\n \n | version | \n table content | \n
\n \n | 1.0.0 | \n cdw, acs, nearest road, and cmaq from 2010 | \n
\n \n | 2.0.0 | \n cdw in FHIR format, acs, nearest road, and cmaq from 2010 | \n
\n \n | 3.0.0 | \n cdw in FHIR format, acs, nearest road, cmaq, and EPR from 2010 to 2016 | \n
\n
",
"termsOfService": "N/A",
"title": "ICEES API",
"version": "4.0.0",
"x-translator": {
"component": "KP",
"team": [
"Exposures Provider"
]
}
},
"paths": {
"/{table}/{year}/cohort": {
"post": {
"description": "Cohort discovery.",
"operationId": "discover_cohort__table___year__cohort_post",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "year",
"required": true,
"schema": {
"title": "Year",
"type": "integer"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"anyOf": [
{
"additionalProperties": {
"anyOf": [
{
"$ref": "#/components/schemas/Comparison"
},
{
"$ref": "#/components/schemas/Between"
},
{
"$ref": "#/components/schemas/In"
}
]
},
"type": "object"
},
{
"items": {
"$ref": "#/components/schemas/FeatureExplicit"
},
"type": "array"
}
],
"example": {},
"title": "Req Features"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Discover Cohort Table Year Cohort Post",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Discover Cohort"
}
},
"/{table}/{year}/cohort/dictionary": {
"get": {
"description": "Get cohort dictionary.",
"operationId": "dictionary__table___year__cohort_dictionary_get",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "year",
"required": true,
"schema": {
"title": "Year",
"type": "integer"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Dictionary Table Year Cohort Dictionary Get",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Dictionary"
}
},
"/{table}/{year}/cohort/{cohort_id}": {
"get": {
"description": "Get definition of a cohort.",
"operationId": "get_cohort__table___year__cohort__cohort_id__get",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "year",
"required": true,
"schema": {
"title": "Year",
"type": "integer"
}
},
{
"in": "path",
"name": "cohort_id",
"required": true,
"schema": {
"title": "Cohort Id",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Get Cohort Table Year Cohort Cohort Id Get",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get Cohort"
},
"put": {
"description": "Cohort discovery.",
"operationId": "edit_cohort__table___year__cohort__cohort_id__put",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "year",
"required": true,
"schema": {
"title": "Year",
"type": "integer"
}
},
{
"in": "path",
"name": "cohort_id",
"required": true,
"schema": {
"title": "Cohort Id",
"type": "string"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"anyOf": [
{
"additionalProperties": {
"anyOf": [
{
"$ref": "#/components/schemas/Comparison"
},
{
"$ref": "#/components/schemas/Between"
},
{
"$ref": "#/components/schemas/In"
}
]
},
"type": "object"
},
{
"items": {
"$ref": "#/components/schemas/FeatureExplicit"
},
"type": "array"
}
],
"example": {},
"title": "Req Features"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Edit Cohort Table Year Cohort Cohort Id Put",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Edit Cohort"
}
},
"/{table}/{year}/cohort/{cohort_id}/feature_association": {
"post": {
"description": "Hypothesis-driven 2 x 2 feature associations.\n\nUsers select a predefined cohort and two feature variables, and the service\nreturns a 2 x 2 feature table with a correspondingChi Square statistic and\nP value.",
"operationId": "feature_association__table___year__cohort__cohort_id__feature_association_post",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "year",
"required": true,
"schema": {
"title": "Year",
"type": "integer"
}
},
{
"in": "path",
"name": "cohort_id",
"required": true,
"schema": {
"title": "Cohort Id",
"type": "string"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/FeatureAssociation"
}
],
"example": {
"feature_a": {
"Sex": {
"operator": "=",
"value": "Female"
}
},
"feature_b": {
"AsthmaDx": {
"operator": "=",
"value": 1
}
}
},
"title": "Obj"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Feature Association Table Year Cohort Cohort Id Feature Association Post",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Feature Association"
}
},
"/{table}/{year}/cohort/{cohort_id}/feature_association2": {
"post": {
"description": "Hypothesis-driven N x N feature associations.\n\nUsers select a predefined cohort, two feature variables, and bins, which\ncan be combined, and the service returns a N x N feature table with a\ncorresponding Chi Square statistic and P value.",
"operationId": "feature_association2__table___year__cohort__cohort_id__feature_association2_post",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "year",
"required": true,
"schema": {
"title": "Year",
"type": "integer"
}
},
{
"in": "path",
"name": "cohort_id",
"required": true,
"schema": {
"title": "Cohort Id",
"type": "string"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/FeatureAssociation2"
}
],
"example": {
"feature_a": {
"Sex": [
{
"operator": "=",
"value": "Female"
},
{
"operator": "=",
"value": "Male"
}
]
},
"feature_b": {
"AsthmaDx": [
{
"operator": "=",
"value": 1
},
{
"operator": "=",
"value": 0
}
]
}
},
"title": "Obj"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Feature Association2 Table Year Cohort Cohort Id Feature Association2 Post",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Feature Association2"
}
},
"/{table}/{year}/cohort/{cohort_id}/associations_to_all_features": {
"post": {
"description": "Exploratory 1 X N feature associations.\n\nUsers select a predefined cohort and a feature variable of interest, and\nthe service returns a 1 x N feature table with corrected Chi Square\nstatistics and associated P values.",
"operationId": "associations_to_all_features__table___year__cohort__cohort_id__associations_to_all_features_post",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "year",
"required": true,
"schema": {
"title": "Year",
"type": "integer"
}
},
{
"in": "path",
"name": "cohort_id",
"required": true,
"schema": {
"title": "Cohort Id",
"type": "string"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/AllFeaturesAssociation"
}
],
"example": {
"correction": {
"method": "bonferroni"
},
"feature": {
"Sex": {
"operator": "=",
"value": "Female"
}
},
"maximum_p_value": 1
},
"title": "Obj"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Associations To All Features Table Year Cohort Cohort Id Associations To All Features Post",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Associations To All Features"
}
},
"/{table}/{year}/cohort/{cohort_id}/associations_to_all_features2": {
"post": {
"description": "Exploratory 1 X N feature associations.\n\nUsers select a predefined cohort and a feature variable of interest and\nbins, which can be combined, and the service returns a 1 x N feature table\nwith corrected Chi Square statistics and associated P values.",
"operationId": "associations_to_all_features2__table___year__cohort__cohort_id__associations_to_all_features2_post",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "year",
"required": true,
"schema": {
"title": "Year",
"type": "integer"
}
},
{
"in": "path",
"name": "cohort_id",
"required": true,
"schema": {
"title": "Cohort Id",
"type": "string"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/AllFeaturesAssociation2"
}
],
"example": {
"correction": {
"method": "bonferroni"
},
"feature": {
"Sex": [
{
"operator": "=",
"value": "Female"
},
{
"operator": "=",
"value": "Male"
}
]
},
"maximum_p_value": 1
},
"title": "Obj"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Associations To All Features2 Table Year Cohort Cohort Id Associations To All Features2 Post",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Associations To All Features2"
}
},
"/{table}/{year}/cohort/{cohort_id}/features": {
"get": {
"description": "Feature-rich cohort discovery.\n\nUsers select a predefined cohort as the input parameter, and the service\nreturns a profile of that cohort in terms of all feature variables.",
"operationId": "features__table___year__cohort__cohort_id__features_get",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "year",
"required": true,
"schema": {
"title": "Year",
"type": "integer"
}
},
{
"in": "path",
"name": "cohort_id",
"required": true,
"schema": {
"title": "Cohort Id",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Features Table Year Cohort Cohort Id Features Get",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Features"
}
},
"/{table}/{feature}/identifiers": {
"get": {
"description": "Feature identifiers.",
"operationId": "identifiers__table___feature__identifiers_get",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "feature",
"required": true,
"schema": {
"title": "Feature",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Identifiers Table Feature Identifiers Get",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Identifiers"
}
},
"/{table}/name/{name}": {
"get": {
"description": "Return cohort id associated with name.",
"operationId": "get_name__table__name__name__get",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "name",
"required": true,
"schema": {
"title": "Name",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Get Name Table Name Name Get",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get Name"
},
"post": {
"description": "Associate name with cohort id.",
"operationId": "post_name__table__name__name__post",
"parameters": [
{
"in": "path",
"name": "table",
"required": true,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "path",
"name": "name",
"required": true,
"schema": {
"title": "Name",
"type": "string"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/AddNameById"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Post Name Table Name Name Post",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Post Name"
}
},
"/knowledge_graph": {
"post": {
"description": "Query for knowledge graph associations between concepts.",
"operationId": "knowledge_graph_knowledge_graph_post",
"parameters": [
{
"in": "query",
"name": "reasoner",
"required": false,
"schema": {
"default": false,
"title": "Reasoner",
"type": "boolean"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {
"e00": {
"object": "n01",
"predicate": "biolink:correlated_with",
"subject": "n00"
}
},
"nodes": {
"n00": {
"category": "biolink:PopulationOfIndividualOrganisms"
},
"n01": {
"category": "biolink:ChemicalSubstance"
}
}
}
},
"query_options": {
"cohort_features": {
"AgeStudyStart": {
"operator": "=",
"value": "0-2"
}
},
"feature": {
"EstResidentialDensity": {
"operator": "<",
"value": 1
}
},
"maximum_p_value": 1,
"table": "patient",
"year": 2010
}
},
"title": "Obj"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Knowledge Graph Knowledge Graph Post",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Knowledge Graph"
}
},
"/knowledge_graph/schema": {
"get": {
"description": "Query the ICEES clinical reasoner for knowledge graph schema.",
"operationId": "knowledge_graph_schema_knowledge_graph_schema_get",
"parameters": [
{
"in": "query",
"name": "reasoner",
"required": false,
"schema": {
"default": false,
"title": "Reasoner",
"type": "boolean"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Knowledge Graph Schema Knowledge Graph Schema Get",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Knowledge Graph Schema"
}
},
"/predicates": {
"get": {
"description": "Get meta-knowledge graph.",
"operationId": "predicates_predicates_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {}
},
"text/tabular": {}
},
"description": "Return the tabular output."
