diff --git a/biolink/openapi.yml b/biolink/openapi.yml
index 7e98a1b1..4cbf5f72 100644
--- a/biolink/openapi.yml
+++ b/biolink/openapi.yml
@@ -1,1545 +1,3393 @@
-openapi: 3.0.3
+openapi: 3.0.3 ## downgrade from 3.1.0 to 3.0.3, which SmartAPI currently supports
info:
contact:
- email: cjm@berkeleybop.org
- name: Chris Mungall
- x-id: https://github.com/cmungall
+ email: info@monarchinitiative.org
+ name: Monarch help desk
x-role: responsible developer
- description: API integration layer for linked biological objects.
- termsOfService: https://github.com/monarch-initiative/biolink-api/
- title: BioLink API
- version: 1.1.14
+ url: https://monarchinitiative.org/help
+ description: >-
+ The [Monarch Application Programming Interface (API)](https://api-v3.monarchinitiative.org/v3/docs#/)
+ is a RESTful API that wraps functionality required by the
+ [Monarch Initiative website](https://monarchinitiative.org/), including the retrieval of disease,
+ gene, and phenotype associations, phenotypic profile comparisons, and other graph operations.
+ termsOfService: https://monarchinitiative.org/terms
+ title: Monarch API
+ version: 0.1.0
x-translator:
- infores: "infores:biolink-api"
+ infores: "infores:monarchinitiative" ## don't use biolink-api?
component: KP
team:
- "Service Provider"
- "Standards Reference Implementation Team"
- biolink-version: "3.5.0"
+ biolink-version: "3.5.3"
servers:
- description: Production server
- url: http://api-v2.monarchinitiative.org/api
+ url: https://api-v3.monarchinitiative.org
x-maturity: production
tags:
-- name: anatomy
-- name: disease
-- name: gene
-- name: phenotype
-- name: pathway
-- name: variant
-- name: annotation
-- name: query
- name: translator
-- name: biolink
paths:
-## - note that this API has a LOT of endpoints. Currently we only include endpoints we are annotating as x-bte operations
-## browse here to find more endpoints: https://api.monarchinitiative.org/api/
-## - not interested in any endpoints using cases, genotypes, models, publications
-## - there are more parameters in the endpoints below. Only included parameters we're using
-## - potentially interesting operation to annotate:
-## - disease -> treatment: doesn't have same output format as the other endpoints...
-## - function <-> gene: looks like GO terms <-> Gene (tricky Gene -> GO because no separation between the sub-ontologies bp/cc/mf)
-## - bioentity/gene/{id}/expression/anatomy: same as gene/anatomy endpoint (already annotated)?
-## - bioentity/gene/{id}/homologs: gene -> gene homologs in other species (could annotate MyGene instead?)
-## - gene <-> pathway
-## - ontology/shared/{subject}/{object}:
-## the shared ancestry operation looks kinda interesting...but it's only for GO terms?
-## - removed / decided not to:
-## - pathway <-> phenotype: only seemed to include non-human REACT pathways (MMU, DRE) connected to MP / HP terms...
-## - phenotype -> anatomy: has a different output format (only has object...)
-## - /bioentity/substance/{id}/participant_in: gives association between chebi chem and...chebi roles/GO MF...
-## - /bioentity/substance/{id}/treats: looks like it's not working
- "/bioentity/anatomy/{id}/genes":
+ /v3/api/association:
get:
- parameters:
- - name: id
- 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
- required: true
- example: "UBERON:0001817" ## same as for anatomy-gene operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
- responses:
- '200':
- description: Success
- summary: Returns genes associated with a given anatomy
- tags:
- - anatomy
x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/anatomy-gene"
- "/bioentity/disease/{id}/genes":
- get:
- parameters:
- - name: id
- description: "CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results"
- in: path
- required: true
- example: "MONDO:0011562" ## same as for disease-gene-1 operation
- schema:
- type: string
- - name: association_type
- description: "Additional filters: causal, non_causal, both"
- in: query
- required: false
- example: "causal"
- schema:
- type: string
- enum:
- - causal
- - non_causal
- - both
- default: "both"
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
- responses:
- '200':
- description: Success
- summary: Returns genes associated with a disease
+ - "$ref": "#/components/x-bte-kgs-operations/gene-anatomy"
+ - "$ref": "#/components/x-bte-kgs-operations/anatomy-gene"
+ - "$ref": "#/components/x-bte-kgs-operations/disease-pheno"
+ - "$ref": "#/components/x-bte-kgs-operations/pheno-disease"
+ - "$ref": "#/components/x-bte-kgs-operations/gene-disease-causal"
+ - "$ref": "#/components/x-bte-kgs-operations/disease-gene-causal"
+ - "$ref": "#/components/x-bte-kgs-operations/gene-disease-contributesTo"
+ - "$ref": "#/components/x-bte-kgs-operations/disease-gene-contributesTo"
+ - "$ref": "#/components/x-bte-kgs-operations/gene-disease-associatedCondition"
+ - "$ref": "#/components/x-bte-kgs-operations/disease-gene-associatedCondition"
+ - "$ref": "#/components/x-bte-kgs-operations/gene-pheno"
+ - "$ref": "#/components/x-bte-kgs-operations/pheno-gene"
+ - "$ref": "#/components/x-bte-kgs-operations/gene-gene-interaction-forward"
+ - "$ref": "#/components/x-bte-kgs-operations/gene-gene-interaction-backward"
tags:
- - disease
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/disease-gene-1"
- - "$ref": "#/components/x-bte-kgs-operations/disease-gene-2"
- "/bioentity/disease/{id}/pathways":
- get:
+ - association
+ summary: ' Get Associations'
+ description: 'Retrieves all associations for a given entity, or between two entities.'
+ operationId: _get_associations_v3_api_association_get
parameters:
- - name: id
- description: "CURIE identifier of disease, e.g. DOID:4450. Equivalent IDs can be used with same results"
- in: path
- required: true
- example: "MONDO:0010524" ## same as for disease-pathway operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: category
+ in: query
+ required: false
+ schema:
+ type: array
+ items:
+ $ref: '#/components/schemas/AssociationCategory'
+ title: Category
+ - name: subject
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Subject
+ - name: subject_category
+ in: query
+ required: false
+ schema:
+ type: array
+ items:
+ $ref: '#/components/schemas/EntityCategory'
+ title: Subject Category
+ - name: subject_namespace
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Subject Namespace
+ - name: subject_taxon
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Subject Taxon
+ - name: predicate
+ in: query
+ required: false
+ schema:
+ type: array
+ items:
+ $ref: '#/components/schemas/AssociationPredicate'
+ title: Predicate
+ - name: object
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Object
+ - name: object_category
+ in: query
+ required: false
+ schema:
+ type: array
+ items:
+ $ref: '#/components/schemas/EntityCategory'
+ title: Object Category
+ - name: object_namespace
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Object Namespace
+ - name: object_taxon
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Object Taxon
+ - name: entity
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Entity
+ - name: direct
+ in: query
+ required: false
+ schema:
+ type: boolean
+ default: false
+ title: Direct
+ - name: format
+ in: query
+ required: false
+ schema:
+ allOf:
+ - $ref: '#/components/schemas/OutputFormat'
+ title: Output format for the response
+ # examples:
+ # - json
+ # - tsv
+ default: json
+ - name: limit
+ in: query
+ required: false
+ schema:
+ type: integer
+ default: 20
+ title: Limit
+ - name: offset
+ in: query
+ required: false
+ schema:
+ type: integer
+ default: 0
+ title: Offset
responses:
'200':
- description: Success
- summary: Returns pathways associated with a disease
- tags:
- - disease
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/disease-pathway"
- "/bioentity/disease/{id}/phenotypes":
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ anyOf:
+ - $ref: '#/components/schemas/AssociationResults'
+ - type: string
+ title: Response Get Associations V3 Api Association Get
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ '/v3/api/entity/{id}':
get:
- parameters:
- - name: id
- description: "CURIE identifier of disease, e.g. OMIM:605543, Orphanet:1934, DOID:678. Equivalent IDs can be used with same results"
- in: path
- required: true
- example: "MONDO:0008974" ## same as for disease-phenotypes operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
- responses:
- '200':
- description: Success
- summary: Returns phenotypes associated with a disease
tags:
- - disease
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/disease-phenotype"
- "/bioentity/disease/{id}/variants":
- get:
+ - entity
+ summary: ' Get Entity'
+ description: |-
+ Retrieves the entity with the specified id
+
+ Args:
+ id (str): ID for the entity to retrieve, ex: MONDO:0019391
+
+ Raises:
+ HTTPException: 404 if the entity is not found
+
+ Returns:
+ Node: Entity details for the specified id
+ operationId: _get_entity_v3_api_entity__id__get
parameters:
- - name: id
- description: "CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results"
- in: path
- required: true
- example: "MONDO:0004747" ## same as for disease-variant operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: id
+ in: path
+ required: true
+ schema:
+ type: string
+ title: ID of the entity to retrieve
+ # examples:
+ # - 'MONDO:0019391'
+ - name: format
+ in: query
+ required: false
+ schema:
+ allOf:
+ - $ref: '#/components/schemas/OutputFormat'
+ title: Output format for the response
+ # examples:
+ # - json
+ # - tsv
+ default: json
responses:
'200':
- description: Success
- summary: Returns variants associated with a disease
- tags:
- - disease
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/disease-variant"
- "/bioentity/gene/{id}/anatomy":
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ anyOf:
+ - $ref: '#/components/schemas/Node'
+ - type: string
+ title: Response Get Entity V3 Api Entity Id Get
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ '/v3/api/entity/{id}/{category}':
get:
+ tags:
+ - entity
+ summary: ' Association Table'
+ description: |-
+ Retrieves association table data for a given entity and association type
+
+ Args:
+ id (str): ID of the entity to retrieve association table data, ex: MONDO:0019391
+ category (str): Category of association to retrieve association table data for, ex: biolink:DiseaseToPhenotypicFeatureAssociation
+ Path (str, optional): Path string to limit results to a subset. Defaults to None.
+ pagination (PaginationParams, optional): Pagination parameters. Defaults to Depends().
+
+ Returns:
+ AssociationResults: Association table data for the specified entity and association type
+ operationId: _association_table_v3_api_entity__id___category__get
parameters:
- - name: id
- description: "CURIE identifier of gene, e.g. NCBIGene:13434"
- in: path
- required: true
- example: "HGNC:8548" ## same as for gene-anatomy operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: id
+ in: path
+ required: true
+ schema:
+ type: string
+ title: ID of the entity to retrieve association table data for
+ # examples:
+ # - 'MONDO:0019391'
+ - name: category
+ in: path
+ required: true
+ schema:
+ allOf:
+ - $ref: '#/components/schemas/AssociationCategory'
+ title: Type of association to retrieve association table data for
+ # examples:
+ # - 'biolink:DiseaseToPhenotypicFeatureAssociation'
+ - name: query
+ in: query
+ required: false
+ schema:
+ type: string
+ title: query string to limit results to a subset
+ # examples:
+ # - thumb
+ - name: sort
+ in: query
+ required: false
+ schema:
+ type: array
+ items:
+ type: string
+ title: Sort results by a list of field + direction statements
+ # examples:
+ # - subject_label asc
+ # - predicate asc
+ # - object_label asc
+ - name: format
+ in: query
+ required: false
+ schema:
+ allOf:
+ - $ref: '#/components/schemas/OutputFormat'
+ title: Output format for the response
+ # examples:
+ # - json
+ # - tsv
+ default: json
+ - name: download
+ in: query
+ required: false
+ schema:
+ type: boolean
+ title: Download the results as a file
+ # examples:
+ # - true
+ # - false
+ default: false
+ - name: limit
+ in: query
+ required: false
+ schema:
+ type: integer
+ default: 20
+ title: Limit
+ - name: offset
+ in: query
+ required: false
+ schema:
+ type: integer
+ default: 0
+ title: Offset
responses:
'200':
- description: Success
- summary: Returns anatomies associated with a gene
- tags:
- - gene
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/gene-anatomy"
- "/bioentity/gene/{id}/diseases":
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ anyOf:
+ - $ref: '#/components/schemas/AssociationTableResults'
+ - type: string
+ title: Response Association Table V3 Api Entity Id Category Get
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ '/v3/api/histopheno/{id}':
get:
+ tags:
+ - histopheno
+ summary: ' Get Histopheno'
+ description: Retrieves the entity with the specified id
+ operationId: _get_histopheno_v3_api_histopheno__id__get
parameters:
- - name: id
- description: "CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results"
- in: path
- required: true
- example: "HGNC:11138" ## same as for gene-disease-1 operation
- schema:
- type: string
- - name: association_type
- description: "Additional filters: causal, non_causal, both"
- in: query
- required: false
- example: "causal"
- schema:
- type: string
- enum:
- - causal
- - non_causal
- - both
- default: "both"
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: id
+ in: path
+ required: true
+ schema:
+ type: string
+ title: ID of the entity to get histopheno data for
+ # examples:
+ # - 'MONDO:0019391'
+ - name: format
+ in: query
+ required: false
+ schema:
+ allOf:
+ - $ref: '#/components/schemas/OutputFormat'
+ title: Output format for the response
+ # examples:
+ # - json
+ # - tsv
+ default: json
responses:
'200':
- description: Success
- summary: Returns diseases associated with a gene
- tags:
- - gene
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/gene-disease-1"
- - "$ref": "#/components/x-bte-kgs-operations/gene-disease-2"
- "/bioentity/gene/{id}/interactions":
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ anyOf:
+ - $ref: '#/components/schemas/HistoPheno'
+ - type: string
+ title: Response Get Histopheno V3 Api Histopheno Id Get
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ /v3/api/search:
get:
+ tags:
+ - search
+ summary: Search
+ description: |-
+ Search for entities by label, with optional filters
+
+ Args:
+ q (str, optional): Query string. Defaults to "*:*".
