BioLink API
API integration layer for linked biological objects
COMMUNITYNO AUTH0 INSTALLS
OpenAPI Specificationv3.0
{
"openapi": "3.0.0",
"servers": [
{
"url": "/api"
}
],
"info": {
"description": "API integration layer for linked biological objects.\n\n __Source:__ https://github.com/biolink/biolink-api/",
"license": {
"name": "BSD3"
},
"title": "BioLink API",
"version": "1.1.14",
"x-apisguru-categories": [
"open_data"
],
"x-origin": [
{
"format": "openapi",
"url": "https://api.monarchinitiative.org/api/swagger.json",
"version": "3.0"
}
],
"x-providerName": "monarchinitiative.org",
"x-logo": {
"url": "https://api.apis.guru/v2/cache/logo/https_apis.guru_assets_images_no-logo.svg"
}
},
"tags": [
{
"description": "Retrieval of domain entities plus associations",
"name": "bioentity"
},
{
"description": "Retrieve associations between entities or entity and descriptors",
"name": "association"
},
{
"description": "Operations on GO Causal Activity Models (GO-CAMs)",
"name": "cam"
},
{
"description": "Operations over sets of entities",
"name": "bioentityset"
},
{
"description": "Map gene IDs to their homologs",
"name": "bioentityset/homologs"
},
{
"description": "maps a set of entities to a slim",
"name": "bioentityset/slimmer"
},
{
"description": "Operations on evidence graphs",
"name": "evidence/graph"
},
{
"description": "Operations to retrieve sequence features",
"name": "genome/features"
},
{
"description": "Operations over data graphs",
"name": "graph"
},
{
"description": "mapping and resolution of identifiers",
"name": "identifier/mapper"
},
{
"description": "identifier prefixes",
"name": "identifier/prefixes"
},
{
"description": "Perform bulk operations",
"name": "mart"
},
{
"description": "annotate text using named entities",
"name": "nlp/annotate"
},
{
"description": "extract a subgraph from an ontology",
"name": "ontol"
},
{
"description": "Assign labels to IDs",
"name": "ontol/labeler"
},
{
"description": "Retrieve IDs for labels",
"name": "ontol/identifier"
},
{
"description": "Operations on Ontology Terms and Subsets",
"name": "ontology"
},
{
"description": "OWL-level operations on an ontology",
"name": "owl/ontology"
},
{
"description": "pairwise similarity between two entities",
"name": "pair/sim"
},
{
"description": "Individual humans (including patients), or organisms",
"name": "individual"
},
{
"description": "Usage of different relationship types",
"name": "relation/usage"
},
{
"description": "Search for entities",
"name": "search"
},
{
"description": "Operations related to sets of variants",
"name": "variation/set"
},
{
"description": "Perform semantic similarity, ranking, and sufficiency scoring",
"name": "sim"
},
{
"description": "Match patients with similar diseases and non-human genes based on their phenotypes",
"name": "mme"
},
{
"description": "Get metadata",
"name": "metadata"
}
],
"paths": {
"/association/between/{subject}/{object}": {
"get": {
"description": "Given two entities (e.g. a particular gene and a particular disease), if these two entities\nare connected (directly or indirectly), then return the association objects describing\nthe connection.",
"operationId": "get_associations_between",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns associations connecting two entities",
"tags": [
"association"
]
},
"parameters": [
{
"description": "Return associations pointing to this node, e.g. MP:0013765. Can also be a biological entity such as a gene",
"in": "path",
"name": "object",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Return associations emanating from this node, e.g. MGI:1342287 (If ID is from an ontology then results would include inferred associations, by default)",
"in": "path",
"name": "subject",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/association/find/{subject_category}": {
"get": {
"operationId": "get_association_by_subject_category_search",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Subject taxon ID, e.g. NCBITaxon:9606 (Includes inferred associations, by default)",
"in": "query",
"name": "subject_taxon",
"schema": {
"type": "string"
}
},
{
"description": "Object taxon ID, e.g. NCBITaxon:10090 (Includes inferred associations, by default)",
"in": "query",
"name": "object_taxon",
"schema": {
"type": "string"
}
},
{
"description": "Filter by relation CURIE, e.g. RO:0002200 (has_phenotype), RO:0002607 (is marker for), RO:HOM0000017 (orthologous to), etc.",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matching associations for a given subject category",
"tags": [
"association"
]
},
"parameters": [
{
"description": "Category of entity at link Subject (source), e.g. gene, disease, phenotype",
"in": "path",
"name": "subject_category",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/association/find/{subject_category}/{object_category}": {
"get": {
"operationId": "get_association_by_subject_and_object_category_search",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Subject CURIE",
"in": "query",
"name": "subject",
"schema": {
"type": "string"
}
},
{
"description": "Object CURIE",
"in": "query",
"name": "object",
"schema": {
"type": "string"
}
},
{
"description": "Subject taxon ID, e.g. NCBITaxon:9606 (Includes inferred associations, by default)",
"in": "query",
"name": "subject_taxon",
"schema": {
"type": "string"
}
},
{
"description": "Object taxon ID, e.g. NCBITaxon:10090 (Includes inferred associations, by default)",
"in": "query",
"name": "object_taxon",
"schema": {
"type": "string"
}
},
{
"description": "Filter by relation CURIE, e.g. RO:0002200 (has_phenotype), RO:0002607 (is marker for), RO:HOM0000017 (orthologous to), etc.",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matching associations between a given subject and object category",
"tags": [
"association"
]
},
"parameters": [
{
"description": "Category of entity at link Object (target), e.g. gene, disease, phenotype",
"in": "path",
"name": "object_category",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Category of entity at link Subject (source), e.g. gene, disease, phenotype",
"in": "path",
"name": "subject_category",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/association/from/{subject}": {
"get": {
"operationId": "get_associations_from",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Object taxon ID, e.g. NCBITaxon:10090 (Includes inferred associations, by default)",
"in": "query",
"name": "object_taxon",
"schema": {
"type": "string"
}
},
{
"description": "Filter by relation CURIE, e.g. RO:0002200 (has_phenotype), RO:0002607 (is marker for), RO:HOM0000017 (orthologous to), etc.",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matching associations starting from a given subject (source)",
"tags": [
"association"
]
},
"parameters": [
{
"description": "Return associations emanating from this node, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357 (If ID is from an ontology then results would include inferred associations, by default)",
"in": "path",
"name": "subject",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/association/to/{object}": {
"get": {
"operationId": "get_associations_to",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matching associations pointing to a given object (target)",
"tags": [
"association"
]
},
"parameters": [
{
"description": "Return associations pointing to this node, e.g. specifying MP:0013765 will return all genes, variants, strains, etc. annotated with this term. Can also be a biological entity such as a gene",
"in": "path",
"name": "object",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/association/type/{association_type}": {
"get": {
"operationId": "get_association_by_subject_and_assoc_type",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Subject CURIE",
"in": "query",
"name": "subject",
"schema": {
"type": "string"
}
},
{
"description": "Object CURIE",
"in": "query",
"name": "object",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matching associations of a given type",
"tags": [
"association"
]
},
"parameters": [
{
"description": "Association type, eg gene_phenotype",
"in": "path",
"name": "association_type",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/association/{id}": {
"get": {
"description": "An association connects, at a minimum, two things, designated subject and object,\nvia some relationship. Associations also include evidence, provenance etc.",
"operationId": "get_association_object",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns the association with a given identifier",
"tags": [
"association"
]
},
"parameters": [
{
"description": "identifier for an association, e.g. f5ba436c-f851-41b3-9d9d-bb2b5fc879d4",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/anatomy/{id}/genes": {
"get": {
"operationId": "get_anatomy_gene_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genes associated with a given anatomy",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of anatomical entity, e.g. GO:0005634 (nucleus), UBERON:0002037 (cerebellum), CL:0000540 (neuron). Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/anatomy/{id}/genes/{taxid}": {
"get": {
"deprecated": true,
"description": "For example, + NCBITaxon:10090 (mouse)",
"operationId": "get_anatomy_gene_by_taxon_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns gene IDs for all genes associated with a given anatomy, filtered by taxon",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "Species or high level taxon grouping, e.g NCBITaxon:10090 (Mus musculus)",
"in": "path",
"name": "taxid",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "CURIE identifier of anatomical entity, e.g. GO:0005634 (nucleus), UBERON:0002037 (cerebellum), CL:0000540 (neuron). Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/case/{id}/diseases": {
"get": {
"operationId": "get_case_disease_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns diseases associated with a case",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a case",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/case/{id}/genotypes": {
"get": {
"operationId": "get_case_genotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genotypes associated with a case",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a case",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/case/{id}/models": {
"get": {
"operationId": "get_case_model_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns models associated with a case",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a case",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/case/{id}/phenotypes": {
"get": {
"operationId": "get_case_phenotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns phenotypes associated with a case",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a case",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/case/{id}/variants": {
"get": {
"operationId": "get_case_variant_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns variants associated with a case",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a case",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/disease/{id}/cases": {
"get": {
"operationId": "get_disease_case_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns cases associated with a disease",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of disease, e.g. MONDO:0007103, MONDO:0010918. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/disease/{id}/genes": {
"get": {
"operationId": "get_disease_gene_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
},
{
"description": "Additional filters: causal, non_causal, both",
"explode": true,
"in": "query",
"name": "association_type",
"schema": {
"default": "both",
"enum": [
"causal",
"non_causal",
"both"
],
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genes associated with a disease",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/disease/{id}/genotypes": {
"get": {
"operationId": "get_disease_genotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genotypes associated with a disease",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of disease, e.g. Orphanet:399158, DOID:0080008. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/disease/{id}/models": {
"get": {
"description": "In the association object returned, the subject will be the disease, and the object will be the model.\nThe model may be a gene or genetic element.\n\nIf the query disease is a general class, the association subject may be to a specific disease.\n\nIn some cases the association will be *direct*, for example if a paper asserts a genotype is a model of a disease.\n\nIn other cases, the association will be *indirect*, for\nexample, chaining over orthology. In these cases the chain\nwill be reflected in the *evidence graph*\n\n* TODO: provide hook into owlsim for dynamic computation of models by similarity",
"operationId": "get_disease_model_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns associations to models of the disease",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/disease/{id}/models/{taxon}": {
"get": {
"deprecated": true,
"description": "See /disease/<id>/models route for full details",
"operationId": "get_disease_model_taxon_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns associations to models of the disease constrained by taxon",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE of organism taxonomy class to constrain models, e.g NCBITaxon:10090 (M. musculus).\n\n Higher level taxa may be used",
"in": "path",
"name": "taxon",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/disease/{id}/pathways": {
"get": {
"operationId": "get_disease_pathway_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns pathways associated with a disease",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of disease, e.g. DOID:4450. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/disease/{id}/phenotypes": {
"get": {
"operationId": "get_disease_phenotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/D2PAssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns phenotypes associated with disease",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of disease, e.g. OMIM:605543, Orphanet:1934, DOID:678. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/disease/{id}/publications": {
"get": {
"operationId": "get_disease_publication_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns publications associated with a disease",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/disease/{id}/treatment": {
