openapi: 3.0.0
servers:
  - url: /api
info:
  description: |-
    API integration layer for linked biological objects.

     __Source:__ https://github.com/biolink/biolink-api/
  license:
    name: BSD3
  title: BioLink API
  version: 1.1.14
  x-apisguru-categories:
    - open_data
  x-origin:
    - format: openapi
      url: https://api.monarchinitiative.org/api/swagger.json
      version: "3.0"
  x-providerName: monarchinitiative.org
tags:
  - description: Retrieval of domain entities plus associations
    name: bioentity
  - description: Retrieve associations between entities or entity and descriptors
    name: association
  - description: Operations on GO Causal Activity Models (GO-CAMs)
    name: cam
  - description: Operations over sets of entities
    name: bioentityset
  - description: Map gene IDs to their homologs
    name: bioentityset/homologs
  - description: maps a set of entities to a slim
    name: bioentityset/slimmer
  - description: Operations on evidence graphs
    name: evidence/graph
  - description: Operations to retrieve sequence features
    name: genome/features
  - description: Operations over data graphs
    name: graph
  - description: mapping and resolution of identifiers
    name: identifier/mapper
  - description: identifier prefixes
    name: identifier/prefixes
  - description: Perform bulk operations
    name: mart
  - description: annotate text using named entities
    name: nlp/annotate
  - description: extract a subgraph from an ontology
    name: ontol
  - description: Assign labels to IDs
    name: ontol/labeler
  - description: Retrieve IDs for labels
    name: ontol/identifier
  - description: Operations on Ontology Terms and Subsets
    name: ontology
  - description: OWL-level operations on an ontology
    name: owl/ontology
  - description: pairwise similarity between two entities
    name: pair/sim
  - description: Individual humans (including patients), or organisms
    name: individual
  - description: Usage of different relationship types
    name: relation/usage
  - description: Search for entities
    name: search
  - description: Operations related to sets of variants
    name: variation/set
  - description: Perform semantic similarity, ranking, and sufficiency scoring
    name: sim
  - description: Match patients with similar diseases and non-human genes based on their phenotypes
    name: mme
  - description: Get metadata
    name: metadata
paths:
  "/association/between/{subject}/{object}":
    get:
      description: |-
        Given two entities (e.g. a particular gene and a particular disease), if these two entities
        are connected (directly or indirectly), then return the association objects describing
        the connection.
      operationId: get_associations_between
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Returns associations connecting two entities
      tags:
        - association
    parameters:
      - description: Return associations pointing to this node, e.g. MP:0013765. Can also be a biological entity such as a gene
        in: path
        name: object
        required: true
        schema:
          type: string
      - description: Return associations emanating from this node, e.g. MGI:1342287 (If ID is from an ontology then results would include inferred associations, by default)
        in: path
        name: subject
        required: true
        schema:
          type: string
  "/association/find/{subject_category}":
    get:
      operationId: get_association_by_subject_category_search
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Subject taxon ID, e.g. NCBITaxon:9606 (Includes inferred associations, by default)
          in: query
          name: subject_taxon
          schema:
            type: string
        - description: Object taxon ID, e.g. NCBITaxon:10090 (Includes inferred associations, by default)
          in: query
          name: object_taxon
          schema:
            type: string
        - description: Filter by relation CURIE, e.g. RO:0002200 (has_phenotype), RO:0002607 (is marker for), RO:HOM0000017 (orthologous to), etc.
          in: query
          name: relation
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Returns list of matching associations for a given subject category
      tags:
        - association
    parameters:
      - description: Category of entity at link Subject (source), e.g. gene, disease, phenotype
        in: path
        name: subject_category
        required: true
        schema:
          type: string
  "/association/find/{subject_category}/{object_category}":
    get:
      operationId: get_association_by_subject_and_object_category_search
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Subject CURIE
          in: query
          name: subject
          schema:
            type: string
        - description: Object CURIE
          in: query
          name: object
          schema:
            type: string
        - description: Subject taxon ID, e.g. NCBITaxon:9606 (Includes inferred associations, by default)
          in: query
          name: subject_taxon
          schema:
            type: string
        - description: Object taxon ID, e.g. NCBITaxon:10090 (Includes inferred associations, by default)
          in: query
          name: object_taxon
          schema:
            type: string
        - description: Filter by relation CURIE, e.g. RO:0002200 (has_phenotype), RO:0002607 (is marker for), RO:HOM0000017 (orthologous to), etc.
          in: query
          name: relation
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Returns list of matching associations between a given subject and object category
      tags:
        - association
    parameters:
      - description: Category of entity at link Object (target), e.g. gene, disease, phenotype
        in: path
        name: object_category
        required: true
        schema:
          type: string
      - description: Category of entity at link Subject (source), e.g. gene, disease, phenotype
        in: path
        name: subject_category
        required: true
        schema:
          type: string
  "/association/from/{subject}":
    get:
      operationId: get_associations_from
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Object taxon ID, e.g. NCBITaxon:10090 (Includes inferred associations, by default)
          in: query
          name: object_taxon
          schema:
            type: string
        - description: Filter by relation CURIE, e.g. RO:0002200 (has_phenotype), RO:0002607 (is marker for), RO:HOM0000017 (orthologous to), etc.
          in: query
          name: relation
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Returns list of matching associations starting from a given subject (source)
      tags:
        - association
    parameters:
      - description: Return associations emanating from this node, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357 (If ID is from an ontology then results would include inferred associations, by default)
        in: path
        name: subject
        required: true
        schema:
          type: string
  "/association/to/{object}":
    get:
      operationId: get_associations_to
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Returns list of matching associations pointing to a given object (target)
      tags:
        - association
    parameters:
      - description: Return associations pointing to this node, e.g. specifying MP:0013765 will return all genes, variants, strains, etc. annotated with this term. Can also be a biological entity such as a gene
        in: path
        name: object
        required: true
        schema:
          type: string
  "/association/type/{association_type}":
    get:
      operationId: get_association_by_subject_and_assoc_type
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Subject CURIE
          in: query
          name: subject
          schema:
            type: string
        - description: Object CURIE
          in: query
          name: object
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Returns list of matching associations of a given type
      tags:
        - association
    parameters:
      - description: Association type, eg gene_phenotype
        in: path
        name: association_type
        required: true
        schema:
          type: string
  "/association/{id}":
    get:
      description: |-
        An association connects, at a minimum, two things, designated subject and object,
        via some relationship. Associations also include evidence, provenance etc.
      operationId: get_association_object
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Returns the association with a given identifier
      tags:
        - association
    parameters:
      - description: identifier for an association, e.g. f5ba436c-f851-41b3-9d9d-bb2b5fc879d4
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/anatomy/{id}/genes":
    get:
      operationId: get_anatomy_gene_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genes associated with a given anatomy
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of anatomical entity, e.g. GO:0005634 (nucleus), UBERON:0002037 (cerebellum), CL:0000540 (neuron). Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/anatomy/{id}/genes/{taxid}":
    get:
      deprecated: true
      description: For example, + NCBITaxon:10090 (mouse)
      operationId: get_anatomy_gene_by_taxon_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: Returns gene IDs for all genes associated with a given anatomy, filtered by taxon
      tags:
        - bioentity
    parameters:
      - description: Species or high level taxon grouping, e.g  NCBITaxon:10090 (Mus musculus)
        in: path
        name: taxid
        required: true
        schema:
          type: string
      - description: CURIE identifier of anatomical entity, e.g. GO:0005634 (nucleus), UBERON:0002037 (cerebellum), CL:0000540 (neuron). Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/case/{id}/diseases":
    get:
      operationId: get_case_disease_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns diseases associated with a case
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a case
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/case/{id}/genotypes":
    get:
      operationId: get_case_genotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genotypes associated with a case
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a case
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/case/{id}/models":
    get:
      operationId: get_case_model_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns models associated with a case
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a case
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/case/{id}/phenotypes":
    get:
      operationId: get_case_phenotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns phenotypes associated with a case
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a case
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/case/{id}/variants":
    get:
      operationId: get_case_variant_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns variants associated with a case
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a case
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/disease/{id}/cases":
    get:
      operationId: get_disease_case_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns cases associated with a disease
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of disease, e.g. MONDO:0007103, MONDO:0010918. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/disease/{id}/genes":
    get:
      operationId: get_disease_gene_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
        - description: "Additional filters: causal, non_causal, both"
          explode: true
          in: query
          name: association_type
          schema:
            default: both
            enum:
              - causal
              - non_causal
              - both
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genes associated with a disease
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/disease/{id}/genotypes":
    get:
      operationId: get_disease_genotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genotypes associated with a disease
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of disease, e.g. Orphanet:399158, DOID:0080008. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/disease/{id}/models":
    get:
      description: |-
        In the association object returned, the subject will be the disease, and the object will be the model.
        The model may be a gene or genetic element.

        If the query disease is a general class, the association subject may be to a specific disease.

        In some cases the association will be *direct*, for example if a paper asserts a genotype is a model of a disease.

        In other cases, the association will be *indirect*, for
        example, chaining over orthology. In these cases the chain
        will be reflected in the *evidence graph*

        * TODO: provide hook into owlsim for dynamic computation of models by similarity
      operationId: get_disease_model_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns associations to models of the disease
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/disease/{id}/models/{taxon}":
    get:
      deprecated: true
      description: See /disease/<id>/models route for full details
      operationId: get_disease_model_taxon_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns associations to models of the disease constrained by taxon
      tags:
        - bioentity
    parameters:
      - description: |-
          CURIE of organism taxonomy class to constrain models, e.g NCBITaxon:10090 (M. musculus).