+ category (str, optional): Filter by biolink model category. Defaults to None.
+ in_taxon_label (str, optional): Filter by taxon label. Defaults to None.
+ offset (int, optional): Offset for pagination. Defaults to 0.
+ limit (int, optional): Limit results. Defaults to 20.
+
+ Returns:
+ EntityResults
+ operationId: search_v3_api_search_get
parameters:
- - name: id
- description: "id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results"
- in: path
- required: true
- example: "HGNC:2950" ## same as for gene-disease-1 operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: q
+ in: query
+ required: false
+ schema:
+ type: string
+ title: Q
+ - name: category
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ $ref: '#/components/schemas/EntityCategory'
+ # - type: 'null'
+ title: Category
+ - name: in_taxon_label
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: In Taxon Label
+ - name: limit
+ in: query
+ required: false
+ schema:
+ type: integer
+ default: 20
+ title: Limit
+ - name: offset
+ in: query
+ required: false
+ schema:
+ type: integer
+ default: 0
+ title: Offset
responses:
'200':
- description: Success
- summary: Returns gene interaction
- tags:
- - gene
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/gene-interaction"
- "/bioentity/gene/{id}/ortholog/diseases":
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/SearchResults'
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ /v3/api/autocomplete:
get:
+ tags:
+ - search
+ summary: Autocomplete
+ description: |-
+ Autocomplete for entities by label
+
+ Args:
+ q (str): Query string to autocomplete against
+
+ Returns:
+ SearchResults
+ operationId: autocomplete_v3_api_autocomplete_get
parameters:
- - name: id
- description: "CURIE identifier of gene, e.g. NCBIGene:4750"
- in: path
- required: true
- example: "HGNC:8548"
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: q
+ in: query
+ required: false
+ schema:
+ type: string
+ title: Query string to autocomplete against
+ # examples:
+ # - fanc
+ # - ehler
+ default: '*:*'
responses:
'200':
- description: Success
- summary: Returns diseases associated with orthologs of a gene
- tags:
- - gene
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/geneOrtholog-disease"
- "/bioentity/gene/{id}/ortholog/phenotypes":
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/SearchResults'
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ /v3/api/mappings:
get:
+ tags:
+ - search
+ summary: Mappings
+ operationId: mappings_v3_api_mappings_get
parameters:
- - name: id
- description: "CURIE identifier of gene, e.g. NCBIGene:4750"
- in: path
- required: true
- example: "HGNC:8548"
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: entity_id
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Entity Id
+ - name: subject_id
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Subject Id
+ - name: predicate_id
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Predicate Id
+ - name: object_id
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Object Id
+ - name: mapping_justification
+ in: query
+ required: false
+ schema:
+ anyOf:
+ - type: array
+ items:
+ type: string
+ # - type: 'null'
+ title: Mapping Justification
+ - name: format
+ in: query
+ required: false
+ schema:
+ allOf:
+ - $ref: '#/components/schemas/OutputFormat'
+ title: Output format for the response
+ # examples:
+ # - json
+ # - tsv
+ default: json
+ - name: limit
+ in: query
+ required: false
+ schema:
+ type: integer
+ default: 20
+ title: Limit
+ - name: offset
+ in: query
+ required: false
+ schema:
+ type: integer
+ default: 0
+ title: Offset
responses:
'200':
- description: Success
- summary: Returns phenotypes associated with orthologs for a gene
- tags:
- - gene
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/geneOrtholog-phenotype"
- "/bioentity/gene/{id}/phenotypes":
+ description: Successful Response
+ content:
+ application/json:
+ schema: {}
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ /v3/api/semsim/autocomplete:
get:
+ tags:
+ - semsim
+ summary: Autocomplete
+ description: >-
+ Autocomplete for semantic similarity lookups, prioritizes entities which
+ have direct phenotype associations.
+
+ Note: This API endpoint is experimental and may evolve or disappear over
+ time.
+
+
+ Args:
+ q (str): Query string to autocomplete against
+
+ Returns:
+ SearchResults
+ operationId: autocomplete_v3_api_semsim_autocomplete_get
parameters:
- - name: id
- description: "CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results"
- in: path
- required: true
- example: "HGNC:2950" ## same as for gene-phenotype operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: q
+ in: query
+ required: false
+ schema:
+ type: string
+ title: Query string to autocomplete against
+ # examples:
+ # - fanc
+ # - ehler
+ default: '*:*'
responses:
'200':
- description: Success
- summary: Returns phenotypes associated with a gene
- tags:
- - gene
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/gene-phenotype"
- "/bioentity/gene/{id}/variants":
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/SearchResults'
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ '/v3/api/semsim/compare/{subjects}/{objects}':
get:
+ tags:
+ - semsim
+ summary: ' Compare'
+ description: |-
+ Get pairwise similarity between two sets of terms
+
+ Args:
+ subjects (str, optional): List of subjects for comparison. Defaults to "".
+ objects (str, optional): List of objects for comparison. Defaults to "".
+
+ Returns:
+ TermSetPairwiseSimilarity: Pairwise similarity between subjects and objects
+ operationId: _compare_v3_api_semsim_compare__subjects___objects__get
parameters:
- - name: id
- description: "CURIE identifier of gene, e.g. HGNC:10896"
- in: path
- required: true
- example: "HGNC:2950" ## same as for gene-variant operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: subjects
+ in: path
+ required: true
+ schema:
+ type: string
+ title: List of subjects for comparison
+ - name: objects
+ in: path
+ required: true
+ schema:
+ type: string
+ title: List of objects for comparison
responses:
'200':
- description: Success
- summary: Returns variants associated with a gene
+ description: Successful Response
+ content:
+ application/json:
+ schema: {}
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ /v3/api/semsim/compare:
+ post:
tags:
- - gene
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/gene-variant"
- "/bioentity/pathway/{id}/diseases":
- get:
- parameters:
- - name: id
- description: "CURIE any pathway element. E.g. REACT:R-HSA-5387390"
- in: path
+ - semsim
+ summary: ' Post Compare'
+ description: |-
+ Pairwise similarity between two sets of terms
+
+ Example:
+
+ {
+ "subjects": ["MP:0010771","MP:0002169","MP:0005391","MP:0005389","MP:0005367"],
+ "objects": ["HP:0004325","HP:0000093","MP:0006144"]
+ }
+
+ operationId: _post_compare_v3_api_semsim_compare_post
+ requestBody:
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/SemsimCompareRequest'
required: true
- example: "REACT:R-HSA-2644606" ## same as for pathway-disease operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
responses:
'200':
- description: Success
- summary: Returns diseases associated with a pathway
- tags:
- - pathway
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/pathway-disease"
- "/bioentity/phenotype/{id}/diseases":
+ description: Successful Response
+ content:
+ application/json:
+ schema: {}
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ '/v3/api/semsim/search/{termset}/{group}':
get:
+ tags:
+ - semsim
+ summary: ' Search'
+ description: |-
+ Search for terms in a termset
+
+ Args:
+ termset (str, optional): Comma separated list of term IDs to find matches for.
+ group (str, optional): Group of entities to search within (e.g. Human Genes)
+ limit (int, optional): Limit the number of results. Defaults to 10.
+
+ Returns:
+ List[str]: List of matching terms
+ operationId: _search_v3_api_semsim_search__termset___group__get
parameters:
- - name: id
- description: "CURIE identifier of phenotype, e.g. HP:0007359. Equivalent IDs can be used with same results"
- in: path
- required: true
- example: "HP:0000272" ## same as for phenotype-disease operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: termset
+ in: path
+ required: true
+ schema:
+ type: string
+ title: Termset to search
+ - name: group
+ in: path
+ required: true
+ schema:
+ allOf:
+ - $ref: '#/components/schemas/SemsimSearchGroup'
+ title: Group of entities to search within (e.g. Human Genes)
+ - name: limit
+ in: query
+ required: false
+ schema:
+ type: integer
+ maximum: 50
+ minimum: 1
+ default: 10
+ title: Limit
responses:
'200':
- description: Success
- summary: Returns diseases associated with a phenotype
+ description: Successful Response
+ content:
+ application/json:
+ schema: {}
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ /v3/api/semsim/search:
+ post:
tags:
- - phenotype
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/phenotype-disease"
- "/bioentity/phenotype/{id}/genes":
- get:
- parameters:
- - name: id
- description: "Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)"
- in: path
+ - semsim
+ summary: ' Post Search'
+ description: |-
+ Search for terms in a termset
+
+ Example:
+
+ {
+ "termset": ["HP:0002104", "HP:0012378", "HP:0012378", "HP:0012378"],
+ "group": "Human Diseases",
+ "limit": 5
+ }
+
+ operationId: _post_search_v3_api_semsim_search_post
+ requestBody:
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/SemsimSearchRequest'
required: true
- example: "HP:0000183" ## same as for phenotype-gene operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
responses:
'200':
- description: Success
- summary: Returns genes associated with a phenotype
- tags:
- - phenotype
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/phenotype-gene"
- "/bioentity/phenotype/{id}/variants":
+ description: Successful Response
+ content:
+ application/json:
+ schema: {}
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ /v3/api/annotate:
get:
+ tags:
+ - text_annotation
+ summary: ' Annotate'
+ operationId: _annotate_v3_api_annotate_get
parameters:
- - name: id
- description: "Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)"
- in: path
- required: true
- example: "HP:0002944" ## same as for phenotype-variant operation
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: text
+ in: query
+ required: false
+ schema:
+ type: string
+ title: The text content to annotate
+ default: ''
responses:
'200':
- description: Success
- summary: Returns variants associated with a phenotype
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ type: string
+ title: Response Annotate V3 Api Annotate Get
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ post:
tags:
- - phenotype
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/phenotype-variant"
- "/bioentity/variant/{id}/diseases":
- get:
- parameters:
- - name: id
- description: "CURIE identifier of variant, e.g. ClinVarVariant:14925"
- in: path
+ - text_annotation
+ summary: ' Post Annotate'
+ operationId: _post_annotate_v3_api_annotate_post
+ requestBody:
required: true
- example: "dbSNP:rs227731" ## same as for variant-disease operation; but they use these as prefix
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/TextAnnotationRequest'
responses:
'200':
- description: Success
- summary: Returns diseases associated with a variant
- tags:
- - variant
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/variant-disease"
- "/bioentity/variant/{id}/genes":
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ type: string
+ title: Response Post Annotate V3 Api Annotate Post
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ /v3/api/annotate/entities:
get:
+ tags:
+ - text_annotation
+ summary: ' Entities'
+ operationId: _entities_v3_api_annotate_entities_get
parameters:
- - name: id
- description: "CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783"
- in: path
- required: true
- example: "dbSNP:rs11879191" ## same as for variant-gene operation; but they use these as prefix
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ - name: text
+ in: query
+ required: false
+ schema:
+ type: string
+ default: ''
+ title: Text
responses:
'200':
- description: Success
- summary: Returns genes associated with a variant
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ type: array
+ items:
+ $ref: '#/components/schemas/TextAnnotationResult'
+ title: Response Entities V3 Api Annotate Entities Get
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ post:
tags:
- - variant
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/variant-gene"
- "/bioentity/variant/{id}/phenotypes":
- get:
- parameters:
- - name: id
- description: "CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783"
- in: path
+ - text_annotation
+ summary: ' Post Entities'
+ operationId: _post_entities_v3_api_annotate_entities_post
+ requestBody:
required: true
- example: "dbSNP:rs115165302" ## same as for variant-phenotype operation; but they use these as prefix
- schema:
- type: string
- - "$ref": "#/components/parameters/rows"
- - "$ref": "#/components/parameters/start"
- - "$ref": "#/components/parameters/facet"
- - "$ref": "#/components/parameters/facet_fields"
- - "$ref": "#/components/parameters/unselect_evidence"
- - "$ref": "#/components/parameters/exclude_automatic_assertions"
- - "$ref": "#/components/parameters/fetch_objects"
- - "$ref": "#/components/parameters/use_compact_associations"
- - "$ref": "#/components/parameters/slim"
- - "$ref": "#/components/parameters/evidence"
- - "$ref": "#/components/parameters/direct"
- - "$ref": "#/components/parameters/taxon"
- - "$ref": "#/components/parameters/direct_taxon"
- - "$ref": "#/components/parameters/relation"
- - "$ref": "#/components/parameters/sort"
- - "$ref": "#/components/parameters/q"
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/TextAnnotationRequest'
responses:
'200':
- description: Success
- summary: Returns phenotypes associated with a variant
- tags:
- - variant
- x-bte-kgs-operations:
- - "$ref": "#/components/x-bte-kgs-operations/variant-phenotype"
+ description: Successful Response
+ content:
+ application/json:
+ schema:
+ type: array
+ items:
+ $ref: '#/components/schemas/TextAnnotationResult'
+ title: Response Post Entities V3 Api Annotate Entities Post
+ '404':
+ description: Not Found
+ '422':
+ description: Validation Error
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/HTTPValidationError'
+ # /:
+ # get:
+ # summary: ' Root'
+ # operationId: _root__get
+ # responses:
+ # '200':
+ # description: Successful Response
+ # content:
+ # application/json:
+ # schema: {}
+ # /api:
+ # get:
+ # summary: ' Api'
+ # operationId: _api_api_get
+ # responses:
+ # '200':
+ # description: Successful Response
+ # content:
+ # application/json:
+ # schema: {}
components:
- parameters:
- rows:
- name: rows
- description: number of rows
- in: query
- required: false
- schema:
- ## default is 100; -1 should get everything back (not sure though)
- type: integer
- default: 100
- start:
- name: start
- description: beginning row
- in: query
- required: false
- schema:
- type: integer
- facet:
- name: facet
- description: Enable faceting
- in: query
- required: false
- schema:
- type: boolean
- facet_fields:
- name: facet_fields
- description: Fields to facet on
- in: query
- required: false
- schema:
- type: array
+ schemas:
+ Association:
+ properties:
+ id:
+ type: string
+ title: Id
+ category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Category
+ subject:
+ type: string
+ title: Subject
+ original_subject:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Original Subject
+ subject_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Subject Namespace
+ description: The namespace/prefix of the subject entity
+ subject_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Subject Category
+ description: The category of the subject entity
+ subject_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Subject Closure
+ description: Field containing subject id and the ids of all of it's ancestors
+ subject_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Subject Label
+ description: The name of the subject entity
+ subject_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Subject Closure Label
+ description: Field containing subject name and the names of all of it's ancestors
+ subject_taxon:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Subject Taxon
+ subject_taxon_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Subject Taxon Label
+ predicate:
+ type: string
+ title: Predicate
+ object:
+ type: string
+ title: Object
+ original_object:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Original Object
+ object_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Object Namespace
+ description: The namespace/prefix of the object entity
+ object_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Object Category
+ description: The category of the object entity
+ object_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Object Closure
+ description: Field containing object id and the ids of all of it's ancestors
+ object_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Object Label
+ description: The name of the object entity
+ object_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Object Closure Label
+ description: Field containing object name and the names of all of it's ancestors
+ object_taxon:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Object Taxon
+ object_taxon_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Object Taxon Label
+ primary_knowledge_source:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Primary Knowledge Source
+ aggregator_knowledge_source:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Aggregator Knowledge Source
+ negated:
+ anyOf:
+ - type: boolean
+ # - type: 'null'
+ title: Negated
+ pathway:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Pathway
+ evidence_count:
+ anyOf:
+ - type: integer
+ # - type: 'null'
+ title: Evidence Count
+ description: >-
+ count of supporting documents, evidence codes, and sources supplying
+ evidence
+ has_evidence:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Evidence
+ has_evidence_links:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/ExpandedCurie'
+ type: array
+ # - type: 'null'
+ title: Has Evidence Links
+ description: List of ExpandedCuries with id and url for evidence
+ grouping_key:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Grouping Key
+ description: >-
+ A concatenation of fields used to group associations with the same
+ essential/defining properties
+ provided_by:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Provided By
+ provided_by_link:
+ anyOf:
+ - $ref: '#/components/schemas/ExpandedCurie'
+ # - type: 'null'
+ description: >-
+ A link to the docs for the knowledge source that provided the
+ node/edge.