"get": {
"description": "e.g. drugs or small molecules used to treat",
"operationId": "get_disease_substance_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns substances associated with a disease",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/disease/{id}/variants": {
"get": {
"operationId": "get_disease_variant_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns variants associated with a disease",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/function/{id}": {
"get": {
"operationId": "get_function_associations",
"parameters": [
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"default": 0,
"type": "integer"
}
},
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"explode": true,
"in": "query",
"name": "evidence",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns annotations associated to a function term",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of a function term (e.g. GO:0044598)",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/function/{id}/genes": {
"get": {
"operationId": "get_function_gene_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
},
{
"description": "relationship type ('involved_in', 'involved_in_regulation_of' or 'acts_upstream_of_or_within')",
"explode": true,
"in": "query",
"name": "relationship_type",
"schema": {
"default": "involved_in",
"enum": [
"involved_in",
"involved_in_regulation_of",
"acts_upstream_of_or_within"
],
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genes associated to a GO term",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of a GO term, e.g. GO:0044598",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/function/{id}/publications": {
"get": {
"operationId": "get_function_publication_associations",
"parameters": [
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"default": 0,
"type": "integer"
}
},
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"explode": true,
"in": "query",
"name": "evidence",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns publications associated to a GO term",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of a GO term, e.g. GO:0044598",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/function/{id}/taxons": {
"get": {
"operationId": "get_function_taxon_associations",
"parameters": [
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"default": 0,
"type": "integer"
}
},
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"explode": true,
"in": "query",
"name": "evidence",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns taxons associated to a GO term",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of a GO term, e.g. GO:0044598",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/anatomy": {
"get": {
"operationId": "get_gene_anatomy_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns anatomical entities associated with a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. NCBIGene:13434",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/cases": {
"get": {
"operationId": "get_gene_case_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns cases associated with a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. HGNC:613, HGNC:11025",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/diseases": {
"get": {
"operationId": "get_gene_disease_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
},
{
"description": "Additional filters: causal, non_causal, both",
"explode": true,
"in": "query",
"name": "association_type",
"schema": {
"default": "both",
"enum": [
"causal",
"non_causal",
"both"
],
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns diseases associated with gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/expression/anatomy": {
"get": {
"operationId": "get_gene_expression_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns expression events for a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/function": {
"get": {
"description": "IMPLEMENTATION DETAILS\n----------------------\n\nNote: currently this is implemented as a query to the GO/AmiGO solr instance.\nThis directly supports IDs such as:\n\n - ZFIN e.g. ZFIN:ZDB-GENE-050417-357\n\nNote that the AmiGO GOlr natively stores MGI annotations to MGI:MGI:nn. However,\nthe standard for biolink is MGI:nnnn, so you should use this (will be transparently\nmapped to legacy ID)\n\nAdditionally, for some species such as Human, GO has the annotation attached to the UniProt ID.\nAgain, this should be transparently handled; e.g. you can use NCBIGene:6469, and this will be\nmapped behind the scenes for querying.",
"operationId": "get_gene_function_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns function associations for a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "id, e.g. NCBIGene:6469. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/genotypes": {
"get": {
"operationId": "get_gene_genotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genotypes associated with a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. ZFIN:ZDB-GENE-980526-166",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/homologs": {
"get": {
"operationId": "get_gene_homolog_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Taxon CURIE of homolog, e.g. NCBITaxon:9606 (Can be an ancestral node in the ontology; includes inferred associations by default)",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "P (paralog), O (Ortholog) or LDO (least-diverged ortholog)",
"explode": true,
"in": "query",
"name": "homology_type",
"schema": {
"enum": [
"P",
"O",
"LDO"
],
"type": "string"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns homologs for a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/interactions": {
"get": {
"operationId": "get_gene_interactions",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns interactions for a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/models": {
"get": {
"operationId": "get_gene_model_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns models associated with a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. NCBIGene:17988",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/ortholog/diseases": {
"get": {
"operationId": "get_gene_ortholog_disease_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Return diseases associated with orthologs of a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. NCBIGene:4750",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/ortholog/phenotypes": {
"get": {
"operationId": "get_gene_ortholog_phenotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Return phenotypes associated with orthologs for a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. NCBIGene:4750",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/pathways": {
"get": {
"operationId": "get_gene_pathway_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns pathways associated with gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. NCBIGene:50846. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/phenotypes": {
"get": {
"operationId": "get_gene_phenotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns phenotypes associated with gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/publications": {
"get": {
"operationId": "get_gene_publication_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns publications associated with a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. NCBIGene:4750",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/gene/{id}/variants": {
"get": {
"operationId": "get_gene_variant_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns variants associated with a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of gene, e.g. HGNC:10896",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/genotype/{id}/cases": {
"get": {
"operationId": "get_genotype_case_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns cases associated with a genotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of genotype, e.g. dbSNPIndividual:10440, dbSNPIndividual:22633",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/genotype/{id}/diseases": {
"get": {
"operationId": "get_genotype_disease_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns diseases associated with a genotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of genotype, e.g. dbSNPIndividual:11441 (if non-human will return models)",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/genotype/{id}/genes": {
"get": {
"operationId": "get_genotype_gene_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genes associated with a genotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/genotype/{id}/genotypes": {
"get": {
"description": "Genotypes may be related to one another according to the GENO model",
"operationId": "get_genotype_genotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genotypes-genotype associations",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/genotype/{id}/models": {
"get": {
"operationId": "get_genotype_model_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns models associated with a genotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/genotype/{id}/phenotypes": {
"get": {
"operationId": "get_genotype_phenotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns phenotypes associated with a genotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/genotype/{id}/publications": {
"get": {
"operationId": "get_genotype_publication_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns publications associated with a genotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/genotype/{id}/variants": {
"get": {
"operationId": "get_genotype_variant_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genotypes-variant associations",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of genotype, e.g. MONARCH:FBgeno422705",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/goterm/{id}/genes": {
"get": {
"deprecated": true,
"operationId": "get_goterm_gene_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "relationship type ('involved_in', 'involved_in_regulation_of' or 'acts_upstream_of_or_within')",
"explode": true,
"in": "query",
"name": "relationship_type",
"schema": {
"default": "involved_in",
"enum": [
"involved_in",
"involved_in_regulation_of",
"acts_upstream_of_or_within"
],
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns associations to GO terms for a gene",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of a GO term, e.g. GO:0044598",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/model/{id}/cases": {
"get": {
"operationId": "get_model_case_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns cases associated with a model",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a model, e.g. Coriell:GM22295, Coriell:HG02187",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/model/{id}/diseases": {
"get": {
"operationId": "get_model_disease_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns diseases associated with a model",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a model, e.g. MGI:5573196",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/model/{id}/genes": {
"get": {
"operationId": "get_model_gene_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genes associated with a model",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a model, e.g. MMRRC:042787",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/model/{id}/genotypes": {
"get": {
"operationId": "get_model_genotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genotypes associated with a model",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a model, e.g. Coriell:NA16660",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/model/{id}/phenotypes": {
"get": {
"operationId": "get_model_phenotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns phenotypes associated with a model",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "id",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/model/{id}/publications": {
"get": {
"operationId": "get_model_publication_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns publications associated with a model",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a model, e.g. MGI:5644542",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/model/{id}/variants": {
"get": {
"operationId": "get_model_variant_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns variants associated with a model",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a model, e.g. MMRRC:042787",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/pathway/{id}/diseases": {
"get": {
"operationId": "get_pathway_disease_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns diseases associated with a pathway",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE any pathway element. E.g. REACT:R-HSA-5387390",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/pathway/{id}/genes": {
"get": {
"operationId": "get_pathway_gene_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genes associated with a pathway",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE any pathway element. E.g. REACT:R-HSA-5387390",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/pathway/{id}/phenotypes": {
"get": {
"operationId": "get_pathway_phenotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns phenotypes associated with a pathway",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE any pathway element. E.g. REACT:R-HSA-5387390",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/phenotype/{id}/anatomy": {
"get": {
"description": "Example IDs:\n\n * MP:0008521 abnormal Bowman membrane",
"operationId": "get_phenotype_anatomy_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/NamedObject"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns anatomical entities associated with a phenotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of phenotype, e.g. MP:0008521. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/phenotype/{id}/cases": {
"get": {
"operationId": "get_phenotype_case_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns cases associated with a phenotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "Pheno class CURIE identifier, e.g HP:0011951 (Aspiration pneumonia), HP:0002450 (Abnormal motor neuron morphology)",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/phenotype/{id}/diseases": {
"get": {