}
},
"summary": "Predicates",
"tags": [
"reasoner"
]
}
},
"/knowledge_graph_overlay": {
"post": {
"description": "Query for knowledge graph co-occurrence overlay.",
"operationId": "knowledge_graph_overlay_knowledge_graph_overlay_post",
"parameters": [
{
"in": "query",
"name": "reasoner",
"required": false,
"schema": {
"default": false,
"title": "Reasoner",
"type": "boolean"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"knowledge_graph": {
"edges": {
"e00": {
"object": "PUBCHEM:281",
"predicate": "biolink:correlated_with",
"subject": "PUBCHEM:2083"
}
},
"nodes": {
"PUBCHEM:2083": {
"category": "biolink:Drug"
},
"PUBCHEM:281": {
"category": "biolink:ChemicalSubstance"
}
}
}
}
},
"title": "Obj"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Knowledge Graph Overlay Knowledge Graph Overlay Post",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Knowledge Graph Overlay"
}
},
"/knowledge_graph_one_hop": {
"post": {
"deprecated": true,
"description": "Query the ICEES clinical reasoner for knowledge graph one hop.",
"operationId": "knowledge_graph_one_hop_knowledge_graph_one_hop_post",
"parameters": [
{
"in": "query",
"name": "reasoner",
"required": false,
"schema": {
"default": true,
"title": "Reasoner",
"type": "boolean"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"knowledge_graph": {
"edges": {},
"nodes": {}
},
"query_graph": {
"edges": {
"e00": {
"object": "n01",
"predicate": "biolink:correlated_with",
"subject": "n00"
}
},
"nodes": {
"n00": {
"category": "biolink:Drug",
"id": "PUBCHEM:2083"
},
"n01": {
"category": "biolink:ChemicalSubstance"
}
}
},
"results": []
}
},
"title": "Obj"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Knowledge Graph One Hop Knowledge Graph One Hop Post",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Knowledge Graph One Hop"
}
},
"/query": {
"post": {
"description": "Query the ICEES clinical reasoner for knowledge graph one hop.",
"operationId": "knowledge_graph_one_hop_query_post",
"parameters": [
{
"in": "query",
"name": "reasoner",
"required": false,
"schema": {
"default": true,
"title": "Reasoner",
"type": "boolean"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"knowledge_graph": {
"edges": {},
"nodes": {}
},
"query_graph": {
"edges": {
"e00": {
"object": "n01",
"predicate": "biolink:correlated_with",
"subject": "n00"
}
},
"nodes": {
"n00": {
"category": "biolink:Drug",
"id": "PUBCHEM:2083"
},
"n01": {
"category": "biolink:ChemicalSubstance"
}
}
},
"results": []
}
},
"title": "Obj"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Knowledge Graph One Hop Query Post",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Knowledge Graph One Hop",
"tags": [
"reasoner"
]
}
},
"/bins": {
"get": {
"description": "Return bin values.",
"operationId": "handle_bins_bins_get",
"parameters": [
{
"in": "query",
"name": "year",
"required": false,
"schema": {
"title": "Year",
"type": "string"
}
},
{
"in": "query",
"name": "table",
"required": false,
"schema": {
"title": "Table",
"type": "string"
}
},
{
"in": "query",
"name": "feature",
"required": false,
"schema": {
"title": "Feature",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Handle Bins Bins Get",
"type": "object"
}
},
"text/tabular": {}
},
"description": "Return the tabular output."
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Handle Bins"
}
}
},
"servers": [
{
"url": "https://icees.renci.org:16340"
}
],
"tags": [
{
"name": "translator"
},
{
"name": "reasoner"
}
]
},
{
"_id": "132da307d445fac70a403a5e623107d5",
"_meta": {
"date_created": "2021-02-04T00:00:37.939131+00:00",
"last_updated": "2021-03-29T07:03:26.875445+00:00",
"url": "https://automat.renci.org/hetio/openapi.json",
"username": "YaphetKG"
},
"_score": 0.6863549,
"info": {
"contact": {
"email": "kebedey@renci.org",
"name": "Yaphet Kebede",
"x-id": "https://github.com/yaphetkg",
"x-role": "contributor"
},
"description": "A graph based on [hetionet (het.io)](het.io).",
"termsOfService": "http://linkmissing",
"title": "Automat Hetio",
"version": "1.0.0",
"x-translator": {
"component": "KP",
"team": [
"Ranking Agent"
]
}
},
"paths": {
"/query": {
"post": {
"description": "Given a question graph return question graph plus answers.",
"operationId": "reasoner_api_query_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Query Reasoner API",
"tags": [
"translator"
]
}
},
"/reasonerapi": {
"get": {
"description": "Returns a list of question templates that can be used to query this plater instance.",
"operationId": "get_reasoner_api_reasonerapi_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Message"
},
"title": "Response Get Reasoner Api Reasonerapi Get",
"type": "array"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get question templates"
},
"post": {
"deprecated": true,
"description": "Handle TRAPI request.",
"operationId": "reasoner_api_reasonerapi_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Reasoner Api"
}
},
"/cypher": {
"post": {
"description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).",
"operationId": "cypher_cypher_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/CypherRequest"
}
],
"example": {
"query": "MATCH (n) RETURN count(n)"
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/CypherResponse"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Run cypher query"
}
},
"/predicates": {
"get": {
"description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.",
"operationId": "predicates_predicates_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"items": {
"type": "string"
},
"type": "array"
},
"type": "object"
},
"title": "Response Predicates Predicates Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types",
"tags": [
"translator"
]
}
},
"/graph/schema": {
"get": {
"deprecated": true,
"description": "Get one-hop connection types",
"operationId": "predicates_graph_schema_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Predicates Graph Schema Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types"
}
},
"/simple_spec": {
"get": {
"description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.",
"operationId": "simple_spec_simple_spec_get",
"parameters": [
{
"in": "query",
"name": "source",
"required": false,
"schema": {
"title": "Source",
"type": "string"
}
},
{
"in": "query",
"name": "target",
"required": false,
"schema": {
"title": "Target",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/SimpleSpecElement"
},
"title": "Response Simple Spec Simple Spec Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one-hop connection schema"
}
},
"/graph/summary": {
"get": {
"description": "Returns a summary of the graph.",
"operationId": "graph_summary_graph_summary_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Graph Summary Graph Summary Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get graph summary"
}
},
"/overlay": {
"post": {
"description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.",
"operationId": "overlay_overlay_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"knowledge_graph": {
"edges": {
"9f7f9d86cb57e7190aafa57f7564eb05": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1610437123.7988985,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_family_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "PANTHER.FAMILY:PTHR12015:SF170",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "PANTHER.FAMILY:PTHR12015:SF170"
},
"dd8ef7a4606c4f8e405e6a5b1b095993": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1584932086.0009434,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "NCBIGene:6352",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "NCBIGene:6352"
}
},
"nodes": {
"NCBIGene:6352": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Gene"
],
"chromosome": "17",
"equivalent_identifiers": [
"ENSEMBL:ENSG00000271503",
"NCBIGene:6352",
"NCBIGene:6352",
"HGNC:10632",
"UniProtKB:P13501"
],
"gene_family": [
"Chemokine ligands"
],
"gene_family_id": [
483
],
"location": "17q12",
"locus_group": "protein-coding gene",
"synonyms": [],
"taxon": 9606
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:MolecularEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:Gene"
],
"name": "CCL5"
},
"PANTHER.FAMILY:PTHR12015": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "SMALL INDUCIBLE CYTOKINE A"
},
"PANTHER.FAMILY:PTHR12015:SF170": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015:SF170"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "C-C MOTIF CHEMOKINE 5"
}
}
},
"query_graph": {
"edges": {
"e12": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n1"
},
"e23": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n3"
}
},
"nodes": {
"n1": {
"category": "biolink:Gene",
"id": "NCBIGene:6352",
"is_set": false
},
"n2": {
"category": "biolink:GeneFamily",
"is_set": false
},
"n3": {
"category": "biolink:GeneFamily",
"is_set": false
}
}
},
"results": [
{
"edge_bindings": {
"e12": [
{
"id": "dd8ef7a4606c4f8e405e6a5b1b095993"
}
],
"e23": [
{
"id": "9f7f9d86cb57e7190aafa57f7564eb05"
}
]
},
"node_bindings": {
"n1": [
{
"id": "NCBIGene:6352"
}
],
"n2": [
{
"id": "PANTHER.FAMILY:PTHR12015"
}
],
"n3": [
{
"id": "PANTHER.FAMILY:PTHR12015:SF170"
}
]
}
}
]
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Message"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Overlay results with available connections between each node.",
"tags": [
"translator"
]
}
},
"/about": {
"get": {
"description": "Returns a JSON describing dataset.",
"operationId": "about_about_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response About About Get"
}
}
},
"description": "Successful Response"
}
},
"summary": "JSON about dataset"
}
},
"/{source_type}/{target_type}/{curie}": {
"get": {
"description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.",
"operationId": "one_hop__source_type___target_type___curie__get",
"parameters": [
{
"in": "path",
"name": "source_type",
"required": true,
"schema": {
"title": "Source Type",
"type": "string"
}
},
{
"in": "path",
"name": "target_type",
"required": true,
"schema": {
"title": "Target Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response One Hop Source Type Target Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source"
}
},
"/{node_type}/{curie}": {
"get": {
"description": "Returns `node` matching `curie`.",
"operationId": "node__node_type___curie__get",
"parameters": [
{
"in": "path",
"name": "node_type",
"required": true,
"schema": {
"title": "Node Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response Node Node Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Find `node` by `curie`"
}
}
},
"servers": [
{
"description": "Default server",
"url": "https://automat.renci.org/hetio"
}
],
"tags": [
{
"name": "translator"
},
{
"name": "automat"
}
]
},
{
"_id": "a3cfb0c18f630ce73ccf86b1db5117db",
"_meta": {
"date_created": "2021-02-03T00:00:38.618714+00:00",
"last_updated": "2021-03-29T07:04:10.254897+00:00",
"url": "https://automat.renci.org/panther/openapi.json",
"username": "YaphetKG"
},
"_score": 0.6863549,
"info": {
"contact": {
"email": "kebedey@renci.org",
"name": "Yaphet Kebede",
"x-id": "https://github.com/yaphetkg",
"x-role": "contributor"
},
"description": " A graph of gene families and pathways from [Panther (pantherdb.org)](pantherdb.org)",
"termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Panther&provider_long=RENCI",
"title": "Automat Panther",
"version": "1.0.0",
"x-translator": {
"component": "KP",
"team": [
"Ranking Agent"
]
}
},
"paths": {
"/query": {
"post": {
"description": "Given a question graph return question graph plus answers.",
"operationId": "reasoner_api_query_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Query Reasoner API",
"tags": [
"translator"
]
}
},
"/reasonerapi": {
"get": {
"description": "Returns a list of question templates that can be used to query this plater instance.",
"operationId": "get_reasoner_api_reasonerapi_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Message"
},
"title": "Response Get Reasoner Api Reasonerapi Get",
"type": "array"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get question templates"
},
"post": {
"deprecated": true,
"description": "Handle TRAPI request.",
"operationId": "reasoner_api_reasonerapi_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Reasoner Api"
}
},
"/cypher": {
"post": {
"description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).",