+ publications:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Publications
+ publications_links:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/ExpandedCurie'
+ type: array
+ # - type: 'null'
+ title: Publications Links
+ description: List of ExpandedCuries with id and url for publications
+ frequency_qualifier:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Frequency Qualifier
+ onset_qualifier:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Onset Qualifier
+ sex_qualifier:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Sex Qualifier
+ stage_qualifier:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Stage Qualifier
+ qualifiers:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifiers
+ qualifiers_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifiers Label
+ description: The name of the frequency_qualifier entity
+ qualifiers_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifiers Namespace
+ description: The namespace/prefix of the frequency_qualifier entity
+ qualifiers_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifiers Category
+ description: The category of the frequency_qualifier entity
+ qualifiers_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifiers Closure
+ description: >-
+ Field containing frequency_qualifier id and the ids of all of it's
+ ancestors
+ qualifiers_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifiers Closure Label
+ description: >-
+ Field containing frequency_qualifier name and the names of all of
+ it's ancestors
+ qualifier:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifier
+ qualifier_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifier Label
+ description: The name of the frequency_qualifier entity
+ qualifier_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifier Namespace
+ description: The namespace/prefix of the frequency_qualifier entity
+ qualifier_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifier Category
+ description: The category of the frequency_qualifier entity
+ qualifier_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifier Closure
+ description: >-
+ Field containing frequency_qualifier id and the ids of all of it's
+ ancestors
+ qualifier_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifier Closure Label
+ description: >-
+ Field containing frequency_qualifier name and the names of all of
+ it's ancestors
+ frequency_qualifier_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Frequency Qualifier Label
+ description: The name of the frequency_qualifier entity
+ frequency_qualifier_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Frequency Qualifier Namespace
+ description: The namespace/prefix of the frequency_qualifier entity
+ frequency_qualifier_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Frequency Qualifier Category
+ description: The category of the frequency_qualifier entity
+ frequency_qualifier_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Frequency Qualifier Closure
+ description: >-
+ Field containing frequency_qualifier id and the ids of all of it's
+ ancestors
+ frequency_qualifier_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Frequency Qualifier Closure Label
+ description: >-
+ Field containing frequency_qualifier name and the names of all of
+ it's ancestors
+ onset_qualifier_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Onset Qualifier Label
+ description: The name of the onset_qualifier entity
+ onset_qualifier_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Onset Qualifier Namespace
+ description: The namespace/prefix of the onset_qualifier entity
+ onset_qualifier_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Onset Qualifier Category
+ description: The category of the onset_qualifier entity
+ onset_qualifier_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Onset Qualifier Closure
+ description: >-
+ Field containing onset_qualifier id and the ids of all of it's
+ ancestors
+ onset_qualifier_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Onset Qualifier Closure Label
+ description: >-
+ Field containing onset_qualifier name and the names of all of it's
+ ancestors
+ sex_qualifier_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Sex Qualifier Label
+ description: The name of the sex_qualifier entity
+ sex_qualifier_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Sex Qualifier Namespace
+ description: The namespace/prefix of the sex_qualifier entity
+ sex_qualifier_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Sex Qualifier Category
+ description: The category of the sex_qualifier entity
+ sex_qualifier_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Sex Qualifier Closure
+ description: >-
+ Field containing sex_qualifier id and the ids of all of it's
+ ancestors
+ sex_qualifier_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Sex Qualifier Closure Label
+ description: >-
+ Field containing sex_qualifier name and the names of all of it's
+ ancestors
+ stage_qualifier_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Stage Qualifier Label
+ description: The name of the stage_qualifier entity
+ stage_qualifier_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Stage Qualifier Namespace
+ description: The namespace/prefix of the stage_qualifier entity
+ stage_qualifier_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Stage Qualifier Category
+ description: The category of the stage_qualifier entity
+ stage_qualifier_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Stage Qualifier Closure
+ description: >-
+ Field containing stage_qualifier id and the ids of all of it's
+ ancestors
+ stage_qualifier_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Stage Qualifier Closure Label
+ description: >-
+ Field containing stage_qualifier name and the names of all of it's
+ ancestors
+ additionalProperties: true
+ type: object
+ required:
+ - id
+ - subject
+ - predicate
+ - object
+ title: Association
+ AssociationCategory:
+ type: string
+ enum:
+ - 'biolink:PairwiseGeneToGeneInteraction'
+ - 'biolink:GeneToExpressionSiteAssociation'
+ - 'biolink:MacromolecularMachineToBiologicalProcessAssociation'
+ - 'biolink:GeneToPhenotypicFeatureAssociation'
+ - 'biolink:MacromolecularMachineToMolecularActivityAssociation'
+ - 'biolink:MacromolecularMachineToCellularComponentAssociation'
+ - 'biolink:Association'
+ - 'biolink:GeneToGeneHomologyAssociation'
+ - 'biolink:DiseaseToPhenotypicFeatureAssociation'
+ - 'biolink:GeneToPathwayAssociation'
+ - 'biolink:ChemicalToPathwayAssociation'
+ - 'biolink:CorrelatedGeneToDiseaseAssociation'
+ - 'biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation'
+ - 'biolink:CausalGeneToDiseaseAssociation'
+ - 'biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation'
+ title: AssociationCategory
+ description: Association categories
+ AssociationCount:
+ properties:
+ label:
+ type: string
+ title: Label
+ count:
+ anyOf:
+ - type: integer
+ # - type: 'null'
+ title: Count
+ description: count of documents
+ category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Category
+ additionalProperties: true
+ type: object
+ required:
+ - label
+ title: AssociationCount
+ AssociationDirectionEnum:
+ type: string
+ enum:
+ - incoming
+ - outgoing
+ title: AssociationDirectionEnum
+ description: >-
+ The directionality of an association as it relates to a specified
+ entity, with edges being categorized as incoming or outgoing
+ AssociationPredicate:
+ type: string
+ enum:
+ - 'biolink:interacts_with'
+ - 'biolink:expressed_in'
+ - 'biolink:has_phenotype'
+ - 'biolink:enables'
+ - 'biolink:actively_involved_in'
+ - 'biolink:orthologous_to'
+ - 'biolink:located_in'
+ - 'biolink:subclass_of'
+ - 'biolink:participates_in'
+ - 'biolink:related_to'
+ - 'biolink:acts_upstream_of_or_within'
+ - 'biolink:active_in'
+ - 'biolink:part_of'
+ - 'biolink:acts_upstream_of'
+ - 'biolink:has_mode_of_inheritance'
+ - 'biolink:gene_associated_with_condition'
+ - 'biolink:contributes_to'
+ - 'biolink:causes'
+ - 'biolink:colocalizes_with'
+ - 'biolink:acts_upstream_of_or_within_positive_effect'
+ - 'biolink:acts_upstream_of_positive_effect'
+ - 'biolink:affects'
+ - 'biolink:acts_upstream_of_or_within_negative_effect'
+ - 'biolink:acts_upstream_of_negative_effect'
+ title: AssociationPredicate
+ description: Association predicates
+ AssociationResults:
+ properties:
+ limit:
+ type: integer
+ title: Limit
+ description: number of items to return in a response
+ offset:
+ type: integer
+ title: Offset
+ description: offset into the total number of items
+ total:
+ type: integer
+ title: Total
+ description: total number of items matching a query
items:
+ items:
+ $ref: '#/components/schemas/Association'
+ type: array
+ title: Items
+ description: 'A collection of items, with the type to be overriden by slot_usage'
+ additionalProperties: true
+ type: object
+ required:
+ - limit
+ - offset
+ - total
+ title: AssociationResults
+ AssociationTableResults:
+ properties:
+ limit:
+ type: integer
+ title: Limit
+ description: number of items to return in a response
+ offset:
+ type: integer
+ title: Offset
+ description: offset into the total number of items
+ total:
+ type: integer
+ title: Total
+ description: total number of items matching a query
+ items:
+ items:
+ $ref: '#/components/schemas/DirectionalAssociation'
+ type: array
+ title: Items
+ description: 'A collection of items, with the type to be overriden by slot_usage'
+ additionalProperties: true
+ type: object
+ required:
+ - limit
+ - offset
+ - total
+ title: AssociationTableResults
+ DirectionalAssociation:
+ properties:
+ id:
+ type: string
+ title: Id
+ category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Category
+ subject:
+ type: string
+ title: Subject
+ original_subject:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Original Subject
+ subject_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Subject Namespace
+ description: The namespace/prefix of the subject entity
+ subject_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Subject Category
+ description: The category of the subject entity
+ subject_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Subject Closure
+ description: Field containing subject id and the ids of all of it's ancestors
+ subject_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Subject Label
+ description: The name of the subject entity
+ subject_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Subject Closure Label
+ description: Field containing subject name and the names of all of it's ancestors
+ subject_taxon:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Subject Taxon
+ subject_taxon_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Subject Taxon Label
+ predicate:
+ type: string
+ title: Predicate
+ object:
type: string
- unselect_evidence:
- name: unselect_evidence
- description: If true, excludes evidence objects in response
- in: query
- required: false
- schema:
- type: boolean
- default: false
- exclude_automatic_assertions:
- name: exclude_automatic_assertions
- description: If true, excludes associations that involve IEAs (ECO:0000501)
- in: query
- required: false
- schema:
- type: boolean
- default: false
- fetch_objects:
- name: fetch_objects
- 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
- required: false
- schema:
- type: boolean
- default: false
- use_compact_associations:
- name: use_compact_associations
- description: If true, returns results in compact associations format
- in: query
- required: false
- schema:
- type: boolean
- default: false
- slim:
- name: slim
- description: "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID"
- in: query
- required: false
- schema:
- type: array
+ title: Object
+ original_object:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Original Object
+ object_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Object Namespace
+ description: The namespace/prefix of the object entity
+ object_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Object Category
+ description: The category of the object entity
+ object_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Object Closure
+ description: Field containing object id and the ids of all of it's ancestors
+ object_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Object Label
+ description: The name of the object entity
+ object_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Object Closure Label
+ description: Field containing object name and the names of all of it's ancestors
+ object_taxon:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Object Taxon
+ object_taxon_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Object Taxon Label
+ primary_knowledge_source:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Primary Knowledge Source
+ aggregator_knowledge_source:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Aggregator Knowledge Source
+ negated:
+ anyOf:
+ - type: boolean
+ # - type: 'null'
+ title: Negated
+ pathway:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Pathway
+ evidence_count:
+ anyOf:
+ - type: integer
+ # - type: 'null'
+ title: Evidence Count
+ description: >-
+ count of supporting documents, evidence codes, and sources supplying
+ evidence
+ has_evidence:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Evidence
+ has_evidence_links:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/ExpandedCurie'
+ type: array
+ # - type: 'null'
+ title: Has Evidence Links
+ description: List of ExpandedCuries with id and url for evidence
+ grouping_key:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Grouping Key
+ description: >-
+ A concatenation of fields used to group associations with the same
+ essential/defining properties
+ provided_by:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Provided By
+ provided_by_link:
+ anyOf:
+ - $ref: '#/components/schemas/ExpandedCurie'
+ # - type: 'null'
+ description: >-
+ A link to the docs for the knowledge source that provided the
+ node/edge.