"operationId": "get_phenotype_disease_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/D2PAssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns diseases associated with a phenotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of phenotype, e.g. HP:0007359. Equivalent IDs can be used with same results",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/phenotype/{id}/gene/{taxid}/ids": {
"get": {
"deprecated": true,
"description": "For example, MP:0001569 + NCBITaxon:10090 (mouse)",
"operationId": "get_phenotype_gene_by_taxon_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns gene IDs for all genes associated with a given phenotype, filtered by taxon",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "Species or high level taxon grouping, e.g NCBITaxon:10090 (Mus musculus)",
"in": "path",
"name": "taxid",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Pheno class CURIE identifier, e.g MP:0001569 (abnormal circulating bilirubin level)",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/phenotype/{id}/genes": {
"get": {
"operationId": "get_phenotype_gene_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genes associated with a phenotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level), ",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/phenotype/{id}/genotypes": {
"get": {
"operationId": "get_phenotype_genotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genotypes associated with a phenotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/phenotype/{id}/pathways": {
"get": {
"operationId": "get_phenotype_pathway_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns pathways associated with a phenotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "Pheno class CURIE identifier, e.g MP:0001569 (abnormal circulating bilirubin level)",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/phenotype/{id}/publications": {
"get": {
"operationId": "get_phenotype_publication_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns publications associated with a phenotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/phenotype/{id}/variants": {
"get": {
"operationId": "get_phenotype_variant_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns variants associated with a phenotype",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/publication/{id}/diseases": {
"get": {
"operationId": "get_publication_disease_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns diseases associated with a publication",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a publication, e.g. PMID:11751940",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/publication/{id}/genes": {
"get": {
"operationId": "get_publication_gene_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genes associated with a publication",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a publication, e.g. PMID:11751940",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/publication/{id}/genotypes": {
"get": {
"operationId": "get_publication_genotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genotypes associated with a publication",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a publication, e.g. PMID:11751940",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/publication/{id}/models": {
"get": {
"operationId": "get_publication_model_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns models associated with a publication",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a publication, e.g. PMID:11751940",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/publication/{id}/phenotypes": {
"get": {
"operationId": "get_publication_phenotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns phenotypes associated with a publication",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a publication, e.g. PMID:11751940",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/publication/{id}/variants": {
"get": {
"operationId": "get_publication_variant_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns variants associated with a publication",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier for a publication, e.g. PMID:11751940",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/substance/{id}/participant_in": {
"get": {
"description": "Examples relationships:\n\n * substance is a metabolite of a process\n * substance is synthesized by a process\n * substance is modified by an activity\n * substance elicits a response program/pathway\n * substance is transported by activity or pathway\n\nFor example, CHEBI:40036 (amitrole)",
"operationId": "get_substance_participant_in_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns associations between an activity and process and the specified substance",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of substance, e.g. CHEBI:40036",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/substance/{id}/roles": {
"get": {
"description": "Roles may be human-oriented (e.g. pesticide) or molecular (e.g. enzyme inhibitor)",
"operationId": "get_substance_role_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns associations between given drug and roles",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of substance, e.g. CHEBI:40036",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/substance/{id}/treats": {
"get": {
"description": "e.g. drugs or small molecules used to treat",
"operationId": "get_substance_treats_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns substances associated with a disease",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of substance, e.g. CHEBI:40036",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/variant/{id}/cases": {
"get": {
"operationId": "get_variant_case_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns cases associated with a variant",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of variant, e.g. OMIM:309550.0004, dbSNP:rs5030868",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/variant/{id}/diseases": {
"get": {
"operationId": "get_variant_disease_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns diseases associated with a variant",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of variant, e.g. ClinVarVariant:14925",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/variant/{id}/genes": {
"get": {
"operationId": "get_variant_gene_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genes associated with a variant",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/variant/{id}/genotypes": {
"get": {
"operationId": "get_variant_genotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns genotypes associated with a variant",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/variant/{id}/models": {
"get": {
"operationId": "get_variant_model_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns models associated with a variant",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of variant, e.g. OMIM:607623.0012, dbSNP:rs5030868",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/variant/{id}/phenotypes": {
"get": {
"operationId": "get_variant_phenotype_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns phenotypes associated with a variant",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/variant/{id}/publications": {
"get": {
"operationId": "get_variant_publication_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns publications associated with a variant",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/{id}": {
"get": {
"operationId": "get_generic_object",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/BioObject"
}
}
},
"description": "Success"
}
},
"summary": "Returns basic info on object of any type",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "id, e.g. NCBIGene:84570",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/{id}/associations": {
"get": {
"operationId": "get_generic_associations",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Set true to exclude inferred taxa",
"in": "query",
"name": "direct_taxon",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "A relation CURIE to filter associations",
"in": "query",
"name": "relation",
"schema": {
"type": "string"
}
},
{
"description": "Sorting responses <field> <desc,asc>",
"in": "query",
"name": "sort",
"schema": {
"type": "string"
}
},
{
"description": "Query string to filter documents",
"in": "query",
"name": "q",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AssociationResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns associations for an entity regardless of the type",
"tags": [
"bioentity"
]
},
"parameters": [
{
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentity/{type}/{id}": {
"get": {
"operationId": "get_generic_object_by_type",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
},
{
"description": "Enable faceting",
"in": "query",
"name": "facet",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Fields to facet on",
"explode": true,
"in": "query",
"name": "facet_fields",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If true, excludes evidence objects in response",
"in": "query",
"name": "unselect_evidence",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload",
"in": "query",
"name": "fetch_objects",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "If true, returns results in compact associations format",
"in": "query",
"name": "use_compact_associations",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
},
{
"description": "Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False",
"in": "query",
"name": "direct",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Get association counts",
"in": "query",
"name": "get_association_counts",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Get distinct counts for associations (to be used in conjunction with 'get_association_counts' parameter)",
"in": "query",
"name": "distinct_counts",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Return basic info on an object for a given type",
"tags": [
"bioentity"
]
},
"parameters": [
{
"description": "bioentity type",
"in": "path",
"name": "type",
"required": true,
"schema": {
"enum": [
"gene",
"variant",
"genotype",
"phenotype",
"disease",
"goterm",
"pathway",
"anatomy",
"substance",
"individual",
"publication",
"model",
"case"
],
"type": "string"
}
},
{
"description": "id, e.g. NCBIGene:84570",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/bioentityset/associations": {
"get": {
"operationId": "get_entity_set_associations",
"parameters": [
{
"description": "Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387",
"explode": true,
"in": "query",
"name": "subject",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests",
"explode": true,
"in": "query",
"name": "background",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "E.g. phenotype, function",
"in": "query",
"name": "object_category",
"schema": {
"type": "string"
}
},
{
"description": "Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED",
"in": "query",
"name": "object_slim",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns compact associations for a given input set",
"tags": [
"bioentityset"
]
}
},
"/bioentityset/descriptor/counts": {
"get": {
"operationId": "get_entity_set_summary",
"parameters": [
{
"description": "Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387",
"explode": true,
"in": "query",
"name": "subject",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests",
"explode": true,
"in": "query",
"name": "background",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "E.g. phenotype, function",
"in": "query",
"name": "object_category",
"schema": {
"type": "string"
}
},
{
"description": "Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED",
"in": "query",
"name": "object_slim",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Summary statistics for objects associated",
"tags": [
"bioentityset"
]
}
},
"/bioentityset/graph": {
"get": {
"operationId": "get_entity_set_graph_resource",
"parameters": [
{
"description": "Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387",
"explode": true,
"in": "query",
"name": "subject",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests",
"explode": true,
"in": "query",
"name": "background",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "E.g. phenotype, function",
"in": "query",
"name": "object_category",
"schema": {
"type": "string"
}
},
{
"description": "Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED",
"in": "query",
"name": "object_slim",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "TODO Graph object spanning all entities",
"tags": [
"bioentityset"
]
}
},
"/bioentityset/homologs/": {
"get": {
"operationId": "get_entity_set_homologs",
"parameters": [
{
"description": "Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387",
"explode": true,
"in": "query",
"name": "subject",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns homology associations for a given input set of genes",
"tags": [
"bioentityset/homologs"
]
}
},
"/bioentityset/overrepresentation": {
"get": {
"operationId": "get_over_representation",
"parameters": [
{
"description": "E.g. phenotype, function",
"in": "query",
"name": "object_category",
"schema": {
"type": "string"
}
},
{
"description": "Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387",
"explode": true,
"in": "query",
"name": "subject",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests",
"explode": true,
"in": "query",
"name": "background",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Default: gene. Other types may be used e.g. disease but statistics may not make sense",
"in": "query",
"name": "subject_category",
"schema": {
"default": "gene",
"type": "string"
}
},
{
"description": "Exclude results with p-value greater than this",
"in": "query",
"name": "max_p_value",
"schema": {
"default": "0.05",
"type": "string"
}
},
{
"description": "ontology id. Must be obo id. Examples: go, mp, hp, uberon (optional: will be inferred if left blank)",
"in": "query",
"name": "ontology",
"schema": {
"type": "string"
}
},
{
"description": "must be NCBITaxon CURIE. Example: NCBITaxon:9606",
"in": "query",
"name": "taxon",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Summary statistics for objects associated",
"tags": [
"bioentityset"
]
}
},
"/bioentityset/slimmer/anatomy": {
"get": {
"operationId": "get_entity_set_anatomy_slimmer",
"parameters": [
{