"operationId": "cypher_cypher_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/CypherRequest"
}
],
"example": {
"query": "MATCH (n) RETURN count(n)"
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/CypherResponse"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Run cypher query"
}
},
"/predicates": {
"get": {
"description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.",
"operationId": "predicates_predicates_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"items": {
"type": "string"
},
"type": "array"
},
"type": "object"
},
"title": "Response Predicates Predicates Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types",
"tags": [
"translator"
]
}
},
"/graph/schema": {
"get": {
"deprecated": true,
"description": "Get one-hop connection types",
"operationId": "predicates_graph_schema_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Predicates Graph Schema Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types"
}
},
"/simple_spec": {
"get": {
"description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.",
"operationId": "simple_spec_simple_spec_get",
"parameters": [
{
"in": "query",
"name": "source",
"required": false,
"schema": {
"title": "Source",
"type": "string"
}
},
{
"in": "query",
"name": "target",
"required": false,
"schema": {
"title": "Target",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/SimpleSpecElement"
},
"title": "Response Simple Spec Simple Spec Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one-hop connection schema"
}
},
"/graph/summary": {
"get": {
"description": "Returns a summary of the graph.",
"operationId": "graph_summary_graph_summary_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Graph Summary Graph Summary Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get graph summary"
}
},
"/overlay": {
"post": {
"description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.",
"operationId": "overlay_overlay_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"knowledge_graph": {
"edges": {
"9f7f9d86cb57e7190aafa57f7564eb05": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1610437123.7988985,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_family_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "PANTHER.FAMILY:PTHR12015:SF170",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "PANTHER.FAMILY:PTHR12015:SF170"
},
"dd8ef7a4606c4f8e405e6a5b1b095993": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1584932086.0009434,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "NCBIGene:6352",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "NCBIGene:6352"
}
},
"nodes": {
"NCBIGene:6352": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Gene"
],
"chromosome": "17",
"equivalent_identifiers": [
"ENSEMBL:ENSG00000271503",
"NCBIGene:6352",
"NCBIGene:6352",
"HGNC:10632",
"UniProtKB:P13501"
],
"gene_family": [
"Chemokine ligands"
],
"gene_family_id": [
483
],
"location": "17q12",
"locus_group": "protein-coding gene",
"synonyms": [],
"taxon": 9606
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:MolecularEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:Gene"
],
"name": "CCL5"
},
"PANTHER.FAMILY:PTHR12015": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "SMALL INDUCIBLE CYTOKINE A"
},
"PANTHER.FAMILY:PTHR12015:SF170": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015:SF170"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "C-C MOTIF CHEMOKINE 5"
}
}
},
"query_graph": {
"edges": {
"e12": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n1"
},
"e23": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n3"
}
},
"nodes": {
"n1": {
"category": "biolink:Gene",
"id": "NCBIGene:6352",
"is_set": false
},
"n2": {
"category": "biolink:GeneFamily",
"is_set": false
},
"n3": {
"category": "biolink:GeneFamily",
"is_set": false
}
}
},
"results": [
{
"edge_bindings": {
"e12": [
{
"id": "dd8ef7a4606c4f8e405e6a5b1b095993"
}
],
"e23": [
{
"id": "9f7f9d86cb57e7190aafa57f7564eb05"
}
]
},
"node_bindings": {
"n1": [
{
"id": "NCBIGene:6352"
}
],
"n2": [
{
"id": "PANTHER.FAMILY:PTHR12015"
}
],
"n3": [
{
"id": "PANTHER.FAMILY:PTHR12015:SF170"
}
]
}
}
]
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Message"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Overlay results with available connections between each node.",
"tags": [
"translator"
]
}
},
"/about": {
"get": {
"description": "Returns a JSON describing dataset.",
"operationId": "about_about_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response About About Get"
}
}
},
"description": "Successful Response"
}
},
"summary": "JSON about dataset"
}
},
"/{source_type}/{target_type}/{curie}": {
"get": {
"description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.",
"operationId": "one_hop__source_type___target_type___curie__get",
"parameters": [
{
"in": "path",
"name": "source_type",
"required": true,
"schema": {
"title": "Source Type",
"type": "string"
}
},
{
"in": "path",
"name": "target_type",
"required": true,
"schema": {
"title": "Target Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response One Hop Source Type Target Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source"
}
},
"/{node_type}/{curie}": {
"get": {
"description": "Returns `node` matching `curie`.",
"operationId": "node__node_type___curie__get",
"parameters": [
{
"in": "path",
"name": "node_type",
"required": true,
"schema": {
"title": "Node Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response Node Node Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Find `node` by `curie`"
}
}
},
"servers": [
{
"description": "Default server",
"url": "https://automat.renci.org/panther"
}
],
"tags": [
{
"name": "translator"
},
{
"name": "automat"
}
]
},
{
"_id": "7c481f0761132876e6b953547623f594",
"_meta": {
"date_created": "2021-01-26T00:03:04.513280+00:00",
"last_updated": "2021-03-29T07:04:04.240631+00:00",
"url": "https://automat.renci.org/pharos/openapi.json",
"username": "YaphetKG"
},
"_score": 0.6863549,
"info": {
"contact": {
"email": "kebedey@renci.org",
"name": "Yaphet Kebede",
"x-id": "https://github.com/yaphetkg",
"x-role": "contributor"
},
"description": "A graph based on [Pharos (pharos.nih.gov)](pharos.nih.gov).",
"termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Pharos&provider_long=RENCI",
"title": "Automat Pharos",
"version": "1.0.0",
"x-translator": {
"component": "KP",
"team": [
"Ranking Agent"
]
}
},
"paths": {
"/query": {
"post": {
"description": "Given a question graph return question graph plus answers.",
"operationId": "reasoner_api_query_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Query Reasoner API",
"tags": [
"translator"
]
}
},
"/reasonerapi": {
"get": {
"description": "Returns a list of question templates that can be used to query this plater instance.",
"operationId": "get_reasoner_api_reasonerapi_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Message"
},
"title": "Response Get Reasoner Api Reasonerapi Get",
"type": "array"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get question templates"
},
"post": {
"deprecated": true,
"description": "Handle TRAPI request.",
"operationId": "reasoner_api_reasonerapi_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Reasoner Api"
}
},
"/cypher": {
"post": {
"description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).",
"operationId": "cypher_cypher_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/CypherRequest"
}
],
"example": {
"query": "MATCH (n) RETURN count(n)"
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/CypherResponse"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Run cypher query"
}
},
"/predicates": {
"get": {
"description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.",
"operationId": "predicates_predicates_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"items": {
"type": "string"
},
"type": "array"
},
"type": "object"
},
"title": "Response Predicates Predicates Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types",
"tags": [
"translator"
]
}
},
"/graph/schema": {
"get": {
"deprecated": true,
"description": "Get one-hop connection types",
"operationId": "predicates_graph_schema_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Predicates Graph Schema Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types"
}
},
"/simple_spec": {
"get": {
"description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.",
"operationId": "simple_spec_simple_spec_get",
"parameters": [
{
"in": "query",
"name": "source",
"required": false,
"schema": {
"title": "Source",
"type": "string"
}
},
{
"in": "query",
"name": "target",
"required": false,
"schema": {
"title": "Target",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/SimpleSpecElement"
},
"title": "Response Simple Spec Simple Spec Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one-hop connection schema"
}
},
"/graph/summary": {
"get": {
"description": "Returns a summary of the graph.",
"operationId": "graph_summary_graph_summary_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Graph Summary Graph Summary Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get graph summary"
}
},
"/overlay": {
"post": {
"description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.",
"operationId": "overlay_overlay_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"knowledge_graph": {
"edges": {
"9f7f9d86cb57e7190aafa57f7564eb05": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1610437123.7988985,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_family_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "PANTHER.FAMILY:PTHR12015:SF170",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "PANTHER.FAMILY:PTHR12015:SF170"
},
"dd8ef7a4606c4f8e405e6a5b1b095993": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1584932086.0009434,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "NCBIGene:6352",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "NCBIGene:6352"
}
},
"nodes": {
"NCBIGene:6352": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Gene"
],
"chromosome": "17",
"equivalent_identifiers": [
"ENSEMBL:ENSG00000271503",
"NCBIGene:6352",
"NCBIGene:6352",
"HGNC:10632",
"UniProtKB:P13501"
],
"gene_family": [
"Chemokine ligands"
],
"gene_family_id": [
483
],
"location": "17q12",
"locus_group": "protein-coding gene",
"synonyms": [],
"taxon": 9606
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:MolecularEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:Gene"
],
"name": "CCL5"
},
"PANTHER.FAMILY:PTHR12015": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "SMALL INDUCIBLE CYTOKINE A"
},
"PANTHER.FAMILY:PTHR12015:SF170": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015:SF170"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "C-C MOTIF CHEMOKINE 5"
}
}
},
"query_graph": {
"edges": {
"e12": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n1"
},
"e23": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n3"
}
},
"nodes": {
"n1": {
"category": "biolink:Gene",
"id": "NCBIGene:6352",
"is_set": false
},
"n2": {
"category": "biolink:GeneFamily",
"is_set": false
},
"n3": {
"category": "biolink:GeneFamily",
"is_set": false
}
}
},
"results": [
{
"edge_bindings": {
"e12": [
{
"id": "dd8ef7a4606c4f8e405e6a5b1b095993"
}
],
"e23": [
{
"id": "9f7f9d86cb57e7190aafa57f7564eb05"
}
]
},
"node_bindings": {
"n1": [
{
"id": "NCBIGene:6352"
}
],
"n2": [
{
"id": "PANTHER.FAMILY:PTHR12015"
}
],
"n3": [
{
"id": "PANTHER.FAMILY:PTHR12015:SF170"
}
]
}
}
]
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Message"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Overlay results with available connections between each node.",
"tags": [
"translator"
]
}
},
"/about": {
"get": {
"description": "Returns a JSON describing dataset.",
"operationId": "about_about_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response About About Get"
}
}
},
"description": "Successful Response"
}
},
"summary": "JSON about dataset"
}
},
"/{source_type}/{target_type}/{curie}": {
"get": {
"description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.",
"operationId": "one_hop__source_type___target_type___curie__get",
"parameters": [
{
"in": "path",
"name": "source_type",
"required": true,
"schema": {
"title": "Source Type",
"type": "string"
}
},
{
"in": "path",
"name": "target_type",
"required": true,
"schema": {
"title": "Target Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response One Hop Source Type Target Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source"
