abstract:\n    name: abstract\n    description: The abstract of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: abstract\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  combined_text:\n    name: combined_text\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: combined_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n  full_text:\n    name: full_text\n    description: The full text of the publication\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: full_text\n    owner: Publication\n    domain_of:\n    - Publication\n    range: string\n\n
"},{"location":"treatment/RelationshipType/","title":"Class: RelationshipType","text":"

URI: treatment:RelationshipType

erDiagram\nRelationshipType {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/RelationshipType/#inheritance","title":"Inheritance","text":""},{"location":"treatment/RelationshipType/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/RelationshipType/#usages","title":"Usages","text":"used by used in type used Triple predicate range RelationshipType"},{"location":"treatment/RelationshipType/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/RelationshipType/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"treatment/RelationshipType/#schema-source","title":"Schema Source","text":""},{"location":"treatment/RelationshipType/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:RelationshipType native treatment:RelationshipType"},{"location":"treatment/RelationshipType/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/RelationshipType/#direct","title":"Direct","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/RelationshipType/#induced","title":"Induced","text":"
name: RelationshipType\nid_prefixes:\n- RO\n- biolink\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: RelationshipType\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"treatment/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/String/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Symptom/","title":"Class: Symptom","text":"

URI: treatment:Symptom

erDiagram\nSymptom {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Symptom/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Symptom/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Symptom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Symptom/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"treatment/Symptom/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:hp"},{"location":"treatment/Symptom/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Symptom/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Symptom native treatment:Symptom"},{"location":"treatment/Symptom/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Symptom/#direct","title":"Direct","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\n\n
"},{"location":"treatment/Symptom/#induced","title":"Induced","text":"
name: Symptom\nid_prefixes:\n- HP\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:hp\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Symptom\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/TextWithTriples/","title":"Class: TextWithTriples","text":"

URI: treatment:TextWithTriples

erDiagram\nTextWithTriples {\n\n}\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\nPublication {\n    string id  \n    string title  \n    string abstract  \n    string combined_text  \n    string full_text  \n}\n\nTextWithTriples ||--|o Publication : \"publication\"\nTextWithTriples ||--}o Triple : \"triples\"\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"treatment/TextWithTriples/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance publication 0..1 Publication direct triples 0..* Triple direct"},{"location":"treatment/TextWithTriples/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/TextWithTriples/#schema-source","title":"Schema Source","text":""},{"location":"treatment/TextWithTriples/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:TextWithTriples native treatment:TextWithTriples"},{"location":"treatment/TextWithTriples/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/TextWithTriples/#direct","title":"Direct","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"treatment/TextWithTriples/#induced","title":"Induced","text":"
name: TextWithTriples\nfrom_schema: http://w3id.org/ontogpt/treatment\nattributes:\n  publication:\n    name: publication\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: publication\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Publication\n    inlined: true\n  triples:\n    name: triples\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: triples\n    owner: TextWithTriples\n    domain_of:\n    - TextWithTriples\n    range: Triple\n    inlined: true\n    inlined_as_list: true\n\n
"},{"location":"treatment/Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:dateTime

"},{"location":"treatment/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Time/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Treatment/","title":"Class: Treatment","text":"