"description": "Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387",
"explode": true,
"in": "query",
"name": "subject",
"required": true,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID (IMPLEMENTED) or subset ID (TODO)",
"explode": true,
"in": "query",
"name": "slim",
"required": true,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If set, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "For a given gene(s), summarize its annotations over a defined set of slim",
"tags": [
"bioentityset/slimmer"
]
}
},
"/bioentityset/slimmer/function": {
"get": {
"operationId": "get_entity_set_function_slimmer",
"parameters": [
{
"description": "relationship type ('involved_in' or 'acts_upstream_of_or_within')",
"explode": true,
"in": "query",
"name": "relationship_type",
"schema": {
"default": "acts_upstream_of_or_within",
"enum": [
"involved_in",
"acts_upstream_of_or_within"
],
"type": "string"
}
},
{
"description": "Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387",
"explode": true,
"in": "query",
"name": "subject",
"required": true,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID (IMPLEMENTED) or subset ID (TODO)",
"explode": true,
"in": "query",
"name": "slim",
"required": true,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If set, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "For a given gene(s), summarize its annotations over a defined set of slim",
"tags": [
"bioentityset/slimmer"
]
}
},
"/bioentityset/slimmer/phenotype": {
"get": {
"operationId": "get_entity_set_phenotype_slimmer",
"parameters": [
{
"description": "Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387",
"explode": true,
"in": "query",
"name": "subject",
"required": true,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID (IMPLEMENTED) or subset ID (TODO)",
"explode": true,
"in": "query",
"name": "slim",
"required": true,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "If set, excludes associations that involve IEAs (ECO:0000501)",
"in": "query",
"name": "exclude_automatic_assertions",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 100,
"type": "integer"
}
},
{
"description": "beginning row",
"in": "query",
"name": "start",
"schema": {
"type": "integer"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "For a given gene(s), summarize its annotations over a defined set of slim",
"tags": [
"bioentityset/slimmer"
]
}
},
"/cam/activity": {
"get": {
"operationId": "get_activity_collection",
"parameters": [
{
"description": "string to search for in title of model",
"in": "query",
"name": "title",
"schema": {
"type": "string"
}
},
{
"description": "string to search for in contributor of model",
"in": "query",
"name": "contributor",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns list of models",
"tags": [
"cam"
]
}
},
"/cam/instance/{id}": {
"get": {
"operationId": "get_instance_object",
"parameters": [
{
"description": "string to search for in title of model",
"in": "query",
"name": "title",
"schema": {
"type": "string"
}
},
{
"description": "string to search for in contributor of model",
"in": "query",
"name": "contributor",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matches",
"tags": [
"cam"
]
},
"parameters": [
{
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/cam/instances": {
"get": {
"operationId": "get_model_instances",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns list of all instances",
"tags": [
"cam"
]
}
},
"/cam/model": {
"get": {
"operationId": "get_model_collection",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns list of ALL models",
"tags": [
"cam"
]
}
},
"/cam/model/contributors": {
"get": {
"operationId": "get_model_contributors",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns list of all contributors across all models",
"tags": [
"cam"
]
}
},
"/cam/model/properties": {
"get": {
"operationId": "get_model_properties",
"parameters": [
{
"description": "string to search for in title of model",
"in": "query",
"name": "title",
"schema": {
"type": "string"
}
},
{
"description": "string to search for in contributor of model",
"in": "query",
"name": "contributor",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns list of all properties used across all models",
"tags": [
"cam"
]
}
},
"/cam/model/property_values": {
"get": {
"operationId": "get_model_property_values",
"parameters": [
{
"description": "string to search for in title of model",
"in": "query",
"name": "title",
"schema": {
"type": "string"
}
},
{
"description": "string to search for in contributor of model",
"in": "query",
"name": "contributor",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns list property-values for all models",
"tags": [
"cam"
]
}
},
"/cam/model/query": {
"get": {
"operationId": "get_model_query",
"parameters": [
{
"description": "string to search for in title of model",
"in": "query",
"name": "title",
"schema": {
"type": "string"
}
},
{
"description": "string to search for in contributor of model",
"in": "query",
"name": "contributor",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns list of models matching query",
"tags": [
"cam"
]
}
},
"/cam/model/{id}": {
"get": {
"operationId": "get_model_object",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns a complete model",
"tags": [
"cam"
]
},
"parameters": [
{
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/cam/physical_interaction": {
"get": {
"operationId": "get_physical_interaction",
"parameters": [
{
"description": "string to search for in title of model",
"in": "query",
"name": "title",
"schema": {
"type": "string"
}
},
{
"description": "string to search for in contributor of model",
"in": "query",
"name": "contributor",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns list of models",
"tags": [
"cam"
]
}
},
"/evidence/graph/{id}": {
"get": {
"description": "Note that every association is assumed to have a unique ID",
"operationId": "get_evidence_graph_object",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Graph"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns evidence graph object for a given association",
"tags": [
"evidence/graph"
]
},
"parameters": [
{
"description": "association id, e.g. 68e686f6-d05b-46b8-ab1f-1da2fff97ada",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/evidence/graph/{id}/table": {
"get": {
"description": "Note that every association is assumed to have a unique ID",
"operationId": "get_evidence_graph_table",
"parameters": [
{
"description": "If true, considers dc:source as edge",
"in": "query",
"name": "is_publication",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns evidence as a association_results object given an association",
"tags": [
"evidence/graph"
]
},
"parameters": [
{
"description": "association id, e.g. 68e686f6-d05b-46b8-ab1f-1da2fff97ada",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/genome/features/within/{build}/{reference}/{begin}/{end}": {
"get": {
"operationId": "get_features_within_resource",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/SequenceFeature"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matches",
"tags": [
"genome/features"
]
},
"parameters": [
{
"in": "path",
"name": "build",
"required": true,
"schema": {
"type": "string"
}
},
{
"in": "path",
"name": "reference",
"required": true,
"schema": {
"type": "string"
}
},
{
"in": "path",
"name": "begin",
"required": true,
"schema": {
"type": "string"
}
},
{
"in": "path",
"name": "end",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/graph/edges/from/{id}": {
"get": {
"operationId": "get_edge_resource",
"parameters": [
{
"description": "How far to traverse for neighbors",
"in": "query",
"name": "depth",
"schema": {
"default": 1,
"type": "integer"
}
},
{
"description": "Which direction to traverse (used only if relationship_type is defined)",
"explode": true,
"in": "query",
"name": "direction",
"schema": {
"default": "BOTH",
"enum": [
"INCOMING",
"OUTGOING",
"BOTH"
],
"type": "string"
}
},
{
"description": "Relationship type to traverse",
"explode": true,
"in": "query",
"name": "relationship_type",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Include sub-properties and equivalent properties",
"in": "query",
"name": "entail",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Which monarch graph to query",
"explode": true,
"in": "query",
"name": "graph",
"schema": {
"default": "data",
"enum": [
"data",
"ontology"
],
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Graph"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns edges emanating from a given node",
"tags": [
"graph"
]
},
"parameters": [
{
"description": "CURIE e.g. HP:0000465",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/graph/node/{id}": {
"get": {
"description": "A node is an abstract representation of some kind of entity. The entity may be a physical thing such as a patient,\na molecular entity such as a gene or protein, or a conceptual entity such as a class from an ontology.",
"operationId": "get_node_resource",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/BioObject"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns a graph node",
"tags": [
"graph"
]
},
"parameters": [
{
"description": "CURIE e.g. HP:0000465",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/identifier/mapper/{source}/{target}/": {
"get": {
"operationId": "get_identifier_mapper",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "TODO maps a list of identifiers from a source to a target",
"tags": [
"identifier/mapper"
]
},
"parameters": [
{
"in": "path",
"name": "source",
"required": true,
"schema": {
"type": "string"
}
},
{
"in": "path",
"name": "target",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/identifier/prefixes/": {
"get": {
"operationId": "get_prefix_collection",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns list of prefixes",
"tags": [
"identifier/prefixes"
]
}
},
"/identifier/prefixes/contract/{uri}": {
"get": {
"operationId": "get_prefix_contract",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns contracted URI",
"tags": [
"identifier/prefixes"
]
},
"parameters": [
{
"description": "URI of entity to be contracted to identifier/CURIE, e.g \"http://www.informatics.jax.org/accession/MGI:1\"",
"in": "path",
"name": "uri",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/identifier/prefixes/expand/{id}": {
"get": {
"operationId": "get_prefix_expand",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns expanded URI",
"tags": [
"identifier/prefixes"
]
},
"parameters": [
{
"description": "ID of entity to be contracted to URI, e.g \"MGI:1\"",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/individual/pedigree/{id}": {
"get": {
"operationId": "get_pedigree",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matches",
"tags": [
"individual"
]
},
"parameters": [
{
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/individual/{id}": {
"get": {
"operationId": "get_individual",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matches",
"tags": [
"individual"
]
},
"parameters": [
{
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/mart/case/{object_category}/{taxon}": {
"get": {
"description": "NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.",
"operationId": "get_mart_case_associations_resource",
"parameters": [
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Bulk download of case associations",
"tags": [
"mart"
]
},
"parameters": [
{
"description": "taxon of case, must be of form NCBITaxon:9606",
"in": "path",
"name": "taxon",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Category of entity at link Subject (target), e.g. phenotype, disease",
"in": "path",
"name": "object_category",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/mart/disease/{object_category}/{taxon}": {
"get": {
"description": "NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.",
"operationId": "get_mart_disease_associations_resource",
"parameters": [
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Bulk download of disease associations",
"tags": [
"mart"
]
},
"parameters": [
{
"description": "taxon of disease, must be of form NCBITaxon:9606",
"in": "path",
"name": "taxon",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Category of entity at link Object (target), e.g. phenotype, disease",
"in": "path",
"name": "object_category",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/mart/gene/{object_category}/{taxon}": {
"get": {
"description": "NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.",
"operationId": "get_mart_gene_associations_resource",
"parameters": [
{
"description": "Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID",
"explode": true,
"in": "query",
"name": "slim",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Bulk download of gene associations",
"tags": [
"mart"
]
},
"parameters": [
{
"description": "taxon of gene, must be of form NCBITaxon:9606",
"in": "path",
"name": "taxon",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Category of entity at link Object (target), e.g. phenotype, disease",
"in": "path",
"name": "object_category",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/mart/ortholog/{taxon1}/{taxon2}": {
"get": {
"operationId": "get_mart_ortholog_associations_resource",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Bulk download of orthologs",
"tags": [
"mart"
]
},
"parameters": [
{
"description": "object taxon, e.g. NCBITaxon:10090",
"in": "path",
"name": "taxon2",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "subject taxon, e.g. NCBITaxon:9606",
"in": "path",
"name": "taxon1",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/mart/paralog/{taxon1}/{taxon2}": {
"get": {
"operationId": "get_mart_paralog_associations_resource",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Bulk download of paralogs",
"tags": [
"mart"
]
},
"parameters": [
{
"description": "object taxon, e.g. NCBITaxon:9606",
"in": "path",
"name": "taxon2",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "subject taxon, e.g. NCBITaxon:9606",
"in": "path",
"name": "taxon1",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/metadata/datasets": {
"get": {
"operationId": "get_metadata_for_datasets",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Get metadata for all datasets from SciGraph",
"tags": [
"metadata"
]
}
},
"/mme/disease": {
"post": {
"operationId": "post_disease_mme",
"requestBody": {
"$ref": "#/components/requestBodies/mme"
},
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Match a patient to diseases based on their phenotypes",