}
},
"/{node_type}/{curie}": {
"get": {
"description": "Returns `node` matching `curie`.",
"operationId": "node__node_type___curie__get",
"parameters": [
{
"in": "path",
"name": "node_type",
"required": true,
"schema": {
"title": "Node Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response Node Node Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Find `node` by `curie`"
}
}
},
"servers": [
{
"description": "Default server",
"url": "https://automat.renci.org/pharos"
}
],
"tags": [
{
"name": "translator"
},
{
"name": "automat"
}
]
},
{
"_id": "e9f69b81e755e163fdf6c41a2b5e07c0",
"_meta": {
"date_created": "2021-01-29T00:00:15.735608+00:00",
"last_updated": "2021-03-29T07:04:11.343019+00:00",
"url": "https://openpredict.semanticscience.org/openapi.json",
"username": "vemonet"
},
"_score": 0.6863549,
"info": {
"contact": {
"email": "vincent.emonet@maastrichtuniversity.nl",
"name": "Institute of Data Science at Maastricht University",
"url": "https://maastrichtuniversity.nl/ids"
},
"description": "Get predicted targets for a given entity: the **potential drugs treating a given disease**, or the **potential diseases a given drug could treat**. \n\n* Use the `/predict` operation to easily retrieve predictions for a given entity (operation annotated for the [BioThings Explorer](https://x-bte-extension.readthedocs.io/en/latest/x-bte-kgs-operations.html)). \n\n* Predictions are currently produced using the [PREDICT method](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159979/) from the [fair-workflows/openpredict](https://github.com/fair-workflows/openpredict) project. \n\n* You can also install the [OpenPredict Python package](https://pypi.org/project/openpredict/) to train and serve a new model yourself. \n\n* More documentation available at [github.com/MaastrichtU-IDS/translator-openpredict](https://github.com/MaastrichtU-IDS/translator-openpredict) \n\n[](https://pypi.org/project/openpredict) [](https://github.com/MaastrichtU-IDS/translator-openpredict/actions?query=workflow%3A%22Run+tests%22) \n\nService supported by the [NCATS Translator project](https://ncats.nih.gov/translator/about)",
"license": {
"name": "MIT License",
"url": "https://opensource.org/licenses/MIT"
},
"termsOfService": "",
"title": "OpenPredict API",
"version": "1.0.0",
"x-translator": {
"component": "KP",
"team": [
"Clinical Data Provider"
]
},
"x-trapi": {
"version": "1.0.0"
}
},
"paths": {
"/embedding": {
"post": {
"description": "Upload your embedding file: select which types do you have in the embeddings, Drugs, Diseases or Both. \n1. provided embeddings will be added to the model\n2. the model will be retrained\n3. the model evaluation will be stored in a triplestore",
"operationId": "openpredict.openpredict_api.post_embedding",
"parameters": [
{
"description": "Types of the entities in the embedding",
"in": "query",
"name": "types",
"required": true,
"schema": {
"default": "Both",
"enum": [
"Drugs",
"Diseases",
"Both"
],
"type": "string"
}
},
{
"description": "Name of embedding (eg. TransE_DrugBank_Drug)",
"in": "query",
"name": "emb_name",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Describe how the embeddings was obtained (eg. rdf2vec on drugbank/omim data)",
"in": "query",
"name": "description",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Provide the ID of the run output you want to use as base model to add the embeddings",
"example": "openpredict-baseline-omim-drugbank",
"in": "query",
"name": "model_id",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"content": {
"multipart/form-data": {
"schema": {
"properties": {
"embedding_file": {
"description": "The embedding file to be uploaded",
"format": "binary",
"type": "string"
}
},
"type": "object"
}
}
}
},
"responses": {
"200": {
"description": "OK"
}
},
"summary": "Upload your embedding for drugs or diseases",
"tags": [
"openpredict"
]
}
},
"/features": {
"get": {
"description": "Return the features trained in the model, for Drugs, Diseases or Both ",
"operationId": "openpredict.openpredict_api.get_features",
"parameters": [
{
"description": "Type of the entities in the features",
"in": "query",
"name": "type",
"required": true,
"schema": {
"default": "All",
"enum": [
"All",
"Drugs",
"Diseases",
"Both"
],
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {}
},
"description": "OK"
}
},
"summary": "Return the features trained in the models",
"tags": [
"openpredict"
]
}
},
"/models": {
"get": {
"description": "Return the models with their training features and scores",
"operationId": "openpredict.openpredict_api.get_models",
"responses": {
"200": {
"content": {
"application/json": {}
},
"description": "OK"
}
},
"summary": "Return the models with their training features and scores",
"tags": [
"openpredict"
]
}
},
"/predicates": {
"get": {
"operationId": "openpredict.openpredict_api.get_predicates",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"description": "Array of predicates",
"items": {
"type": "string"
},
"type": "array"
},
"description": "Target map",
"type": "object"
},
"description": "Source map",
"example": {
"biolink:ChemicalSubstance": {
"biolink:Gene": [
"biolink:directly_interacts_with",
"biolink:decreases_activity_of"
]
}
},
"type": "object"
}
}
},
"description": "Predicates by source and target"
}
},
"summary": "Get supported relationships by source and target",
"tags": [
"translator"
]
}
},
"/predict": {
"get": {
"description": "Return the predicted targets for a given entity: drug (DrugBank ID) or disease (OMIM ID), with confidence scores. Only a drug_id or a disease_id can be provided, the disease_id will be ignored if drug_id is provided This operation is annotated with x-bte-kgs-operations, and follow the BioThings API recommendations.",
"operationId": "openpredict.openpredict_api.get_predict",
"parameters": [
{
"description": "CURIE of the drug to get prediction of diseases it could treat (e.g. DRUGBANK:DB00394)",
"example": "DRUGBANK:DB00394",
"in": "query",
"name": "drug_id",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "CURIE of the disease to get prediction of drugs it could be treated with (e.g. OMIM:246300). Ignored if drug_id provided.",
"in": "query",
"name": "disease_id",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Provide the ID of the run output you want to use as model to use to predict associations",
"example": "openpredict-baseline-omim-drugbank",
"in": "query",
"name": "model_id",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Minimum score of predictions to return (0 to 1)",
"in": "query",
"name": "min_score",
"required": false,
"schema": {
"format": "double",
"maximum": 1,
"minimum": 0,
"type": "number"
}
},
{
"description": "Maximum score of predictions to return (0 to 1)",
"in": "query",
"name": "max_score",
"required": false,
"schema": {
"format": "double",
"maximum": 1,
"minimum": 0,
"type": "number"
}
},
{
"description": "Maximum number of results to return, ordered from best score (e.g. 42)",
"in": "query",
"name": "n_results",
"required": false,
"schema": {
"format": "int32",
"minimum": 0,
"type": "integer"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {}
},
"description": "Successful Operation"
}
},
"summary": "Get predicted targets for a given entity",
"tags": [
"biothings"
],
"x-bte-kgs-operations": [
{
"inputs": [
{
"id": "biolink:DRUGBANK",
"semantic": "biolink:ChemicalSubstance"
}
],
"outputs": [
{
"id": "biolink:OMIM",
"semantic": "biolink:Disease"
}
],
"parameters": {
"drug_id": "{inputs[0]}"
},
"predicate": "biolink:treats",
"responseMapping": {
"OMIM": "hits.id"
},
"supportBatch": false
},
{
"inputs": [
{
"id": "biolink:OMIM",
"semantic": "biolink:Disease"
}
],
"outputs": [
{
"id": "biolink:DRUGBANK",
"semantic": "biolink:ChemicalSubstance"
}
],
"parameters": {
"disease_id": "{inputs[0]}"
},
"predicate": "biolink:treated_by",
"responseMapping": {
"DRUGBANK": "hits.id"
},
"supportBatch": false
}
]
}
},
"/query": {
"post": {
"description": "Send a [ReasonerAPI](https://github.com/NCATSTranslator/ReasonerAPI) query to request the predicted targets given: a source node, and the relation to predict. Use classes and relations from the [BioLink model](https://biolink.github.io/biolink-model)",
"operationId": "openpredict.openpredict_api.post_reasoner_predict",
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Query information to be submitted",
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
}
},
"description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."
},
"400": {
"content": {
"application/json": {
"schema": {
"type": "string"
}
}
},
"description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."
},
"500": {
"content": {
"application/json": {
"schema": {
"type": "string"
}
}
},
"description": "Internal server error."
},
"501": {
"content": {
"application/json": {
"schema": {
"type": "string"
}
}
},
"description": "Not implemented."
}
},
"summary": "Query reasoner via one of several inputs",
"tags": [
"trapi"
],
"x-swagger-router-controller": "swagger_server.controllers.query_controller"
}
}
},
"servers": [
{
"url": "https://openpredict.semanticscience.org"
}
],
"tags": [
{
"description": "Get relationships supported by this API",
"name": "translator"
},
{
"description": "Query the models using the Reasoner API",
"name": "trapi"
}
]
},
{
"_id": "89054eff6ee6d91641d278d9ffdb3993",
"_meta": {
"date_created": "2021-01-20T00:00:12.144499+00:00",
"last_updated": "2021-03-29T07:04:12.761521+00:00",
"url": "https://api.collaboratory.semanticscience.org/openapi.json",
"username": "vemonet"
},
"_score": 0.6863549,
"info": {
"contact": {
"email": "vincent.emonet@maastrichtuniversity.nl"
},
"description": "Translator Reasoner API for the Knowledge Collaboratory, hosted on the [Nanopublications network](http://nanopub.org/wordpress/), for annotated drug indications or any other BioLink-compliant claims. \n\n This Open API supports [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI) version `1.0.0` queries and the [`KGX`](https://github.com/biolink/kgx) format \n\nSee the API GitHub repository: [github.com/MaastrichtU-IDS/knowledge-collaboratory-api](https://github.com/MaastrichtU-IDS/knowledge-collaboratory-api) \n\nThis service is supported by the [NCATS Translator project](https://ncats.nih.gov/translator/about)",
"license": {
"name": "MIT license",
"url": "https://opensource.org/licenses/MIT"
},
"termsOfService": "https://github.com/MaastrichtU-IDS/knowledge-collaboratory-api/blob/master/LICENSE",
"title": "Translator Knowledge Collaboratory API",
"version": "1.0.0",
"x-translator": {
"component": "KP",
"team": [
"Clinical Data Provider"
]
},
"x-trapi": {
"version": "1.0.0"
}
},
"paths": {
"/kgx": {
"get": {
"operationId": "api.get_kgx",
"responses": {
"200": {
"content": {
"application/zip": {
"schema": {
"format": "binary",
"type": "string"
}
}
},
"description": "Zip file with nodes and edges files in KGX TSV format"
}
},
"summary": "Get the Knowledge Collaboratory drug indications in KGX TSV format (TSV files in a .zip)",
"tags": [
"translator"
]
}
},
"/predicates": {
"get": {
"operationId": "api.get_predicates",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"description": "Array of predicates",
"items": {
"type": "string"
},
"type": "array"
},
"description": "Target map",
"type": "object"
},
"description": "Source map",
"example": {
"biolink:ChemicalSubstance": {
"biolink:Gene": [
"biolink:directly_interacts_with",
"biolink:decreases_activity_of"
]
}
},
"type": "object"
}
}
},
"description": "Predicates by source and target"
}
},
"summary": "Get supported relationships by source and target",
"tags": [
"translator"
]
}
},
"/query": {
"post": {
"description": "Send a [ReasonerAPI](https://github.com/NCATSTranslator/ReasonerAPI) query to request the predicted targets given: a source node, and the relation to predict. Use classes and relations from the [BioLink model](https://biolink.github.io/biolink-model)",
"operationId": "api.post_reasoner_query",
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Query information to be submitted",
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
}
},
"description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."
},
"400": {
"content": {
"application/json": {
"schema": {
"type": "string"
}
}
},
"description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."