           Higher level taxa may be used
        in: path
        name: taxon
        required: true
        schema:
          type: string
      - description: CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/disease/{id}/pathways":
    get:
      operationId: get_disease_pathway_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns pathways associated with a disease
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of disease, e.g. DOID:4450. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/disease/{id}/phenotypes":
    get:
      operationId: get_disease_phenotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/D2PAssociationResults"
          description: Success
      summary: Returns phenotypes associated with disease
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of disease, e.g. OMIM:605543, Orphanet:1934, DOID:678. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/disease/{id}/publications":
    get:
      operationId: get_disease_publication_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns publications associated with a disease
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/disease/{id}/treatment":
    get:
      description: e.g. drugs or small molecules used to treat
      operationId: get_disease_substance_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          description: Success
      summary: Returns substances associated with a disease
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/disease/{id}/variants":
    get:
      operationId: get_disease_variant_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns variants associated with a disease
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/function/{id}":
    get:
      operationId: get_function_associations
      parameters:
        - description: beginning row
          in: query
          name: start
          schema:
            default: 0
            type: integer
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          explode: true
          in: query
          name: evidence
          schema:
            items:
              type: string
            type: array
      responses:
        "200":
          description: Success
      summary: Returns annotations associated to a function term
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of a function term (e.g. GO:0044598)
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/function/{id}/genes":
    get:
      operationId: get_function_gene_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
        - description: relationship type ('involved_in', 'involved_in_regulation_of' or 'acts_upstream_of_or_within')
          explode: true
          in: query
          name: relationship_type
          schema:
            default: involved_in
            enum:
              - involved_in
              - involved_in_regulation_of
              - acts_upstream_of_or_within
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genes associated to a GO term
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of a GO term, e.g. GO:0044598
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/function/{id}/publications":
    get:
      operationId: get_function_publication_associations
      parameters:
        - description: beginning row
          in: query
          name: start
          schema:
            default: 0
            type: integer
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          explode: true
          in: query
          name: evidence
          schema:
            items:
              type: string
            type: array
      responses:
        "200":
          description: Success
      summary: Returns publications associated to a GO term
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of a GO term, e.g. GO:0044598
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/function/{id}/taxons":
    get:
      operationId: get_function_taxon_associations
      parameters:
        - description: beginning row
          in: query
          name: start
          schema:
            default: 0
            type: integer
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          explode: true
          in: query
          name: evidence
          schema:
            items:
              type: string
            type: array
      responses:
        "200":
          description: Success
      summary: Returns taxons associated to a GO term
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of a GO term, e.g. GO:0044598
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/anatomy":
    get:
      operationId: get_gene_anatomy_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns anatomical entities associated with a gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. NCBIGene:13434
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/cases":
    get:
      operationId: get_gene_case_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns cases associated with a gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. HGNC:613, HGNC:11025
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/diseases":
    get:
      operationId: get_gene_disease_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
        - description: "Additional filters: causal, non_causal, both"
          explode: true
          in: query
          name: association_type
          schema:
            default: both
            enum:
              - causal
              - non_causal
              - both
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns diseases associated with gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/expression/anatomy":
    get:
      operationId: get_gene_expression_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns expression events for a gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/function":
    get:
      description: |-
        IMPLEMENTATION DETAILS
        ----------------------

        Note: currently this is implemented as a query to the GO/AmiGO solr instance.
        This directly supports IDs such as:

         - ZFIN e.g. ZFIN:ZDB-GENE-050417-357

        Note that the AmiGO GOlr natively stores MGI annotations to MGI:MGI:nn. However,
        the standard for biolink is MGI:nnnn, so you should use this (will be transparently
        mapped to legacy ID)

        Additionally, for some species such as Human, GO has the annotation attached to the UniProt ID.
        Again, this should be transparently handled; e.g. you can use NCBIGene:6469, and this will be
        mapped behind the scenes for querying.
      operationId: get_gene_function_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns function associations for a gene
      tags:
        - bioentity
    parameters:
      - description: id, e.g. NCBIGene:6469. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/genotypes":
    get:
      operationId: get_gene_genotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genotypes associated with a gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. ZFIN:ZDB-GENE-980526-166
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/homologs":
    get:
      operationId: get_gene_homolog_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: Taxon CURIE of homolog, e.g. NCBITaxon:9606 (Can be an ancestral node in the ontology; includes inferred associations by default)
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: P (paralog), O (Ortholog) or LDO (least-diverged ortholog)
          explode: true
          in: query
          name: homology_type
          schema:
            enum:
              - P
              - O
              - LDO
            type: string
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns homologs for a gene
      tags:
        - bioentity
    parameters:
      - description: id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/interactions":
    get:
      operationId: get_gene_interactions
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns interactions for a gene
      tags:
        - bioentity
    parameters:
      - description: id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/models":
    get:
      operationId: get_gene_model_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns models associated with a gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. NCBIGene:17988
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/ortholog/diseases":
    get:
      operationId: get_gene_ortholog_disease_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Return diseases associated with orthologs of a gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. NCBIGene:4750
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/ortholog/phenotypes":
    get:
      operationId: get_gene_ortholog_phenotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Return phenotypes associated with orthologs for a gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. NCBIGene:4750
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/pathways":
    get:
      operationId: get_gene_pathway_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns pathways associated with gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. NCBIGene:50846. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/phenotypes":
    get:
      operationId: get_gene_phenotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns phenotypes associated with gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/publications":
    get:
      operationId: get_gene_publication_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns publications associated with a gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. NCBIGene:4750
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/gene/{id}/variants":
    get:
      operationId: get_gene_variant_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns variants associated with a gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of gene, e.g. HGNC:10896
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/genotype/{id}/cases":
    get:
      operationId: get_genotype_case_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns cases associated with a genotype
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of genotype, e.g. dbSNPIndividual:10440, dbSNPIndividual:22633
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/genotype/{id}/diseases":
    get:
      operationId: get_genotype_disease_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns diseases associated with a genotype
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of genotype, e.g. dbSNPIndividual:11441 (if non-human will return models)
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/genotype/{id}/genes":
    get:
      operationId: get_genotype_gene_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genes associated with a genotype
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/genotype/{id}/genotypes":
    get:
      description: Genotypes may be related to one another according to the GENO model
      operationId: get_genotype_genotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genotypes-genotype associations
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/genotype/{id}/models":
    get:
      operationId: get_genotype_model_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns models associated with a genotype
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/genotype/{id}/phenotypes":
    get:
      operationId: get_genotype_phenotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns phenotypes associated with a genotype
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/genotype/{id}/publications":
    get:
      operationId: get_genotype_publication_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns publications associated with a genotype
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/genotype/{id}/variants":
    get:
      operationId: get_genotype_variant_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genotypes-variant associations
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of genotype, e.g. MONARCH:FBgeno422705
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/goterm/{id}/genes":
    get:
      deprecated: true
      operationId: get_goterm_gene_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: relationship type ('involved_in', 'involved_in_regulation_of' or 'acts_upstream_of_or_within')
          explode: true
          in: query
          name: relationship_type
          schema:
            default: involved_in
            enum:
              - involved_in
              - involved_in_regulation_of
              - acts_upstream_of_or_within
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns associations to GO terms for a gene
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of a GO term, e.g. GO:0044598
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/model/{id}/cases":
    get:
      operationId: get_model_case_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns cases associated with a model
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a model, e.g. Coriell:GM22295, Coriell:HG02187
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/model/{id}/diseases":
    get:
      operationId: get_model_disease_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns diseases associated with a model
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a model, e.g. MGI:5573196
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/model/{id}/genes":
    get:
      operationId: get_model_gene_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genes associated with a model
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a model, e.g. MMRRC:042787
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/model/{id}/genotypes":
    get:
      operationId: get_model_genotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genotypes associated with a model
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a model, e.g. Coriell:NA16660
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/model/{id}/phenotypes":
    get:
      operationId: get_model_phenotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns phenotypes associated with a model
      tags:
        - bioentity
    parameters:
      - description: id
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/model/{id}/publications":
    get:
      operationId: get_model_publication_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns publications associated with a model
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a model, e.g. MGI:5644542
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/model/{id}/variants":
    get:
      operationId: get_model_variant_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns variants associated with a model
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a model, e.g. MMRRC:042787
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/pathway/{id}/diseases":
    get:
      operationId: get_pathway_disease_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns diseases associated with a pathway
      tags:
        - bioentity
    parameters:
      - description: CURIE any pathway element. E.g. REACT:R-HSA-5387390
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/pathway/{id}/genes":
    get:
      operationId: get_pathway_gene_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genes associated with a pathway
      tags:
        - bioentity
    parameters:
      - description: CURIE any pathway element. E.g. REACT:R-HSA-5387390
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/pathway/{id}/phenotypes":
    get:
      operationId: get_pathway_phenotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns phenotypes associated with a pathway
      tags:
        - bioentity
    parameters:
      - description: CURIE any pathway element. E.g. REACT:R-HSA-5387390
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/phenotype/{id}/anatomy":
    get:
      description: |-
        Example IDs:

         * MP:0008521 abnormal Bowman membrane
      operationId: get_phenotype_anatomy_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/NamedObject"
                type: array
          description: Success
      summary: Returns anatomical entities associated with a phenotype
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of phenotype, e.g. MP:0008521. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/phenotype/{id}/cases":
    get:
      operationId: get_phenotype_case_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns cases associated with a phenotype
      tags:
        - bioentity
    parameters:
      - description: Pheno class CURIE identifier, e.g  HP:0011951 (Aspiration pneumonia), HP:0002450 (Abnormal motor neuron morphology)
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/phenotype/{id}/diseases":
    get:
      operationId: get_phenotype_disease_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/D2PAssociationResults"
          description: Success
      summary: Returns diseases associated with a phenotype
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of phenotype, e.g. HP:0007359. Equivalent IDs can be used with same results
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/phenotype/{id}/gene/{taxid}/ids":
    get:
      deprecated: true
      description: For example, MP:0001569 + NCBITaxon:10090 (mouse)
      operationId: get_phenotype_gene_by_taxon_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          description: Success
      summary: Returns gene IDs for all genes associated with a given phenotype, filtered by taxon
      tags:
        - bioentity
    parameters:
      - description: Species or high level taxon grouping, e.g  NCBITaxon:10090 (Mus musculus)
        in: path
        name: taxid
        required: true
        schema:
          type: string
      - description: Pheno class CURIE identifier, e.g  MP:0001569 (abnormal circulating bilirubin level)
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/phenotype/{id}/genes":
    get:
      operationId: get_phenotype_gene_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genes associated with a phenotype
      tags:
        - bioentity
    parameters:
      - description: "Pheno class CURIE identifier, e.g  WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level), "
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/phenotype/{id}/genotypes":
    get:
      operationId: get_phenotype_genotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genotypes associated with a phenotype
      tags:
        - bioentity
    parameters:
      - description: Pheno class CURIE identifier, e.g  WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/phenotype/{id}/pathways":
    get:
      operationId: get_phenotype_pathway_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns pathways associated with a phenotype
      tags:
        - bioentity
    parameters:
      - description: Pheno class CURIE identifier, e.g  MP:0001569 (abnormal circulating bilirubin level)
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/phenotype/{id}/publications":
    get:
      operationId: get_phenotype_publication_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns publications associated with a phenotype
      tags:
        - bioentity
    parameters:
      - description: Pheno class CURIE identifier, e.g  WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/phenotype/{id}/variants":
    get:
      operationId: get_phenotype_variant_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns variants associated with a phenotype
      tags:
        - bioentity
    parameters:
      - description: Pheno class CURIE identifier, e.g  WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/publication/{id}/diseases":
    get:
      operationId: get_publication_disease_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns diseases associated with a publication
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a publication, e.g. PMID:11751940
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/publication/{id}/genes":
    get:
      operationId: get_publication_gene_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genes associated with a publication
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a publication, e.g. PMID:11751940
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/publication/{id}/genotypes":
    get:
      operationId: get_publication_genotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genotypes associated with a publication
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a publication, e.g. PMID:11751940
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/publication/{id}/models":
    get:
      operationId: get_publication_model_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns models associated with a publication
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a publication, e.g. PMID:11751940
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/publication/{id}/phenotypes":
    get:
      operationId: get_publication_phenotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns phenotypes associated with a publication
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a publication, e.g. PMID:11751940
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/publication/{id}/variants":
    get:
      operationId: get_publication_variant_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns variants associated with a publication
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier for a publication, e.g. PMID:11751940
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/substance/{id}/participant_in":
    get:
      description: |-
        Examples relationships:

         * substance is a metabolite of a process
         * substance is synthesized by a process
         * substance is modified by an activity
         * substance elicits a response program/pathway
         * substance is transported by activity or pathway

        For example, CHEBI:40036 (amitrole)
      operationId: get_substance_participant_in_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Association"
                type: array
          description: Success
      summary: Returns associations between an activity and process and the specified substance
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of substance, e.g. CHEBI:40036
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/substance/{id}/roles":
    get:
      description: Roles may be human-oriented (e.g. pesticide) or molecular (e.g. enzyme inhibitor)
      operationId: get_substance_role_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Association"
                type: array
          description: Success
      summary: Returns associations between given drug and roles
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of substance, e.g. CHEBI:40036
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/substance/{id}/treats":
    get:
      description: e.g. drugs or small molecules used to treat
      operationId: get_substance_treats_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          description: Success
      summary: Returns substances associated with a disease
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of substance, e.g. CHEBI:40036
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/variant/{id}/cases":
    get:
      operationId: get_variant_case_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns cases associated with a variant
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of variant, e.g. OMIM:309550.0004, dbSNP:rs5030868
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/variant/{id}/diseases":
    get:
      operationId: get_variant_disease_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns diseases associated with a variant
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of variant, e.g. ClinVarVariant:14925
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/variant/{id}/genes":
    get:
      operationId: get_variant_gene_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genes associated with a variant
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/variant/{id}/genotypes":
    get:
      operationId: get_variant_genotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns genotypes associated with a variant
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/variant/{id}/models":
    get:
      operationId: get_variant_model_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns models associated with a variant
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of variant, e.g. OMIM:607623.0012, dbSNP:rs5030868
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/variant/{id}/phenotypes":
    get:
      operationId: get_variant_phenotype_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns phenotypes associated with a variant
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/variant/{id}/publications":
    get:
      operationId: get_variant_publication_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns publications associated with a variant
      tags:
        - bioentity
    parameters:
      - description: CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/{id}":
    get:
      operationId: get_generic_object
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/BioObject"
          description: Success
      summary: Returns basic info on object of any type
      tags:
        - bioentity
    parameters:
      - description: id, e.g. NCBIGene:84570
        in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/{id}/associations":
    get:
      operationId: get_generic_associations
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: Set true to exclude inferred taxa
          in: query
          name: direct_taxon
          schema:
            default: false
            type: boolean
        - description: A relation CURIE to filter associations
          in: query
          name: relation
          schema:
            type: string
        - description: Sorting responses <field> <desc,asc>
          in: query
          name: sort
          schema:
            type: string
        - description: Query string to filter documents
          in: query
          name: q
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AssociationResults"
          description: Success
      summary: Returns associations for an entity regardless of the type
      tags:
        - bioentity
    parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
  "/bioentity/{type}/{id}":
    get:
      operationId: get_generic_object_by_type
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
        - description: Enable faceting
          in: query
          name: facet
          schema:
            default: false
            type: boolean
        - description: Fields to facet on
          explode: true
          in: query
          name: facet_fields
          schema:
            items:
              type: string
            type: array
        - description: If true, excludes evidence objects in response
          in: query
          name: unselect_evidence
          schema:
            default: false
            type: boolean
        - description: If true, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
          in: query
          name: fetch_objects
          schema:
            default: false
            type: boolean
        - description: If true, returns results in compact associations format
          in: query
          name: use_compact_associations
          schema:
            default: false
            type: boolean
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
        - description: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
          in: query
          name: evidence
          schema:
            type: string
        - description: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
          in: query
          name: direct
          schema:
            default: false
            type: boolean
        - description: Get association counts
          in: query
          name: get_association_counts
          schema:
            default: false
            type: boolean
        - description: Get distinct counts for associations (to be used in conjunction with 'get_association_counts' parameter)
          in: query
          name: distinct_counts
          schema:
            default: false
            type: boolean
      responses:
        "200":
          description: Success
      summary: Return basic info on an object for a given type
      tags:
        - bioentity
    parameters:
      - description: bioentity type
        in: path
        name: type
        required: true
        schema:
          enum:
            - gene
            - variant
            - genotype
            - phenotype
            - disease
            - goterm
            - pathway
            - anatomy
            - substance
            - individual
            - publication
            - model
            - case
          type: string
      - description: id, e.g. NCBIGene:84570
        in: path
        name: id
        required: true
        schema:
          type: string
  /bioentityset/associations:
    get:
      operationId: get_entity_set_associations
      parameters:
        - description: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
          explode: true
          in: query
          name: subject
          schema:
            items:
              type: string
            type: array
        - description: Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests
          explode: true
          in: query
          name: background
          schema:
            items:
              type: string
            type: array
        - description: E.g. phenotype, function
          in: query
          name: object_category
          schema:
            type: string
        - description: Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED
          in: query
          name: object_slim
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Returns compact associations for a given input set
      tags:
        - bioentityset
  /bioentityset/descriptor/counts:
    get:
      operationId: get_entity_set_summary
      parameters:
        - description: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
          explode: true
          in: query
          name: subject
          schema:
            items:
              type: string
            type: array
        - description: Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests
          explode: true
          in: query
          name: background
          schema:
            items:
              type: string
            type: array
        - description: E.g. phenotype, function
          in: query
          name: object_category
          schema:
            type: string
        - description: Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED
          in: query
          name: object_slim
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: Summary statistics for objects associated
      tags:
        - bioentityset
  /bioentityset/graph:
    get:
      operationId: get_entity_set_graph_resource
      parameters:
        - description: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
          explode: true
          in: query
          name: subject
          schema:
            items:
              type: string
            type: array
        - description: Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests
          explode: true
          in: query
          name: background
          schema:
            items:
              type: string
            type: array
        - description: E.g. phenotype, function
          in: query
          name: object_category
          schema:
            type: string
        - description: Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED
          in: query
          name: object_slim
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: TODO Graph object spanning all entities
      tags:
        - bioentityset
  /bioentityset/homologs/:
    get:
      operationId: get_entity_set_homologs
      parameters:
        - description: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
          explode: true
          in: query
          name: subject
          schema:
            items:
              type: string
            type: array
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Returns homology associations for a given input set of genes
      tags:
        - bioentityset/homologs
  /bioentityset/overrepresentation:
    get:
      operationId: get_over_representation
      parameters:
        - description: E.g. phenotype, function
          in: query
          name: object_category
          schema:
            type: string
        - description: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
          explode: true
          in: query
          name: subject
          schema:
            items:
              type: string
            type: array
        - description: Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests
          explode: true
          in: query
          name: background
          schema:
            items:
              type: string
            type: array
        - description: "Default: gene. Other types may be used e.g. disease but statistics may not make sense"
          in: query
          name: subject_category
          schema:
            default: gene
            type: string
        - description: Exclude results with p-value greater than this
          in: query
          name: max_p_value
          schema:
            default: "0.05"
            type: string
        - description: "ontology id. Must be obo id. Examples: go, mp, hp, uberon (optional: will be inferred if left blank)"
          in: query
          name: ontology
          schema:
            type: string
        - description: "must be NCBITaxon CURIE. Example: NCBITaxon:9606"
          in: query
          name: taxon
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: Summary statistics for objects associated
      tags:
        - bioentityset
  /bioentityset/slimmer/anatomy:
    get:
      operationId: get_entity_set_anatomy_slimmer
      parameters:
        - description: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
          explode: true
          in: query
          name: subject
          required: true
          schema:
            items:
              type: string
            type: array
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID (IMPLEMENTED) or subset ID (TODO)
          explode: true
          in: query
          name: slim
          required: true
          schema:
            items:
              type: string
            type: array
        - description: If set, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
      responses:
        "200":
          description: Success
      summary: For a given gene(s), summarize its annotations over a defined set of slim
      tags:
        - bioentityset/slimmer
  /bioentityset/slimmer/function:
    get:
      operationId: get_entity_set_function_slimmer
      parameters:
        - description: relationship type ('involved_in' or 'acts_upstream_of_or_within')
          explode: true
          in: query
          name: relationship_type
          schema:
            default: acts_upstream_of_or_within
            enum:
              - involved_in
              - acts_upstream_of_or_within
            type: string
        - description: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
          explode: true
          in: query
          name: subject
          required: true
          schema:
            items:
              type: string
            type: array
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID (IMPLEMENTED) or subset ID (TODO)
          explode: true
          in: query
          name: slim
          required: true
          schema:
            items:
              type: string
            type: array
        - description: If set, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
      responses:
        "200":
          description: Success
      summary: For a given gene(s), summarize its annotations over a defined set of slim
      tags:
        - bioentityset/slimmer
  /bioentityset/slimmer/phenotype:
    get:
      operationId: get_entity_set_phenotype_slimmer
      parameters:
        - description: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
          explode: true
          in: query
          name: subject
          required: true
          schema:
            items:
              type: string
            type: array
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID (IMPLEMENTED) or subset ID (TODO)
          explode: true
          in: query
          name: slim
          required: true
          schema:
            items:
              type: string
            type: array
        - description: If set, excludes associations that involve IEAs (ECO:0000501)
          in: query
          name: exclude_automatic_assertions
          schema:
            default: false
            type: boolean
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 100
            type: integer
        - description: beginning row
          in: query
          name: start
          schema:
            type: integer
      responses:
        "200":
          description: Success
      summary: For a given gene(s), summarize its annotations over a defined set of slim
      tags:
        - bioentityset/slimmer
  /cam/activity:
    get:
      operationId: get_activity_collection
      parameters:
        - description: string to search for in title of model
          in: query
          name: title
          schema:
            type: string
        - description: string to search for in contributor of model
          in: query
          name: contributor
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: Returns list of models
      tags:
        - cam
  "/cam/instance/{id}":
    get:
      operationId: get_instance_object
      parameters:
        - description: string to search for in title of model
          in: query
          name: title
          schema:
            type: string
        - description: string to search for in contributor of model
          in: query
          name: contributor
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Association"
                type: array
          description: Success
      summary: Returns list of matches
      tags:
        - cam
    parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
  /cam/instances:
    get:
      operationId: get_model_instances
      responses:
        "200":
          description: Success
      summary: Returns list of all instances
      tags:
        - cam
  /cam/model:
    get:
      operationId: get_model_collection
      responses:
        "200":
          description: Success
      summary: Returns list of ALL models
      tags:
        - cam
  /cam/model/contributors:
    get:
      operationId: get_model_contributors
      responses:
        "200":
          description: Success
      summary: Returns list of all contributors across all models
      tags:
        - cam
  /cam/model/properties:
    get:
      operationId: get_model_properties
      parameters:
        - description: string to search for in title of model
          in: query
          name: title
          schema:
            type: string
        - description: string to search for in contributor of model
          in: query
          name: contributor
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: Returns list of all properties used across all models
      tags:
        - cam
  /cam/model/property_values:
    get:
      operationId: get_model_property_values
      parameters:
        - description: string to search for in title of model
          in: query
          name: title
          schema:
            type: string
        - description: string to search for in contributor of model
          in: query
          name: contributor
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: Returns list property-values for all models
      tags:
        - cam
  /cam/model/query:
    get:
      operationId: get_model_query
      parameters:
        - description: string to search for in title of model
          in: query
          name: title
          schema:
            type: string
        - description: string to search for in contributor of model
          in: query
          name: contributor
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: Returns list of models matching query
      tags:
        - cam
  "/cam/model/{id}":
    get:
      operationId: get_model_object
      responses:
        "200":
          description: Success
      summary: Returns a complete model
      tags:
        - cam
    parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
  /cam/physical_interaction:
    get:
      operationId: get_physical_interaction
      parameters:
        - description: string to search for in title of model
          in: query
          name: title
          schema:
            type: string
        - description: string to search for in contributor of model
          in: query
          name: contributor
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: Returns list of models
      tags:
        - cam
  "/evidence/graph/{id}":
    get:
      description: Note that every association is assumed to have a unique ID
      operationId: get_evidence_graph_object