"tags": [
"mme"
]
}
},
"/mme/fly": {
"post": {
"operationId": "post_fly_mme",
"requestBody": {
"$ref": "#/components/requestBodies/mme"
},
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Match a patient to fruit fly genes based on similar phenotypes",
"tags": [
"mme"
]
}
},
"/mme/mouse": {
"post": {
"operationId": "post_mouse_mme",
"requestBody": {
"$ref": "#/components/requestBodies/mme"
},
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Match a patient to mouse genes based on similar phenotypes",
"tags": [
"mme"
]
}
},
"/mme/nematode": {
"post": {
"operationId": "post_nematode_mme",
"requestBody": {
"$ref": "#/components/requestBodies/mme"
},
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Match a patient to nematode genes based on similar phenotypes",
"tags": [
"mme"
]
}
},
"/mme/zebrafish": {
"post": {
"operationId": "post_zebrafish_mme",
"requestBody": {
"$ref": "#/components/requestBodies/mme"
},
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Match a patient to zebrafish genes based on similar phenotypes",
"tags": [
"mme"
]
}
},
"/nlp/annotate/": {
"get": {
"operationId": "get_annotate",
"parameters": [
{
"description": "The text content to annotate",
"in": "query",
"name": "content",
"schema": {
"type": "string"
}
},
{
"description": "Categories to include for annotation",
"explode": true,
"in": "query",
"name": "include_category",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Categories to exclude for annotation",
"explode": true,
"in": "query",
"name": "exclude_category",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "The minimum number of characters in the annotated entity",
"in": "query",
"name": "min_length",
"schema": {
"default": 4,
"type": "string"
}
},
{
"description": "Should only the longest entity be returned for an overlapping group",
"in": "query",
"name": "longest_only",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should abbreviations be included",
"in": "query",
"name": "include_abbreviation",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should acronyms be included",
"in": "query",
"name": "include_acronym",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should numbers be included",
"in": "query",
"name": "include_numbers",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Annotate a given text using SciGraph annotator",
"tags": [
"nlp/annotate"
]
},
"post": {
"operationId": "post_annotate",
"parameters": [
{
"description": "The text content to annotate",
"in": "query",
"name": "content",
"schema": {
"type": "string"
}
},
{
"description": "Categories to include for annotation",
"explode": true,
"in": "query",
"name": "include_category",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Categories to exclude for annotation",
"explode": true,
"in": "query",
"name": "exclude_category",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "The minimum number of characters in the annotated entity",
"in": "query",
"name": "min_length",
"schema": {
"default": 4,
"type": "string"
}
},
{
"description": "Should only the longest entity be returned for an overlapping group",
"in": "query",
"name": "longest_only",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should abbreviations be included",
"in": "query",
"name": "include_abbreviation",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should acronyms be included",
"in": "query",
"name": "include_acronym",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should numbers be included",
"in": "query",
"name": "include_numbers",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Annotate a given text using SciGraph annotator",
"tags": [
"nlp/annotate"
]
}
},
"/nlp/annotate/entities": {
"get": {
"operationId": "get_annotate_entities",
"parameters": [
{
"description": "The text content to annotate",
"in": "query",
"name": "content",
"schema": {
"type": "string"
}
},
{
"description": "Categories to include for annotation",
"explode": true,
"in": "query",
"name": "include_category",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Categories to exclude for annotation",
"explode": true,
"in": "query",
"name": "exclude_category",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "The minimum number of characters in the annotated entity",
"in": "query",
"name": "min_length",
"schema": {
"default": 4,
"type": "string"
}
},
{
"description": "Should only the longest entity be returned for an overlapping group",
"in": "query",
"name": "longest_only",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should abbreviations be included",
"in": "query",
"name": "include_abbreviation",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should acronyms be included",
"in": "query",
"name": "include_acronym",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should numbers be included",
"in": "query",
"name": "include_numbers",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/EntityAnnotationResult"
}
}
},
"description": "Success"
}
},
"summary": "Annotate a given content using SciGraph annotator and get all entities from content",
"tags": [
"nlp/annotate"
]
},
"post": {
"operationId": "post_annotate_entities",
"parameters": [
{
"description": "The text content to annotate",
"in": "query",
"name": "content",
"schema": {
"type": "string"
}
},
{
"description": "Categories to include for annotation",
"explode": true,
"in": "query",
"name": "include_category",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Categories to exclude for annotation",
"explode": true,
"in": "query",
"name": "exclude_category",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "The minimum number of characters in the annotated entity",
"in": "query",
"name": "min_length",
"schema": {
"default": 4,
"type": "string"
}
},
{
"description": "Should only the longest entity be returned for an overlapping group",
"in": "query",
"name": "longest_only",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should abbreviations be included",
"in": "query",
"name": "include_abbreviation",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should acronyms be included",
"in": "query",
"name": "include_acronym",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "Should numbers be included",
"in": "query",
"name": "include_numbers",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/EntityAnnotationResult"
}
}
},
"description": "Success"
}
},
"summary": "Annotate a given content using SciGraph annotator and get all entities from content",
"tags": [
"nlp/annotate"
]
}
},
"/ontol/identifier/": {
"get": {
"operationId": "get_ontol_identifier_resource",
"parameters": [
{
"description": "List of labels",
"explode": true,
"in": "query",
"name": "label",
"required": true,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Fetches a map from CURIEs/IDs to labels",
"tags": [
"ontol/identifier"
]
},
"post": {
"description": "Takes 'label' list argument either as a querystring argument or as a key\nin the POST body when content-type is application/json.",
"operationId": "post_ontol_identifier_resource",
"parameters": [
{
"description": "List of labels",
"explode": true,
"in": "query",
"name": "label",
"required": true,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Fetches a map from CURIEs/IDs to labels",
"tags": [
"ontol/identifier"
]
}
},
"/ontol/information_content/{subject_category}/{object_category}/{subject_taxon}": {
"get": {
"description": "```\nIC = -log2( freq(t) / popSize )\n```\n\nHere the frequency and population is calculated for a particular dataset:\ne.g. all human disease-phenotype associations",
"operationId": "get_information_content_resource",
"parameters": [
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)\n or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.\n ",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns information content (IC) for a set of relevant ontology classes",
"tags": [
"ontol"
]
},
"parameters": [
{
"in": "path",
"name": "subject_category",
"required": true,
"schema": {
"type": "string"
}
},
{
"in": "path",
"name": "object_category",
"required": true,
"schema": {
"type": "string"
}
},
{
"in": "path",
"name": "subject_taxon",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/ontol/labeler/": {
"get": {
"operationId": "get_ontol_labeler_resource",
"parameters": [
{
"description": "List of ids",
"explode": true,
"in": "query",
"name": "id",
"required": true,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Fetches a map from CURIEs/IDs to labels",
"tags": [
"ontol/labeler"
]
}
},
"/ontol/subgraph/{ontology}/{node}": {
"get": {
"operationId": "get_extract_ontology_subgraph_resource",
"parameters": [
{
"description": "Additional classes",
"explode": true,
"in": "query",
"name": "cnode",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Include Ancestors",
"in": "query",
"name": "include_ancestors",
"schema": {
"default": true,
"type": "boolean"
}
},
{
"description": "Include Descendants",
"in": "query",
"name": "include_descendants",
"schema": {
"type": "boolean"
}
},
{
"description": "Additional classes",
"explode": true,
"in": "query",
"name": "relation",
"schema": {
"default": [
"subClassOf",
"BFO:0000050"
],
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Include metadata in response",
"in": "query",
"name": "include_meta",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Extract a subgraph from an ontology",
"tags": [
"ontol"
]
},
"parameters": [
{
"description": "class ID, e.g. HP:0001288",
"in": "path",
"name": "node",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "ontology ID, e.g. go, uberon, mp, hp",
"in": "path",
"name": "ontology",
"required": true,
"schema": {
"type": "string"
}
}
],
"post": {
"operationId": "post_extract_ontology_subgraph_resource",
"parameters": [
{
"description": "Additional classes",
"explode": true,
"in": "query",
"name": "cnode",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Include Ancestors",
"in": "query",
"name": "include_ancestors",
"schema": {
"default": true,
"type": "boolean"
}
},
{
"description": "Include Descendants",
"in": "query",
"name": "include_descendants",
"schema": {
"type": "boolean"
}
},
{
"description": "Additional classes",
"explode": true,
"in": "query",
"name": "relation",
"schema": {
"default": [
"subClassOf",
"BFO:0000050"
],
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Include metadata in response",
"in": "query",
"name": "include_meta",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Extract a subgraph from an ontology",
"tags": [
"ontol"
]
}
},
"/ontology/shared/{subject}/{object}": {
"get": {
"operationId": "get_ontology_terms_shared_ancestor",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns the ancestor ontology terms shared by two ontology terms",
"tags": [
"ontology"
]
},
"parameters": [
{
"description": "CURIE identifier of a GO term, e.g. GO:0006259",
"in": "path",
"name": "subject",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "CURIE identifier of a GO term, e.g. GO:0046483",
"in": "path",
"name": "object",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/ontology/subset/{id}": {
"get": {
"operationId": "get_ontology_subset",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns meta data of an ontology subset (slim)",
"tags": [
"ontology"
]
},
"parameters": [
{
"description": "name of a slim subset, e.g. goslim_agr, goslim_generic",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/ontology/term/{id}": {
"get": {
"operationId": "get_ontology_term",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns meta data of an ontology term",
"tags": [
"ontology"
]
},
"parameters": [
{
"description": "CURIE identifier of a GO term, e.g. GO:0003677",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/ontology/term/{id}/graph": {
"get": {
"operationId": "get_ontology_term_graph",
"parameters": [
{
"description": "graph type ('topology_graph', 'regulates_transitivity_graph' or 'neighborhood_graph')",
"explode": true,
"in": "query",
"name": "graph_type",
"schema": {
"default": "topology_graph",
"enum": [
"topology_graph",
"regulates_transitivity_graph",
"neighborhood_graph",
"neighborhood_limited_graph"
],
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns graph of an ontology term",
"tags": [
"ontology"
]
},
"parameters": [
{
"description": "CURIE identifier of a GO term, e.g. GO:0000981",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/ontology/term/{id}/subgraph": {
"get": {
"operationId": "get_ontology_term_subgraph",
"parameters": [
{
"description": "Additional classes",
"explode": true,
"in": "query",
"name": "cnode",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Include Ancestors",
"in": "query",
"name": "include_ancestors",
"schema": {
"default": true,
"type": "boolean"
}
},
{
"description": "Include Descendants",
"in": "query",
"name": "include_descendants",
"schema": {
"type": "boolean"
}
},
{
"description": "Additional classes",
"explode": true,
"in": "query",
"name": "relation",
"schema": {
"default": [
"subClassOf",
"BFO:0000050"
],
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Include metadata in response",
"in": "query",
"name": "include_meta",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Extract a subgraph from an ontology term",
"tags": [
"ontology"
]
},
"parameters": [
{
"description": "CURIE identifier of a GO term, e.g. GO:0007275",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/ontology/term/{id}/subsets": {
"get": {
"operationId": "get_ontology_term_subsets",
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Returns subsets (slims) associated to an ontology term",
"tags": [
"ontology"
]
},
"parameters": [
{
"description": "CURIE identifier of a GO term, e.g. GO:0006259",
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/owl/ontology/dlquery/{query}": {
"get": {
"operationId": "get_dl_query",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Placeholder - use OWLery for now",
"tags": [
"owl/ontology"
]
},
"parameters": [
{
"in": "path",
"name": "query",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/owl/ontology/sparql/{query}": {
"get": {
"operationId": "get_sparql_query",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Placeholder - use direct SPARQL endpoint for now",
"tags": [
"owl/ontology"
]
},
"parameters": [
{
"in": "path",
"name": "query",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/pair/sim/jaccard/{id1}/{id2}": {
"get": {