URI: treatment:Treatment

erDiagram\nTreatment {\n    string id  \n    string label  \n}\n\n\n\n
"},{"location":"treatment/Treatment/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Treatment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1..1 String A unique identifier for the named entity NamedEntity label 0..1 String The label (name) of the named thing NamedEntity"},{"location":"treatment/Treatment/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary treatments range Treatment DiseaseTreatmentSummary contraindications range Treatment TreatmentMechanism treatment range Treatment TreatmentAdverseEffect treatment range Treatment TreatmentEfficacy treatment range Treatment"},{"location":"treatment/Treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Treatment/#annotations","title":"Annotations","text":"property value annotators sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi"},{"location":"treatment/Treatment/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Treatment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Treatment native treatment:Treatment"},{"location":"treatment/Treatment/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Treatment/#direct","title":"Direct","text":"
name: Treatment\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nvalues_from:\n- NCITDrugType\n- NCITTreatmentType\n- NCITActivityType\n- MAXOTreatmentType\n- MESHTherapeuticType\n- CHEBIDrugType\n\n
"},{"location":"treatment/Treatment/#induced","title":"Induced","text":"
name: Treatment\nannotations:\n  annotators:\n    tag: annotators\n    value: sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: NamedEntity\nvalues_from:\n- NCITDrugType\n- NCITTreatmentType\n- NCITActivityType\n- MAXOTreatmentType\n- MESHTherapeuticType\n- CHEBIDrugType\nattributes:\n  id:\n    name: id\n    annotations:\n      prompt.skip:\n        tag: prompt.skip\n        value: 'true'\n    description: A unique identifier for the named entity\n    comments:\n    - this is populated during the grounding and normalization step\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    - Publication\n    range: string\n    required: true\n  label:\n    name: label\n    annotations:\n      owl:\n        tag: owl\n        value: AnnotationProperty, AnnotationAssertion\n    description: The label (name) of the named thing\n    from_schema: http://w3id.org/ontogpt/treatment\n    aliases:\n    - name\n    rank: 1000\n    slot_uri: rdfs:label\n    alias: label\n    owner: Treatment\n    domain_of:\n    - NamedEntity\n    range: string\n\n
"},{"location":"treatment/TreatmentAdverseEffect/","title":"Class: TreatmentAdverseEffect","text":"

URI: treatment:TreatmentAdverseEffect

erDiagram\nTreatmentAdverseEffect {\n\n}\nAdverseEffect {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentAdverseEffect ||--|o Treatment : \"treatment\"\nTreatmentAdverseEffect ||--}o AdverseEffect : \"adverse_effects\"\n\n
"},{"location":"treatment/TreatmentAdverseEffect/#inheritance","title":"Inheritance","text":""},{"location":"treatment/TreatmentAdverseEffect/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct adverse_effects 0..* AdverseEffect direct"},{"location":"treatment/TreatmentAdverseEffect/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary treatment_adverse_effects range TreatmentAdverseEffect"},{"location":"treatment/TreatmentAdverseEffect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/TreatmentAdverseEffect/#schema-source","title":"Schema Source","text":""},{"location":"treatment/TreatmentAdverseEffect/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:TreatmentAdverseEffect native treatment:TreatmentAdverseEffect"},{"location":"treatment/TreatmentAdverseEffect/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/TreatmentAdverseEffect/#direct","title":"Direct","text":"
name: TreatmentAdverseEffect\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    range: Treatment\n  adverse_effects:\n    name: adverse_effects\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    range: AdverseEffect\n\n
"},{"location":"treatment/TreatmentAdverseEffect/#induced","title":"Induced","text":"
name: TreatmentAdverseEffect\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    alias: treatment\n    owner: TreatmentAdverseEffect\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  adverse_effects:\n    name: adverse_effects\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    multivalued: true\n    alias: adverse_effects\n    owner: TreatmentAdverseEffect\n    domain_of:\n    - TreatmentAdverseEffect\n    range: AdverseEffect\n\n
"},{"location":"treatment/TreatmentEfficacy/","title":"Class: TreatmentEfficacy","text":"

URI: treatment:TreatmentEfficacy

erDiagram\nTreatmentEfficacy {\n    string efficacy  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentEfficacy ||--|o Treatment : \"treatment\"\n\n
"},{"location":"treatment/TreatmentEfficacy/#inheritance","title":"Inheritance","text":""},{"location":"treatment/TreatmentEfficacy/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct efficacy 0..1 String direct"},{"location":"treatment/TreatmentEfficacy/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary treatment_efficacies range TreatmentEfficacy"},{"location":"treatment/TreatmentEfficacy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/TreatmentEfficacy/#schema-source","title":"Schema Source","text":""},{"location":"treatment/TreatmentEfficacy/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:TreatmentEfficacy native treatment:TreatmentEfficacy"},{"location":"treatment/TreatmentEfficacy/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/TreatmentEfficacy/#direct","title":"Direct","text":"
name: TreatmentEfficacy\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    range: Treatment\n  efficacy:\n    name: efficacy\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: string\n\n
"},{"location":"treatment/TreatmentEfficacy/#induced","title":"Induced","text":"
name: TreatmentEfficacy\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    alias: treatment\n    owner: TreatmentEfficacy\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  efficacy:\n    name: efficacy\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: efficacy\n    owner: TreatmentEfficacy\n    domain_of:\n    - TreatmentEfficacy\n    range: string\n\n
"},{"location":"treatment/TreatmentMechanism/","title":"Class: TreatmentMechanism","text":"