+ publications:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Publications
+ publications_links:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/ExpandedCurie'
+ type: array
+ # - type: 'null'
+ title: Publications Links
+ description: List of ExpandedCuries with id and url for publications
+ frequency_qualifier:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Frequency Qualifier
+ onset_qualifier:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Onset Qualifier
+ sex_qualifier:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Sex Qualifier
+ stage_qualifier:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Stage Qualifier
+ qualifiers:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifiers
+ qualifiers_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifiers Label
+ description: The name of the frequency_qualifier entity
+ qualifiers_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifiers Namespace
+ description: The namespace/prefix of the frequency_qualifier entity
+ qualifiers_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifiers Category
+ description: The category of the frequency_qualifier entity
+ qualifiers_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifiers Closure
+ description: >-
+ Field containing frequency_qualifier id and the ids of all of it's
+ ancestors
+ qualifiers_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifiers Closure Label
+ description: >-
+ Field containing frequency_qualifier name and the names of all of
+ it's ancestors
+ qualifier:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifier
+ qualifier_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifier Label
+ description: The name of the frequency_qualifier entity
+ qualifier_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifier Namespace
+ description: The namespace/prefix of the frequency_qualifier entity
+ qualifier_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Qualifier Category
+ description: The category of the frequency_qualifier entity
+ qualifier_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifier Closure
+ description: >-
+ Field containing frequency_qualifier id and the ids of all of it's
+ ancestors
+ qualifier_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Qualifier Closure Label
+ description: >-
+ Field containing frequency_qualifier name and the names of all of
+ it's ancestors
+ frequency_qualifier_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Frequency Qualifier Label
+ description: The name of the frequency_qualifier entity
+ frequency_qualifier_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Frequency Qualifier Namespace
+ description: The namespace/prefix of the frequency_qualifier entity
+ frequency_qualifier_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Frequency Qualifier Category
+ description: The category of the frequency_qualifier entity
+ frequency_qualifier_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Frequency Qualifier Closure
+ description: >-
+ Field containing frequency_qualifier id and the ids of all of it's
+ ancestors
+ frequency_qualifier_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Frequency Qualifier Closure Label
+ description: >-
+ Field containing frequency_qualifier name and the names of all of
+ it's ancestors
+ onset_qualifier_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Onset Qualifier Label
+ description: The name of the onset_qualifier entity
+ onset_qualifier_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Onset Qualifier Namespace
+ description: The namespace/prefix of the onset_qualifier entity
+ onset_qualifier_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Onset Qualifier Category
+ description: The category of the onset_qualifier entity
+ onset_qualifier_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Onset Qualifier Closure
+ description: >-
+ Field containing onset_qualifier id and the ids of all of it's
+ ancestors
+ onset_qualifier_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Onset Qualifier Closure Label
+ description: >-
+ Field containing onset_qualifier name and the names of all of it's
+ ancestors
+ sex_qualifier_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Sex Qualifier Label
+ description: The name of the sex_qualifier entity
+ sex_qualifier_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Sex Qualifier Namespace
+ description: The namespace/prefix of the sex_qualifier entity
+ sex_qualifier_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Sex Qualifier Category
+ description: The category of the sex_qualifier entity
+ sex_qualifier_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Sex Qualifier Closure
+ description: >-
+ Field containing sex_qualifier id and the ids of all of it's
+ ancestors
+ sex_qualifier_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Sex Qualifier Closure Label
+ description: >-
+ Field containing sex_qualifier name and the names of all of it's
+ ancestors
+ stage_qualifier_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Stage Qualifier Label
+ description: The name of the stage_qualifier entity
+ stage_qualifier_namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Stage Qualifier Namespace
+ description: The namespace/prefix of the stage_qualifier entity
+ stage_qualifier_category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Stage Qualifier Category
+ description: The category of the stage_qualifier entity
+ stage_qualifier_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Stage Qualifier Closure
+ description: >-
+ Field containing stage_qualifier id and the ids of all of it's
+ ancestors
+ stage_qualifier_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Stage Qualifier Closure Label
+ description: >-
+ Field containing stage_qualifier name and the names of all of it's
+ ancestors
+ direction:
+ allOf:
+ - $ref: '#/components/schemas/AssociationDirectionEnum'
+ description: >-
+ The directionality of the association relative to a given entity for
+ an association_count. If the entity is the subject or in the subject
+ closure, the direction is forwards, if it is the object or in the
+ object closure, the direction is backwards.
+ additionalProperties: true
+ type: object
+ required:
+ - id
+ - subject
+ - predicate
+ - object
+ - direction
+ title: DirectionalAssociation
+ description: An association that gives it's direction relative to a specified entity
+ Entity:
+ properties:
+ id:
+ type: string
+ title: Id
+ category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Category
+ name:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Name
+ full_name:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Full Name
+ description: The long form name of an entity
+ deprecated:
+ anyOf:
+ - type: boolean
+ # - type: 'null'
+ title: Deprecated
+ description: >-
+ A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ description:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Description
+ xref:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Xref
+ provided_by:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Provided By
+ in_taxon:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: In Taxon
+ description: The biolink taxon that the entity is in the closure of.
+ in_taxon_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: In Taxon Label
+ description: The label of the biolink taxon that the entity is in the closure of.
+ symbol:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Symbol
+ synonym:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Synonym
+ uri:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Uri
+ description: The URI of the entity
+ namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Namespace
+ description: The namespace/prefix portion of this entity's identifier
+ has_phenotype:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype
+ description: >-
+ A list of phenotype identifiers that are known to be associated with
+ this entity
+ has_phenotype_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype Label
+ description: >-
+ A list of phenotype labels that are known to be associated with this
+ entity
+ has_phenotype_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype Closure
+ description: >-
+ A list of phenotype identifiers that are known to be associated with
+ this entity expanded to include all ancestors
+ has_phenotype_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype Closure Label
+ description: >-
+ A list of phenotype labels that are known to be associated with this
+ entity expanded to include all ancestors
+ has_phenotype_count:
+ anyOf:
+ - type: integer
+ # - type: 'null'
+ title: Has Phenotype Count
+ description: >-
+ A count of the number of phenotypes that are known to be associated
+ with this entity
+ additionalProperties: true
+ type: object
+ required:
+ - id
+ title: Entity
+ description: Represents an Entity in the Monarch KG data model
+ EntityCategory:
+ type: string
+ enum:
+ - 'biolink:Gene'
+ - 'biolink:PhenotypicFeature'
+ - 'biolink:BiologicalProcessOrActivity'
+ - 'biolink:GrossAnatomicalStructure'
+ - 'biolink:Disease'
+ - 'biolink:Pathway'
+ - 'biolink:Cell'
+ - 'biolink:NamedThing'
+ - 'biolink:AnatomicalEntity'
+ - 'biolink:CellularComponent'
+ - 'biolink:MolecularEntity'
+ - 'biolink:BiologicalProcess'
+ - 'biolink:MacromolecularComplex'
+ - 'biolink:MolecularActivity'
+ - 'biolink:Protein'
+ - 'biolink:CellularOrganism'
+ - 'biolink:PhenotypicQuality'
+ - 'biolink:Vertebrate'
+ - 'biolink:Virus'
+ - 'biolink:BehavioralFeature'
+ - 'biolink:LifeStage'
+ - 'biolink:PathologicalProcess'
+ - 'biolink:ChemicalEntity'
+ - 'biolink:Drug'
+ - 'biolink:InformationContentEntity'
+ - 'biolink:SequenceVariant'
+ - 'biolink:SmallMolecule'
+ - 'biolink:OrganismTaxon'
+ - 'biolink:NucleicAcidEntity'
+ - 'biolink:EvidenceType'
+ - 'biolink:GeographicExposure'
+ - 'biolink:RNAProduct'
+ - 'biolink:Transcript'
+ - 'biolink:Fungus'
+ - 'biolink:Plant'
+ - 'biolink:PopulationOfIndividualOrganisms'
+ - 'biolink:Invertebrate'
+ - 'biolink:ProteinDomain'
+ - 'biolink:ProteinFamily'
+ - 'biolink:Activity'
+ - 'biolink:Agent'
+ - 'biolink:ChemicalExposure'
+ - 'biolink:ConfidenceLevel'
+ - 'biolink:Dataset'
+ - 'biolink:EnvironmentalFeature'
+ - 'biolink:Exon'
+ - 'biolink:GeneticInheritance'
+ - 'biolink:Genome'
+ - 'biolink:Genotype'
+ - 'biolink:Haplotype'
+ - 'biolink:Human'
+ - 'biolink:IndividualOrganism'
+ - 'biolink:Mammal'
+ - 'biolink:MaterialSample'
+ - 'biolink:MicroRNA'
+ - 'biolink:Patent'
+ - 'biolink:Publication'
+ - 'biolink:RegulatoryRegion'
+ - 'biolink:Study'
+ - 'biolink:Treatment'
+ - 'biolink:WebPage'
+ - 'biolink:AccessibleDnaRegion'
+ - 'biolink:Article'
+ - 'biolink:Attribute'
+ - 'biolink:Bacterium'
+ - 'biolink:BiologicalEntity'
+ - 'biolink:BiologicalSex'
+ - 'biolink:CellLine'
+ - 'biolink:ChemicalMixture'
+ - 'biolink:CodingSequence'
+ - 'biolink:DatasetDistribution'
+ - 'biolink:DiagnosticAid'
+ - 'biolink:DrugExposure'
+ - 'biolink:EnvironmentalProcess'
+ - 'biolink:Event'
+ - 'biolink:GenotypicSex'
+ - 'biolink:NoncodingRNAProduct'
+ - 'biolink:OrganismalEntity'
+ - 'biolink:PhenotypicSex'
+ - 'biolink:Polypeptide'
+ - 'biolink:Procedure'
+ - 'biolink:ProcessedMaterial'
+ - 'biolink:ReagentTargetedGene'
+ - 'biolink:SiRNA'
+ - 'biolink:Snv'
+ - 'biolink:StudyVariable'
+ - 'biolink:TranscriptionFactorBindingSite'
+ - 'biolink:Zygosity'
+ title: EntityCategory
+ description: Entity categories
+ ExpandedCurie:
+ properties:
+ id:
+ type: string
+ title: Id
+ url:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Url
+ additionalProperties: true
+ type: object
+ required:
+ - id
+ title: ExpandedCurie
+ description: A curie bundled along with its expanded url
+ FacetField:
+ properties:
+ label:
+ type: string
+ title: Label
+ facet_values:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/FacetValue'
+ type: array
+ # - type: 'null'
+ title: Facet Values
+ description: >-
+ Collection of FacetValue label/value instances belonging to a
+ FacetField
+ additionalProperties: true
+ type: object
+ required:
+ - label
+ title: FacetField
+ FacetValue:
+ properties:
+ label:
+ type: string
+ title: Label
+ count:
+ anyOf:
+ - type: integer
+ # - type: 'null'
+ title: Count
+ description: count of documents
+ additionalProperties: true
+ type: object
+ required:
+ - label
+ title: FacetValue
+ HTTPValidationError:
+ properties:
+ detail:
+ items:
+ $ref: '#/components/schemas/ValidationError'
+ type: array
+ title: Detail
+ type: object
+ title: HTTPValidationError
+ HistoBin:
+ properties:
+ label:
+ type: string
+ title: Label
+ count:
+ anyOf:
+ - type: integer
+ # - type: 'null'
+ title: Count
+ description: count of documents
+ id:
+ type: string
+ title: Id
+ additionalProperties: true
+ type: object
+ required:
+ - label
+ - id
+ title: HistoBin
+ HistoPheno:
+ properties:
+ id:
+ type: string
+ title: Id
items:
+ items:
+ $ref: '#/components/schemas/HistoBin'
+ type: array
+ title: Items
+ description: 'A collection of items, with the type to be overriden by slot_usage'
+ additionalProperties: true
+ type: object
+ required:
+ - id
+ title: HistoPheno
+ Node:
+ properties:
+ id:
+ type: string
+ title: Id
+ category:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Category
+ name:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Name
+ full_name:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Full Name
+ description: The long form name of an entity
+ deprecated:
+ anyOf:
+ - type: boolean
+ # - type: 'null'
+ title: Deprecated
+ description: >-
+ A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ description:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Description
+ xref:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Xref
+ provided_by:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Provided By
+ in_taxon:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: In Taxon
+ description: The biolink taxon that the entity is in the closure of.
+ in_taxon_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: In Taxon Label
+ description: The label of the biolink taxon that the entity is in the closure of.