},
"500": {
"content": {
"application/json": {
"schema": {
"type": "string"
}
}
},
"description": "Internal server error."
},
"501": {
"content": {
"application/json": {
"schema": {
"type": "string"
}
}
},
"description": "Not implemented."
}
},
"summary": "Query reasoner via one of several inputs",
"tags": [
"trapi"
],
"x-swagger-router-controller": "swagger_server.controllers.query_controller"
}
}
},
"servers": [
{
"url": "https://api.collaboratory.semanticscience.org"
}
],
"tags": [
{
"description": "Query reasoner using a predefined question type",
"name": "trapi"
},
{
"name": "translator"
}
]
},
{
"_id": "dca415f2d792976af9d642b7e73f7a41",
"_meta": {
"date_created": "2020-12-07T23:08:24.199007+00:00",
"last_updated": "2021-03-29T07:03:32.230606+00:00",
"url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/litvar/smartapi.yaml",
"username": "kevinxin90"
},
"_score": 0.6863549,
"components": {
"x-bte-kgs-operations": {
"variant_located_in_gene": [
{
"inputs": [
{
"id": "DBSNP",
"semantic": "SequenceVariant"
}
],
"outputs": [
{
"id": "SYMBOL",
"semantic": "Gene"
}
],
"parameters": {
"variantid": "{inputs[0]}%23%23"
},
"predicate": "located_in",
"response_mapping": {
"$ref": "#/components/x-bte-response-mapping/variant_located_in_gene"
},
"source": "dbsnp",
"supportBatch": false
}
]
},
"x-bte-response-mapping": {
"variant_located_in_gene": {
"SYMBOL": "gene.name"
}
}
},
"info": {
"contact": {
"email": "luzh@ncbi.nlm.nih.gov",
"name": "Zhiyong Lu"
},
"description": "LitVar allows the search and retrieval of variant relevant information from the biomedical literature and shows key biological relations between a variant and its close related entities (e.g. genes, diseases, and drugs). The LitVar results are automatically extracted (with regular updates) from over 27 million PubMed articles as well as applicable full-text articles in PubMed Central.",
"termsOfService": "https://www.ncbi.nlm.nih.gov/home/about/policies/",
"title": "LitVar API",
"version": "1.0.0",
"x-translator": {
"component": "KP",
"team": [
"Service Provider"
]
}
},
"paths": {
"/entity/litvar/{variantid}": {
"get": {
"parameters": [
{
"description": "rsid",
"example": "rs121913527",
"in": "path",
"name": "variantid",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "publications mentioned the submitted variant"
}
},
"summary": "Retrieve PMIDs of publications mentioning submitted variants",
"x-bte-kgs-operations": [
{
"$ref": "#/components/x-bte-kgs-operations/variant_located_in_gene"
}
]
}
}
},
"servers": [
{
"description": "Production server",
"url": "https://www.ncbi.nlm.nih.gov/research/bionlp/litvar/api/v1"
}
],
"tags": [
{
"name": "variant"
},
{
"name": "translator"
}
]
},
{
"_id": "786e41a17dbb75399f22e09858f828b7",
"_meta": {
"date_created": "2021-01-26T00:02:48.347118+00:00",
"last_updated": "2021-03-29T07:03:51.419861+00:00",
"url": "https://automat.renci.org/chembio/openapi.json",
"username": "YaphetKG"
},
"_score": 0.6863549,
"info": {
"contact": {
"email": "kebedey@renci.org",
"name": "Yaphet Kebede",
"x-id": "https://github.com/yaphetkg",
"x-role": "contributor"
},
"description": "A graph based on [chem2bio2rdf (http://cheminfov.informatics.indiana.edu:8080/c2b2r/)](http://cheminfov.informatics.indiana.edu:8080/c2b2r/).",
"termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Chembio&provider_long=RENCI",
"title": "Automat Chembio",
"version": "1.0.0",
"x-translator": {
"component": "KP",
"team": [
"Ranking Agent"
]
}
},
"paths": {
"/query": {
"post": {
"description": "Given a question graph return question graph plus answers.",
"operationId": "reasoner_api_query_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Query Reasoner API",
"tags": [
"translator"
]
}
},
"/reasonerapi": {
"get": {
"description": "Returns a list of question templates that can be used to query this plater instance.",
"operationId": "get_reasoner_api_reasonerapi_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Message"
},
"title": "Response Get Reasoner Api Reasonerapi Get",
"type": "array"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get question templates"
},
"post": {
"deprecated": true,
"description": "Handle TRAPI request.",
"operationId": "reasoner_api_reasonerapi_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Reasoner Api"
}
},
"/cypher": {
"post": {
"description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).",
"operationId": "cypher_cypher_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/CypherRequest"
}
],
"example": {
"query": "MATCH (n) RETURN count(n)"
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/CypherResponse"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Run cypher query"
}
},
"/predicates": {
"get": {
"description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.",
"operationId": "predicates_predicates_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"items": {
"type": "string"
},
"type": "array"
},
"type": "object"
},
"title": "Response Predicates Predicates Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types",
"tags": [
"translator"
]
}
},
"/graph/schema": {
"get": {
"deprecated": true,
"description": "Get one-hop connection types",
"operationId": "predicates_graph_schema_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Predicates Graph Schema Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types"
}
},
"/simple_spec": {
"get": {
"description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.",
"operationId": "simple_spec_simple_spec_get",
"parameters": [
{
"in": "query",
"name": "source",
"required": false,
"schema": {
"title": "Source",
"type": "string"
}
},
{
"in": "query",
"name": "target",
"required": false,
"schema": {
"title": "Target",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/SimpleSpecElement"
},
"title": "Response Simple Spec Simple Spec Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one-hop connection schema"
}
},
"/graph/summary": {
"get": {
"description": "Returns a summary of the graph.",
"operationId": "graph_summary_graph_summary_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Graph Summary Graph Summary Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get graph summary"
}
},
"/overlay": {
"post": {
"description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.",
"operationId": "overlay_overlay_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"knowledge_graph": {
"edges": {
"9f7f9d86cb57e7190aafa57f7564eb05": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1610437123.7988985,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_family_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "PANTHER.FAMILY:PTHR12015:SF170",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "PANTHER.FAMILY:PTHR12015:SF170"
},
"dd8ef7a4606c4f8e405e6a5b1b095993": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1584932086.0009434,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "NCBIGene:6352",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "NCBIGene:6352"
}
},
"nodes": {
"NCBIGene:6352": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Gene"
],
"chromosome": "17",
"equivalent_identifiers": [
"ENSEMBL:ENSG00000271503",
"NCBIGene:6352",
"NCBIGene:6352",
"HGNC:10632",
"UniProtKB:P13501"
],
"gene_family": [
"Chemokine ligands"
],
"gene_family_id": [
483
],
"location": "17q12",
"locus_group": "protein-coding gene",
"synonyms": [],
"taxon": 9606
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:MolecularEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:Gene"
],
"name": "CCL5"
},
"PANTHER.FAMILY:PTHR12015": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "SMALL INDUCIBLE CYTOKINE A"
},
"PANTHER.FAMILY:PTHR12015:SF170": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015:SF170"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "C-C MOTIF CHEMOKINE 5"
}
}
},
"query_graph": {
"edges": {
"e12": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n1"
},
"e23": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n3"
}
},
"nodes": {
"n1": {
"category": "biolink:Gene",
"id": "NCBIGene:6352",
"is_set": false
},
"n2": {
"category": "biolink:GeneFamily",
"is_set": false
},
"n3": {
"category": "biolink:GeneFamily",
"is_set": false
}
}
},
"results": [
{
"edge_bindings": {
"e12": [
{
"id": "dd8ef7a4606c4f8e405e6a5b1b095993"
}
],
"e23": [
{
"id": "9f7f9d86cb57e7190aafa57f7564eb05"
}
]
},
"node_bindings": {
"n1": [
{
"id": "NCBIGene:6352"
}
],
"n2": [
{
"id": "PANTHER.FAMILY:PTHR12015"
}
],
"n3": [
{
"id": "PANTHER.FAMILY:PTHR12015:SF170"
}
]
}
}
]
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Message"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Overlay results with available connections between each node.",
"tags": [
"translator"
]
}
},
"/about": {
"get": {
"description": "Returns a JSON describing dataset.",
"operationId": "about_about_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response About About Get"
}
}
},
"description": "Successful Response"
}
},
"summary": "JSON about dataset"
}
},
"/{source_type}/{target_type}/{curie}": {
"get": {
"description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.",
"operationId": "one_hop__source_type___target_type___curie__get",
"parameters": [
{
"in": "path",
"name": "source_type",
"required": true,
"schema": {
"title": "Source Type",
"type": "string"
}
},
{
"in": "path",
"name": "target_type",
"required": true,
"schema": {
"title": "Target Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response One Hop Source Type Target Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source"
}
},
"/{node_type}/{curie}": {
"get": {
"description": "Returns `node` matching `curie`.",
"operationId": "node__node_type___curie__get",
"parameters": [
{
"in": "path",
"name": "node_type",
"required": true,
"schema": {
"title": "Node Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response Node Node Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Find `node` by `curie`"
}
}
},
"servers": [
{
"description": "Default server",
"url": "https://automat.renci.org/chembio"
}
],
"tags": [
{
"name": "translator"
},
{
"name": "automat"
}
]
},
{
"_id": "9d7ab69df070c2c1b9ce89e750569b5b",
"_meta": {
"date_created": "2021-01-26T00:00:59.341300+00:00",
"last_updated": "2021-03-29T07:03:51.982362+00:00",
"url": "https://automat.renci.org/chemical-normalization/openapi.json",
"username": "YaphetKG"
},
"_score": 0.6863549,
"info": {
"contact": {
"email": "kebedey@renci.org",
"name": "Yaphet Kebede",
"x-id": "https://github.com/yaphetkg",
"x-role": "contributor"
},
"description": "A graph linking together similar compounds. Two compounds are linked by an edge in the graph if they are equivalent when charge, salts, and stereochemistry are ignored.",
"termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Chemical Normalization&provider_long=RENCI",
"title": "Automat Chemical normalization",
"version": "1.0.0",
"x-translator": {
"component": "KP",
"team": [
"Ranking Agent"
]
}
},
"paths": {
"/query": {
"post": {
"description": "Given a question graph return question graph plus answers.",
"operationId": "reasoner_api_query_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Query Reasoner API",
"tags": [
"translator"
]
}
},
"/reasonerapi": {
"get": {
"description": "Returns a list of question templates that can be used to query this plater instance.",
"operationId": "get_reasoner_api_reasonerapi_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Message"
},
"title": "Response Get Reasoner Api Reasonerapi Get",
"type": "array"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get question templates"
},
"post": {
"deprecated": true,
"description": "Handle TRAPI request.",
"operationId": "reasoner_api_reasonerapi_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Reasoner Api"
}
},
"/cypher": {
"post": {
"description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).",
"operationId": "cypher_cypher_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/CypherRequest"
}
],
"example": {
"query": "MATCH (n) RETURN count(n)"
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/CypherResponse"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Run cypher query"
}
},
"/predicates": {
"get": {
"description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.",
"operationId": "predicates_predicates_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"items": {
"type": "string"
},
"type": "array"
},
"type": "object"
},
"title": "Response Predicates Predicates Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types",
"tags": [
"translator"
]
}
},
"/graph/schema": {
"get": {
"deprecated": true,
"description": "Get one-hop connection types",
"operationId": "predicates_graph_schema_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Predicates Graph Schema Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types"
}
},
"/simple_spec": {
"get": {
"description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.",