URI: treatment:TreatmentMechanism

erDiagram\nTreatmentMechanism {\n\n}\nMechanism {\n    string id  \n    string label  \n}\nTreatment {\n    string id  \n    string label  \n}\n\nTreatmentMechanism ||--|o Treatment : \"treatment\"\nTreatmentMechanism ||--|o Mechanism : \"mechanism\"\n\n
"},{"location":"treatment/TreatmentMechanism/#inheritance","title":"Inheritance","text":""},{"location":"treatment/TreatmentMechanism/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance treatment 0..1 Treatment direct mechanism 0..1 Mechanism direct"},{"location":"treatment/TreatmentMechanism/#usages","title":"Usages","text":"used by used in type used DiseaseTreatmentSummary treatment_mechanisms range TreatmentMechanism"},{"location":"treatment/TreatmentMechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/TreatmentMechanism/#schema-source","title":"Schema Source","text":""},{"location":"treatment/TreatmentMechanism/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:TreatmentMechanism native treatment:TreatmentMechanism"},{"location":"treatment/TreatmentMechanism/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/TreatmentMechanism/#direct","title":"Direct","text":"
name: TreatmentMechanism\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: Treatment\n  mechanism:\n    name: mechanism\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: Mechanism\n\n
"},{"location":"treatment/TreatmentMechanism/#induced","title":"Induced","text":"
name: TreatmentMechanism\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nattributes:\n  treatment:\n    name: treatment\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: treatment\n    owner: TreatmentMechanism\n    domain_of:\n    - TreatmentMechanism\n    - TreatmentAdverseEffect\n    - TreatmentEfficacy\n    range: Treatment\n  mechanism:\n    name: mechanism\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: mechanism\n    owner: TreatmentMechanism\n    domain_of:\n    - TreatmentMechanism\n    range: Mechanism\n\n
"},{"location":"treatment/Triple/","title":"Class: Triple","text":"

Abstract parent for Relation Extraction tasks

URI: treatment:Triple

erDiagram\nTriple {\n    string qualifier  \n}\nNamedEntity {\n    string id  \n    string label  \n}\nRelationshipType {\n    string id  \n    string label  \n}\n\nTriple ||--|o NamedEntity : \"subject\"\nTriple ||--|o RelationshipType : \"predicate\"\nTriple ||--|o NamedEntity : \"object\"\nTriple ||--|o NamedEntity : \"subject_qualifier\"\nTriple ||--|o NamedEntity : \"object_qualifier\"\n\n
"},{"location":"treatment/Triple/#inheritance","title":"Inheritance","text":""},{"location":"treatment/Triple/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 0..1 NamedEntity direct predicate 0..1 RelationshipType direct object 0..1 NamedEntity direct qualifier 0..1 String A qualifier for the statements, e direct subject_qualifier 0..1 NamedEntity An optional qualifier or modifier for the subject of the statement, e direct object_qualifier 0..1 NamedEntity An optional qualifier or modifier for the object of the statement, e direct"},{"location":"treatment/Triple/#usages","title":"Usages","text":"used by used in type used TextWithTriples triples range Triple"},{"location":"treatment/Triple/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Triple/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Triple/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self treatment:Triple native treatment:Triple"},{"location":"treatment/Triple/#linkml-source","title":"LinkML Source","text":""},{"location":"treatment/Triple/#direct","title":"Direct","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    range: NamedEntity\n\n
"},{"location":"treatment/Triple/#induced","title":"Induced","text":"
name: Triple\ndescription: Abstract parent for Relation Extraction tasks\nfrom_schema: http://w3id.org/ontogpt/treatment\nis_a: CompoundExpression\nabstract: true\nattributes:\n  subject:\n    name: subject\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: subject\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  predicate:\n    name: predicate\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: predicate\n    owner: Triple\n    domain_of:\n    - Triple\n    range: RelationshipType\n  object:\n    name: object\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: object\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  qualifier:\n    name: qualifier\n    description: A qualifier for the statements, e.g. \"NOT\" for negation\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: string\n  subject_qualifier:\n    name: subject_qualifier\n    description: An optional qualifier or modifier for the subject of the statement,\n      e.g. \"high dose\" or \"intravenously administered\"\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: subject_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n  object_qualifier:\n    name: object_qualifier\n    description: An optional qualifier or modifier for the object of the statement,\n      e.g. \"severe\" or \"with additional complications\"\n    from_schema: http://w3id.org/ontogpt/treatment\n    rank: 1000\n    alias: object_qualifier\n    owner: Triple\n    domain_of:\n    - Triple\n    range: NamedEntity\n\n
"},{"location":"treatment/Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"treatment/Uri/#comments","title":"Comments","text":""},{"location":"treatment/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Uri/#schema-source","title":"Schema Source","text":""},{"location":"treatment/Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"treatment/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"treatment/abstract/","title":"Slot: abstract","text":"