+ symbol:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Symbol
+ synonym:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Synonym
+ uri:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Uri
+ description: The URI of the entity
+ namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Namespace
+ description: The namespace/prefix portion of this entity's identifier
+ has_phenotype:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype
+ description: >-
+ A list of phenotype identifiers that are known to be associated with
+ this entity
+ has_phenotype_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype Label
+ description: >-
+ A list of phenotype labels that are known to be associated with this
+ entity
+ has_phenotype_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype Closure
+ description: >-
+ A list of phenotype identifiers that are known to be associated with
+ this entity expanded to include all ancestors
+ has_phenotype_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype Closure Label
+ description: >-
+ A list of phenotype labels that are known to be associated with this
+ entity expanded to include all ancestors
+ has_phenotype_count:
+ anyOf:
+ - type: integer
+ # - type: 'null'
+ title: Has Phenotype Count
+ description: >-
+ A count of the number of phenotypes that are known to be associated
+ with this entity
+ inheritance:
+ anyOf:
+ - $ref: '#/components/schemas/Entity'
+ # - type: 'null'
+ causal_gene:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/Entity'
+ type: array
+ # - type: 'null'
+ title: Causal Gene
+ description: >-
+ A list of genes that are known to be causally associated with a
+ disease
+ causes_disease:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/Entity'
+ type: array
+ # - type: 'null'
+ title: Causes Disease
+ description: >-
+ A list of diseases that are known to be causally associated with a
+ gene
+ mappings:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/ExpandedCurie'
+ type: array
+ # - type: 'null'
+ title: Mappings
+ description: List of ExpandedCuries with id and url for mapped entities
+ external_links:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/ExpandedCurie'
+ type: array
+ # - type: 'null'
+ title: External Links
+ description: ExpandedCurie with id and url for xrefs
+ provided_by_link:
+ anyOf:
+ - $ref: '#/components/schemas/ExpandedCurie'
+ # - type: 'null'
+ description: >-
+ A link to the docs for the knowledge source that provided the
+ node/edge.
+ association_counts:
+ items:
+ $ref: '#/components/schemas/AssociationCount'
+ type: array
+ title: Association Counts
+ node_hierarchy:
+ anyOf:
+ - $ref: '#/components/schemas/NodeHierarchy'
+ # - type: 'null'
+ additionalProperties: true
+ type: object
+ required:
+ - id
+ title: Node
+ description: UI container class extending Entity with additional information
+ NodeHierarchy:
+ properties:
+ super_classes:
+ items:
+ $ref: '#/components/schemas/Entity'
+ type: array
+ title: Super Classes
+ sub_classes:
+ items:
+ $ref: '#/components/schemas/Entity'
+ type: array
+ title: Sub Classes
+ additionalProperties: true
+ type: object
+ title: NodeHierarchy
+ OutputFormat:
+ type: string
+ enum:
+ - json
+ - tsv
+ title: OutputFormat
+ SearchResult:
+ properties:
+ id:
+ type: string
+ title: Id
+ category:
type: string
- evidence:
- name: evidence
- 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
- required: false
- schema:
- type: string
- direct:
- name: direct
- description: "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False"
- in: query
- required: false
- schema:
- type: boolean
- default: false
- taxon:
- name: taxon
- description: "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default"
- in: query
- required: false
- schema:
- type: array
+ title: Category
+ name:
+ type: string
+ title: Name
+ full_name:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Full Name
+ description: The long form name of an entity
+ deprecated:
+ anyOf:
+ - type: boolean
+ # - type: 'null'
+ title: Deprecated
+ description: >-
+ A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ description:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Description
+ xref:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Xref
+ provided_by:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Provided By
+ in_taxon:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: In Taxon
+ description: The biolink taxon that the entity is in the closure of.
+ in_taxon_label:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: In Taxon Label
+ description: The label of the biolink taxon that the entity is in the closure of.
+ symbol:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Symbol
+ synonym:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Synonym
+ uri:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Uri
+ description: The URI of the entity
+ namespace:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Namespace
+ description: The namespace/prefix portion of this entity's identifier
+ has_phenotype:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype
+ description: >-
+ A list of phenotype identifiers that are known to be associated with
+ this entity
+ has_phenotype_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype Label
+ description: >-
+ A list of phenotype labels that are known to be associated with this
+ entity
+ has_phenotype_closure:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype Closure
+ description: >-
+ A list of phenotype identifiers that are known to be associated with
+ this entity expanded to include all ancestors
+ has_phenotype_closure_label:
+ anyOf:
+ - items:
+ type: string
+ type: array
+ # - type: 'null'
+ title: Has Phenotype Closure Label
+ description: >-
+ A list of phenotype labels that are known to be associated with this
+ entity expanded to include all ancestors
+ has_phenotype_count:
+ anyOf:
+ - type: integer
+ # - type: 'null'
+ title: Has Phenotype Count
+ description: >-
+ A count of the number of phenotypes that are known to be associated
+ with this entity
+ highlight:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Highlight
+ description: matching text snippet containing html tags
+ score:
+ anyOf:
+ - type: number
+ # - type: 'null'
+ title: Score
+ additionalProperties: true
+ type: object
+ required:
+ - id
+ - category
+ - name
+ title: SearchResult
+ SearchResults:
+ properties:
+ limit:
+ type: integer
+ title: Limit
+ description: number of items to return in a response
+ offset:
+ type: integer
+ title: Offset
+ description: offset into the total number of items
+ total:
+ type: integer
+ title: Total
+ description: total number of items matching a query
items:
+ items:
+ $ref: '#/components/schemas/SearchResult'
+ type: array
+ title: Items
+ description: 'A collection of items, with the type to be overriden by slot_usage'
+ facet_fields:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/FacetField'
+ type: array
+ # - type: 'null'
+ title: Facet Fields
+ description: Collection of facet field responses with the field values and counts
+ facet_queries:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/FacetValue'
+ type: array
+ # - type: 'null'
+ title: Facet Queries
+ description: >-
+ Collection of facet query responses with the query string values and
+ counts
+ additionalProperties: true
+ type: object
+ required:
+ - limit
+ - offset
+ - total
+ title: SearchResults
+ SemsimCompareRequest:
+ properties:
+ subjects:
+ items:
+ type: string
+ type: array
+ title: List of subjects for comparison
+ objects:
+ items:
+ type: string
+ type: array
+ title: List of objects for comparison
+ type: object
+ required:
+ - subjects
+ - objects
+ title: SemsimCompareRequest
+ SemsimSearchGroup:
+ type: string
+ enum:
+ - Human Genes
+ - Mouse Genes
+ - Rat Genes
+ - Zebrafish Genes
+ - C. Elegans Genes
+ - Human Diseases
+ title: SemsimSearchGroup
+ SemsimSearchRequest:
+ properties:
+ termset:
+ items:
+ type: string
+ type: array
+ title: Termset to search
+ group:
+ allOf:
+ - $ref: '#/components/schemas/SemsimSearchGroup'
+ title: Group of entities to search within (e.g. Human Genes)
+ limit:
+ anyOf:
+ - type: integer
+ maximum: 50
+ minimum: 1
+ # - type: 'null'
+ title: Limit the number of results
+ default: 10
+ type: object
+ required:
+ - termset
+ - group
+ title: SemsimSearchRequest
+ TextAnnotationRequest:
+ properties:
+ content:
+ type: string
+ title: The text content to annotate
+ type: object
+ required:
+ - content
+ title: TextAnnotationRequest
+ TextAnnotationResult:
+ properties:
+ text:
+ anyOf:
+ - type: string
+ # - type: 'null'
+ title: Text
+ description: text without tokens
+ tokens:
+ anyOf:
+ - items:
+ $ref: '#/components/schemas/Entity'
+ type: array
+ # - type: 'null'
+ title: Tokens
+ description: A collection of entities or concepts
+ start:
+ anyOf:
+ - type: integer
+ # - type: 'null'
+ title: Start
+ description: start position of the annotation
+ end:
+ anyOf:
+ - type: integer
+ # - type: 'null'
+ title: End
+ description: end position of the annotation
+ additionalProperties: true
+ type: object
+ title: TextAnnotationResult
+ ValidationError:
+ properties:
+ loc:
+ items:
+ anyOf:
+ - type: string
+ - type: integer
+ type: array
+ title: Location
+ msg:
+ type: string
+ title: Message
+ type:
type: string
- direct_taxon:
- name: direct_taxon
- description: Set true to exclude inferred taxa
- in: query
- required: false
- schema:
- type: boolean
- default: false
- relation:
- name: relation
- description: A relation CURIE to filter associations
- in: query
- required: false
- schema:
- type: string
- sort:
- name: sort
- description: "Sorting responses "
- in: query
- required: false
- schema:
- type: string
- q:
- name: q
- description: Query string to filter documents
- in: query
- required: false
- schema:
- type: string
- ## there's a special api-response-transform. So object ID can be specified this way...
+ title: Error Type
+ type: object
+ required:
+ - loc
+ - msg
+ - type
+ title: ValidationError
x-bte-response-mapping:
- gene-hgnc:
- HGNC: associations.object.HGNC
- ref_pmid: associations.publications.id
- ## commenting out because data-processing / biolink-modeling issues
- # monarch_source_database: associations.provided_by
- # ## there's also a relation.id and relation.inverse.
- # ## this often has "expressed in" with inverse: true. Meaning the actual relation should be "expresses"
- # "biolink:original_predicate": associations.relation.label
- gene-hgnc-dbsnp-start:
- HGNC: associations.object.HGNC
- input_name: associations.subject.label ## for the dbsnp input
- ref_pmid: associations.publications.id
- ## commenting out because data-processing / biolink-modeling issues
- # monarch_source_database: associations.provided_by
- # ## there's also a relation.id and relation.inverse.
- # ## this often has "expressed in" with inverse: true. Meaning the actual relation should be "expresses"
- # "biolink:original_predicate": associations.relation.label
- pathway-react:
- REACT: associations.object.REACT
- ref_pmid: associations.publications.id
- ## commenting out because data-processing / biolink-modeling issues
- # monarch_source_database: associations.provided_by
- # "biolink:original_predicate": associations.relation.label
- phenotype-hp:
- HP: associations.object.HP
- ref_pmid: associations.publications.id
- ## commenting out because data-processing / biolink-modeling issues
- # monarch_source_database: associations.provided_by
- # "biolink:original_predicate": associations.relation.label
- phenotype-hp-dbsnp-start:
- HP: associations.object.HP
- input_name: associations.subject.label ## for the dbsnp input
- ref_pmid: associations.publications.id
- ## commenting out because data-processing / biolink-modeling issues
- # monarch_source_database: associations.provided_by
- # "biolink:original_predicate": associations.relation.label
- variant-dbsnp:
- DBSNP: associations.object.dbSNP
- output_name: associations.object.label
- ref_pmid: associations.publications.id
- ## commenting out because data-processing / biolink-modeling issues
- # monarch_source_database: associations.provided_by
- # "biolink:original_predicate": associations.relation.label
- anatomy-uberon:
- UBERON: associations.object.UBERON
- ref_pmid: associations.publications.id
- ## commenting out because data-processing / biolink-modeling issues
- # monarch_source_database: associations.provided_by
- # "biolink:original_predicate": associations.relation.label
- disease-mondo:
- MONDO: associations.object.MONDO
- ref_pmid: associations.publications.id
- ## commenting out because data-processing / biolink-modeling issues
- # monarch_source_database: associations.provided_by
- # "biolink:original_predicate": associations.relation.label
- disease-mondo-dbsnp-start:
- MONDO: associations.object.MONDO
- input_name: associations.subject.label ## for the dbsnp input
- ref_pmid: associations.publications.id
- ## commenting out because data-processing / biolink-modeling issues
- # monarch_source_database: associations.provided_by
- # "biolink:original_predicate": associations.relation.label
- orthologGene2diseaseMondo:
- MONDO: associations.object.MONDO
- ref_pmid: associations.publications.id ## not all of these are pubmed though...saw some WormBase:WBPaper ones
- ## commenting out because data-processing / biolink-modeling issues
- # homologous_gene_model_id: associations.subject.id ## what is directly annotated to the disease
- # homologous_gene_model_name: associations.subject.label
- # monarch_source_database: associations.provided_by
- # "biolink:original_predicate": associations.relation.label
- orthologGene2phenoHP:
- HP: associations.object.HP
- ref_pmid: associations.publications.id ## not all of these are pubmed though...saw some WormBase:WBPaper ones
- ## commenting out because data-processing / biolink-modeling issues
- # homologous_gene_model_id: associations.subject.id ## what is directly annotated to the disease
- # homologous_gene_model_name: associations.subject.label
- # monarch_source_database: associations.provided_by
- # "biolink:original_predicate": associations.relation.label
+ ## items.sources: BTE does post-processing on the primary_knowledge_source and aggregator_knowledge_source fields
+ ## and creates this custom field with the info formatted for TRAPI.
+ ## we can then ingest this the same way we do for multiomics/text-mining APIs
+ ## not using because I'm unsure and there's data-processing / biolink-model mapping and TRAPI-structure issues
+ ## - subject_taxon, object_taxon: do we need this? Sometimes the value is null
+ ## - negated: is this ever true? I only ever see it as null
+ ## - has_evidence: ECO codes for where this edge came from / how?, list of curies
+ ## - provided_by: strangely, this can differ from the knowledge source fields
+ ## - qualifier fields
+ object-anatomy-uberon:
+ UBERON: items.object
+ output_name: items.object_label
+ input_name: items.subject_label
+ ref_pmid: items.publications
+ trapi_sources: items.sources
+ object-disease-mondo:
+ MONDO: items.object
+ output_name: items.object_label
+ input_name: items.subject_label
+ ref_pmid: items.publications
+ trapi_sources: items.sources
+ object-gene-hgnc:
+ HGNC: items.object
+ output_name: items.object_label
+ input_name: items.subject_label
+ ref_pmid: items.publications
+ trapi_sources: items.sources
+ object-pheno-hp:
+ HP: items.object
+ output_name: items.object_label
+ input_name: items.subject_label
+ ref_pmid: items.publications
+ trapi_sources: items.sources
+ subject-disease-mondo:
+ MONDO: items.subject
+ output_name: items.subject_label
+ input_name: items.object_label
+ ref_pmid: items.publications
+ trapi_sources: items.sources
+ subject-gene-hgnc:
+ HGNC: items.subject
+ output_name: items.subject_label
+ input_name: items.object_label
+ ref_pmid: items.publications
+ trapi_sources: items.sources
x-bte-kgs-operations:
- ## other useful endpoints for x-bte annotation are...
