standards_schema.yaml

id: https://w3id.org/bridge2ai/standards-schema
name: standards-schema
title: standards-schema
description: |-
  High-level classes for Bridge2AI Standards schemas.
license: MIT
see_also:
  - https://bridge2ai.github.io/standards-schema

prefixes:
  B2AI: https://w3id.org/bridge2ai/standards-schema/
  biolink: https://w3id.org/biolink/vocab/
  edam.data: http://edamontology.org/data_
  edam.format: http://edamontology.org/format_
  edam.operation: http://edamontology.org/operation_
  edam.topic: http://edamontology.org/topic_
  linkml: https://w3id.org/linkml/
  mesh: http://id.nlm.nih.gov/mesh/
  ncit: http://purl.obolibrary.org/obo/NCIT_
  pato: http://purl.obolibrary.org/obo/PATO_
  rdfs: http://www.w3.org/2000/01/rdf-schema#
  schema: http://schema.org/
  uberon: http://purl.obolibrary.org/obo/uberon/core#
  wikidata: http://www.wikidata.org/wiki/
default_prefix: B2AI
default_range: string

imports:
  - linkml:types

types:
  category_type:
    typeof: uriorcurie
    description: >-
      A primitive type in which the value denotes a class within the model.
  edam_identifier:
    description: Identifier from EDAM ontology
    typeof: uriorcurie
    id_prefixes:
      - edam.data
      - edam.format
      - edam.operation
      - edam.topic
  mesh_identifier:
    description: >-
      Identifier from Medical Subject Headings (MeSH) biomedical vocabulary.
    typeof: uriorcurie
    id_prefixes:
      - mesh
  ncit_identifier:
    description: >-
      Identifier from NCIT reference terminology with broad
      coverage of the cancer domain.
    typeof: uriorcurie
    id_prefixes:
      - NCIT

classes:

  NamedThing:
    description: >-
      A generic grouping for any identifiable entity
    slots:
      - id
      - category
      - name
      - description
      - subclass_of
      - related_to
      - contributor_name
      - contributor_github_name
      - contributor_orcid
      - contribution_date
    class_uri: schema:Thing

  AnatomicalEntity:  # Based on Biolink Model v.3.2.6
    is_a: NamedThing
    description: >-
      A subcellular location, cell type or gross anatomical part
    exact_mappings:
      - uberon:0001062
      - wikidata:Q4936952
    narrow_mappings:
      - ncit:C12219 # human anatomical entity
    id_prefixes:
      - uberon

slots:
  node_property:
    description: >-
      A grouping for any property that holds
      between a node and a value.
    domain: NamedThing
  id:
    identifier: true
    slot_uri: schema:identifier
    range: uriorcurie
    description: A unique identifier for a thing.
    required: true
  type:
    description: >-
      A generic slot for any label corresponding to the label 
      for an entity type associated to the class.
    domain: NamedThing
  category:
    is_a: type
    domain: NamedThing
    range: category_type
    designates_type: true
    description: >-
      Name of the high level ontology class in which this entity is categorized.
      Corresponds to the label for the entity type class, e.g., "BiomedicalStandard".
  name:
    slot_uri: schema:name
    description: A human-readable name for a thing.
    range: string
  description:
    slot_uri: schema:description
    description: A human-readable description for a thing.
    range: string
  edam_id:
    description: Unique EDAM identifier
    examples:
      - value: edam.data:0006
    range: edam_identifier
    values_from:
      - edam.data
      - edam.format
      - edam.operation
      - edam.topic
  mesh_id:
    description: Unique MeSH identifier
    examples:
      - value: MeSH:D014831
    range: mesh_identifier
    values_from:
      - MeSH
  ncit_id:
    description: Unique NCIt Identifier
    examples:
      - value: NCIT:C92692
    range: ncit_identifier
    values_from:
      - NCIT
  url:
    is_a: node_property
    range: uriorcurie
    description: >-
      URL for basic documentation of the standard
      or tool.
  xref:
    is_a: node_property
    aliases: [ 'dbxref', 'Dbxref', 'DbXref' ]
    domain: NamedThing
    range: uriorcurie
    description: >-
      URI of corresponding class in an ontology
      of experimental procedures, in CURIE form.
    multivalued: true

  contributor_name:
    is_a: node_property
    range: string
    description: The name of the person who added this node.
  contributor_github_name:
    is_a: node_property
    range: string
    description: The name of the github user who added this node.
  contributor_orcid:
    is_a: node_property
    range: uriorcurie
    description: The ORCiD of the person who added this node.
    examples:
      - value: "ORCID:0000-0001-1234-5678"
  contribution_date:
    is_a: node_property
    range: date
    description: The date on which the node was added.
    examples:
      - value: "2023-03-20"

  related_to:
    description: >-
      A relationship that is asserted between two named things.
    domain: NamedThing
    range: NamedThing
    multivalued: true
    inherited: true
    symmetric: true

  # TODO: Could be more specific with is_a relationships.
  subclass_of:
    is_a: related_to
    description: >-
      Holds between two classes where the domain class is
      a specialization of the range class.
    domain: NamedThing
    range: NamedThing
    multivalued: True
    exact_mappings:
      - rdfs:subClassOf
      - MESH:isa
    narrow_mappings:
      - rdfs:subPropertyOf

enums:
  DataGeneratingProject:
    description: One of the Bridge2AI Data Generating Projects.
    permissible_values:
      aireadi:
        description: >-
          AI-READI: Uncovering the details of how human health is restored
          after disease, using type 2 diabetes as a model.
        meaning: https://reporter.nih.gov/project-details/10471118
      chorus:
        description: >-
          CHoRUS: Collaborative Hospital Repository Uniting Standards.
          Using imaging, clinical, and other data collected in
          an ICU setting for diagnosis and risk prediction.
        meaning: https://reporter.nih.gov/project-details/10472824
      cm4ai:
        description: >-
          CM4AI: Cell Maps for AI. Mapping spatiotemporal architecture
          of human cells to interpret cell structure/function in health
          and disease.
        meaning: https://reporter.nih.gov/project-details/10473403
      voice:
        description: >-
          Voice as a Biomarker of Health: Building an ethically
          sourced, bioaccoustic database to understand disease
          like never before.
        meaning: https://reporter.nih.gov/project-details/10473236