The abstract of the publication

URI: treatment:abstract

"},{"location":"treatment/abstract/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"treatment/abstract/#properties","title":"Properties","text":""},{"location":"treatment/abstract/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/abstract/#schema-source","title":"Schema Source","text":""},{"location":"treatment/abstract/#linkml-source","title":"LinkML Source","text":"
name: abstract\ndescription: The abstract of the publication\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: abstract\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"treatment/adverse_effects/","title":"Slot: adverse_effects","text":"

URI: treatment:adverse_effects

"},{"location":"treatment/adverse_effects/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentAdverseEffect no"},{"location":"treatment/adverse_effects/#properties","title":"Properties","text":""},{"location":"treatment/adverse_effects/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/adverse_effects/#schema-source","title":"Schema Source","text":""},{"location":"treatment/adverse_effects/#linkml-source","title":"LinkML Source","text":"
name: adverse_effects\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: adverse_effects\nowner: TreatmentAdverseEffect\ndomain_of:\n- TreatmentAdverseEffect\nrange: AdverseEffect\n\n
"},{"location":"treatment/combined_text/","title":"Slot: combined_text","text":"

URI: treatment:combined_text

"},{"location":"treatment/combined_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"treatment/combined_text/#properties","title":"Properties","text":""},{"location":"treatment/combined_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/combined_text/#schema-source","title":"Schema Source","text":""},{"location":"treatment/combined_text/#linkml-source","title":"LinkML Source","text":"
name: combined_text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: combined_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"treatment/contraindications/","title":"Slot: contraindications","text":"

semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.

URI: treatment:contraindications

"},{"location":"treatment/contraindications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/contraindications/#properties","title":"Properties","text":""},{"location":"treatment/contraindications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/contraindications/#annotations","title":"Annotations","text":"property value prompt.examples Beta-blockers, exercise, surgery"},{"location":"treatment/contraindications/#schema-source","title":"Schema Source","text":""},{"location":"treatment/contraindications/#linkml-source","title":"LinkML Source","text":"
name: contraindications\nannotations:\n  prompt.examples:\n    tag: prompt.examples\n    value: Beta-blockers, exercise, surgery\ndescription: semicolon-separated list of therapies and treatments that are contra-indicated\n  for the disease, and should not be used, due to risk of adverse effects.\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: contraindications\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: Treatment\n\n
"},{"location":"treatment/disease/","title":"Slot: disease","text":"

the name of the disease that is treated.