- ## /relation/usage/between/{subject_category}/{object_category}
- ## /association/find/{subject_category}/{object_category}
- ## note that anatomy is "anatomical entity" for this lookup
- anatomy-gene:
- ## supposedly I could use this endpoint with CellularComponent (GO) and Cell (CL) terms
- ## but I haven't been successful in getting results when trying this out
- ## to find examples with /association/find, set subject_category as "gene" and object category as "anatomical entity"
+ ## commenting out the x-bte source field: replaced with the post-processed trapi_sources info
+ ## Parameters
+ ## - `limit`: max seems to be 500
+ gene-anatomy:
+ ## 161069 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:GeneToExpressionSiteAssociation&subject_namespace=HGNC&subject_taxon=NCBITaxon:9606&predicate=biolink:expressed_in&object_namespace=UBERON&direct=true&format=json&limit=10
- supportBatch: false
useTemplating: true
inputs:
- - id: UBERON
- semantic: GrossAnatomicalStructure
- parameters:
- id: "{{ queryInputs }}" ## current BTE automatically adds UBERON prefix to IDs
- rows: -1 ## should allow all results to be returned (above default max of 200)
- direct: true ## don't traverse ontology for anatomy ID to find connection to its subclass terms
- unselect_evidence: true ## don't include nested / verbose evidence info
- taxon: "NCBITaxon:9606" ## currently setting it to human-only
- outputs:
- - id: HGNC ## Monarch seems to prefer HGNC IDs for human genes
+ - id: HGNC
semantic: Gene
- predicate: expresses
- source: "infores:monarchinitiative"
- response_mapping:
- "$ref": "#/components/x-bte-response-mapping/gene-hgnc"
- testExamples:
- - qInput: "UBERON:0001817" ## lacrimal gland
- oneOutput: "HGNC:8548" ## P4HB aka NCBIGene:5034
- - qInput: "UBERON:0002110" ## gall bladder
- oneOutput: "HGNC:8548" ## P4HB aka NCBIGene:5034
- disease-gene-1:
- ## put multiple causal relations here by using association_type parameter
- ## to find examples with /association/find, set relation
- - supportBatch: false
- useTemplating: true
- inputs:
- - id: MONDO
- semantic: Disease
parameters:
- id: "{{ queryInputs }}" ## current BTE automatically adds MONDO prefix to IDs
- rows: -1
+ subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix
+ category: "biolink:GeneToExpressionSiteAssociation"
+ subject_namespace: HGNC
+ subject_taxon: "NCBITaxon:9606"
+ predicate: "biolink:expressed_in"
+ object_namespace: UBERON
direct: true
- unselect_evidence: true
- taxon: "NCBITaxon:9606" ## currently setting it to human-only
- association_type: "causal"
- ## includes multiple relationships, see testExamples
+ format: json
+ limit: 500
outputs:
- - id: HGNC
- semantic: Gene
- predicate: caused_by
- source: "infores:monarchinitiative"
+ - id: UBERON
+ semantic: GrossAnatomicalStructure
+ predicate: expressed_in
+ ## knowledge_source info encountered:
+ ## - primary: "infores:bgee"
+ ## - aggregator: ["infores:monarchinitiative"]
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/gene-hgnc"
+ "$ref": "#/components/x-bte-response-mapping/object-anatomy-uberon"
+ # Examples don't have publication info
testExamples:
- # for "causes condition" / RO:0003303
- - qInput: "MONDO:0011562" ## autosomal dominant Parkinson disease 4
- oneOutput: "HGNC:11138" ## SNCA aka NCBIGene:6622
- # for "causal germline mutation in" / RO:0004013
- - qInput: "MONDO:0019600" ## Xeroderma pigmentosum
- oneOutput: "HGNC:3434" ## ERCC2 aka NCBIGene:2068
- # for "causal loss of function germline mutation of in" / RO:0004012
- - qInput: "MONDO:0009889" ## autosomal recessive polycystic kidney disease
- oneOutput: "HGNC:9016" ## PKHD1 aka NCBIGene:5314
- # for "is marker for" / RO:0002607
- - qInput: "MONDO:0009861" ## phenylketonuria
- oneOutput: "HGNC:8582" ## PAH aka NCBIGene:5053
- # for "is causal somatic mutation in" / RO:0004014
- - qInput: "MONDO:0004948" ## B-cell chronic lymphocytic leukemia
- oneOutput: "HGNC:17284" ## POT1 aka NCBIGene:25913
- # for "causal gain of function germline mutation of in" / RO:0004011
- - qInput: "MONDO:0013648" ## familial progressive hyperpigmentation
- oneOutput: "HGNC:6343" ## KITLG aka NCBIGene:4254
- disease-gene-2:
- ## put non-causal relations together here
- ## to find examples with /association/find, set relation
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:28264&category=biolink:GeneToExpressionSiteAssociation&subject_namespace=HGNC&subject_taxon=NCBITaxon:9606&predicate=biolink:expressed_in&object_namespace=UBERON&direct=true&format=json&limit=500
+ - qInput: "HGNC:28264" ## PCGF5 aka NCBIGene:84333
+ oneOutput: "UBERON:0006566" ## left ventricle myocardium
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:9360&category=biolink:GeneToExpressionSiteAssociation&subject_namespace=HGNC&subject_taxon=NCBITaxon:9606&predicate=biolink:expressed_in&object_namespace=UBERON&direct=true&format=json&limit=500
+ - qInput: "HGNC:9360" ## PRF1 aka NCBIGene:5551
+ oneOutput: "UBERON:0002450" ## decidua
+ anatomy-gene:
- supportBatch: false
useTemplating: true
inputs:
- - id: MONDO
- semantic: Disease
+ - id: UBERON
+ semantic: GrossAnatomicalStructure
parameters:
- id: "{{ queryInputs }}" ## current BTE automatically adds MONDO prefix to IDs
- rows: -1
+ object: "{{ queryInputs | replPrefix('UBERON') }}" ## has prefix
+ category: "biolink:GeneToExpressionSiteAssociation"
+ subject_namespace: HGNC
+ subject_taxon: "NCBITaxon:9606"
+ predicate: "biolink:expressed_in"
+ object_namespace: UBERON
direct: true
- unselect_evidence: true
- taxon: "NCBITaxon:9606" ## currently setting it to human-only
- association_type: "non_causal"
- ## includes multiple relationships, see testExamples
+ format: json
+ limit: 500
outputs:
- id: HGNC
semantic: Gene
- ## more specific than contribution_from
- predicate: condition_associated_with_gene
- source: "infores:monarchinitiative"
- response_mapping:
- "$ref": "#/components/x-bte-response-mapping/gene-hgnc"
- testExamples:
- # for "contributes to condition" / RO:0003304
- - qInput: "MONDO:0019171" ## familial long QT syndrome
- oneOutput: "HGNC:6294" ## KCNQ1 aka NCBIGene:3784
- # for "contributes to" / RO:0002326
- - qInput: "MONDO:0007915" ## systemic lupus erythematosus (disease)
- oneOutput: "HGNC:9652" ## PTPN22 aka NCBIGene:26191
- # for "has phenotype" / RO:0002200
- - qInput: "MONDO:0009131" ## Riley-Day syndrome
- oneOutput: "HGNC:4878" ## HEXA aka NCBIGene:3073
- # for "is causal susceptibility factor for" / RO:0004015
- - qInput: "MONDO:0018961" ## familial melanoma
- oneOutput: "HGNC:1787" ## CDKN2A aka NCBIGene:1029
- # for "pathogenic_for_condition" / GENO:0000840
- - qInput: "MONDO:0008647" ## hypertrophic cardiomyopathy 1
- oneOutput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607
- # for "is causal germline mutation partially giving rise to" / RO:0004016
- - qInput: "MONDO:0018875" ## Li-Fraumeni syndrome
- oneOutput: "HGNC:6973" ## MDM2 aka NCBIGene:4193
- # for "likely_pathogenic_for_condition" / GENO:0000841
- - qInput: "MONDO:0019497" ## nonsyndromic genetic deafness
- oneOutput: "HGNC:7605" ## MYO6 aka NCBIGene:4646
- disease-pathway:
- ## will include non-human pathways because Monarch doesn't include the taxon for pathways
- ## but REACT prefixes show the species (MMU = mouse)
- ## data has weird relation direction. says disease involved_in pathway...
- ## I'm flipping it so disease involves pathway...
- ## to find examples with /association/find, set subject_category as "pathway" and object category as "disease"
- - supportBatch: false
- useTemplating: true
- inputs:
- - id: MONDO
- semantic: Disease
- parameters:
- id: "{{ queryInputs }}" ## current BTE automatically adds MONDO prefix to IDs
- rows: -1
- direct: true
- unselect_evidence: true
- outputs:
- - id: REACT
- semantic: Pathway
- ## biolink 2.2.13 maps to RO:0002331 involved_in
- predicate: actively_involves
- source: "infores:monarchinitiative"
+ predicate: expresses
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/pathway-react"
+ "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc"
+ # Examples have publication pmids
testExamples:
- - qInput: "MONDO:0010524" ## X-linked sideroblastic anemia with ataxia
- oneOutput: "REACT:R-HSA-1369007" ## Mitochondrial ABC transporters
- - qInput: "MONDO:0010665" ## Wilson-Turner syndrome
- oneOutput: "REACT:R-HSA-2467813" ## Separation of Sister Chromatids
- disease-phenotype:
- ## will include non-human phenotypes because Monarch doesn't include the taxon for phenotypes
- ## but prefixes show the species (MP = mouse)
- ## use monarch website to find examples
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=UBERON:0001817&category=biolink:GeneToExpressionSiteAssociation&subject_taxon=NCBITaxon:9606&predicate=biolink:expressed_in&object_namespace=UBERON&direct=true&format=json&limit=500
+ - qInput: "UBERON:0001817" ## lacrimal gland
+ oneOutput: "HGNC:16430" ## LACRT aka NCBIGene:90070
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=UBERON:0002073&category=biolink:GeneToExpressionSiteAssociation&subject_taxon=NCBITaxon:9606&predicate=biolink:expressed_in&object_namespace=UBERON&direct=true&format=json&limit=500
+ - qInput: "UBERON:0002073" ## hair follicle
+ oneOutput: "HGNC:25851" ## GINS3 aka NCBIGene:64785
+ disease-pheno:
+ ## 242009 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:DiseaseToPhenotypicFeatureAssociation&subject_namespace=MONDO&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=10
- supportBatch: false
useTemplating: true
inputs:
- id: MONDO
semantic: Disease
parameters:
- id: "{{ queryInputs }}" ## current BTE automatically adds MONDO prefix to IDs
- rows: -1
+ subject: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix
+ category: "biolink:DiseaseToPhenotypicFeatureAssociation"
+ subject_namespace: MONDO
+ predicate: "biolink:has_phenotype"
+ object_namespace: HP
direct: true
- unselect_evidence: true
+ format: json
+ limit: 500
outputs:
- id: HP
semantic: PhenotypicFeature
predicate: has_phenotype
- source: "infores:monarchinitiative"
+ ## knowledge_source info encountered:
+ ## - primary: "infores:hpo-annotations"
+ ## - aggregator: ["infores:monarchinitiative"]
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/phenotype-hp"
+ "$ref": "#/components/x-bte-response-mapping/object-pheno-hp"
+ # Examples have publication pmids, involves merging multiple hits where some don't have pmids
testExamples:
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=MONDO:0007298&category=biolink:DiseaseToPhenotypicFeatureAssociation&subject_namespace=MONDO&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=500
+ - qInput: "MONDO:0007298" ## spinocerebellar ataxia type 29
+ oneOutput: "HP:0006855" ## Cerebellar vermis atrophy
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=MONDO:0008974&category=biolink:DiseaseToPhenotypicFeatureAssociation&subject_namespace=MONDO&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=500
- qInput: "MONDO:0008974" ## Greenberg dysplasia
- oneOutput: "HP:0000272" ## Malar flattening
- - qInput: "MONDO:0010524" ## X-linked sideroblastic anemia with ataxia
- oneOutput: "HP:0002470" ## Nonprogressive cerebellar ataxia
- disease-variant:
- ## not using:
- ## - GENO:0000840 (pathogenic_for_condition). seems to use ClinVarVariant (ClinVarVariant:13417)
- ## - GENO:0000841 (likely_pathogenic_for_condition). seems to use ClinVarVariant (ClinVarVariant:370820)
- ## to find examples with /association/find, set subject_category as "variant" and object category as "disease"
- ## also set relation
- - supportBatch: false
- useTemplating: true
- inputs:
- - id: MONDO
- semantic: Disease
- parameters:
- id: "{{ queryInputs }}" ## current BTE automatically adds MONDO prefix to IDs
- rows: -1
- direct: true
- unselect_evidence: true
- taxon: "NCBITaxon:9606" ## currently setting it to human-only
- relation: "RO:0003304" ## contributes to condition
- outputs:
- - id: DBSNP
- semantic: SequenceVariant
- predicate: contribution_from
- source: "infores:monarchinitiative"
- response_mapping:
- "$ref": "#/components/x-bte-response-mapping/variant-dbsnp"
- testExamples:
- - qInput: "MONDO:0004747" ## cleft lip (disease)
- oneOutput: "DBSNP:rs227731"
- - qInput: "MONDO:0005150" ## age-related macular degeneration
- oneOutput: "DBSNP:rs2230199"
- gene-anatomy:
- ## see anatomy-gene operation for more details
+ oneOutput: "HP:0000926" ## Platyspondyly
+ pheno-disease:
- supportBatch: false
useTemplating: true
inputs:
- - id: HGNC ## Monarch seems to prefer HGNC IDs for human genes
- semantic: Gene
+ - id: HP
+ semantic: PhenotypicFeature
parameters:
- id: "{{ queryInputs | replPrefix('HGNC') }}"
- ## add prefix since Monarch expects this, while BTE automatically removes
- rows: -1
+ object: "{{ queryInputs | replPrefix('HP') }}" ## has prefix
+ category: "biolink:DiseaseToPhenotypicFeatureAssociation"
+ subject_namespace: MONDO
+ predicate: "biolink:has_phenotype"
+ object_namespace: HP
direct: true
- unselect_evidence: true
- ## don't need to set anatomy to human-only...