"operationId": "simple_spec_simple_spec_get",
"parameters": [
{
"in": "query",
"name": "source",
"required": false,
"schema": {
"title": "Source",
"type": "string"
}
},
{
"in": "query",
"name": "target",
"required": false,
"schema": {
"title": "Target",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/SimpleSpecElement"
},
"title": "Response Simple Spec Simple Spec Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one-hop connection schema"
}
},
"/graph/summary": {
"get": {
"description": "Returns a summary of the graph.",
"operationId": "graph_summary_graph_summary_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Graph Summary Graph Summary Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get graph summary"
}
},
"/overlay": {
"post": {
"description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.",
"operationId": "overlay_overlay_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"knowledge_graph": {
"edges": {
"9f7f9d86cb57e7190aafa57f7564eb05": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1610437123.7988985,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_family_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "PANTHER.FAMILY:PTHR12015:SF170",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "PANTHER.FAMILY:PTHR12015:SF170"
},
"dd8ef7a4606c4f8e405e6a5b1b095993": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1584932086.0009434,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "NCBIGene:6352",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "NCBIGene:6352"
}
},
"nodes": {
"NCBIGene:6352": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Gene"
],
"chromosome": "17",
"equivalent_identifiers": [
"ENSEMBL:ENSG00000271503",
"NCBIGene:6352",
"NCBIGene:6352",
"HGNC:10632",
"UniProtKB:P13501"
],
"gene_family": [
"Chemokine ligands"
],
"gene_family_id": [
483
],
"location": "17q12",
"locus_group": "protein-coding gene",
"synonyms": [],
"taxon": 9606
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:MolecularEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:Gene"
],
"name": "CCL5"
},
"PANTHER.FAMILY:PTHR12015": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "SMALL INDUCIBLE CYTOKINE A"
},
"PANTHER.FAMILY:PTHR12015:SF170": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015:SF170"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "C-C MOTIF CHEMOKINE 5"
}
}
},
"query_graph": {
"edges": {
"e12": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n1"
},
"e23": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n3"
}
},
"nodes": {
"n1": {
"category": "biolink:Gene",
"id": "NCBIGene:6352",
"is_set": false
},
"n2": {
"category": "biolink:GeneFamily",
"is_set": false
},
"n3": {
"category": "biolink:GeneFamily",
"is_set": false
}
}
},
"results": [
{
"edge_bindings": {
"e12": [
{
"id": "dd8ef7a4606c4f8e405e6a5b1b095993"
}
],
"e23": [
{
"id": "9f7f9d86cb57e7190aafa57f7564eb05"
}
]
},
"node_bindings": {
"n1": [
{
"id": "NCBIGene:6352"
}
],
"n2": [
{
"id": "PANTHER.FAMILY:PTHR12015"
}
],
"n3": [
{
"id": "PANTHER.FAMILY:PTHR12015:SF170"
}
]
}
}
]
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Message"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Overlay results with available connections between each node.",
"tags": [
"translator"
]
}
},
"/about": {
"get": {
"description": "Returns a JSON describing dataset.",
"operationId": "about_about_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response About About Get"
}
}
},
"description": "Successful Response"
}
},
"summary": "JSON about dataset"
}
},
"/{source_type}/{target_type}/{curie}": {
"get": {
"description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.",
"operationId": "one_hop__source_type___target_type___curie__get",
"parameters": [
{
"in": "path",
"name": "source_type",
"required": true,
"schema": {
"title": "Source Type",
"type": "string"
}
},
{
"in": "path",
"name": "target_type",
"required": true,
"schema": {
"title": "Target Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response One Hop Source Type Target Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source"
}
},
"/{node_type}/{curie}": {
"get": {
"description": "Returns `node` matching `curie`.",
"operationId": "node__node_type___curie__get",
"parameters": [
{
"in": "path",
"name": "node_type",
"required": true,
"schema": {
"title": "Node Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response Node Node Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Find `node` by `curie`"
}
}
},
"servers": [
{
"description": "Default server",
"url": "https://automat.renci.org/chemical-normalization"
}
],
"tags": [
{
"name": "translator"
},
{
"name": "automat"
}
]
},
{
"_id": "1c0aff2a70b1ed677867c0db8011746f",
"_meta": {
"date_created": "2021-02-03T16:03:16.375825+00:00",
"last_updated": "2021-03-29T07:04:13.339365+00:00",
"url": "https://automat.renci.org/ontological-hierarchy/openapi.json",
"username": "YaphetKG"
},
"_score": 0.6863549,
"info": {
"contact": {
"email": "kebedey@renci.org",
"name": "Yaphet Kebede",
"x-id": "https://github.com/yaphetkg",
"x-role": "contributor"
},
"description": "A graph for ontological hierarchy extracted from Uberongraph.",
"termsOfService": "http://linkmissing",
"title": "Automat Ontological Hierarchy",
"version": "1.0.0",
"x-translator": {
"component": "KP",
"team": [
"Ranking Agent"
]
}
},
"paths": {
"/query": {
"post": {
"description": "Given a question graph return question graph plus answers.",
"operationId": "reasoner_api_query_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Query Reasoner API",
"tags": [
"translator"
]
}
},
"/reasonerapi": {
"get": {
"description": "Returns a list of question templates that can be used to query this plater instance.",
"operationId": "get_reasoner_api_reasonerapi_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Message"
},
"title": "Response Get Reasoner Api Reasonerapi Get",
"type": "array"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get question templates"
},
"post": {
"deprecated": true,
"description": "Handle TRAPI request.",
"operationId": "reasoner_api_reasonerapi_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Reasoner Api"
}
},
"/cypher": {
"post": {
"description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).",
"operationId": "cypher_cypher_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/CypherRequest"
}
],
"example": {
"query": "MATCH (n) RETURN count(n)"
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/CypherResponse"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Run cypher query"
}
},
"/predicates": {
"get": {
"description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.",
"operationId": "predicates_predicates_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"items": {
"type": "string"
},
"type": "array"
},
"type": "object"
},
"title": "Response Predicates Predicates Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types",
"tags": [
"translator"
]
}
},
"/graph/schema": {
"get": {
"deprecated": true,
"description": "Get one-hop connection types",
"operationId": "predicates_graph_schema_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Predicates Graph Schema Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types"
}
},
"/simple_spec": {
"get": {
"description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.",
"operationId": "simple_spec_simple_spec_get",
"parameters": [
{
"in": "query",
"name": "source",
"required": false,
"schema": {
"title": "Source",
"type": "string"
}
},
{
"in": "query",
"name": "target",
"required": false,
"schema": {
"title": "Target",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/SimpleSpecElement"
},
"title": "Response Simple Spec Simple Spec Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one-hop connection schema"
}
},
"/graph/summary": {
"get": {
"description": "Returns a summary of the graph.",
"operationId": "graph_summary_graph_summary_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Graph Summary Graph Summary Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get graph summary"
}
},
"/overlay": {
"post": {
"description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.",
"operationId": "overlay_overlay_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"knowledge_graph": {
"edges": {
"9f7f9d86cb57e7190aafa57f7564eb05": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1610437123.7988985,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_family_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "PANTHER.FAMILY:PTHR12015:SF170",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "PANTHER.FAMILY:PTHR12015:SF170"
},
"dd8ef7a4606c4f8e405e6a5b1b095993": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1584932086.0009434,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "NCBIGene:6352",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "NCBIGene:6352"
}
},
"nodes": {
"NCBIGene:6352": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Gene"
],
"chromosome": "17",
"equivalent_identifiers": [
"ENSEMBL:ENSG00000271503",
"NCBIGene:6352",
"NCBIGene:6352",
"HGNC:10632",
"UniProtKB:P13501"
],
"gene_family": [
"Chemokine ligands"
],
"gene_family_id": [
483
],
"location": "17q12",
"locus_group": "protein-coding gene",
"synonyms": [],
"taxon": 9606
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:MolecularEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:Gene"
],
"name": "CCL5"
},
"PANTHER.FAMILY:PTHR12015": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "SMALL INDUCIBLE CYTOKINE A"
},
"PANTHER.FAMILY:PTHR12015:SF170": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015:SF170"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "C-C MOTIF CHEMOKINE 5"
}
}
},
"query_graph": {
"edges": {
"e12": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n1"
},
"e23": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n3"
}
},
"nodes": {
"n1": {
"category": "biolink:Gene",
"id": "NCBIGene:6352",
"is_set": false
},
"n2": {
"category": "biolink:GeneFamily",
"is_set": false
},
"n3": {
"category": "biolink:GeneFamily",
"is_set": false
}
}
},
"results": [
{
"edge_bindings": {
"e12": [
{
"id": "dd8ef7a4606c4f8e405e6a5b1b095993"
}
],
"e23": [
{
"id": "9f7f9d86cb57e7190aafa57f7564eb05"
}
]
},
"node_bindings": {
"n1": [
{
"id": "NCBIGene:6352"
}
],
"n2": [
{
"id": "PANTHER.FAMILY:PTHR12015"
}
],
"n3": [
{
"id": "PANTHER.FAMILY:PTHR12015:SF170"
}
]
}
}
]
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Message"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Overlay results with available connections between each node.",
"tags": [
"translator"
]
}
},
"/about": {
"get": {
"description": "Returns a JSON describing dataset.",
"operationId": "about_about_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response About About Get"
}
}
},
"description": "Successful Response"
}
},
"summary": "JSON about dataset"
}
},
"/{source_type}/{target_type}/{curie}": {
"get": {
"description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.",
"operationId": "one_hop__source_type___target_type___curie__get",
"parameters": [
{
"in": "path",
"name": "source_type",
"required": true,
"schema": {
"title": "Source Type",
"type": "string"
}
},
{
"in": "path",
"name": "target_type",
"required": true,
"schema": {
"title": "Target Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response One Hop Source Type Target Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source"
}
},
"/{node_type}/{curie}": {
"get": {
"description": "Returns `node` matching `curie`.",
"operationId": "node__node_type___curie__get",
"parameters": [
{
"in": "path",
"name": "node_type",
"required": true,
"schema": {
"title": "Node Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response Node Node Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Find `node` by `curie`"
}
}
},
"servers": [
{
"description": "Default server",
"url": "https://automat.renci.org/ontological-hierarchy"
}
],
"tags": [
{
"name": "translator"
},
{
"name": "Automat"
}
]
},
{
"_id": "a49ee52f6fb81a71cca84e9806732b76",
"_meta": {
"date_created": "2021-01-26T00:02:43.141214+00:00",
"last_updated": "2021-03-29T07:04:13.892270+00:00",
"url": "https://automat.renci.org/foodb/openapi.json",
"username": "YaphetKG"
},
"_score": 0.6863549,
"info": {
"contact": {
"email": "kebedey@renci.org",
"name": "Yaphet Kebede",
"x-id": "https://github.com/yaphetkg",
"x-role": "contributor"
},
"description": "A graph of the food/chemical relationships in [foodb.ca](foodb.ca).",
"termsOfService": "http://robokop.renci.org:7055/tos?service_long=Automat Foodb&provider_long=RENCI",
"title": "Automat Foodb",
"version": "1.0.0",
"x-translator": {
"component": "KP",
"team": [
"Ranking Agent"
]
}
},
"paths": {
"/query": {
"post": {
"description": "Given a question graph return question graph plus answers.",
"operationId": "reasoner_api_query_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Query Reasoner API",