"operationId": "get_pair_sim_jaccard_resource",
"parameters": [
{
"description": "e.g. disease, phenotype, gene. Two subjects will be compared based on overlap between associations to objects in this category",
"in": "query",
"name": "object_category",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Get pairwise similarity",
"tags": [
"pair/sim"
]
},
"parameters": [
{
"description": "id, e.g. NCBIGene:1200; ZFIN:ZDB-GENE-980528-2059; UniProtKB:P12644",
"in": "path",
"name": "id2",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "id, e.g. NCBIGene:10891; ZFIN:ZDB-GENE-980526-166; UniProtKB:Q15465",
"in": "path",
"name": "id1",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/relation/usage/": {
"get": {
"operationId": "get_relation_usage_resource",
"parameters": [
{
"description": "SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default",
"in": "query",
"name": "subject_taxon",
"schema": {
"type": "string"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)\n or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.\n ",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "All relations used plus count of associations",
"tags": [
"relation/usage"
]
}
},
"/relation/usage/between/{subject_category}/{object_category}": {
"get": {
"operationId": "get_relation_usage_between_resource",
"parameters": [
{
"description": "SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default",
"in": "query",
"name": "subject_taxon",
"schema": {
"type": "string"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)\n or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.\n ",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "All relations used plus count of associations",
"tags": [
"relation/usage"
]
},
"parameters": [
{
"in": "path",
"name": "subject_category",
"required": true,
"schema": {
"type": "string"
}
},
{
"in": "path",
"name": "object_category",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/relation/usage/pivot": {
"get": {
"operationId": "get_relation_usage_pivot_resource",
"parameters": [
{
"description": "SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default",
"in": "query",
"name": "subject_taxon",
"schema": {
"type": "string"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)\n or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.\n ",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Relation usage count for all subj x obj category combinations",
"tags": [
"relation/usage"
]
}
},
"/relation/usage/pivot/label": {
"get": {
"operationId": "get_relation_usage_pivot_label_resource",
"parameters": [
{
"description": "SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default",
"in": "query",
"name": "subject_taxon",
"schema": {
"type": "string"
}
},
{
"description": "Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)\n or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.\n ",
"in": "query",
"name": "evidence",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/AssociationResults"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Relation usage count for all subj x obj category combinations, showing label",
"tags": [
"relation/usage"
]
}
},
"/search/entity/autocomplete/{term}": {
"get": {
"operationId": "get_autocomplete",
"parameters": [
{
"description": "fq string passed directly to solr, note that multiple filters will be combined with an AND operator. Combining fq_string with other parameters may result in unexpected behavior.",
"explode": true,
"in": "query",
"name": "fq",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "e.g. gene, disease",
"explode": true,
"in": "query",
"name": "category",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "ontology prefix: HP, -MONDO",
"explode": true,
"in": "query",
"name": "prefix",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Include equivalent ids in prefix filter",
"in": "query",
"name": "include_eqs",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "boost function e.g. pow(edges,0.334)",
"explode": true,
"in": "query",
"name": "boost_fx",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "boost query e.g. category:genotype^-10",
"explode": true,
"in": "query",
"name": "boost_q",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "taxon filter, eg NCBITaxon:9606, includes inferred taxa",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 20,
"type": "integer"
}
},
{
"description": "row number to start from",
"in": "query",
"name": "start",
"schema": {
"default": "0",
"type": "string"
}
},
{
"description": "highlight class",
"in": "query",
"name": "highlight_class",
"schema": {
"type": "string"
}
},
{
"description": "minimum should match parameter, see solr docs for details",
"in": "query",
"name": "min_match",
"schema": {
"type": "string"
}
},
{
"description": "Exclude grouping classes (classes with subclasses)",
"in": "query",
"name": "exclude_groups",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "set to true to use the minimal tokenizer, good for variants and genotypes",
"in": "query",
"name": "minimal_tokenizer",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AutocompleteResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matching concepts or entities using lexical search",
"tags": [
"search"
]
},
"parameters": [
{
"in": "path",
"name": "term",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/search/entity/hpo-pl/{term}": {
"get": {
"operationId": "get_search_hpo_entities",
"parameters": [
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 10,
"type": "integer"
}
},
{
"description": "row number to start from",
"in": "query",
"name": "start",
"schema": {
"default": "0",
"type": "string"
}
},
{
"description": "phenotype group id",
"in": "query",
"name": "phenotype_group",
"schema": {
"type": "string"
}
},
{
"description": "phenotype group label",
"in": "query",
"name": "phenotype_group_label",
"schema": {
"type": "string"
}
},
{
"description": "anatomical system id",
"in": "query",
"name": "anatomical_system",
"schema": {
"type": "string"
}
},
{
"description": "anatomical system label",
"in": "query",
"name": "anatomical_system_label",
"schema": {
"type": "string"
}
},
{
"description": "highlight class",
"in": "query",
"name": "highlight_class",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/LayResults"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matching concepts or entities using lexical search",
"tags": [
"search"
]
},
"parameters": [
{
"description": "search string, e.g. muscle atrophy, frequent infections",
"in": "path",
"name": "term",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/search/entity/{term}": {
"get": {
"operationId": "get_search_entities",
"parameters": [
{
"description": "fq string passed directly to solr, note that multiple filters will be combined with an AND operator. Combining fq_string with other parameters may result in unexpected behavior.",
"explode": true,
"in": "query",
"name": "fq",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "e.g. gene, disease",
"explode": true,
"in": "query",
"name": "category",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "ontology prefix: HP, -MONDO",
"explode": true,
"in": "query",
"name": "prefix",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Include equivalent ids in prefix filter",
"in": "query",
"name": "include_eqs",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "boost function e.g. pow(edges,0.334)",
"explode": true,
"in": "query",
"name": "boost_fx",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "boost query e.g. category:genotype^-10",
"explode": true,
"in": "query",
"name": "boost_q",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "taxon filter, eg NCBITaxon:9606, includes inferred taxa",
"explode": true,
"in": "query",
"name": "taxon",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "number of rows",
"in": "query",
"name": "rows",
"schema": {
"default": 20,
"type": "integer"
}
},
{
"description": "row number to start from",
"in": "query",
"name": "start",
"schema": {
"default": "0",
"type": "string"
}
},
{
"description": "highlight class",
"in": "query",
"name": "highlight_class",
"schema": {
"type": "string"
}
},
{
"description": "minimum should match parameter, see solr docs for details",
"in": "query",
"name": "min_match",
"schema": {
"type": "string"
}
},
{
"description": "Exclude grouping classes (classes with subclasses)",
"in": "query",
"name": "exclude_groups",
"schema": {
"default": false,
"type": "boolean"
}
},
{
"description": "set to true to use the minimal tokenizer, good for variants and genotypes",
"in": "query",
"name": "minimal_tokenizer",
"schema": {
"default": false,
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/SearchResult"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matching concepts or entities using lexical search",
"tags": [
"search"
]
},
"parameters": [
{
"description": "search string, e.g. shh, parkinson, femur",
"in": "path",
"name": "term",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/sim/compare": {
"get": {
"operationId": "get_sim_compare",
"parameters": [
{
"description": "set to true if *all* input ids are phenotypic features, else set to false",
"in": "query",
"name": "is_feature_set",
"schema": {
"default": true,
"type": "boolean"
}
},
{
"description": "Metric for computing similarity",
"explode": true,
"in": "query",
"name": "metric",
"schema": {
"default": "phenodigm",
"enum": [
"phenodigm",
"jaccard",
"simGIC",
"resnik",
"symmetric_resnik"
],
"type": "string"
}
},
{
"description": "A phenotype or identifier that is composed of phenotypes (eg disease, gene)",
"explode": true,
"in": "query",
"name": "ref_id",
"schema": {
"default": [],
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "A phenotype or identifier that is composed of phenotypes (eg disease, gene)",
"explode": true,
"in": "query",
"name": "query_id",
"schema": {
"default": [],
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/SimResult"
}
}
},
"description": "Success"
}
},
"summary": "Compare a reference profile vs one profiles",
"tags": [
"sim"
]
},
"post": {
"operationId": "post_sim_compare",
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/CompareInput"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/SimResult"
}
}
},
"description": "Success"
}
},
"summary": "Compare a reference profile vs one or more profiles",
"tags": [
"sim"
]
}
},
"/sim/score": {
"get": {
"operationId": "get_annotation_score",
"parameters": [
{
"description": "Phenotype identifier (eg HP:0004935)",
"explode": true,
"in": "query",
"name": "id",
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "absent phenotype (eg HP:0002828)",
"explode": true,
"in": "query",
"name": "absent_id",
"schema": {
"default": [],
"items": {
"type": "string"
},
"type": "array"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/SufficiencyOutput"
}
}
},
"description": "Success"
}
},
"summary": "Get annotation score",
"tags": [
"sim"
]
},
"post": {
"operationId": "post_annotation_score",
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/SufficiencyPostInput"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/SufficiencyOutput"
}
}
},
"description": "Success"
}
},
"summary": "Get annotation score",
"tags": [
"sim"
]
}
},
"/sim/search": {
"get": {
"operationId": "get_sim_search",
"parameters": [
{
"description": "set to true if *all* input ids are phenotypic features, else set to false",
"in": "query",
"name": "is_feature_set",
"schema": {
"default": true,
"type": "boolean"
}
},
{
"description": "Metric for computing similarity",
"explode": true,
"in": "query",
"name": "metric",
"schema": {
"default": "phenodigm",
"enum": [
"phenodigm",
"jaccard",
"simGIC",
"resnik",
"symmetric_resnik"
],
"type": "string"
}
},
{
"description": "A phenotype or identifier that is composed of phenotypes (eg disease, gene)",
"explode": true,
"in": "query",
"name": "id",
"schema": {
"default": [],
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "number of rows, max 500",
"in": "query",
"name": "limit",
"schema": {
"default": 20,
"type": "integer"
}
},
{
"description": "ncbi taxon id",
"in": "query",
"name": "taxon",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/SimResult"
}
}
},
"description": "Success"
}
},
"summary": "Search for phenotypically similar diseases or model genes",
"tags": [
"sim"
]
}
},
"/variation/set/": {
"get": {
"operationId": "get_variant_sets_collection",
"parameters": [
{
"description": "Page number",
"in": "query",
"name": "page",
"schema": {
"default": 1,
"type": "integer"
}
},
{
"description": "Results per page {error_msg}",
"explode": true,
"in": "query",
"name": "per_page",
"schema": {
"default": 10,
"enum": [
2,
10,
20,
30,
40,
50
],
"type": "integer"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Page_of_variant_sets"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of variant sets",
"tags": [
"variation/set"
]
},
"post": {
"operationId": "post_variant_sets_collection",
"requestBody": {
"$ref": "#/components/requestBodies/variant_set"
},
"responses": {
"200": {
"description": "Success"
}
},
"summary": "Creates a new variant set",
"tags": [
"variation/set"
]
}
},
"/variation/set/analyze/{id}": {
"get": {
"operationId": "get_variant_analyze",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of matches",
"tags": [
"variation/set"
]
},
"parameters": [
{
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
]
},
"/variation/set/archive/{year}/{month}/{day}": {
"get": {
"operationId": "get_variant_sets_archive_collection",
"parameters": [
{
"description": "Page number",
"in": "query",
"name": "page",
"schema": {
"default": 1,
"type": "integer"
}
},
{
"description": "Results per page {error_msg}",
"explode": true,
"in": "query",
"name": "per_page",
"schema": {
"default": 10,
"enum": [
2,
10,
20,
30,
40,
50
],
"type": "integer"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Page_of_variant_sets"
}
}
},
"description": "Success"
}
},
"summary": "Returns list of variant sets from a specified time period",
"tags": [
"variation/set"
]
},
"parameters": [
{
"in": "path",
"name": "year",
"required": true,
"schema": {
"type": "integer"
}
},
{
"in": "path",
"name": "month",
"required": true,
"schema": {
"type": "integer"
}
},
{
"in": "path",
"name": "day",
"required": true,
"schema": {
"type": "integer"
}
}
]
},
"/variation/set/{id}": {
"delete": {
"operationId": "delete_variant_set_item",
"responses": {
"204": {
"description": "VariantSet successfully deleted."