+ format: json
+ limit: 500
outputs:
- - id: UBERON
- semantic: GrossAnatomicalStructure
- predicate: expressed_in
- source: "infores:monarchinitiative"
+ - id: MONDO
+ semantic: Disease
+ predicate: phenotype_of
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/anatomy-uberon"
+ "$ref": "#/components/x-bte-response-mapping/subject-disease-mondo"
+ # Examples have publication pmids
testExamples:
- - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034
- oneOutput: "UBERON:0000970" ## eye
- - qInput: "HGNC:11138" ## SNCA aka NCBIGene:6622
- oneOutput: "UBERON:0001017" ## central nervous system
- gene-disease-1:
- ## see disease-gene-1 for details
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=HP:0031629&category=biolink:DiseaseToPhenotypicFeatureAssociation&subject_namespace=MONDO&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=500
+ - qInput: "HP:0031629" ## Impaired tandem gait
+ oneOutput: "MONDO:0030458" ## Charcot-Marie-Tooth disease, axonal, Type 2HH"
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=HP:0006855&category=biolink:DiseaseToPhenotypicFeatureAssociation&subject_namespace=MONDO&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=500
+ - qInput: "HP:0006855" ## Cerebellar vermis atrophy
+ oneOutput: "MONDO:0010041" ## Charlevoix-Saguenay spastic ataxia
+ gene-disease-causal:
+ ## 6668 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CausalGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:causes&object_namespace=MONDO&direct=true&format=json&limit=10
- supportBatch: false
useTemplating: true
inputs:
- id: HGNC
semantic: Gene
parameters:
- id: "{{ queryInputs | replPrefix('HGNC') }}"
- ## add prefix since Monarch expects this, while BTE automatically removes
- rows: -1
+ subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix
+ category: "biolink:CausalGeneToDiseaseAssociation"
+ subject_namespace: HGNC
+ predicate: "biolink:causes"
+ object_namespace: MONDO
direct: true
- unselect_evidence: true
- association_type: "causal"
- ## don't need to set disease to human-only...
+ format: json
+ limit: 500
outputs:
- id: MONDO
semantic: Disease
predicate: causes
- source: "infores:monarchinitiative"
+ ## knowledge_source info encountered:
+ ## - primary: "infores:omim"
+ ## - aggregator: ["infores:monarchinitiative", "infores:medgen"]
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/disease-mondo"
+ "$ref": "#/components/x-bte-response-mapping/object-disease-mondo"
+ # Examples don't have publication info
testExamples:
- # for "causes condition" / RO:0003303
- - qInput: "HGNC:11138" ## SNCA aka NCBIGene:6622
- oneOutput: "MONDO:0011562" ## autosomal dominant Parkinson disease 4
- # for "causal gain of function germline mutation of in" / RO:0004011
- - qInput: "HGNC:6343" ## KITLG aka NCBIGene:4254
- oneOutput: "MONDO:0013648" ## familial progressive hyperpigmentation
- gene-disease-2:
- ## see disease-gene-2 for details
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:11138&category=biolink:CausalGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:causes&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "HGNC:11138" ## SNCA aka NCBIGene:6622
+ oneOutput: "MONDO:0007488" ## Lewy body dementia
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:3434&category=biolink:CausalGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:causes&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "HGNC:3434" ## ERCC2 aka NCBIGene:2068
+ oneOutput: "MONDO:0012553" ## cerebrooculofacioskeletal syndrome 2
+ disease-gene-causal:
- supportBatch: false
useTemplating: true
inputs:
- - id: HGNC
- semantic: Gene
- parameters:
- id: "{{ queryInputs | replPrefix('HGNC') }}"
- ## add prefix since Monarch expects this, while BTE automatically removes
- rows: -1
- direct: true
- unselect_evidence: true
- association_type: "non_causal"
- ## don't need to set disease to human-only...
- outputs:
- id: MONDO
semantic: Disease
- predicate: gene_associated_with_condition
- source: "infores:monarchinitiative"
- response_mapping:
- "$ref": "#/components/x-bte-response-mapping/disease-mondo"
- testExamples:
- # for "contributes to condition" / RO:0003304
- - qInput: "HGNC:6294" ## KCNQ1 aka NCBIGene:3784
- oneOutput: "MONDO:0019171" ## familial long QT syndrome
- # for "pathogenic_for_condition" / GENO:0000840
- - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607
- oneOutput: "MONDO:0008647" ## hypertrophic cardiomyopathy 1
- gene-interaction:
- - supportBatch: false
- useTemplating: true
- inputs:
- - id: HGNC
- semantic: Gene
parameters:
- id: "{{ queryInputs | replPrefix('HGNC') }}"
- rows: -1
+ object: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix
+ category: "biolink:CausalGeneToDiseaseAssociation"
+ subject_namespace: HGNC
+ predicate: "biolink:causes"
+ object_namespace: MONDO
direct: true
- unselect_evidence: true
- taxon: "NCBITaxon:9606" ## currently setting it to human-only
+ format: json
+ limit: 500
outputs:
- id: HGNC
semantic: Gene
- ## looks like they are using biogrid? And it looks like there's all kinds of interactions
- ## with all levels of certainty https://wiki.thebiogrid.org/doku.php/experimental_systems
- predicate: interacts_with
- source: "infores:monarchinitiative"
+ predicate: caused_by
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/gene-hgnc"
+ "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc"
+ # Examples don't have publication info
testExamples:
- - qInput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767
- oneOutput: "HGNC:9069" ## PLEC aka NCBIGene:5339
- - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607
- oneOutput: "HGNC:16007" ## TRIM63 aka NCBIGene:84676
- geneOrtholog-disease:
- ## - starting with HGNC = starting with human gene, getting non-human gene orthologs
- ## then finding directly-related diseases
- ## finds info that isn't found through gene-phenotype direct relationships
- ## - don't have a way to get information in reverse direction (Disease -> human gene through ortholog)
- ## can get from Disease -> gene-ortholog
- ## - noticed Wormbase-related data/homologs (C. elegans)
- ## - can find more examples from /relation/usage/between/model/disease
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=MONDO:0011562&category=biolink:CausalGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:causes&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "MONDO:0011562" ## autosomal dominant Parkinson disease 4
+ oneOutput: "HGNC:11138" ## SNCA aka NCBIGene:6622
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=MONDO:0009861&category=biolink:CausalGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:causes&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "MONDO:0009861" ## phenylketonuria
+ oneOutput: "HGNC:8582" ## PAH aka NCBIGene:5053
+ gene-disease-contributesTo:
+ ## 590 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:contributes_to&object_namespace=MONDO&direct=true&format=json&limit=10
- supportBatch: false
useTemplating: true
inputs:
- id: HGNC
- semantic: Gene ## aka start with human gene
+ semantic: Gene
parameters:
- id: "{{ queryInputs | replPrefix('HGNC') }}"
- ## add prefix since Monarch expects this, while BTE automatically removes
- rows: -1
+ subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix
+ category: "biolink:CorrelatedGeneToDiseaseAssociation"
+ subject_namespace: HGNC
+ predicate: "biolink:contributes_to"
+ object_namespace: MONDO
direct: true
- unselect_evidence: true
- ## don't need to set disease to human-only...
+ format: json
+ limit: 500
outputs:
- id: MONDO
semantic: Disease
- ## gene -> gene ortholog -(is model of)-> disease...not sure what predicate to use
- predicate: related_to
- source: "infores:monarchinitiative"
+ predicate: contributes_to
+ ## knowledge_source info encountered:
+ ## - primary: "infores:omim"
+ ## - aggregator: ["infores:monarchinitiative", "infores:medgen"]
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/orthologGene2diseaseMondo"
+ "$ref": "#/components/x-bte-response-mapping/object-disease-mondo"
+ # Examples don't have publication info
testExamples:
- - qInput: "HGNC:9508" ## PSEN1 aka NCBIGene:5663
- oneOutput: "MONDO:0006559" ## hidradenitis suppurativa, not found through gene-disease endpoints
- geneOrtholog-phenotype:
- ## - starting with HGNC = starting with human gene, getting non-human gene orthologs
- ## then finding directly-related phenotypes
- ## finds info that isn't found through gene-phenotype direct relationships
- ## - don't have a way to get information in reverse direction (Phenotype -> human gene through ortholog)
- ## can get from Phenotype -> gene-ortholog
- ## - noticed MGI-related data/homologs
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:6294&category=biolink:CorrelatedGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:contributes_to&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "HGNC:6294" ## KCNQ1 aka NCBIGene:3784
+ oneOutput: "MONDO:0100316" ## long QT syndrome 1
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:9652&category=biolink:CorrelatedGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:contributes_to&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "HGNC:9652" ## PTPN22 aka NCBIGene:26191
+ oneOutput: "MONDO:0007915" ## systemic lupus erythematosus
+ disease-gene-contributesTo:
- supportBatch: false
useTemplating: true
inputs:
- - id: HGNC
- semantic: Gene ## aka start with human gene
+ - id: MONDO
+ semantic: Disease
parameters:
- id: "{{ queryInputs | replPrefix('HGNC') }}"
- ## add prefix since Monarch expects this, while BTE automatically removes
- rows: -1
+ object: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix
+ category: "biolink:CorrelatedGeneToDiseaseAssociation"
+ subject_namespace: HGNC
+ predicate: "biolink:contributes_to"
+ object_namespace: MONDO
direct: true
- unselect_evidence: true
- ## don't need to set phenotype to human-only...
+ format: json
+ limit: 500
outputs:
- - id: HP
- semantic: PhenotypicFeature
- ## gene -> gene ortholog -(has phenotype)-> phenotype...not sure what predicate to use
- predicate: related_to
- source: "infores:monarchinitiative"
+ - id: HGNC
+ semantic: Gene
+ predicate: contribution_from
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/orthologGene2phenoHP"
+ "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc"
+ # Examples don't have publication info
testExamples:
- - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034
- oneOutput: "HP:0003540" ## Impaired platelet aggregation, not found from gene-phenotype operation
- - qInput: "HGNC:9508" ## PSEN1 aka NCBIGene:5663
- oneOutput: "HP:0009121" ## Abnormal axial skeleton morphology
- gene-phenotype:
- ## will include non-human phenotypes because Monarch doesn't include the taxon for phenotypes
- ## but prefixes show the species (MP = mouse)
- ## to find examples with /association/find, set subject_category as "gene" and object category as "phenotype"
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=MONDO:0014629&category=biolink:CorrelatedGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:contributes_to&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "MONDO:0014629" ## autoimmune interstitial lung disease-arthritis syndrome
+ oneOutput: "HGNC:2230" ## COPA aka NCBIGene:1314
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=MONDO:0013416&category=biolink:CorrelatedGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:contributes_to&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "MONDO:0013416" ## age related macular degeneration 8
+ oneOutput: "HGNC:32685" ## ARMS2 aka NCBIGene:387715
+ gene-disease-associatedCondition:
+ ## 7997 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:gene_associated_with_condition&object_namespace=MONDO&direct=true&format=json&limit=10
- supportBatch: false
useTemplating: true
inputs:
- id: HGNC
semantic: Gene
parameters:
- id: "{{ queryInputs | replPrefix('HGNC') }}"
- rows: -1
+ subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix
+ category: "biolink:CorrelatedGeneToDiseaseAssociation"
+ subject_namespace: HGNC
+ predicate: "biolink:gene_associated_with_condition"
+ object_namespace: MONDO
direct: true
- unselect_evidence: true
+ format: json
+ limit: 500
outputs:
- - id: HP
- semantic: PhenotypicFeature
+ - id: MONDO
+ semantic: Disease
predicate: gene_associated_with_condition
- source: "infores:monarchinitiative"
+ ## knowledge_source info encountered:
+ ## - primary: "infores:orphanet"
+ ## - aggregator: ["infores:monarchinitiative"]
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/phenotype-hp"
+ "$ref": "#/components/x-bte-response-mapping/object-disease-mondo"
+ # Examples don't have publication info
testExamples:
- - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034
- oneOutput: "HP:0000944" ## Abnormal metaphysis morphology
- - qInput: "HGNC:9508" ## PSEN1 aka NCBIGene:5663
- oneOutput: HP:0000751" ## Personality changes
- # other possible inputs: HGNC:7551 / MYBPC3, HGNC:9508 / DNAH5
- gene-variant:
- ## can take human or non-human genes as input...