"tags": [
"translator"
]
}
},
"/reasonerapi": {
"get": {
"description": "Returns a list of question templates that can be used to query this plater instance.",
"operationId": "get_reasoner_api_reasonerapi_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/Message"
},
"title": "Response Get Reasoner Api Reasonerapi Get",
"type": "array"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get question templates"
},
"post": {
"deprecated": true,
"description": "Handle TRAPI request.",
"operationId": "reasoner_api_reasonerapi_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"query_graph": {
"edges": {},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "NCBIGene:15"
}
}
}
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Reasoner Api"
}
},
"/cypher": {
"post": {
"description": "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).",
"operationId": "cypher_cypher_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/CypherRequest"
}
],
"example": {
"query": "MATCH (n) RETURN count(n)"
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/CypherResponse"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Run cypher query"
}
},
"/predicates": {
"get": {
"description": "Returns an object where outer keys represent source types with second level keys as targets. And the values of the second level keys is the type of possible edge typesthat connect these concepts.",
"operationId": "predicates_predicates_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"items": {
"type": "string"
},
"type": "array"
},
"type": "object"
},
"title": "Response Predicates Predicates Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types",
"tags": [
"translator"
]
}
},
"/graph/schema": {
"get": {
"deprecated": true,
"description": "Get one-hop connection types",
"operationId": "predicates_graph_schema_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Predicates Graph Schema Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get one-hop connection types"
}
},
"/simple_spec": {
"get": {
"description": "Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.",
"operationId": "simple_spec_simple_spec_get",
"parameters": [
{
"in": "query",
"name": "source",
"required": false,
"schema": {
"title": "Source",
"type": "string"
}
},
{
"in": "query",
"name": "target",
"required": false,
"schema": {
"title": "Target",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {
"$ref": "#/components/schemas/SimpleSpecElement"
},
"title": "Response Simple Spec Simple Spec Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one-hop connection schema"
}
},
"/graph/summary": {
"get": {
"description": "Returns a summary of the graph.",
"operationId": "graph_summary_graph_summary_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response Graph Summary Graph Summary Get",
"type": "object"
}
}
},
"description": "Successful Response"
}
},
"summary": "Get graph summary"
}
},
"/overlay": {
"post": {
"description": "Given a ReasonerAPI graph, add support edges for any nodes linked in result bindings.",
"operationId": "overlay_overlay_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"allOf": [
{
"$ref": "#/components/schemas/Query"
}
],
"example": {
"message": {
"knowledge_graph": {
"edges": {
"9f7f9d86cb57e7190aafa57f7564eb05": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1610437123.7988985,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_family_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "PANTHER.FAMILY:PTHR12015:SF170",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "PANTHER.FAMILY:PTHR12015:SF170"
},
"dd8ef7a4606c4f8e405e6a5b1b095993": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"ctime": 1584932086.0009434,
"predicate": "biolink:part_of",
"provided_by": "panther.get_gene_by_gene_family",
"publications": [],
"relation": "BFO:0000050",
"relation_label": "part of",
"source_database": "panther",
"source_id": "NCBIGene:6352",
"target_id": "PANTHER.FAMILY:PTHR12015"
}
}
],
"object": "PANTHER.FAMILY:PTHR12015",
"predicate": "biolink:part_of",
"subject": "NCBIGene:6352"
}
},
"nodes": {
"NCBIGene:6352": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Gene"
],
"chromosome": "17",
"equivalent_identifiers": [
"ENSEMBL:ENSG00000271503",
"NCBIGene:6352",
"NCBIGene:6352",
"HGNC:10632",
"UniProtKB:P13501"
],
"gene_family": [
"Chemokine ligands"
],
"gene_family_id": [
483
],
"location": "17q12",
"locus_group": "protein-coding gene",
"synonyms": [],
"taxon": 9606
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:MolecularEntity",
"biolink:GenomicEntity",
"biolink:GeneOrGeneProduct",
"biolink:MacromolecularMachine",
"biolink:Gene"
],
"name": "CCL5"
},
"PANTHER.FAMILY:PTHR12015": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "SMALL INDUCIBLE CYTOKINE A"
},
"PANTHER.FAMILY:PTHR12015:SF170": {
"attributes": [
{
"type": "WIKIDATA:Q80585",
"value": {
"category": [
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:NamedThing",
"biolink:MolecularEntity",
"biolink:Entity"
],
"equivalent_identifiers": [
"PANTHER.FAMILY:PTHR12015:SF170"
],
"synonyms": []
}
}
],
"category": [
"biolink:NamedThing",
"biolink:BiologicalEntity",
"biolink:GeneFamily",
"biolink:MolecularEntity",
"biolink:Entity"
],
"name": "C-C MOTIF CHEMOKINE 5"
}
}
},
"query_graph": {
"edges": {
"e12": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n1"
},
"e23": {
"object": "n2",
"predicate": "biolink:part_of",
"subject": "n3"
}
},
"nodes": {
"n1": {
"category": "biolink:Gene",
"id": "NCBIGene:6352",
"is_set": false
},
"n2": {
"category": "biolink:GeneFamily",
"is_set": false
},
"n3": {
"category": "biolink:GeneFamily",
"is_set": false
}
}
},
"results": [
{
"edge_bindings": {
"e12": [
{
"id": "dd8ef7a4606c4f8e405e6a5b1b095993"
}
],
"e23": [
{
"id": "9f7f9d86cb57e7190aafa57f7564eb05"
}
]
},
"node_bindings": {
"n1": [
{
"id": "NCBIGene:6352"
}
],
"n2": [
{
"id": "PANTHER.FAMILY:PTHR12015"
}
],
"n3": [
{
"id": "PANTHER.FAMILY:PTHR12015:SF170"
}
]
}
}
]
}
},
"title": "Request"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Message"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Overlay results with available connections between each node.",
"tags": [
"translator"
]
}
},
"/about": {
"get": {
"description": "Returns a JSON describing dataset.",
"operationId": "about_about_get",
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"title": "Response About About Get"
}
}
},
"description": "Successful Response"
}
},
"summary": "JSON about dataset"
}
},
"/{source_type}/{target_type}/{curie}": {
"get": {
"description": "Returns one hop paths from `source_node_type` with `curie` to `target_node_type`.",
"operationId": "one_hop__source_type___target_type___curie__get",
"parameters": [
{
"in": "path",
"name": "source_type",
"required": true,
"schema": {
"title": "Source Type",
"type": "string"
}
},
{
"in": "path",
"name": "target_type",
"required": true,
"schema": {
"title": "Target Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response One Hop Source Type Target Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Get one hop results from source type to target type. Note: Please GET /predicates to determine what target goes with a source"
}
},
"/{node_type}/{curie}": {
"get": {
"description": "Returns `node` matching `curie`.",
"operationId": "node__node_type___curie__get",
"parameters": [
{
"in": "path",
"name": "node_type",
"required": true,
"schema": {
"title": "Node Type",
"type": "string"
}
},
{
"in": "path",
"name": "curie",
"required": true,
"schema": {
"title": "Curie",
"type": "string"
}
}
],
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"items": {},
"title": "Response Node Node Type Curie Get",
"type": "array"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Find `node` by `curie`"
}
}
},
"servers": [
{
"description": "Default server",
"url": "https://automat.renci.org/foodb"
}
],
"tags": [
{
"name": "translator"
},
{
"name": "automat"
}
]
},
{
"_id": "4f7b6f661ac61ed64190d5b26d87aff5",
"_meta": {
"date_created": "2020-03-12T16:25:03.083494+00:00",
"last_updated": "2021-02-17T07:42:23.333398+00:00",
"url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/robokop_extend/smartapi.yaml",
"username": "kevinxin90"
},
"_score": 0.6863549,
"components": {
"x-bte-kgs-operations": {
"associatedWith": {
"inputs": [
{
"id": "hgnc",
"semantic": "Gene"
}
],
"outputs": [
{
"id": "chembl",
"semantic": "ChemicalSubstance"
}
],
"parameters": {
"chemical_id": "HGNC:{input1}"
},
"response-mapping": {
"$ref": "#/components/x-bte-response-mapping/gene-chemical"
},
"supportBatch": false
},
"contraindication": {
"inputs": [
{
"id": "chembl",
"semantic": "ChemicalSubstance"
}
],
"outputs": [
{
"id": "mondo",
"semantic": "DiseaseOrPhenotypicFeature"
}
],
"parameters": {
"chemical_id": "CHEMBL:{input1}"
},
"response-mapping": {
"$ref": "#/components/x-bte-response-mapping/chemical-disease"
},
"supportBatch": false
},
"partOf": {
"inputs": [
{
"id": "hgnc",
"semantic": "Gene"
}
],
"outputs": [
{
"id": "panther",
"semantic": "GeneFamily"
}
],
"parameters": {
"chemical_id": "HGNC:{input1}"
},
"response-mapping": {
"$ref": "#/components/x-bte-response-mapping/gene-genefamily"
},
"supportBatch": false
},
"treats": {
"inputs": [
{
"id": "chembl",
"semantic": "ChemicalSubstance"
}
],
"outputs": [
{
"id": "mondo",
"semantic": "DiseaseOrPhenotypicFeature"
}
],
"parameters": {
"chemical_id": "CHEMBL:{input1}"
},
"response-mapping": {
"$ref": "#/components/x-bte-response-mapping/chemical-disease"
},
"supportBatch": false
}
},
"x-bte-response-mapping": {
"chemical-disease": {
"@context": "http://schema.org",
"@type": "ChemicalSubstance",
"bts:chembl": "treats.source_id",
"bts:contraindication": {
"$input": "bts:chembl",
"$source": "robokop",
"@type": "DiseaseOrPhenotypicFeature",
"bts:mondo": "contraindicated_for.mondo",
"bts:pubmed": "contraindicated_for.publications",
"bts:source": "contraindicated_for.source_database"
},
"bts:treats": {
"$input": "bts:chembl",
"$source": "robokop",
"@type": "DiseaseOrPhenotypicFeature",
"bts:mondo": "treats.mondo",
"bts:pubmed": "treats.publications",
"bts:source": "treats.source_database"
}
},
"gene-chemical": {
"@context": "http://schema.org",
"@type": "Gene",
"bts:associatedWith": {
"$input": "bts:hgnc",
"$source": "robokop",
"@type": "ChemicalSubstance",
"bts:chembl": "literature_co-occurrence.chembl",
"bts:source": "literature_co-occurrence.source_database"
},
"bts:hgnc": "literature_co-occurrence.source_id"
},
"gene-genefamily": {
"@context": "http://schema.org",
"@type": "Gene",
"bts:hgnc": "part_of.source_id",
"bts:partOf": {
"$input": "bts:hgnc",
"$source": "panther",
"@type": "GeneFamily",
"bts:panther": "part_of.panther",
"bts:pubmed": "part_of.publications",
"bts:source": "part_of.source_database"
}
}
}
},
"info": {
"contact": {
"email": "patrick@covar.com",
"name": "Patrick Wang",
"url": "robokop.renci.org"
},
"description": "An API for answering biomedical questions",
"termsOfService": "https://robokop.renci.org/termsofservice/",
"title": "ROBOKOP",
"version": "1.0"
},
"paths": {
"/simple/expand/chemical_substance/{chemical_id}/disease_or_phenotypic_feature/": {
"get": {
"parameters": [
{
"description": "chembl id",
"example": "CHEMBL:CHEMBL744",
"in": "path",
"name": "chemical_id",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "A association object",
"x-bte-response-mapping": {
"$ref": "#/components/x-bte-response-mapping/chemical-disease"
}
}
},
"summary": "retrieve diseases related to chemical",
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"treats": {
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}
}
}
},
"/simple/expand/gene/{gene_id}/gene_family/": {
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{
"description": "hgnc id",
"example": "HGNC:1771",
"in": "path",
"name": "gene_id",
"required": true,
"schema": {
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}
}
],
"responses": {
"200": {
"description": "A association object",
"x-bte-response-mapping": {
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}
}
},
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"x-bte-kgs-operations": {
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"$ref": "#/components/x-bte-kgs-operations/partOf"
}
}
}
},
"/simple/expand/gene/{gene_id}/chemical_substance/": {
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{
"description": "hgnc id",
"example": "HGNC:1771",
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"schema": {
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}
],
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"x-bte-response-mapping": {
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}
},
"summary": "retrieve chemicals related to gene",
"x-bte-kgs-operations": {
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}
}
}
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],
"outputs": [
{
"id": "chembl",
"semantic": "Gene"
}
],