URI: treatment:disease

"},{"location":"treatment/disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/disease/#properties","title":"Properties","text":""},{"location":"treatment/disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/disease/#schema-source","title":"Schema Source","text":""},{"location":"treatment/disease/#linkml-source","title":"LinkML Source","text":"
name: disease\ndescription: the name of the disease that is treated.\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: disease\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: Disease\n\n
"},{"location":"treatment/drugs/","title":"Slot: drugs","text":"

semicolon-separated list of named small molecule drugs

URI: treatment:drugs

"},{"location":"treatment/drugs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/drugs/#properties","title":"Properties","text":""},{"location":"treatment/drugs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/drugs/#schema-source","title":"Schema Source","text":""},{"location":"treatment/drugs/#linkml-source","title":"LinkML Source","text":"
name: drugs\ndescription: semicolon-separated list of named small molecule drugs\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: drugs\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: Drug\n\n
"},{"location":"treatment/efficacy/","title":"Slot: efficacy","text":"

URI: treatment:efficacy

"},{"location":"treatment/efficacy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentEfficacy no"},{"location":"treatment/efficacy/#properties","title":"Properties","text":""},{"location":"treatment/efficacy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/efficacy/#schema-source","title":"Schema Source","text":""},{"location":"treatment/efficacy/#linkml-source","title":"LinkML Source","text":"
name: efficacy\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: efficacy\nowner: TreatmentEfficacy\ndomain_of:\n- TreatmentEfficacy\nrange: string\n\n
"},{"location":"treatment/extracted_object/","title":"Slot: extracted_object","text":"

The complex objects extracted from the text

URI: treatment:extracted_object

"},{"location":"treatment/extracted_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/extracted_object/#properties","title":"Properties","text":""},{"location":"treatment/extracted_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/extracted_object/#schema-source","title":"Schema Source","text":""},{"location":"treatment/extracted_object/#linkml-source","title":"LinkML Source","text":"
name: extracted_object\ndescription: The complex objects extracted from the text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: extracted_object\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\n\n
"},{"location":"treatment/full_text/","title":"Slot: full_text","text":"

The full text of the publication

URI: treatment:full_text

"},{"location":"treatment/full_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Publication no"},{"location":"treatment/full_text/#properties","title":"Properties","text":""},{"location":"treatment/full_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/full_text/#schema-source","title":"Schema Source","text":""},{"location":"treatment/full_text/#linkml-source","title":"LinkML Source","text":"
name: full_text\ndescription: The full text of the publication\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: full_text\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"treatment/id/","title":"Slot: id","text":"

URI: treatment:id

"},{"location":"treatment/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Symptom no Disease no AdverseEffect no Treatment no Mechanism no Drug no NamedEntity no RelationshipType no Publication no"},{"location":"treatment/id/#properties","title":"Properties","text":""},{"location":"treatment/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/id/#linkml-source","title":"LinkML Source","text":"
name: id\nalias: id\ndomain_of:\n- NamedEntity\n- Publication\nrange: string\n\n
"},{"location":"treatment/input_id/","title":"Slot: input_id","text":"

URI: treatment:input_id

"},{"location":"treatment/input_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/input_id/#properties","title":"Properties","text":""},{"location":"treatment/input_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/input_id/#schema-source","title":"Schema Source","text":""},{"location":"treatment/input_id/#linkml-source","title":"LinkML Source","text":"
name: input_id\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: input_id\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"treatment/input_text/","title":"Slot: input_text","text":"

URI: treatment:input_text

"},{"location":"treatment/input_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/input_text/#properties","title":"Properties","text":""},{"location":"treatment/input_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/input_text/#schema-source","title":"Schema Source","text":""},{"location":"treatment/input_text/#linkml-source","title":"LinkML Source","text":"
name: input_text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: input_text\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"treatment/input_title/","title":"Slot: input_title","text":"

URI: treatment:input_title

"},{"location":"treatment/input_title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/input_title/#properties","title":"Properties","text":""},{"location":"treatment/input_title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/input_title/#schema-source","title":"Schema Source","text":""},{"location":"treatment/input_title/#linkml-source","title":"LinkML Source","text":"
name: input_title\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: input_title\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"treatment/label/","title":"Slot: label","text":"