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Graph"
                type: array
          description: Success
      summary: Returns evidence graph object for a given association
      tags:
        - evidence/graph
    parameters:
      - description: association id, e.g. 68e686f6-d05b-46b8-ab1f-1da2fff97ada
        in: path
        name: id
        required: true
        schema:
          type: string
  "/evidence/graph/{id}/table":
    get:
      description: Note that every association is assumed to have a unique ID
      operationId: get_evidence_graph_table
      parameters:
        - description: If true, considers dc:source as edge
          in: query
          name: is_publication
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Returns evidence as a association_results object given an association
      tags:
        - evidence/graph
    parameters:
      - description: association id, e.g. 68e686f6-d05b-46b8-ab1f-1da2fff97ada
        in: path
        name: id
        required: true
        schema:
          type: string
  "/genome/features/within/{build}/{reference}/{begin}/{end}":
    get:
      operationId: get_features_within_resource
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/SequenceFeature"
                type: array
          description: Success
      summary: Returns list of matches
      tags:
        - genome/features
    parameters:
      - in: path
        name: build
        required: true
        schema:
          type: string
      - in: path
        name: reference
        required: true
        schema:
          type: string
      - in: path
        name: begin
        required: true
        schema:
          type: string
      - in: path
        name: end
        required: true
        schema:
          type: string
  "/graph/edges/from/{id}":
    get:
      operationId: get_edge_resource
      parameters:
        - description: How far to traverse for neighbors
          in: query
          name: depth
          schema:
            default: 1
            type: integer
        - description: Which direction to traverse (used only if relationship_type is defined)
          explode: true
          in: query
          name: direction
          schema:
            default: BOTH
            enum:
              - INCOMING
              - OUTGOING
              - BOTH
            type: string
        - description: Relationship type to traverse
          explode: true
          in: query
          name: relationship_type
          schema:
            items:
              type: string
            type: array
        - description: Include sub-properties and equivalent properties
          in: query
          name: entail
          schema:
            default: false
            type: boolean
        - description: Which monarch graph to query
          explode: true
          in: query
          name: graph
          schema:
            default: data
            enum:
              - data
              - ontology
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Graph"
                type: array
          description: Success
      summary: Returns edges emanating from a given node
      tags:
        - graph
    parameters:
      - description: CURIE e.g. HP:0000465
        in: path
        name: id
        required: true
        schema:
          type: string
  "/graph/node/{id}":
    get:
      description: |-
        A node is an abstract representation of some kind of entity. The entity may be a physical thing such as a patient,
        a molecular entity such as a gene or protein, or a conceptual entity such as a class from an ontology.
      operationId: get_node_resource
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/BioObject"
                type: array
          description: Success
      summary: Returns a graph node
      tags:
        - graph
    parameters:
      - description: CURIE e.g. HP:0000465
        in: path
        name: id
        required: true
        schema:
          type: string
  "/identifier/mapper/{source}/{target}/":
    get:
      operationId: get_identifier_mapper
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Association"
                type: array
          description: Success
      summary: TODO maps a list of identifiers from a source to a target
      tags:
        - identifier/mapper
    parameters:
      - in: path
        name: source
        required: true
        schema:
          type: string
      - in: path
        name: target
        required: true
        schema:
          type: string
  /identifier/prefixes/:
    get:
      operationId: get_prefix_collection
      responses:
        "200":
          description: Success
      summary: Returns list of prefixes
      tags:
        - identifier/prefixes
  "/identifier/prefixes/contract/{uri}":
    get:
      operationId: get_prefix_contract
      responses:
        "200":
          description: Success
      summary: Returns contracted URI
      tags:
        - identifier/prefixes
    parameters:
      - description: URI of entity to be contracted to identifier/CURIE, e.g "http://www.informatics.jax.org/accession/MGI:1"
        in: path
        name: uri
        required: true
        schema:
          type: string
  "/identifier/prefixes/expand/{id}":
    get:
      operationId: get_prefix_expand
      responses:
        "200":
          description: Success
      summary: Returns expanded URI
      tags:
        - identifier/prefixes
    parameters:
      - description: ID of entity to be contracted to URI, e.g "MGI:1"
        in: path
        name: id
        required: true
        schema:
          type: string
  "/individual/pedigree/{id}":
    get:
      operationId: get_pedigree
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Association"
                type: array
          description: Success
      summary: Returns list of matches
      tags:
        - individual
    parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
  "/individual/{id}":
    get:
      operationId: get_individual
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Association"
                type: array
          description: Success
      summary: Returns list of matches
      tags:
        - individual
    parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
  "/mart/case/{object_category}/{taxon}":
    get:
      description: "NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully."
      operationId: get_mart_case_associations_resource
      parameters:
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
      responses:
        "200":
          description: Success
      summary: Bulk download of case associations
      tags:
        - mart
    parameters:
      - description: taxon of case, must be of form NCBITaxon:9606
        in: path
        name: taxon
        required: true
        schema:
          type: string
      - description: Category of entity at link Subject (target), e.g. phenotype, disease
        in: path
        name: object_category
        required: true
        schema:
          type: string
  "/mart/disease/{object_category}/{taxon}":
    get:
      description: "NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully."
      operationId: get_mart_disease_associations_resource
      parameters:
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
      responses:
        "200":
          description: Success
      summary: Bulk download of disease associations
      tags:
        - mart
    parameters:
      - description: taxon of disease, must be of form NCBITaxon:9606
        in: path
        name: taxon
        required: true
        schema:
          type: string
      - description: Category of entity at link Object (target), e.g. phenotype, disease
        in: path
        name: object_category
        required: true
        schema:
          type: string
  "/mart/gene/{object_category}/{taxon}":
    get:
      description: "NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully."
      operationId: get_mart_gene_associations_resource
      parameters:
        - description: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
          explode: true
          in: query
          name: slim
          schema:
            items:
              type: string
            type: array
      responses:
        "200":
          description: Success
      summary: Bulk download of gene associations
      tags:
        - mart
    parameters:
      - description: taxon of gene, must be of form NCBITaxon:9606
        in: path
        name: taxon
        required: true
        schema:
          type: string
      - description: Category of entity at link Object (target), e.g. phenotype, disease
        in: path
        name: object_category
        required: true
        schema:
          type: string
  "/mart/ortholog/{taxon1}/{taxon2}":
    get:
      operationId: get_mart_ortholog_associations_resource
      responses:
        "200":
          description: Success
      summary: Bulk download of orthologs
      tags:
        - mart
    parameters:
      - description: object taxon, e.g. NCBITaxon:10090
        in: path
        name: taxon2
        required: true
        schema:
          type: string
      - description: subject taxon, e.g. NCBITaxon:9606
        in: path
        name: taxon1
        required: true
        schema:
          type: string
  "/mart/paralog/{taxon1}/{taxon2}":
    get:
      operationId: get_mart_paralog_associations_resource
      responses:
        "200":
          description: Success
      summary: Bulk download of paralogs
      tags:
        - mart
    parameters:
      - description: object taxon, e.g. NCBITaxon:9606
        in: path
        name: taxon2
        required: true
        schema:
          type: string
      - description: subject taxon, e.g. NCBITaxon:9606
        in: path
        name: taxon1
        required: true
        schema:
          type: string
  /metadata/datasets:
    get:
      operationId: get_metadata_for_datasets
      responses:
        "200":
          description: Success
      summary: Get metadata for all datasets from SciGraph
      tags:
        - metadata
  /mme/disease:
    post:
      operationId: post_disease_mme
      requestBody:
        $ref: "#/components/requestBodies/mme"
      responses:
        "200":
          description: Success
      summary: Match a patient to diseases based on their phenotypes
      tags:
        - mme
  /mme/fly:
    post:
      operationId: post_fly_mme
      requestBody:
        $ref: "#/components/requestBodies/mme"
      responses:
        "200":
          description: Success
      summary: Match a patient to fruit fly genes based on similar phenotypes
      tags:
        - mme
  /mme/mouse:
    post:
      operationId: post_mouse_mme
      requestBody:
        $ref: "#/components/requestBodies/mme"
      responses:
        "200":
          description: Success
      summary: Match a patient to mouse genes based on similar phenotypes
      tags:
        - mme
  /mme/nematode:
    post:
      operationId: post_nematode_mme
      requestBody:
        $ref: "#/components/requestBodies/mme"
      responses:
        "200":
          description: Success
      summary: Match a patient to nematode genes based on similar phenotypes
      tags:
        - mme
  /mme/zebrafish:
    post:
      operationId: post_zebrafish_mme
      requestBody:
        $ref: "#/components/requestBodies/mme"
      responses:
        "200":
          description: Success
      summary: Match a patient to zebrafish genes based on similar phenotypes
      tags:
        - mme
  /nlp/annotate/:
    get:
      operationId: get_annotate
      parameters:
        - description: The text content to annotate
          in: query
          name: content
          schema:
            type: string
        - description: Categories to include for annotation
          explode: true
          in: query
          name: include_category
          schema:
            items:
              type: string
            type: array
        - description: Categories to exclude for annotation
          explode: true
          in: query
          name: exclude_category
          schema:
            items:
              type: string
            type: array
        - description: The minimum number of characters in the annotated entity
          in: query
          name: min_length
          schema:
            default: 4
            type: string
        - description: Should only the longest entity be returned for an overlapping group
          in: query
          name: longest_only
          schema:
            default: false
            type: boolean
        - description: Should abbreviations be included
          in: query
          name: include_abbreviation
          schema:
            default: false
            type: boolean
        - description: Should acronyms be included
          in: query
          name: include_acronym
          schema:
            default: false
            type: boolean
        - description: Should numbers be included
          in: query
          name: include_numbers
          schema:
            default: false
            type: boolean
      responses:
        "200":
          description: Success
      summary: Annotate a given text using SciGraph annotator
      tags:
        - nlp/annotate
    post:
      operationId: post_annotate
      parameters:
        - description: The text content to annotate
          in: query
          name: content
          schema:
            type: string
        - description: Categories to include for annotation
          explode: true
          in: query
          name: include_category
          schema:
            items:
              type: string
            type: array
        - description: Categories to exclude for annotation
          explode: true
          in: query
          name: exclude_category
          schema:
            items:
              type: string
            type: array
        - description: The minimum number of characters in the annotated entity
          in: query
          name: min_length
          schema:
            default: 4
            type: string
        - description: Should only the longest entity be returned for an overlapping group
          in: query
          name: longest_only
          schema:
            default: false
            type: boolean
        - description: Should abbreviations be included
          in: query
          name: include_abbreviation
          schema:
            default: false
            type: boolean
        - description: Should acronyms be included
          in: query
          name: include_acronym
          schema:
            default: false
            type: boolean
        - description: Should numbers be included
          in: query
          name: include_numbers
          schema:
            default: false
            type: boolean
      responses:
        "200":
          description: Success
      summary: Annotate a given text using SciGraph annotator
      tags:
        - nlp/annotate
  /nlp/annotate/entities:
    get:
      operationId: get_annotate_entities
      parameters:
        - description: The text content to annotate
          in: query
          name: content
          schema:
            type: string
        - description: Categories to include for annotation
          explode: true
          in: query
          name: include_category
          schema:
            items:
              type: string
            type: array
        - description: Categories to exclude for annotation
          explode: true
          in: query
          name: exclude_category
          schema:
            items:
              type: string
            type: array
        - description: The minimum number of characters in the annotated entity
          in: query
          name: min_length
          schema:
            default: 4
            type: string
        - description: Should only the longest entity be returned for an overlapping group
          in: query
          name: longest_only
          schema:
            default: false
            type: boolean
        - description: Should abbreviations be included
          in: query
          name: include_abbreviation
          schema:
            default: false
            type: boolean
        - description: Should acronyms be included
          in: query
          name: include_acronym
          schema:
            default: false
            type: boolean
        - description: Should numbers be included
          in: query
          name: include_numbers
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/EntityAnnotationResult"
          description: Success
      summary: Annotate a given content using SciGraph annotator and get all entities from content
      tags:
        - nlp/annotate
    post:
      operationId: post_annotate_entities
      parameters:
        - description: The text content to annotate
          in: query
          name: content
          schema:
            type: string
        - description: Categories to include for annotation
          explode: true
          in: query
          name: include_category
          schema:
            items:
              type: string
            type: array
        - description: Categories to exclude for annotation
          explode: true
          in: query
          name: exclude_category
          schema:
            items:
              type: string
            type: array
        - description: The minimum number of characters in the annotated entity
          in: query
          name: min_length
          schema:
            default: 4
            type: string
        - description: Should only the longest entity be returned for an overlapping group
          in: query
          name: longest_only
          schema:
            default: false
            type: boolean
        - description: Should abbreviations be included
          in: query
          name: include_abbreviation
          schema:
            default: false
            type: boolean
        - description: Should acronyms be included
          in: query
          name: include_acronym
          schema:
            default: false
            type: boolean
        - description: Should numbers be included
          in: query
          name: include_numbers
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/EntityAnnotationResult"
          description: Success
      summary: Annotate a given content using SciGraph annotator and get all entities from content
      tags:
        - nlp/annotate
  /ontol/identifier/:
    get:
      operationId: get_ontol_identifier_resource
      parameters:
        - description: List of labels
          explode: true
          in: query
          name: label
          required: true
          schema:
            items:
              type: string
            type: array
      responses:
        "200":
          description: Success
      summary: Fetches a map from CURIEs/IDs to labels
      tags:
        - ontol/identifier
    post:
      description: |-
        Takes 'label' list argument either as a querystring argument or as a key
        in the POST body when content-type is application/json.
      operationId: post_ontol_identifier_resource
      parameters:
        - description: List of labels
          explode: true
          in: query
          name: label
          required: true
          schema:
            items:
              type: string
            type: array
      responses:
        "200":
          description: Success
      summary: Fetches a map from CURIEs/IDs to labels
      tags:
        - ontol/identifier
  "/ontol/information_content/{subject_category}/{object_category}/{subject_taxon}":
    get:
      description: |-
        ```
        IC = -log2( freq(t) / popSize )
        ```