},
"404": {
"description": "VariantSet not found."
}
},
"summary": "Deletes variant set",
"tags": [
"variation/set"
]
},
"get": {
"operationId": "get_variant_set_item",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/variant_set"
}
}
},
"description": "Success"
},
"404": {
"description": "VariantSet not found."
}
},
"summary": "Returns a variant set",
"tags": [
"variation/set"
]
},
"parameters": [
{
"in": "path",
"name": "id",
"required": true,
"schema": {
"type": "string"
}
}
],
"put": {
"operationId": "put_variant_set_item",
"requestBody": {
"$ref": "#/components/requestBodies/variant_set"
},
"responses": {
"204": {
"description": "VariantSet successfully updated."
},
"404": {
"description": "VariantSet not found."
}
},
"summary": "Updates a variant set",
"tags": [
"variation/set"
]
}
}
},
"components": {
"requestBodies": {
"mme": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/mme"
}
}
},
"required": true
},
"variant_set": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/variant_set"
}
}
},
"required": true
}
},
"responses": {
"AmbiguousPrefix": {
"description": "Error handler to handle AmbiguousPrefix"
},
"InvalidSyntax": {
"description": "Error handler to handle InvalidSyntax"
},
"MaskError": {
"description": "When any error occurs on mask"
},
"NoContraction": {
"description": "Error handler to handle NoContraction"
},
"NoExpansion": {
"description": "Error handler to handle NoExpansion"
},
"NoPrefix": {
"description": "Error handler to handle NoPrefix"
},
"NoResultFound": {
"description": ""
},
"NoResultFoundException": {
"description": "Error handler to handle NoResultFoundException"
},
"ParseError": {
"description": "When a mask can't be parsed"
},
"RouteNotImplementedException": {
"description": "Error handler to handle RouteNotImplementedException"
},
"UnhandledException": {
"description": "Error handler to handle UnhandledException"
},
"UnrecognizedBioentityTypeException": {
"description": "Error handler to handle UnrecognizedBioentityTypeException"
}
},
"schemas": {
"A_page_of_results": {
"properties": {
"page": {
"description": "Number of this page of results",
"type": "integer"
},
"pages": {
"description": "Total number of pages of results",
"type": "integer"
},
"per_page": {
"description": "Number of items per page of results",
"type": "integer"
},
"total": {
"description": "Total number of results",
"type": "integer"
}
},
"type": "object"
},
"AbstractPropertyValue": {
"properties": {
"pred": {
"description": "predicate (attribute) part",
"type": "string"
},
"val": {
"description": "value part",
"type": "string"
},
"xrefs": {
"description": "Xrefs provenance for property-value",
"items": {
"type": "string"
},
"type": "array"
}
},
"type": "object"
},
"AnnotationExtension": {
"properties": {
"filler": {
"allOf": [
{
"$ref": "#/components/schemas/NamedObject"
}
],
"description": "Extension interpreted as OWL expression (r1 some r2 some .. some filler)."
},
"relation_chain": {
"description": "Relationship type. If more than one value, interpreted as chain",
"items": {
"$ref": "#/components/schemas/Relation"
},
"type": "array"
}
},
"type": "object"
},
"Association": {
"properties": {
"evidence_graph": {
"allOf": [
{
"$ref": "#/components/schemas/Graph"
}
],
"description": "An indirect association is a join between two or more direct assocations, e.g. gene to disease via ortholog. We record the full set of associations as a graph object"
},
"evidence_types": {
"description": "Evidence types (ECO classes)",
"items": {
"$ref": "#/components/schemas/EntityReference"
},
"type": "array"
},
"id": {
"description": "Association/annotation unique ID",
"type": "string"
},
"negated": {
"description": "True if association is negated",
"type": "boolean"
},
"object": {
"allOf": [
{
"$ref": "#/components/schemas/BioObjectCore"
}
],
"description": "Object (sensu RDF), aka target, e.g. HP:0000448, MP:0002109, DOID:14330"
},
"object_eq": {
"description": "Equivalent identifiers to object node",
"items": {
"type": "string"
},
"type": "array"
},
"object_extensions": {
"items": {
"allOf": [
{
"$ref": "#/components/schemas/AnnotationExtension"
}
],
"description": "Additional properties of the object in the context of this association. See http://www.biomedcentral.com/1471-2105/15/155"
},
"type": "array"
},
"provided_by": {
"description": "Provider of association, e.g. Orphanet, ClinVar",
"items": {
"type": "string"
},
"type": "array"
},
"publications": {
"description": "Publications supporting association, extracted from evidence graph",
"items": {
"$ref": "#/components/schemas/EntityReference"
},
"type": "array"
},
"qualifiers": {
"description": "Qualifier on the association",
"items": {
"type": "string"
},
"type": "array"
},
"relation": {
"allOf": [
{
"$ref": "#/components/schemas/RelationRef"
}
],
"description": "Relationship type connecting subject and object"
},
"slim": {
"description": "Objects mapped to a slim",
"items": {
"type": "string"
},
"type": "array"
},
"subject": {
"allOf": [
{
"$ref": "#/components/schemas/BioObjectCore"
}
],
"description": "Subject of association (what it is about), e.g. ClinVar:nnn, MGI:1201606"
},
"subject_eq": {
"description": "Equivalent identifiers to subject node",
"items": {
"type": "string"
},
"type": "array"
},
"subject_extensions": {
"items": {
"allOf": [
{
"$ref": "#/components/schemas/AnnotationExtension"
}
],
"description": "Additional properties of the subject in the context of this association."
},
"type": "array"
},
"type": {
"description": "Type of association, e.g. gene-phenotype",
"type": "string"
}
},
"required": [
"id",
"object",
"relation",
"subject"
],
"type": "object"
},
"AssociationResults": {
"allOf": [
{
"$ref": "#/components/schemas/SearchResult"
},
{
"properties": {
"associations": {
"description": "Complete representation of full association object, plus evidence",
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
},
"compact_associations": {
"description": "Compact representation in which objects (e.g. phenotypes) are collected for subject-predicate pairs",
"items": {
"$ref": "#/components/schemas/CompactAssociationSet"
},
"type": "array"
},
"objects": {
"description": "List of distinct objects used",
"items": {
"type": "string"
},
"type": "array"
}
},
"type": "object"
}
]
},
"AutocompleteResult": {
"properties": {
"category": {
"description": "node categories",
"items": {
"type": "string"
},
"type": "array"
},
"equivalent_ids": {
"description": "Equivalent IDs",
"items": {
"type": "string"
},
"type": "array"
},
"has_highlight": {
"description": "True if highlight can be interpreted as html, else False",
"type": "boolean"
},
"highlight": {
"description": "solr highlight",
"type": "string"
},
"id": {
"description": "curie formatted id",
"type": "string"
},
"label": {
"description": "primary label (rdfs:label)",
"items": {
"type": "string"
},
"type": "array"
},
"match": {
"description": "matched part of document (may be primary label, synonym, id, etc)",
"type": "string"
},
"taxon": {
"description": "taxon as NCBITaxon curie",
"type": "string"
},
"taxon_label": {
"description": "taxon label",
"type": "string"
}
},
"type": "object"
},
"AutocompleteResults": {
"properties": {
"docs": {
"description": "list of AutocompleteResult docs",
"items": {
"$ref": "#/components/schemas/AutocompleteResult"
},
"type": "array"
}
},
"type": "object"
},
"BioObject": {
"allOf": [
{
"$ref": "#/components/schemas/NamedObject"
},
{
"properties": {
"association_counts": {
"description": "association counts",
"type": "object"
},
"taxon": {
"allOf": [
{
"$ref": "#/components/schemas/Taxon"
}
],
"description": "Taxon to which the object belongs"
},
"xrefs": {
"description": "Database cross-references. These are usually CURIEs, but may also be URLs. E.g. ENSEMBL:ENSG00000099940 ",
"items": {
"type": "string"
},
"type": "array"
}
},
"type": "object"
}
]
},
"BioObjectCore": {
"allOf": [
{
"$ref": "#/components/schemas/NamedObjectCore"
},
{
"properties": {
"taxon": {
"allOf": [
{
"$ref": "#/components/schemas/Taxon"
}
],
"description": "Taxon to which the object belongs"
}
},
"type": "object"
}
]
},
"CompactAssociationSet": {
"properties": {
"objects": {
"description": "List of O, for a given (S,R) pair, yielding (S,R,O) triples. E.g. list of MPs for (MGI:nnn, has_phenotype)",
"items": {
"type": "string"
},
"type": "array"
},
"relation": {
"description": "Relationship type connecting subject and object list",
"type": "string"
},
"subject": {
"description": "Subject of association (what it is about), e.g. MGI:1201606",
"type": "string"
}
},
"required": [
"objects",
"relation",
"subject"
],
"type": "object"
},
"CompareInput": {
"properties": {
"query_ids": {
"description": "list of query profiles",
"items": {
"description": "list of ids",
"items": {
"description": "curie formatted id",
"type": "string"
},
"type": "array"
},
"type": "array"
},
"reference_ids": {
"description": "list of ids",
"items": {
"description": "curie formatted id",
"type": "string"
},
"type": "array"
}
},
"type": "object"
},
"D2PAssociation": {
"allOf": [
{
"$ref": "#/components/schemas/Association"
},
{
"properties": {
"frequency": {
"allOf": [
{
"$ref": "#/components/schemas/EntityReference"
}
],
"description": "Frequency of phenotype in patients with disease"
},
"onset": {
"allOf": [
{
"$ref": "#/components/schemas/EntityReference"
}
],
"description": "Onset of phenotype in disease process"
}
},
"type": "object"
}
]
},
"D2PAssociationResults": {
"allOf": [
{
"$ref": "#/components/schemas/SearchResult"
},
{
"properties": {
"associations": {
"description": "Complete representation of full disease to phenotype association, plus evidence",
"items": {
"$ref": "#/components/schemas/D2PAssociation"
},
"type": "array"
},
"compact_associations": {
"description": "Compact representation in which objects (e.g. phenotypes) are collected for subject-predicate pairs",
"items": {
"$ref": "#/components/schemas/CompactAssociationSet"
},
"type": "array"
},
"objects": {
"description": "List of distinct objects used",
"items": {
"type": "string"
},
"type": "array"
}
},
"type": "object"
}
]
},
"Edge": {
"properties": {
"meta": {
"description": "metadata about the Edge",
"type": "object"
},
"obj": {