The label (name) of the named thing

URI: rdfs:label

"},{"location":"treatment/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Gene no Symptom no Disease no AdverseEffect no Treatment no Mechanism no Drug no NamedEntity no RelationshipType no"},{"location":"treatment/label/#properties","title":"Properties","text":""},{"location":"treatment/label/#aliases","title":"Aliases","text":""},{"location":"treatment/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/label/#annotations","title":"Annotations","text":"property value owl AnnotationProperty, AnnotationAssertion"},{"location":"treatment/label/#schema-source","title":"Schema Source","text":""},{"location":"treatment/label/#linkml-source","title":"LinkML Source","text":"
name: label\nannotations:\n  owl:\n    tag: owl\n    value: AnnotationProperty, AnnotationAssertion\ndescription: The label (name) of the named thing\nfrom_schema: http://w3id.org/ontogpt/treatment\naliases:\n- name\nrank: 1000\nslot_uri: rdfs:label\nalias: label\nowner: NamedEntity\ndomain_of:\n- NamedEntity\nrange: string\n\n
"},{"location":"treatment/mechanism/","title":"Slot: mechanism","text":"

URI: treatment:mechanism

"},{"location":"treatment/mechanism/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentMechanism no"},{"location":"treatment/mechanism/#properties","title":"Properties","text":""},{"location":"treatment/mechanism/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/mechanism/#schema-source","title":"Schema Source","text":""},{"location":"treatment/mechanism/#linkml-source","title":"LinkML Source","text":"
name: mechanism\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: mechanism\nowner: TreatmentMechanism\ndomain_of:\n- TreatmentMechanism\nrange: Mechanism\n\n
"},{"location":"treatment/named_entities/","title":"Slot: named_entities","text":"

Named entities extracted from the text

URI: treatment:named_entities

"},{"location":"treatment/named_entities/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/named_entities/#properties","title":"Properties","text":""},{"location":"treatment/named_entities/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/named_entities/#schema-source","title":"Schema Source","text":""},{"location":"treatment/named_entities/#linkml-source","title":"LinkML Source","text":"
name: named_entities\ndescription: Named entities extracted from the text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: named_entities\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: Any\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"treatment/object/","title":"Slot: object","text":"

URI: treatment:object

"},{"location":"treatment/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"treatment/object/#properties","title":"Properties","text":""},{"location":"treatment/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/object/#schema-source","title":"Schema Source","text":""},{"location":"treatment/object/#linkml-source","title":"LinkML Source","text":"
name: object\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: object\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"treatment/object_id/","title":"Slot: object_id","text":"

URI: treatment:object_id

"},{"location":"treatment/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"treatment/object_id/#properties","title":"Properties","text":""},{"location":"treatment/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/object_id/#schema-source","title":"Schema Source","text":""},{"location":"treatment/object_id/#linkml-source","title":"LinkML Source","text":"
name: object_id\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: object_id\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"treatment/object_qualifier/","title":"Slot: object_qualifier","text":"

An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"

URI: treatment:object_qualifier

"},{"location":"treatment/object_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"treatment/object_qualifier/#properties","title":"Properties","text":""},{"location":"treatment/object_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/object_qualifier/#schema-source","title":"Schema Source","text":""},{"location":"treatment/object_qualifier/#linkml-source","title":"LinkML Source","text":"
name: object_qualifier\ndescription: An optional qualifier or modifier for the object of the statement, e.g.\n  \"severe\" or \"with additional complications\"\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: object_qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: NamedEntity\n\n
"},{"location":"treatment/object_text/","title":"Slot: object_text","text":"

URI: treatment:object_text

"},{"location":"treatment/object_text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AnnotatorResult no"},{"location":"treatment/object_text/#properties","title":"Properties","text":""},{"location":"treatment/object_text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/object_text/#schema-source","title":"Schema Source","text":""},{"location":"treatment/object_text/#linkml-source","title":"LinkML Source","text":"
name: object_text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: object_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"treatment/predicate/","title":"Slot: predicate","text":"