        Here the frequency and population is calculated for a particular dataset:
        e.g. all human disease-phenotype associations
      operationId: get_information_content_resource
      parameters:
        - description: "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)

            \                    or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.

            \                    "
          in: query
          name: evidence
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: Returns information content (IC) for a set of relevant ontology classes
      tags:
        - ontol
    parameters:
      - in: path
        name: subject_category
        required: true
        schema:
          type: string
      - in: path
        name: object_category
        required: true
        schema:
          type: string
      - in: path
        name: subject_taxon
        required: true
        schema:
          type: string
  /ontol/labeler/:
    get:
      operationId: get_ontol_labeler_resource
      parameters:
        - description: List of ids
          explode: true
          in: query
          name: id
          required: true
          schema:
            items:
              type: string
            type: array
      responses:
        "200":
          description: Success
      summary: Fetches a map from CURIEs/IDs to labels
      tags:
        - ontol/labeler
  "/ontol/subgraph/{ontology}/{node}":
    get:
      operationId: get_extract_ontology_subgraph_resource
      parameters:
        - description: Additional classes
          explode: true
          in: query
          name: cnode
          schema:
            items:
              type: string
            type: array
        - description: Include Ancestors
          in: query
          name: include_ancestors
          schema:
            default: true
            type: boolean
        - description: Include Descendants
          in: query
          name: include_descendants
          schema:
            type: boolean
        - description: Additional classes
          explode: true
          in: query
          name: relation
          schema:
            default:
              - subClassOf
              - BFO:0000050
            items:
              type: string
            type: array
        - description: Include metadata in response
          in: query
          name: include_meta
          schema:
            default: false
            type: boolean
      responses:
        "200":
          description: Success
      summary: Extract a subgraph from an ontology
      tags:
        - ontol
    parameters:
      - description: class ID, e.g. HP:0001288
        in: path
        name: node
        required: true
        schema:
          type: string
      - description: ontology ID, e.g. go, uberon, mp, hp
        in: path
        name: ontology
        required: true
        schema:
          type: string
    post:
      operationId: post_extract_ontology_subgraph_resource
      parameters:
        - description: Additional classes
          explode: true
          in: query
          name: cnode
          schema:
            items:
              type: string
            type: array
        - description: Include Ancestors
          in: query
          name: include_ancestors
          schema:
            default: true
            type: boolean
        - description: Include Descendants
          in: query
          name: include_descendants
          schema:
            type: boolean
        - description: Additional classes
          explode: true
          in: query
          name: relation
          schema:
            default:
              - subClassOf
              - BFO:0000050
            items:
              type: string
            type: array
        - description: Include metadata in response
          in: query
          name: include_meta
          schema:
            default: false
            type: boolean
      responses:
        "200":
          description: Success
      summary: Extract a subgraph from an ontology
      tags:
        - ontol
  "/ontology/shared/{subject}/{object}":
    get:
      operationId: get_ontology_terms_shared_ancestor
      responses:
        "200":
          description: Success
      summary: Returns the ancestor ontology terms shared by two ontology terms
      tags:
        - ontology
    parameters:
      - description: CURIE identifier of a GO term, e.g. GO:0006259
        in: path
        name: subject
        required: true
        schema:
          type: string
      - description: CURIE identifier of a GO term, e.g. GO:0046483
        in: path
        name: object
        required: true
        schema:
          type: string
  "/ontology/subset/{id}":
    get:
      operationId: get_ontology_subset
      responses:
        "200":
          description: Success
      summary: Returns meta data of an ontology subset (slim)
      tags:
        - ontology
    parameters:
      - description: name of a slim subset, e.g. goslim_agr, goslim_generic
        in: path
        name: id
        required: true
        schema:
          type: string
  "/ontology/term/{id}":
    get:
      operationId: get_ontology_term
      responses:
        "200":
          description: Success
      summary: Returns meta data of an ontology term
      tags:
        - ontology
    parameters:
      - description: CURIE identifier of a GO term, e.g. GO:0003677
        in: path
        name: id
        required: true
        schema:
          type: string
  "/ontology/term/{id}/graph":
    get:
      operationId: get_ontology_term_graph
      parameters:
        - description: graph type ('topology_graph', 'regulates_transitivity_graph' or 'neighborhood_graph')
          explode: true
          in: query
          name: graph_type
          schema:
            default: topology_graph
            enum:
              - topology_graph
              - regulates_transitivity_graph
              - neighborhood_graph
              - neighborhood_limited_graph
            type: string
      responses:
        "200":
          description: Success
      summary: Returns graph of an ontology term
      tags:
        - ontology
    parameters:
      - description: CURIE identifier of a GO term, e.g. GO:0000981
        in: path
        name: id
        required: true
        schema:
          type: string
  "/ontology/term/{id}/subgraph":
    get:
      operationId: get_ontology_term_subgraph
      parameters:
        - description: Additional classes
          explode: true
          in: query
          name: cnode
          schema:
            items:
              type: string
            type: array
        - description: Include Ancestors
          in: query
          name: include_ancestors
          schema:
            default: true
            type: boolean
        - description: Include Descendants
          in: query
          name: include_descendants
          schema:
            type: boolean
        - description: Additional classes
          explode: true
          in: query
          name: relation
          schema:
            default:
              - subClassOf
              - BFO:0000050
            items:
              type: string
            type: array
        - description: Include metadata in response
          in: query
          name: include_meta
          schema:
            default: false
            type: boolean
      responses:
        "200":
          description: Success
      summary: Extract a subgraph from an ontology term
      tags:
        - ontology
    parameters:
      - description: CURIE identifier of a GO term, e.g. GO:0007275
        in: path
        name: id
        required: true
        schema:
          type: string
  "/ontology/term/{id}/subsets":
    get:
      operationId: get_ontology_term_subsets
      responses:
        "200":
          description: Success
      summary: Returns subsets (slims) associated to an ontology term
      tags:
        - ontology
    parameters:
      - description: CURIE identifier of a GO term, e.g. GO:0006259
        in: path
        name: id
        required: true
        schema:
          type: string
  "/owl/ontology/dlquery/{query}":
    get:
      operationId: get_dl_query
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Association"
                type: array
          description: Success
      summary: Placeholder - use OWLery for now
      tags:
        - owl/ontology
    parameters:
      - in: path
        name: query
        required: true
        schema:
          type: string
  "/owl/ontology/sparql/{query}":
    get:
      operationId: get_sparql_query
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Association"
                type: array
          description: Success
      summary: Placeholder - use direct SPARQL endpoint for now
      tags:
        - owl/ontology
    parameters:
      - in: path
        name: query
        required: true
        schema:
          type: string
  "/pair/sim/jaccard/{id1}/{id2}":
    get:
      operationId: get_pair_sim_jaccard_resource
      parameters:
        - description: e.g. disease, phenotype, gene. Two subjects will be compared based on overlap between associations to objects in this category
          in: query
          name: object_category
          schema:
            type: string
      responses:
        "200":
          description: Success
      summary: Get pairwise similarity
      tags:
        - pair/sim
    parameters:
      - description: id, e.g. NCBIGene:1200; ZFIN:ZDB-GENE-980528-2059; UniProtKB:P12644
        in: path
        name: id2
        required: true
        schema:
          type: string
      - description: id, e.g. NCBIGene:10891; ZFIN:ZDB-GENE-980526-166; UniProtKB:Q15465
        in: path
        name: id1
        required: true
        schema:
          type: string
  /relation/usage/:
    get:
      operationId: get_relation_usage_resource
      parameters:
        - description: SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
          in: query
          name: subject_taxon
          schema:
            type: string
        - description: "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)

