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docs/evaluations.md

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 # Evaluations
 
-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:
-
-```bash
-ontogpt eval EvalCTD 
-```
-
-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:
-
-```bash
-ontogpt eval --num-tests 1 EvalCTD
-```
-
-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.
-
-## BC5CDR
-
-*Test Name:* EvalCTD
-*Input Count:* 500
-
-Results for OntoGPT on the [BioCreative V Chemical Disease Relation Task (BC5CDR)](https://biocreative.bioinformatics.udel.edu/media/store/files/2015/BC5CDR_overview.final.pdf) 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`).
-
-### Template
-
-This evaluation uses the following schema template:
-
-```yaml
-id: http://w3id.org/ontogpt/ctd
-name: ctd
-title: Chemical to Disease Template
-description: >-
-  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).
-see_also:
-  - https://biocreative.bioinformatics.udel.edu/media/store/files/2015/BC5CDR_overview.final.pdf
-  - https://academic.oup.com/database/article/doi/10.1093/database/baw068/2630414
-source: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/track-3-cdr/
-license: https://creativecommons.org/publicdomain/zero/1.0/
-prefixes:
-  linkml: https://w3id.org/linkml/
-  drug: http://w3id.org/ontogpt/drug/
-
-default_prefix: drug
-default_range: string
-
-imports:
-  - linkml:types
-  - core
-
-classes:
-
-  ChemicalToDiseaseDocument:
-    description: A document that contains chemical to disease relations.
-    is_a: TextWithTriples
-    slot_usage:
-      triples:
-        range: ChemicalToDiseaseRelationship
-        annotations:
-          prompt: >-
-            A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES
-            or TREATS.
-            for example: Lidocaine INDUCES cardiac asystole; 
-            Hydroxychloroquine NOT TREATS COVID-19;
-            Methyldopa INDUCES Hypotension;
-            Monosodium Glutamate NOT INDUCES Headache;
-            Imatinib TREATS cancer
-          exclude: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer
-
-
-  ChemicalToDiseaseRelationship:
-    is_a: Triple
-    description: A triple where the subject is a chemical and the object is a disease.
-    slot_usage:
-      subject:
-        range: Chemical
-        description: >-
-          The chemical substance, drug, or small molecule. 
-          For example: Lidocaine, Monosodium Glutamate, Imatinib.
-      object:
-        range: Disease
-        description: >-
-          The disease or condition that is being treated or induced by the chemical.
-          For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache.
-      predicate:
-        range: ChemicalToDiseasePredicate
-        description: The relationship type, e.g. INDUCES, TREATS.
-      subject_qualifier:
-        range: NamedEntity
-        description: >-
-          An optional qualifier or modifier for the chemical, e.g. "high dose" or "intravenously administered"
-      object_qualifier:
-        range: NamedEntity
-        description: >-
-          An optional qualifier or modifier for the disease, e.g. "severe" or "with additional complications"
-
-  Disease:
-    is_a: NamedEntity
-    annotations:
-      annotators: "sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra"
-      prompt.examples: cardiac asystole, COVID-19, Headache, cancer
-    id_prefixes:
-      - MESH
-    slot_usage:
-      id:
-        pattern: "^MESH:[CD][0-9]{6}$"
-        values_from:
-          - MeshDiseaseIdentifier
-
-  Chemical:
-    is_a: NamedEntity
-    annotations:
-      annotators: "sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:"
-      prompt.examples: Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib
-    id_prefixes:
-      - MESH
-    slot_usage:
-      id:
-        pattern: "^MESH:[CD][0-9]{6}$"
-        values_from:
-          - MeshChemicalIdentifier
-
-  ChemicalToDiseasePredicate:
-    is_a: RelationshipType
-    description: >-
-      A predicate for chemical to disease relationships
-    comments:
-      - for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored.
-
-enums:
-
-  MeshChemicalIdentifier:
-    reachable_from:
-      source_ontology: obo:mesh
-      source_nodes:
-        - MESH:D000602 ## Amino Acids, Peptides, and Proteins
-        - MESH:D001685 ## Biological Factors
-        - MESH:D002241 ## Carbohydrates
-        - MESH:D004364 ## Pharmaceutical Preparations
-        - MESH:D006571 ## Heterocyclic Compounds
-        - MESH:D007287 ## Inorganic Chemicals
-        - MESH:D008055 ## Lipids
-        - MESH:D009706 ## Nucleic Acids, Nucleotides, and Nucleosides
-        - MESH:D009930 ## Organic Chemicals
-        - MESH:D011083 ## Polycyclic Compounds
-        - MESH:D013812 ## Therapeutics
-        - MESH:D019602 ## Food and Beverages
-        - MESH:D045424 ## Complex Mixtures
-        - MESH:D045762 ## Enzymes and Coenzymes
-        - MESH:D046911 ## Macromolecular Substances
-  MeshDiseaseIdentifier:
-    reachable_from:
-      source_ontology: obo:mesh
-      source_nodes:
-        - MESH:D001423 ## Bacterial Infections and Mycoses
-        - MESH:D001523 ## Mental Disorders
-        - MESH:D002318 ## Cardiovascular Diseases
-        - MESH:D002943 ## Circulatory and Respiratory Physiological Phenomena
-        - MESH:D004066 ## Digestive System Diseases
-        - MESH:D004700 ## Endocrine System Diseases
-        - MESH:D005128 ## Eye Diseases
-        - MESH:D005261 ## Female Urogenital Diseases and Pregnancy Complications
-        - MESH:D006425 ## Hemic and Lymphatic Diseases
-        - MESH:D007154 ## Immune System Diseases
-        - MESH:D007280 ## Disorders of Environmental Origin
-        - MESH:D009057 ## Stomatognathic Diseases
-        - MESH:D009140 ## Musculoskeletal Diseases
-        - MESH:D009358 ## Congenital, Hereditary, and Neonatal Diseases and Abnormalities
-        - MESH:D009369 ## Neoplasms
-        - MESH:D009422 ## Nervous System Diseases
-        - MESH:D009750 ## Nutritional and Metabolic Diseases
-        - MESH:D009784 ## Occupational Diseases
-        - MESH:D010038 ## Otorhinolaryngologic Diseases
-        - MESH:D010272 ## Parasitic Diseases
-        - MESH:D012140 ## Respiratory Tract Diseases
-        - MESH:D013568 ## Pathological Conditions, Signs and Symptoms
-        - MESH:D014777 ## Virus Diseases
-        - MESH:D014947 ## Wounds and Injuries
-        - MESH:D017437 ## Skin and Connective Tissue Diseases
-        - MESH:D052801 ## Male Urogenital Diseases
-        - MESH:D064419 ## Chemically-Induced Disorders
-```
+TODO