URI: treatment:predicate

"},{"location":"treatment/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"treatment/predicate/#properties","title":"Properties","text":""},{"location":"treatment/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/predicate/#schema-source","title":"Schema Source","text":""},{"location":"treatment/predicate/#linkml-source","title":"LinkML Source","text":"
name: predicate\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: predicate\nowner: Triple\ndomain_of:\n- Triple\nrange: RelationshipType\n\n
"},{"location":"treatment/prompt/","title":"Slot: prompt","text":"

URI: treatment:prompt

"},{"location":"treatment/prompt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/prompt/#properties","title":"Properties","text":""},{"location":"treatment/prompt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/prompt/#schema-source","title":"Schema Source","text":""},{"location":"treatment/prompt/#linkml-source","title":"LinkML Source","text":"
name: prompt\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: prompt\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"treatment/publication/","title":"Slot: publication","text":"

URI: treatment:publication

"},{"location":"treatment/publication/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextWithTriples no"},{"location":"treatment/publication/#properties","title":"Properties","text":""},{"location":"treatment/publication/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/publication/#annotations","title":"Annotations","text":"property value prompt.skip true"},{"location":"treatment/publication/#schema-source","title":"Schema Source","text":""},{"location":"treatment/publication/#linkml-source","title":"LinkML Source","text":"
name: publication\nannotations:\n  prompt.skip:\n    tag: prompt.skip\n    value: 'true'\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: publication\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Publication\ninlined: true\n\n
"},{"location":"treatment/qualifier/","title":"Slot: qualifier","text":"

A qualifier for the statements, e.g. \"NOT\" for negation

URI: treatment:qualifier

"},{"location":"treatment/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Triple Abstract parent for Relation Extraction tasks no"},{"location":"treatment/qualifier/#properties","title":"Properties","text":""},{"location":"treatment/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/qualifier/#schema-source","title":"Schema Source","text":""},{"location":"treatment/qualifier/#linkml-source","title":"LinkML Source","text":"
name: qualifier\ndescription: A qualifier for the statements, e.g. \"NOT\" for negation\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: qualifier\nowner: Triple\ndomain_of:\n- Triple\nrange: string\n\n
"},{"location":"treatment/raw_completion_output/","title":"Slot: raw_completion_output","text":"

URI: treatment:raw_completion_output

"},{"location":"treatment/raw_completion_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExtractionResult A result of extracting knowledge on text no"},{"location":"treatment/raw_completion_output/#properties","title":"Properties","text":""},{"location":"treatment/raw_completion_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/raw_completion_output/#schema-source","title":"Schema Source","text":""},{"location":"treatment/raw_completion_output/#linkml-source","title":"LinkML Source","text":"
name: raw_completion_output\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: raw_completion_output\nowner: ExtractionResult\ndomain_of:\n- ExtractionResult\nrange: string\n\n
"},{"location":"treatment/subject/","title":"Slot: subject","text":"

URI: treatment:subject

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"},{"location":"treatment/subject_qualifier/","title":"Slot: subject_qualifier","text":"

An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"

URI: treatment:subject_qualifier

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"},{"location":"treatment/subject_text/","title":"Slot: subject_text","text":"

URI: treatment:subject_text

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name: subject_text\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: subject_text\nowner: AnnotatorResult\ndomain_of:\n- AnnotatorResult\nrange: string\n\n
"},{"location":"treatment/title/","title":"Slot: title","text":"

The title of the publication

URI: treatment:title

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name: title\ndescription: The title of the publication\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nalias: title\nowner: Publication\ndomain_of:\n- Publication\nrange: string\n\n
"},{"location":"treatment/treatment-template/","title":"treatment-template","text":"

A template for MAXO treatments

URI: http://w3id.org/ontogpt/treatment

"},{"location":"treatment/treatment/","title":"Slot: treatment","text":"