            \                    or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.

            \                    "
          in: query
          name: evidence
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: All relations used plus count of associations
      tags:
        - relation/usage
  "/relation/usage/between/{subject_category}/{object_category}":
    get:
      operationId: get_relation_usage_between_resource
      parameters:
        - description: SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
          in: query
          name: subject_taxon
          schema:
            type: string
        - description: "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)

            \                    or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.

            \                    "
          in: query
          name: evidence
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: All relations used plus count of associations
      tags:
        - relation/usage
    parameters:
      - in: path
        name: subject_category
        required: true
        schema:
          type: string
      - in: path
        name: object_category
        required: true
        schema:
          type: string
  /relation/usage/pivot:
    get:
      operationId: get_relation_usage_pivot_resource
      parameters:
        - description: SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
          in: query
          name: subject_taxon
          schema:
            type: string
        - description: "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)

            \                    or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.

            \                    "
          in: query
          name: evidence
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Relation usage count for all subj x obj category combinations
      tags:
        - relation/usage
  /relation/usage/pivot/label:
    get:
      operationId: get_relation_usage_pivot_label_resource
      parameters:
        - description: SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
          in: query
          name: subject_taxon
          schema:
            type: string
        - description: "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)

            \                    or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.

            \                    "
          in: query
          name: evidence
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AssociationResults"
                type: array
          description: Success
      summary: Relation usage count for all subj x obj category combinations, showing label
      tags:
        - relation/usage
  "/search/entity/autocomplete/{term}":
    get:
      operationId: get_autocomplete
      parameters:
        - description: fq string passed directly to solr, note that multiple filters will be combined with an AND operator. Combining fq_string with other parameters may result in unexpected behavior.
          explode: true
          in: query
          name: fq
          schema:
            items:
              type: string
            type: array
        - description: e.g. gene, disease
          explode: true
          in: query
          name: category
          schema:
            items:
              type: string
            type: array
        - description: "ontology prefix: HP, -MONDO"
          explode: true
          in: query
          name: prefix
          schema:
            items:
              type: string
            type: array
        - description: Include equivalent ids in prefix filter
          in: query
          name: include_eqs
          schema:
            default: false
            type: boolean
        - description: boost function e.g. pow(edges,0.334)
          explode: true
          in: query
          name: boost_fx
          schema:
            items:
              type: string
            type: array
        - description: boost query e.g. category:genotype^-10
          explode: true
          in: query
          name: boost_q
          schema:
            items:
              type: string
            type: array
        - description: taxon filter, eg NCBITaxon:9606, includes inferred taxa
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 20
            type: integer
        - description: row number to start from
          in: query
          name: start
          schema:
            default: "0"
            type: string
        - description: highlight class
          in: query
          name: highlight_class
          schema:
            type: string
        - description: minimum should match parameter, see solr docs for details
          in: query
          name: min_match
          schema:
            type: string
        - description: Exclude grouping classes (classes with subclasses)
          in: query
          name: exclude_groups
          schema:
            default: false
            type: boolean
        - description: set to true to use the minimal tokenizer, good for variants and genotypes
          in: query
          name: minimal_tokenizer
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/AutocompleteResults"
          description: Success
      summary: Returns list of matching concepts or entities using lexical search
      tags:
        - search
    parameters:
      - in: path
        name: term
        required: true
        schema:
          type: string
  "/search/entity/hpo-pl/{term}":
    get:
      operationId: get_search_hpo_entities
      parameters:
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 10
            type: integer
        - description: row number to start from
          in: query
          name: start
          schema:
            default: "0"
            type: string
        - description: phenotype group id
          in: query
          name: phenotype_group
          schema:
            type: string
        - description: phenotype group label
          in: query
          name: phenotype_group_label
          schema:
            type: string
        - description: anatomical system id
          in: query
          name: anatomical_system
          schema:
            type: string
        - description: anatomical system label
          in: query
          name: anatomical_system_label
          schema:
            type: string
        - description: highlight class
          in: query
          name: highlight_class
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/LayResults"
          description: Success
      summary: Returns list of matching concepts or entities using lexical search
      tags:
        - search
    parameters:
      - description: search string, e.g. muscle atrophy, frequent infections
        in: path
        name: term
        required: true
        schema:
          type: string
  "/search/entity/{term}":
    get:
      operationId: get_search_entities
      parameters:
        - description: fq string passed directly to solr, note that multiple filters will be combined with an AND operator. Combining fq_string with other parameters may result in unexpected behavior.
          explode: true
          in: query
          name: fq
          schema:
            items:
              type: string
            type: array
        - description: e.g. gene, disease
          explode: true
          in: query
          name: category
          schema:
            items:
              type: string
            type: array
        - description: "ontology prefix: HP, -MONDO"
          explode: true
          in: query
          name: prefix
          schema:
            items:
              type: string
            type: array
        - description: Include equivalent ids in prefix filter
          in: query
          name: include_eqs
          schema:
            default: false
            type: boolean
        - description: boost function e.g. pow(edges,0.334)
          explode: true
          in: query
          name: boost_fx
          schema:
            items:
              type: string
            type: array
        - description: boost query e.g. category:genotype^-10
          explode: true
          in: query
          name: boost_q
          schema:
            items:
              type: string
            type: array
        - description: taxon filter, eg NCBITaxon:9606, includes inferred taxa
          explode: true
          in: query
          name: taxon
          schema:
            items:
              type: string
            type: array
        - description: number of rows
          in: query
          name: rows
          schema:
            default: 20
            type: integer
        - description: row number to start from
          in: query
          name: start
          schema:
            default: "0"
            type: string
        - description: highlight class
          in: query
          name: highlight_class
          schema:
            type: string
        - description: minimum should match parameter, see solr docs for details
          in: query
          name: min_match
          schema:
            type: string
        - description: Exclude grouping classes (classes with subclasses)
          in: query
          name: exclude_groups
          schema:
            default: false
            type: boolean
        - description: set to true to use the minimal tokenizer, good for variants and genotypes
          in: query
          name: minimal_tokenizer
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/SearchResult"
          description: Success
      summary: Returns list of matching concepts or entities using lexical search
      tags:
        - search
    parameters:
      - description: search string, e.g. shh, parkinson, femur
        in: path
        name: term
        required: true
        schema:
          type: string
  /sim/compare:
    get:
      operationId: get_sim_compare
      parameters:
        - description: set to true if *all* input ids are phenotypic features, else set to false
          in: query
          name: is_feature_set
          schema:
            default: true
            type: boolean
        - description: Metric for computing similarity
          explode: true
          in: query
          name: metric
          schema:
            default: phenodigm
            enum:
              - phenodigm
              - jaccard
              - simGIC
              - resnik
              - symmetric_resnik
            type: string
        - description: A phenotype or identifier that is composed of phenotypes (eg disease, gene)
          explode: true
          in: query
          name: ref_id
          schema:
            default: []
            items:
              type: string
            type: array
        - description: A phenotype or identifier that is composed of phenotypes (eg disease, gene)
          explode: true
          in: query
          name: query_id
          schema:
            default: []
            items:
              type: string
            type: array
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/SimResult"
          description: Success
      summary: Compare a reference profile vs one profiles
      tags:
        - sim
    post:
      operationId: post_sim_compare
      requestBody:
        content:
          application/json:
            schema:
              $ref: "#/components/schemas/CompareInput"
        required: true
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/SimResult"
          description: Success
      summary: Compare a reference profile vs one or more profiles
      tags:
        - sim
  /sim/score:
    get:
      operationId: get_annotation_score
      parameters:
        - description: Phenotype identifier (eg HP:0004935)
          explode: true
          in: query
          name: id
          schema:
            items:
              type: string
            type: array
        - description: absent phenotype (eg HP:0002828)
          explode: true
          in: query
          name: absent_id
          schema:
            default: []
            items:
              type: string
            type: array
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/SufficiencyOutput"
          description: Success
      summary: Get annotation score
      tags:
        - sim
    post:
      operationId: post_annotation_score
      requestBody:
        content:
          application/json:
            schema:
              $ref: "#/components/schemas/SufficiencyPostInput"
        required: true
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/SufficiencyOutput"
          description: Success
      summary: Get annotation score
      tags:
        - sim
  /sim/search:
    get:
      operationId: get_sim_search
      parameters:
        - description: set to true if *all* input ids are phenotypic features, else set to false
          in: query
          name: is_feature_set
          schema:
            default: true
            type: boolean
        - description: Metric for computing similarity
          explode: true
          in: query
          name: metric
          schema:
            default: phenodigm
            enum:
              - phenodigm
              - jaccard
              - simGIC
              - resnik
              - symmetric_resnik
            type: string