- ## to find examples with /association/find, set subject_category as "variant" and object category as "gene"
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:6493&category=biolink:CorrelatedGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:gene_associated_with_condition&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "HGNC:6493" ## LAMC2 aka NCBIGene:3918
+ oneOutput: "MONDO:0009182" ## junctional epidermolysis bullosa Herlitz type
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:9462&category=biolink:CorrelatedGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:gene_associated_with_condition&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "HGNC:9462" ## PRPS1 aka NCBIGene:5631
+ oneOutput: "MONDO:0010699" ## Charcot-Marie-Tooth disease X-linked recessive 5
+ disease-gene-associatedCondition:
- supportBatch: false
useTemplating: true
inputs:
- - id: HGNC
- semantic: Gene
+ - id: MONDO
+ semantic: Disease
parameters:
- id: "{{ queryInputs | replPrefix('HGNC') }}"
- rows: -1
+ object: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix
+ category: "biolink:CorrelatedGeneToDiseaseAssociation"
+ subject_namespace: HGNC
+ predicate: "biolink:gene_associated_with_condition"
+ object_namespace: MONDO
direct: true
- unselect_evidence: true
+ format: json
+ limit: 500
outputs:
- - id: DBSNP
- semantic: SequenceVariant
- predicate: has_sequence_variant
- source: "infores:monarchinitiative"
+ - id: HGNC
+ semantic: Gene
+ predicate: condition_associated_with_gene
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/variant-dbsnp"
+ "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc"
+ # Examples don't have publication info
testExamples:
- - qInput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767
- oneOutput: "dbSNP:rs795544"
- - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607
- oneOutput: "dbSNP:rs2071305"
- pathway-disease:
- ## see disease-pathway for details
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=MONDO:0018961&category=biolink:CorrelatedGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:gene_associated_with_condition&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "MONDO:0018961" ## familial melanoma
+ oneOutput: "HGNC:1787" ## CDKN2A aka NCBIGene:1029
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=MONDO:0018875&category=biolink:CorrelatedGeneToDiseaseAssociation&subject_namespace=HGNC&predicate=biolink:gene_associated_with_condition&object_namespace=MONDO&direct=true&format=json&limit=500
+ - qInput: "MONDO:0018875" ## Li-Fraumeni syndrome
+ oneOutput: "HGNC:6973" ## MDM2 aka NCBIGene:4193
+ gene-pheno:
+ ## 303962 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:GeneToPhenotypicFeatureAssociation&subject_namespace=HGNC&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=10
- supportBatch: false
useTemplating: true
inputs:
- - id: REACT
- semantic: Pathway
+ - id: HGNC
+ semantic: Gene
parameters:
- id: "{{ queryInputs | replPrefix('REACT') }}"
- ## add prefix since Monarch expects this, while BTE automatically removes
- rows: -1
+ subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix
+ category: "biolink:GeneToPhenotypicFeatureAssociation"
+ subject_namespace: HGNC
+ predicate: "biolink:has_phenotype"
+ object_namespace: HP
direct: true
- unselect_evidence: true
- ## don't need to set disease to human-only...
+ format: json
+ limit: 500
outputs:
- - id: MONDO
- semantic: Disease
- predicate: actively_involved_in
- source: "infores:monarchinitiative"
- response_mapping:
- "$ref": "#/components/x-bte-response-mapping/disease-mondo"
- testExamples:
- - qInput: "REACT:R-HSA-2644606" ## Constitutive Signaling by NOTCH1 PEST Domain Mutants
- oneOutput: "MONDO:0010665" ## Wilson-Turner syndrome
- - qInput: "REACT:R-HSA-1369007" ## Mitochondrial ABC transporters
- oneOutput: "MONDO:0012204" ## familial pseudohyperkalemia
- phenotype-disease:
- ## see disease-phenotype for details
- - supportBatch: false
- useTemplating: true
- inputs:
- id: HP
semantic: PhenotypicFeature
- parameters:
- id: "{{ queryInputs }}" ## current BTE automatically adds prefix for HP terms
- rows: -1
- direct: true
- unselect_evidence: true
- outputs:
- - id: MONDO
- semantic: Disease
- predicate: phenotype_of
- source: "infores:monarchinitiative"
+ ## I previously used gene_associated_with_condition
+ predicate: has_phenotype
+ ## knowledge_source info encountered:
+ ## - primary: "infores:hpo-annotations"
+ ## - aggregator: ["infores:monarchinitiative"]
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/disease-mondo"
+ "$ref": "#/components/x-bte-response-mapping/object-pheno-hp"
+ # Examples don't have publication info
testExamples:
- - qInput: "HP:0000272" ## Malar flattening
- oneOutput: "MONDO:0008974" ## Greenberg dysplasia
- - qInput: "HP:0032543" ## Lithoptysis
- oneOutput: "MONDO:0016575" ## primary ciliary dyskinesia
- phenotype-gene:
- ## see gene-phenotype for details
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:8548&category=biolink:GeneToPhenotypicFeatureAssociation&subject_namespace=HGNC&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=500
+ - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034
+ oneOutput: "HP:0000944" ## Abnormal metaphysis morphology
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:7551&category=biolink:GeneToPhenotypicFeatureAssociation&subject_namespace=HGNC&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=500
+ - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607
+ oneOutput: "HP:0011675" ## Arrhythmia aka MONDO:0007263
+ pheno-gene:
- supportBatch: false
useTemplating: true
inputs:
- id: HP
semantic: PhenotypicFeature
parameters:
- id: "{{ queryInputs }}" ## current BTE automatically adds prefix for HP terms
- rows: -1
+ object: "{{ queryInputs | replPrefix('HP') }}" ## has prefix
+ category: "biolink:GeneToPhenotypicFeatureAssociation"
+ subject_namespace: HGNC
+ predicate: "biolink:has_phenotype"
+ object_namespace: HP
direct: true
- unselect_evidence: true
- taxon: "NCBITaxon:9606" ## currently setting it to human-only
+ format: json
+ limit: 500
outputs:
- id: HGNC
semantic: Gene
- predicate: condition_associated_with_gene
- source: "infores:monarchinitiative"
+ predicate: phenotype_of
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/gene-hgnc"
+ "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc"
+ # Examples don't have publication info
testExamples:
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=HP:0000183&category=biolink:GeneToPhenotypicFeatureAssociation&subject_namespace=HGNC&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=500
- qInput: "HP:0000183" ## Difficulty in tongue movements
- oneOutput: "HGNC:4065" ## GAA
+ oneOutput: "HGNC:4065" ## GAA aka NCBIGene:2548
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=HP:0032543&category=biolink:GeneToPhenotypicFeatureAssociation&subject_namespace=HGNC&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=500
- qInput: "HP:0032543" ## Lithoptysis
oneOutput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767
- phenotype-variant:
- ## could also use OMIM IDs...
- ## note: relation RO:0003304 (contributes to condition) seems to use EFO terms, rather than HP...
- ## to find examples with /association/find, set subject_category as "variant" and object category as "phenotype"
- - supportBatch: false
- useTemplating: true
- inputs:
- - id: HP
- semantic: PhenotypicFeature
- parameters:
- id: "{{ queryInputs }}" ## current BTE automatically adds prefix for HP terms
- rows: -1
- direct: true
- unselect_evidence: true
- taxon: "NCBITaxon:9606" ## currently setting it to human-only
- outputs:
- - id: DBSNP
- semantic: SequenceVariant
- ## main relations: has phenotype, is marker for, contributes to condition...
- predicate: related_to
- source: "infores:monarchinitiative"
- response_mapping:
- "$ref": "#/components/x-bte-response-mapping/variant-dbsnp"
- testExamples:
- - qInput: "HP:0002944" ## Thoracolumbar scoliosis
- oneOutput: "DBSNP:rs115165302"
- - qInput: "HP:0000183" ## Difficulty in tongue movements
- oneOutput: "DBSNP:rs771684665"
- variant-disease:
- ## see disease-variant for details
+ gene-gene-interaction-forward:
+ ## 1324672 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:PairwiseGeneToGeneInteraction&subject_namespace=HGNC&predicate=biolink:interacts_with&object_namespace=HGNC&direct=true&format=json&limit=10
- supportBatch: false
useTemplating: true
inputs:
- - id: DBSNP
- semantic: SequenceVariant
- parameters:
- id: "{{ queryInputs | replPrefix('dbSNP') }}"
- ## add prefix since Monarch expects this in this form, while BTE automatically removes
- rows: -1
- direct: true
- unselect_evidence: true
- taxon: "NCBITaxon:9606" ## currently setting it to human-only
- relation: "RO:0003304" ## contributes to condition
- outputs:
- - id: MONDO
- semantic: Disease
- predicate: contributes_to
- source: "infores:monarchinitiative"
- response_mapping:
- "$ref": "#/components/x-bte-response-mapping/disease-mondo-dbsnp-start"
- ## examples have publications!!!
- testExamples:
- - qInput: "DBSNP:rs227731"
- oneOutput: "MONDO:0004747" ## cleft lip (disease)
- - qInput: "DBSNP:rs2230199"
- oneOutput: "MONDO:0005150" ## age-related macular degeneration
- variant-gene:
- ## see gene-variant for details
- - supportBatch: false
- useTemplating: true
- inputs:
- - id: DBSNP
- semantic: SequenceVariant
+ - id: HGNC
+ semantic: Gene
parameters:
- id: "{{ queryInputs | replPrefix('dbSNP') }}"
- ## add prefix since Monarch expects this in this form, while BTE automatically removes
- rows: -1
+ subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix
+ category: "biolink:PairwiseGeneToGeneInteraction"
+ subject_namespace: HGNC
+ predicate: "biolink:interacts_with"
+ object_namespace: HGNC
direct: true
- unselect_evidence: true
+ format: json
+ limit: 500
outputs:
- id: HGNC
semantic: Gene
- predicate: is_sequence_variant_of
- source: "infores:monarchinitiative"
+ ## could this predicate be more specific? like genetically_interacts_with?
+ predicate: interacts_with
+ ## knowledge_source info encountered:
+ ## - primary: "infores:string" OR "infores:biogrid"
+ ## - aggregator: ["infores:monarchinitiative"]
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/gene-hgnc-dbsnp-start"
+ "$ref": "#/components/x-bte-response-mapping/object-gene-hgnc"
+ # Examples have publication pmids
testExamples:
- - qInput: "DBSNP:rs11879191"
- oneOutput: "HGNC:1735" ## CDC37 aka NCBIGene:11140
- - qInput: "DBSNP:rs2230199"
- oneOutput: "HGNC:1318" ## C3 aka NCBIGene:718
- variant-phenotype:
- ## see phenotype-variant for details
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:2950&category=biolink:PairwiseGeneToGeneInteraction&subject_namespace=HGNC&predicate=biolink:interacts_with&object_namespace=HGNC&direct=true&format=json&limit=500
+ - qInput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767
+ oneOutput: "HGNC:13671" ## H2AC12 aka NCBIGene:85235
+ # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:7551&category=biolink:PairwiseGeneToGeneInteraction&subject_namespace=HGNC&predicate=biolink:interacts_with&object_namespace=HGNC&direct=true&format=json&limit=500
+ - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607
+ oneOutput: "HGNC:16007" ## TRIM63 aka NCBIGene:84676
+ gene-gene-interaction-backward:
- supportBatch: false
useTemplating: true
inputs:
- - id: DBSNP
- semantic: SequenceVariant
+ - id: HGNC
+ semantic: Gene
parameters:
- id: "{{ queryInputs | replPrefix('dbSNP') }}"
- ## add prefix since Monarch expects this in this form, while BTE automatically removes
- rows: -1
+ object: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix
+ category: "biolink:PairwiseGeneToGeneInteraction"
+ subject_namespace: HGNC
+ predicate: "biolink:interacts_with"
+ object_namespace: HGNC
direct: true
- unselect_evidence: true
- taxon: "NCBITaxon:9606" ## currently setting it to human-only
+ format: json
+ limit: 500
outputs:
- - id: HP
- semantic: PhenotypicFeature
- ## main relations: has phenotype, is marker for, contributes to condition...
- predicate: related_to
- source: "infores:monarchinitiative"
+ - id: HGNC
+ semantic: Gene
+ predicate: interacts_with
+ # source: "infores:monarchinitiative"
response_mapping:
- "$ref": "#/components/x-bte-response-mapping/phenotype-hp-dbsnp-start"
+ "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc"
testExamples:
- - qInput: "DBSNP:rs115165302"
- oneOutput: "HP:0002944" ## Thoracolumbar scoliosis
- - qInput: "DBSNP:rs771684665"
- oneOutput: "HP:0200055" ## Small hand
-
\ No newline at end of file
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=HGNC:2950&category=biolink:PairwiseGeneToGeneInteraction&subject_namespace=HGNC&predicate=biolink:interacts_with&object_namespace=HGNC&direct=true&format=json&limit=500
+ - qInput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767
+ oneOutput: "HGNC:8607" ## PRKN aka NCBIGene:5071
+ # link https://api-v3.monarchinitiative.org/v3/api/association?object=HGNC:7551&category=biolink:PairwiseGeneToGeneInteraction&subject_namespace=HGNC&predicate=biolink:interacts_with&object_namespace=HGNC&direct=true&format=json&limit=500
+ - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607
+ oneOutput: "HGNC:1476" ## CAPN1 aka NCBIGene:823