"description": "Object (target) Node ID",
"type": "string"
},
"pred": {
"description": "Predicate (relation) ID",
"type": "string"
},
"sub": {
"description": "Subject (source) Node ID",
"type": "string"
}
},
"type": "object"
},
"EntityAnnotationResult": {
"properties": {
"content": {
"default": "The content from which the entities are extracted from",
"type": "string"
},
"spans": {
"description": "A marked-up span of text",
"items": {
"$ref": "#/components/schemas/Span"
},
"type": "array"
}
},
"type": "object"
},
"EntityReference": {
"properties": {
"id": {
"description": "ID or CURIE e.g. MGI:1201606",
"type": "string"
},
"label": {
"description": "RDFS Label",
"type": "string"
}
},
"type": "object"
},
"Feature": {
"properties": {
"id": {
"description": "curie formatted id",
"type": "string"
},
"isPresent": {
"description": "is the feature present",
"type": "boolean"
},
"label": {
"description": "curie formatted id",
"type": "string"
},
"type": {
"description": "feature type (only phenotype supported)",
"type": "string"
}
},
"type": "object"
},
"Graph": {
"properties": {
"edges": {
"description": "All edges in graph",
"items": {
"$ref": "#/components/schemas/Edge"
},
"type": "array"
},
"nodes": {
"description": "All nodes in graph",
"items": {
"$ref": "#/components/schemas/Node"
},
"type": "array"
}
},
"type": "object"
},
"IcNode": {
"allOf": [
{
"$ref": "#/components/schemas/Node"
},
{
"properties": {
"IC": {
"description": "Information content",
"type": "number"
}
},
"type": "object"
}
]
},
"LayAutocomplete": {
"properties": {
"highlight": {
"description": "solr highlight",
"type": "string"
},
"id": {
"description": "curie formatted id",
"type": "string"
},
"label": {
"description": "primary label (rdfs:label)",
"type": "string"
},
"matched_synonym": {
"description": "matched synonym",
"type": "string"
}
},
"type": "object"
},
"LayResults": {
"properties": {
"results": {
"description": "list of AutocompleteResult docs",
"items": {
"$ref": "#/components/schemas/LayAutocomplete"
},
"type": "array"
}
},
"type": "object"
},
"NamedObject": {
"allOf": [
{
"$ref": "#/components/schemas/NamedObjectCore"
},
{
"properties": {
"consider": {
"items": {
"description": "Potential replacement object (if named object is obsoleted)",
"type": "string"
},
"type": "array"
},
"deprecated": {
"description": "True if the node is deprecated/obsoleted.",
"type": "boolean"
},
"description": {
"description": "Descriptive text for the entity. For ontology classes, this will be a definition.",
"type": "string"
},
"replaced_by": {
"items": {
"description": "Direct 1:1 replacement (if named object is obsoleted)",
"type": "string"
},
"type": "array"
},
"synonyms": {
"description": "list of synonyms or alternate labels",
"items": {
"$ref": "#/components/schemas/SynonymPropertyValue"
},
"type": "array"
},
"types": {
"items": {
"description": "Type of object (direct)",
"type": "string"
},
"type": "array"
}
},
"type": "object"
}
]
},
"NamedObjectCore": {
"properties": {
"category": {
"items": {
"description": "Type of object",
"type": "string"
},
"type": "array"
},
"id": {
"description": "ID or CURIE e.g. MGI:1201606",
"type": "string"
},
"iri": {
"description": "IRI",
"type": "string"
},
"label": {
"description": "RDFS Label",
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
},
"Node": {
"properties": {
"id": {
"description": "ID or CURIE e.g. MGI:1201606",
"type": "string"
},
"label": {
"description": "RDFS Label",
"type": "string"
}
},
"required": [
"id"
],
"type": "object"
},
"Page_of_variant_sets": {
"allOf": [
{
"$ref": "#/components/schemas/A_page_of_results"
},
{
"properties": {
"items": {
"items": {
"$ref": "#/components/schemas/variant_set"
},
"type": "array"
}
},
"type": "object"
}
]
},
"PairwiseMatch": {
"properties": {
"lcs": {
"allOf": [
{
"$ref": "#/components/schemas/IcNode"
}
],
"description": "lowest common subsumer"
},
"match": {
"allOf": [
{
"$ref": "#/components/schemas/IcNode"
}
],
"description": "match id"
},
"reference": {
"allOf": [
{
"$ref": "#/components/schemas/IcNode"
}
],
"description": "reference id"
}
},
"type": "object"
},
"Relation": {
"allOf": [
{
"$ref": "#/components/schemas/NamedObject"
},
{
"properties": {},
"type": "object"
}
]
},
"RelationRef": {
"allOf": [
{
"$ref": "#/components/schemas/NamedObjectCore"
},
{
"properties": {
"inverse": {
"default": false,
"description": "is relation inverted",
"type": "boolean"
}
},
"type": "object"
}
]
},
"SearchResult": {
"properties": {
"docs": {
"description": "solr docs",
"items": {
"type": "object"
},
"type": "array"
},
"facet_counts": {
"description": "Mapping between field names and association counts",
"type": "object"
},
"highlighting": {
"description": "Mapping between id and solr highlight",
"type": "object"
},
"numFound": {
"description": "total number of associations matching query",
"type": "integer"
}
},
"type": "object"
},
"Seq": {
"allOf": [
{
"$ref": "#/components/schemas/BioObject"
},
{
"properties": {
"alphabet": {
"description": "one of: DNA, RNA or AA",
"type": "string"
},
"md5checksum": {
"description": "checksum",
"type": "string"
},
"residues": {
"description": "string representing sequence of residues",
"type": "string"
},
"seqlen": {
"description": "length of sequence",
"type": "string"
}
},
"type": "object"
}
]
},
"SequenceFeature": {
"allOf": [
{
"$ref": "#/components/schemas/BioObject"
},
{
"properties": {
"homology_associations": {
"items": {
"$ref": "#/components/schemas/Association"
},
"type": "array"
},
"locations": {
"items": {
"$ref": "#/components/schemas/SequenceLocation"
},
"type": "array"
},
"seq": {
"$ref": "#/components/schemas/Seq"
}
},
"type": "object"
}
]
},
"SequenceLocation": {
"allOf": [
{
"$ref": "#/components/schemas/BioObject"
},
{
"properties": {
"end": {
"$ref": "#/components/schemas/SequencePosition"
},
"phase": {
"type": "integer"
},
"score": {
"type": "integer"
},
"start": {
"$ref": "#/components/schemas/SequencePosition"
},
"strand": {
"description": "Strand direction: 1=='+', -1=='-', 0 or null infers unknown.",
"type": "integer"
}
},
"type": "object"
}
]
},
"SequencePosition": {
"properties": {
"position": {
"type": "integer"
},
"reference": {
"type": "string"
}
},
"type": "object"
},
"SimMatch": {
"allOf": [
{
"$ref": "#/components/schemas/TypedNode"
},
{
"properties": {
"pairwise_match": {
"items": {
"allOf": [
{
"$ref": "#/components/schemas/PairwiseMatch"
}
],
"description": "list of pairwise matches"
},
"type": "array"
},
"rank": {
"description": "rank",
"type": "string"
},
"score": {
"description": "sim score",
"type": "number"
},
"significance": {
"description": "p-value",
"type": "string"
}
},
"type": "object"
}
]
},
"SimMetadata": {
"properties": {
"max_max_ic": {
"description": "max IC",
"type": "number"
}
},
"type": "object"
},
"SimQuery": {
"properties": {
"ids": {
"items": {
"allOf": [
{
"$ref": "#/components/schemas/Node"
}
],
"description": "list of ids"
},
"type": "array"
},
"negated_ids": {
"items": {
"allOf": [
{
"$ref": "#/components/schemas/Node"
}
],
"description": "list of ids"
},
"type": "array"
},
"reference": {
"allOf": [
{
"$ref": "#/components/schemas/TypedNode"
}
],
"description": "reference individual or class (eg gene, disease)"
},
"target_ids": {
"items": {
"items": {
"allOf": [
{
"$ref": "#/components/schemas/Node"
}
],
"description": "query ids"
},
"type": "array"
},
"type": "array"
},
"unresolved_ids": {
"description": "list of unresolved ids",
"items": {
"description": "curie formatted id",
"type": "string"
},
"type": "array"
}
},
"type": "object"
},
"SimResult": {
"properties": {
"matches": {
"items": {
"allOf": [
{
"$ref": "#/components/schemas/SimMatch"
}
],
"description": "list of matches"
},
"type": "array"
},
"metadata": {
"$ref": "#/components/schemas/SimMetadata"
},
"query": {
"$ref": "#/components/schemas/SimQuery"
}
},
"type": "object"
},
"Span": {
"properties": {
"end": {
"description": "end of span text relative to content",
"type": "integer"
},
"start": {
"description": "start of span text relative to content",
"type": "integer"
},
"text": {
"description": "span text",
"type": "string"
},
"token": {
"description": "A token or entity extracted from the span text",
"items": {
"$ref": "#/components/schemas/Token"
},
"type": "array"
}
},
"type": "object"
},
"SufficiencyOutput": {
"properties": {
"categorical_score": {
"description": "categorical score",
"type": "number"
},
"scaled_score": {
"description": "scaled score",
"type": "number"
},
"simple_score": {
"description": "simple score",
"type": "number"
}
},
"type": "object"
},
"SufficiencyPostInput": {
"properties": {
"features": {
"description": "list of features",
"items": {
"$ref": "#/components/schemas/Feature"
},
"type": "array"
},
"id": {
"description": "curie formatted id",
"type": "string"
}
},
"type": "object"
},
"SynonymPropertyValue": {
"allOf": [
{
"$ref": "#/components/schemas/AbstractPropertyValue"
},
{
"properties": {},
"type": "object"
}
]
},
"Taxon": {
"properties": {
"id": {
"description": "CURIE ID, e.g. NCBITaxon:9606",
"type": "string"
},
"label": {
"description": "RDFS Label",
"type": "string"
}
},
"type": "object"
},
"Token": {
"properties": {
"categories": {
"description": "entity categories",
"items": {
"type": "string"
},
"type": "array"
},
"id": {
"description": "The CURIE for the entity or token",
"type": "string"
},
"terms": {
"description": "terms",
"items": {
"type": "string"
},
"type": "array"
}
},
"type": "object"
},
"TypedNode": {
"allOf": [
{
"$ref": "#/components/schemas/Node"
},
{
"properties": {
"taxon": {
"allOf": [
{
"$ref": "#/components/schemas/Node"
}
],
"description": "taxon"
},
"type": {
"description": "node type (eg phenotype, disease)",
"type": "string"
}
},
"type": "object"
}
]
},
"mme": {
"properties": {},
"type": "object"
},
"variant_set": {
"properties": {
"body": {
"description": "Article content",
"type": "string"
},
"category": {
"type": "string"
},
"category_id": {
"type": "integer"
},
"id": {
"description": "The unique identifier of a variant set",
"type": "integer"
},
"pub_date": {
"format": "date-time",
"type": "string"
},
"title": {
"description": "Article title",
"type": "string"
}
},
"required": [
"body",
"title"
],
"type": "object"
}
}
}
}