URI: treatment:treatment

"},{"location":"treatment/treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TreatmentMechanism no TreatmentAdverseEffect no TreatmentEfficacy no"},{"location":"treatment/treatment/#properties","title":"Properties","text":""},{"location":"treatment/treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/treatment/#linkml-source","title":"LinkML Source","text":"
name: treatment\nalias: treatment\ndomain_of:\n- TreatmentMechanism\n- TreatmentAdverseEffect\n- TreatmentEfficacy\nrange: string\n\n
"},{"location":"treatment/treatment_adverse_effects/","title":"Slot: treatment_adverse_effects","text":"

semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea

URI: treatment:treatment_adverse_effects

"},{"location":"treatment/treatment_adverse_effects/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/treatment_adverse_effects/#properties","title":"Properties","text":""},{"location":"treatment/treatment_adverse_effects/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/treatment_adverse_effects/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"treatment/treatment_adverse_effects/#schema-source","title":"Schema Source","text":""},{"location":"treatment/treatment_adverse_effects/#linkml-source","title":"LinkML Source","text":"
name: treatment_adverse_effects\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to adverse effect associations,\n  e.g. Imatinib*nausea\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: treatment_adverse_effects\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: TreatmentAdverseEffect\n\n
"},{"location":"treatment/treatment_efficacies/","title":"Slot: treatment_efficacies","text":"

semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective

URI: treatment:treatment_efficacies

"},{"location":"treatment/treatment_efficacies/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/treatment_efficacies/#properties","title":"Properties","text":""},{"location":"treatment/treatment_efficacies/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/treatment_efficacies/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"treatment/treatment_efficacies/#schema-source","title":"Schema Source","text":""},{"location":"treatment/treatment_efficacies/#linkml-source","title":"LinkML Source","text":"
name: treatment_efficacies\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to efficacy associations, e.g.\n  Imatinib*effective\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: treatment_efficacies\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: TreatmentEfficacy\n\n
"},{"location":"treatment/treatment_mechanisms/","title":"Slot: treatment_mechanisms","text":"

semicolon-separated list of treatment to asterisk-separated mechanism associations

URI: treatment:treatment_mechanisms

"},{"location":"treatment/treatment_mechanisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/treatment_mechanisms/#properties","title":"Properties","text":""},{"location":"treatment/treatment_mechanisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/treatment_mechanisms/#annotations","title":"Annotations","text":"property value prompt.separator *"},{"location":"treatment/treatment_mechanisms/#schema-source","title":"Schema Source","text":""},{"location":"treatment/treatment_mechanisms/#linkml-source","title":"LinkML Source","text":"
name: treatment_mechanisms\nannotations:\n  prompt.separator:\n    tag: prompt.separator\n    value: '*'\ndescription: semicolon-separated list of treatment to asterisk-separated mechanism\n  associations\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: treatment_mechanisms\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: TreatmentMechanism\n\n
"},{"location":"treatment/treatments/","title":"Slot: treatments","text":"

semicolon-separated list of therapies and treatments are indicated for treating the disease.

URI: treatment:treatments

"},{"location":"treatment/treatments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DiseaseTreatmentSummary no"},{"location":"treatment/treatments/#properties","title":"Properties","text":""},{"location":"treatment/treatments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"treatment/treatments/#annotations","title":"Annotations","text":"property value prompt.examples Imatinib, exercise, surgery"},{"location":"treatment/treatments/#schema-source","title":"Schema Source","text":""},{"location":"treatment/treatments/#linkml-source","title":"LinkML Source","text":"
name: treatments\nannotations:\n  prompt.examples:\n    tag: prompt.examples\n    value: Imatinib, exercise, surgery\ndescription: semicolon-separated list of therapies and treatments are indicated for\n  treating the disease.\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: treatments\nowner: DiseaseTreatmentSummary\ndomain_of:\n- DiseaseTreatmentSummary\nrange: Treatment\n\n
"},{"location":"treatment/triples/","title":"Slot: triples","text":"

URI: treatment:triples

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name: triples\nfrom_schema: http://w3id.org/ontogpt/treatment\nrank: 1000\nmultivalued: true\nalias: triples\nowner: TextWithTriples\ndomain_of:\n- TextWithTriples\nrange: Triple\ninlined: true\ninlined_as_list: true\n\n
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