        - description: A phenotype or identifier that is composed of phenotypes (eg disease, gene)
          explode: true
          in: query
          name: id
          schema:
            default: []
            items:
              type: string
            type: array
        - description: number of rows, max 500
          in: query
          name: limit
          schema:
            default: 20
            type: integer
        - description: ncbi taxon id
          in: query
          name: taxon
          schema:
            type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/SimResult"
          description: Success
      summary: Search for phenotypically similar diseases or model genes
      tags:
        - sim
  /variation/set/:
    get:
      operationId: get_variant_sets_collection
      parameters:
        - description: Page number
          in: query
          name: page
          schema:
            default: 1
            type: integer
        - description: Results per page {error_msg}
          explode: true
          in: query
          name: per_page
          schema:
            default: 10
            enum:
              - 2
              - 10
              - 20
              - 30
              - 40
              - 50
            type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Page_of_variant_sets"
          description: Success
      summary: Returns list of variant sets
      tags:
        - variation/set
    post:
      operationId: post_variant_sets_collection
      requestBody:
        $ref: "#/components/requestBodies/variant_set"
      responses:
        "200":
          description: Success
      summary: Creates a new variant set
      tags:
        - variation/set
  "/variation/set/analyze/{id}":
    get:
      operationId: get_variant_analyze
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Association"
                type: array
          description: Success
      summary: Returns list of matches
      tags:
        - variation/set
    parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
  "/variation/set/archive/{year}/{month}/{day}":
    get:
      operationId: get_variant_sets_archive_collection
      parameters:
        - description: Page number
          in: query
          name: page
          schema:
            default: 1
            type: integer
        - description: Results per page {error_msg}
          explode: true
          in: query
          name: per_page
          schema:
            default: 10
            enum:
              - 2
              - 10
              - 20
              - 30
              - 40
              - 50
            type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Page_of_variant_sets"
          description: Success
      summary: Returns list of variant sets from a specified time period
      tags:
        - variation/set
    parameters:
      - in: path
        name: year
        required: true
        schema:
          type: integer
      - in: path
        name: month
        required: true
        schema:
          type: integer
      - in: path
        name: day
        required: true
        schema:
          type: integer
  "/variation/set/{id}":
    delete:
      operationId: delete_variant_set_item
      responses:
        "204":
          description: VariantSet successfully deleted.
        "404":
          description: VariantSet not found.
      summary: Deletes variant set
      tags:
        - variation/set
    get:
      operationId: get_variant_set_item
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/variant_set"
          description: Success
        "404":
          description: VariantSet not found.
      summary: Returns a variant set
      tags:
        - variation/set
    parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
    put:
      operationId: put_variant_set_item
      requestBody:
        $ref: "#/components/requestBodies/variant_set"
      responses:
        "204":
          description: VariantSet successfully updated.
        "404":
          description: VariantSet not found.
      summary: Updates a variant set
      tags:
        - variation/set
components:
  requestBodies:
    mme:
      content:
        application/json:
          schema:
            $ref: "#/components/schemas/mme"
      required: true
    variant_set:
      content:
        application/json:
          schema:
            $ref: "#/components/schemas/variant_set"
      required: true
  responses:
    AmbiguousPrefix:
      description: Error handler to handle AmbiguousPrefix
    InvalidSyntax:
      description: Error handler to handle InvalidSyntax
    MaskError:
      description: When any error occurs on mask
    NoContraction:
      description: Error handler to handle NoContraction
    NoExpansion:
      description: Error handler to handle NoExpansion
    NoPrefix:
      description: Error handler to handle NoPrefix
    NoResultFound:
      description: ""
    NoResultFoundException:
      description: Error handler to handle NoResultFoundException
    ParseError:
      description: When a mask can't be parsed
    RouteNotImplementedException:
      description: Error handler to handle RouteNotImplementedException
    UnhandledException:
      description: Error handler to handle UnhandledException
    UnrecognizedBioentityTypeException:
      description: Error handler to handle UnrecognizedBioentityTypeException
  schemas:
    A_page_of_results:
      properties:
        page:
          description: Number of this page of results
          type: integer
        pages:
          description: Total number of pages of results
          type: integer
        per_page:
          description: Number of items per page of results
          type: integer
        total:
          description: Total number of results
          type: integer
      type: object
    AbstractPropertyValue:
      properties:
        pred:
          description: predicate (attribute) part
          type: string
        val:
          description: value part
          type: string
        xrefs:
          description: Xrefs provenance for property-value
          items:
            type: string
          type: array
      type: object
    AnnotationExtension:
      properties:
        filler:
          allOf:
            - $ref: "#/components/schemas/NamedObject"
          description: Extension interpreted as OWL expression (r1 some r2 some .. some filler).
        relation_chain:
          description: Relationship type. If more than one value, interpreted as chain
          items:
            $ref: "#/components/schemas/Relation"
          type: array
      type: object
    Association:
      properties:
        evidence_graph:
          allOf:
            - $ref: "#/components/schemas/Graph"
          description: An indirect association is a join between two or more direct assocations, e.g. gene to disease via ortholog. We record the full set of associations as a graph object
        evidence_types:
          description: Evidence types (ECO classes)
          items:
            $ref: "#/components/schemas/EntityReference"
          type: array
        id:
          description: Association/annotation unique ID
          type: string
        negated:
          description: True if association is negated
          type: boolean
        object:
          allOf:
            - $ref: "#/components/schemas/BioObjectCore"
          description: Object (sensu RDF), aka target, e.g. HP:0000448, MP:0002109, DOID:14330
        object_eq:
          description: Equivalent identifiers to object node
          items:
            type: string
          type: array
        object_extensions:
          items:
            allOf:
              - $ref: "#/components/schemas/AnnotationExtension"
            description: Additional properties of the object in the context of this association. See http://www.biomedcentral.com/1471-2105/15/155
          type: array
        provided_by:
          description: Provider of association, e.g. Orphanet, ClinVar
          items:
            type: string
          type: array
        publications:
          description: Publications supporting association, extracted from evidence graph
          items:
            $ref: "#/components/schemas/EntityReference"
          type: array
        qualifiers:
          description: Qualifier on the association
          items:
            type: string
          type: array
        relation:
          allOf:
            - $ref: "#/components/schemas/RelationRef"
          description: Relationship type connecting subject and object
        slim:
          description: Objects mapped to a slim
          items:
            type: string
          type: array
        subject:
          allOf:
            - $ref: "#/components/schemas/BioObjectCore"
          description: Subject of association (what it is about), e.g. ClinVar:nnn, MGI:1201606
        subject_eq:
          description: Equivalent identifiers to subject node
          items:
            type: string
          type: array
        subject_extensions:
          items:
            allOf:
              - $ref: "#/components/schemas/AnnotationExtension"
            description: Additional properties of the subject in the context of this association.
          type: array
        type:
          description: Type of association, e.g. gene-phenotype
          type: string
      required:
        - id
        - object
        - relation
        - subject
      type: object
    AssociationResults:
      allOf:
        - $ref: "#/components/schemas/SearchResult"
        - properties:
            associations:
              description: Complete representation of full association object, plus evidence
              items:
                $ref: "#/components/schemas/Association"
              type: array
            compact_associations:
              description: Compact representation in which objects (e.g. phenotypes) are collected for subject-predicate pairs
              items:
                $ref: "#/components/schemas/CompactAssociationSet"
              type: array
            objects:
              description: List of distinct objects used
              items:
                type: string
              type: array
          type: object
    AutocompleteResult:
      properties:
        category:
          description: node categories
          items:
            type: string
          type: array
        equivalent_ids:
          description: Equivalent IDs
          items:
            type: string
          type: array
        has_highlight:
          description: True if highlight can be interpreted as html, else False
          type: boolean
        highlight:
          description: solr highlight
          type: string
        id:
          description: curie formatted id
          type: string
        label:
          description: primary label (rdfs:label)
          items:
            type: string
          type: array
        match:
          description: matched part of document (may be primary label, synonym, id, etc)
          type: string
        taxon:
          description: taxon as NCBITaxon curie
          type: string
        taxon_label:
          description: taxon label
          type: string
      type: object
    AutocompleteResults:
      properties:
        docs:
          description: list of AutocompleteResult docs
          items:
            $ref: "#/components/schemas/AutocompleteResult"
          type: array
      type: object
    BioObject:
      allOf:
        - $ref: "#/components/schemas/NamedObject"
        - properties:
            association_counts:
              description: association counts
              type: object
            taxon:
              allOf:
                - $ref: "#/components/schemas/Taxon"
              description: Taxon to which the object belongs
            xrefs:
              description: "Database cross-references. These are usually CURIEs, but may also be URLs. E.g. ENSEMBL:ENSG00000099940 "
              items:
                type: string
              type: array
          type: object
    BioObjectCore:
      allOf:
        - $ref: "#/components/schemas/NamedObjectCore"
        - properties:
            taxon:
              allOf:
                - $ref: "#/components/schemas/Taxon"
              description: Taxon to which the object belongs
          type: object
    CompactAssociationSet:
      properties:
        objects:
          description: List of O, for a given (S,R) pair, yielding (S,R,O) triples. E.g. list of MPs for (MGI:nnn, has_phenotype)
          items:
            type: string
          type: array
        relation:
          description: Relationship type connecting subject and object list
          type: string
        subject:
          description: Subject of association (what it is about), e.g. MGI:1201606
          type: string
      required:
        - objects
        - relation
        - subject
      type: object
    CompareInput:
      properties:
        query_ids:
          description: list of query profiles
          items:
            description: list of ids
            items:
              description: curie formatted id
              type: string
            type: array
          type: array
        reference_ids:
          description: list of ids
          items:
            description: curie formatted id
            type: string
          type: array
      type: object
    D2PAssociation:
      allOf:
        - $ref: "#/components/schemas/Association"
        - properties:
            frequency:
              allOf:
                - $ref: "#/components/schemas/EntityReference"
              description: Frequency of phenotype in patients with disease
            onset:
              allOf:
                - $ref: "#/components/schemas/EntityReference"
              description: Onset of phenotype in disease process
          type: object
    D2PAssociationResults:
      allOf:
        - $ref: "#/components/schemas/SearchResult"
        - properties:
            associations:
              description: Complete representation of full disease to phenotype association, plus evidence
              items:
                $ref: "#/components/schemas/D2PAssociation"
              type: array
            compact_associations:
              description: Compact representation in which objects (e.g. phenotypes) are collected for subject-predicate pairs
              items:
                $ref: "#/components/schemas/CompactAssociationSet"
              type: array
            objects:
              description: List of distinct objects used
              items:
                type: string
              type: array
          type: object
    Edge:
      properties:
        meta:
          description: metadata about the Edge
          type: object
        obj:
          description: Object (target) Node ID
          type: string
        pred:
          description: Predicate (relation) ID
          type: string
        sub:
          description: Subject (source) Node ID
          type: string
      type: object
    EntityAnnotationResult:
      properties:
        content:
          default: The content from which the entities are extracted from
          type: string
        spans:
          description: A marked-up span of text
          items:
            $ref: "#/components/schemas/Span"
          type: array
      type: object
    EntityReference:
      properties:
        id:
          description: ID or CURIE e.g. MGI:1201606
          type: string
        label:
          description: RDFS Label
          type: string
      type: object
    Feature:
      properties:
        id:
          description: curie formatted id
          type: string
        isPresent:
          description: is the feature present
          type: boolean
        label:
          description: curie formatted id
          type: string
        type:
          description: feature type (only phenotype supported)
          type: string
      type: object
    Graph:
      properties:
        edges:
          description: All edges in graph
          items:
            $ref: "#/components/schemas/Edge"
          type: array
        nodes:
          description: All nodes in graph
          items:
            $ref: "#/components/schemas/Node"
          type: array
      type: object
    IcNode:
      allOf:
        - $ref: "#/components/schemas/Node"
        - properties:
            IC:
              description: Information content
              type: number
          type: object
    LayAutocomplete:
      properties:
        highlight:
          description: solr highlight
          type: string
        id:
          description: curie formatted id
          type: string
        label:
          description: primary label (rdfs:label)
          type: string
        matched_synonym:
          description: matched synonym
          type: string
      type: object
    LayResults:
      properties:
        results:
          description: list of AutocompleteResult docs
          items:
            $ref: "#/components/schemas/LayAutocomplete"
          type: array
      type: object
    NamedObject:
      allOf:
        - $ref: "#/components/schemas/NamedObjectCore"
        - properties:
            consider:
              items:
                description: Potential replacement object (if named object is obsoleted)
                type: string
              type: array
            deprecated:
              description: True if the node is deprecated/obsoleted.
              type: boolean
            description:
              description: Descriptive text for the entity. For ontology classes, this will be a definition.
              type: string
            replaced_by:
              items:
                description: Direct 1:1 replacement (if named object is obsoleted)
                type: string
              type: array
            synonyms:
              description: list of synonyms or alternate labels
              items:
                $ref: "#/components/schemas/SynonymPropertyValue"
              type: array
            types:
              items:
                description: Type of object (direct)
                type: string
              type: array
          type: object
    NamedObjectCore:
      properties:
        category:
          items:
            description: Type of object
            type: string
          type: array
        id:
          description: ID or CURIE e.g. MGI:1201606
          type: string
        iri:
          description: IRI
          type: string
        label:
          description: RDFS Label
          type: string
      required:
        - id
      type: object
    Node:
      properties:
        id:
          description: ID or CURIE e.g. MGI:1201606
          type: string
        label:
          description: RDFS Label
          type: string
      required:
        - id
      type: object
    Page_of_variant_sets:
      allOf:
        - $ref: "#/components/schemas/A_page_of_results"
        - properties:
            items:
              items:
                $ref: "#/components/schemas/variant_set"
              type: array
          type: object
    PairwiseMatch:
      properties:
        lcs:
          allOf:
            - $ref: "#/components/schemas/IcNode"
          description: lowest common subsumer
        match:
          allOf:
            - $ref: "#/components/schemas/IcNode"
          description: match id
        reference:
          allOf:
            - $ref: "#/components/schemas/IcNode"
          description: reference id
      type: object
    Relation:
      allOf:
        - $ref: "#/components/schemas/NamedObject"
        - properties: {}
          type: object
    RelationRef:
      allOf:
        - $ref: "#/components/schemas/NamedObjectCore"
        - properties:
            inverse:
              default: false
              description: is relation inverted
              type: boolean
          type: object
    SearchResult:
      properties:
        docs:
          description: solr docs
          items:
            type: object
          type: array
        facet_counts:
          description: Mapping between field names and association counts
          type: object
        highlighting:
          description: Mapping between id and solr highlight
          type: object
        numFound:
          description: total number of associations matching query
          type: integer
      type: object
    Seq:
      allOf:
        - $ref: "#/components/schemas/BioObject"
        - properties:
            alphabet:
              description: "one of: DNA, RNA or AA"
              type: string
            md5checksum:
              description: checksum
              type: string
            residues:
              description: string representing sequence of residues
              type: string
            seqlen:
              description: length of sequence
              type: string
          type: object
    SequenceFeature:
      allOf:
        - $ref: "#/components/schemas/BioObject"
        - properties:
            homology_associations:
              items:
                $ref: "#/components/schemas/Association"
              type: array
            locations:
              items:
                $ref: "#/components/schemas/SequenceLocation"
              type: array
            seq:
              $ref: "#/components/schemas/Seq"
          type: object
    SequenceLocation:
      allOf:
        - $ref: "#/components/schemas/BioObject"
        - properties:
            end:
              $ref: "#/components/schemas/SequencePosition"
            phase:
              type: integer
            score:
              type: integer
            start:
              $ref: "#/components/schemas/SequencePosition"
            strand:
              description: "Strand direction: 1=='+', -1=='-', 0 or null infers unknown."
              type: integer
          type: object
    SequencePosition:
      properties:
        position:
          type: integer
        reference:
          type: string
      type: object
    SimMatch:
      allOf:
        - $ref: "#/components/schemas/TypedNode"
        - properties:
            pairwise_match:
              items:
                allOf:
                  - $ref: "#/components/schemas/PairwiseMatch"
                description: list of pairwise matches
              type: array
            rank:
              description: rank
              type: string
            score:
              description: sim score
              type: number
            significance:
              description: p-value
              type: string
          type: object
    SimMetadata:
      properties:
        max_max_ic:
          description: max IC
          type: number
      type: object
    SimQuery:
      properties:
        ids:
          items:
            allOf:
              - $ref: "#/components/schemas/Node"
            description: list of ids
          type: array
        negated_ids:
          items:
            allOf:
              - $ref: "#/components/schemas/Node"
            description: list of ids
          type: array
        reference:
          allOf:
            - $ref: "#/components/schemas/TypedNode"
          description: reference individual or class (eg gene, disease)
        target_ids:
          items:
            items:
              allOf:
                - $ref: "#/components/schemas/Node"
              description: query ids
            type: array
          type: array
        unresolved_ids:
          description: list of unresolved ids
          items:
            description: curie formatted id
            type: string
          type: array
      type: object
    SimResult:
      properties:
        matches:
          items:
            allOf:
              - $ref: "#/components/schemas/SimMatch"
            description: list of matches
          type: array
        metadata:
          $ref: "#/components/schemas/SimMetadata"
        query:
          $ref: "#/components/schemas/SimQuery"
      type: object
    Span:
      properties:
        end:
          description: end of span text relative to content
          type: integer
        start:
          description: start of span text relative to content
          type: integer
        text:
          description: span text
          type: string
        token:
          description: A token or entity extracted from the span text
          items:
            $ref: "#/components/schemas/Token"
          type: array
      type: object
    SufficiencyOutput:
      properties:
        categorical_score:
          description: categorical score
          type: number
        scaled_score:
          description: scaled score
          type: number
        simple_score:
          description: simple score
          type: number
      type: object
    SufficiencyPostInput:
      properties:
        features:
          description: list of features
          items:
            $ref: "#/components/schemas/Feature"
          type: array
        id:
          description: curie formatted id
          type: string
      type: object
    SynonymPropertyValue:
      allOf:
        - $ref: "#/components/schemas/AbstractPropertyValue"
        - properties: {}
          type: object
    Taxon:
      properties:
        id:
          description: CURIE ID, e.g. NCBITaxon:9606
          type: string
        label:
          description: RDFS Label
          type: string
      type: object
    Token:
      properties:
        categories:
          description: entity categories
          items:
            type: string
          type: array
        id:
          description: The CURIE for the entity or token
          type: string
        terms:
          description: terms
          items:
            type: string
          type: array
      type: object
    TypedNode:
      allOf:
        - $ref: "#/components/schemas/Node"
        - properties:
            taxon:
              allOf:
                - $ref: "#/components/schemas/Node"
              description: taxon
            type:
              description: node type (eg phenotype, disease)
              type: string
          type: object
    mme:
      properties: {}
      type: object
    variant_set:
      properties:
        body:
          description: Article content
          type: string
        category:
          type: string
        category_id:
          type: integer
        id:
          description: The unique identifier of a variant set
          type: integer
        pub_date:
          format: date-time
          type: string
        title:
          description: Article title
          type: string
      required:
        - body
        - title
      type: object