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},
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},
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}
},
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"@type": "Gene",
"bts:action": "mechanisms.action_type",
"bts:chembl": "mechanisms.target_chembl_id",
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}
},
"info": {
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"name": "chembl help desk",
"x-role": "responsible developer"
},
"description": "The ChEMBL API",
"termsOfService": "http://www.ebi.ac.uk/chembl",
"title": "ChEMBL API",
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{
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"required": true,
"schema": {
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}
],
"responses": {
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"x-bte-response-mapping": {
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},
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"url": "https://aragorn.renci.org/openapi.json",
"username": "PhillipsOwen"
},
"_score": 0.6863549,
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"name": "Patrick Wang",
"x-id": "https://github.com/patrickkwang",
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"description": "ARAGORN: Performs a query operation which compiles data from numerous ARAGORN ranking agent services.",
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"nodes": {
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"id": "MONDO:0004979"
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"n1": {
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"tags": [
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}
},
"servers": [
{
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"url": "https://aragorn.renci.org"
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{
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"url": "https://strider.renci.org/openapi.json",
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"name": "Patrick Wang",
"x-id": "https://github.com/patrickkwang",
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"team": [
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"parameters": [
{
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"required": false,
"schema": {
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"predicate": "biolink:has_phenotype",
"subject": "n0"
}
},
"nodes": {
"n0": {
"category": "biolink:Disease",
"id": "MONDO:0005148"
},
"n1": {
"category": "biolink:PhenotypicFeature"
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}
}
}
},
"title": "Query"
}
}
},
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},
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"content": {
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"summary": "Async Query"
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"operationId": "get_results_query_result_post",
"parameters": [
{
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"name": "qid",
"required": true,
"schema": {
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"type": "string"
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"200": {
"content": {
"application/json": {
"schema": {
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"422": {
"content": {
"application/json": {
"schema": {
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}
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},
"summary": "Get Results"
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"/query": {
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"parameters": [
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"required": false,
"schema": {
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"schema": {
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{
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"predicate": "biolink:has_phenotype",
"subject": "n0"
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},
"nodes": {
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"category": "biolink:Disease",
"id": "MONDO:0005148"
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"n1": {
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}
}
}
}
},
"title": "Query"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
}
},
"description": "Successful Response"
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"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Sync Query",
"tags": [
"reasoner"
]
}
},
"/ars": {
"post": {
"description": "Handle ARS message.",
"operationId": "handle_ars_ars_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"title": "Data",
"type": "object"
}
}
},
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"content": {
"application/json": {
"schema": {}
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"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
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}
},
"summary": "Handle Ars"
}
},
"/plan": {
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"operationId": "generate_traversal_plan_plan_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
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"content": {
"application/json": {
"schema": {
"items": {
"type": "object"
},
"title": "Response Generate Traversal Plan Plan Post",
"type": "array"
}
}
},
"description": "Successful Response"
},
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"schema": {
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}
}
},
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}
},
"summary": "Generate Traversal Plan"
}
},
"/score": {
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"description": "Score results.",
"operationId": "score_results_score_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
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},
"summary": "Score Results"
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}
},
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}
],
"tags": [
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},
{
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"last_updated": "2021-03-09T08:01:08.262488+00:00",
"url": "https://raw.githubusercontent.com/broadinstitute/genetics-kp-dev/master/transaltorRegistry.yaml",
"username": "marcdubybroad"
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"info": {
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"url": "https://github.com/broadinstitute/genetics-kp-dev"
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"description": "A Translator API for Genetic Disease Asociation",
"termsOfService": "http://www.apache.org/licenses/LICENSE-2.0.html",
"title": "Genetics Provider",
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"x-reasoner_standard_version": "1.0.0",
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"team": [
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"/query": {
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}
}
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"schema": {
"$ref": "#/components/schemas/Query"
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},
"description": "Query information to be submitted",
"required": true
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"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
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"description": "OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."
},
"400": {
"content": {
"application/json": {
"schema": {
"type": "string"
}
}
},
"description": "Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."
},
"500": {
"content": {
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"schema": {
"type": "string"
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"description": "Internal server error."
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"501": {
"content": {
"application/json": {
"schema": {
"type": "string"
}
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},
"description": "Not implemented."
}
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"summary": "Query Genetics Provider TRAPI API as KP",
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"1.0.0"
],
"x-swagger-router-controller": "swagger_server.controllers.query_controller"
}
}
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"tags": [
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{
"name": "translator"
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{
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{
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{
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{
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"url": "https://raw.githubusercontent.com/di2ag/chp_metadata/master/smartapi.yaml",
"username": "veenhouse"
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"_score": 0.6217669,
"info": {
"contact": {
"email": "luke.j.veenhuis@dartmouth.edu",
"name": "Luke Veenhuis",
"x-id": "LukeVeenhuis",
"x-role": "responsible developer"
},
"description": "A Translator Reasoner API for the Connections Hypothesis Provider",
"license": {
"name": "Apache 2.0",
"url": "http://www.apache.org/licenses/LICENSE-2.0.html"
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"termsOfService": "https://github.com/di2ag/chp_api/blob/master/terms%20of%20service",
"title": "Connections Hypothesis Provider API",
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"x-reasoner_standard_version": 1,
"x-translator": {
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"team": [
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"biolink:Gene": {
"biolink:Disease": [
"biolink:GeneToDiseaseAssociation"
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}
},
"type": "object"
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"description": "Predicates by source and target"
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"summary": "Get supported relationships by source and target",
"tags": [
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],
"x-accessRestriction": "none"
}
},
"/versions": {
"get": {
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"description": "object of service versions",
"items": {
"type": "string"
},
"type": "object"
}
},
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"chp_client": "0.2.1",
"chp_data": "0.1.1",
"pybkb": "1.1.0"
},
"type": "object"
}
}
},
"description": "versions of our service"
}
},
"summary": "Get a list of versions of our service repositories",
"tags": [
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]
}
},
"/query": {
"post": {
"externalDocs": {
"url": "https://github.com/di2ag/chp_client"
},
"requestBody": {
"content": {
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"example": {
"message": {
"query_graph": {
"edges": {
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"object": "n2",
"predicate": "biolink:GeneToDiseaseAssociation",
"subject": "n0"
},
"e1": {
"object": "n2",
"predicate": "biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation",
"subject": "n1"
},
"e2": {
"object": "n3",
"predicate": "biolink:DiseaseToPhenotypicFeatureAssociation",
"properties": {
"days": 500,
"qualifier": ">="
},
"subject": "n2"
}
},
"nodes": {
"n0": {
"category": "biolink:Gene",
"id": "ENSEMBL:ENSG00000132155"
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"n1": {
"category": "biolink:Drug",
"id": "CHEMBL:CHEMBL1201585"
},
"n2": {
"category": "biolink:Disease",
"id": "MONDO:0007254"
},
"n3": {
"category": "biolink:PhenotypicFeature",
"id": "EFO:0000714"
}
}
}
}
},
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "A message with question graph.",
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Message"
}
}
},
"description": "A message with knowledge graph and answers."
}
},
"summary": "Get answers to a question",
"tags": [
"Query"
],
"x-accessRestriction": "none"
}
},
"/curies": {
"get": {
"externalDocs": {
"url": "https://github.com/di2ag/chp_client"
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"description": "object of supported curies",
"items": {
"type": "string"
},
"type": "object"
}
},
"example": {
"biolink:Disease": [
{
"id": "MONDO:0007254",
"name": "breast_cancer"
}
],
"biolink:Drug": [
{
"id": "CHEMBL:CHEMBL1201247",
"name": "ZOLADEX"
}
],
"biolink:Gene": [
{
"id": "ENSEMBL:ENSG00000106665",
"name": "CLIP2"
}
],
"biolink:PhenotypicFeature": [
{
"id": "EFO:0000714",
"name": "survival_time"
}
]
},
"type": "object"
}
}
},
"description": "set of curies currently supported by our service"
}
},
"summary": "Get a set of curies currently supported by our service",
"tags": [
"Curies"
],
"x-accessRestriction": "none"
}
}
},
"servers": [
{
"description": "Production Server",
"url": "http://chp.thayer.dartmouth.edu/"
}
],
"tags": [
{
"name": "bayesian"
},
{
"name": "translator"
},
{
"name": "1.0.0"
}
]
},
{
"_id": "bfe51132e3f325e9f74a7fa40dc81583",
"_meta": {
"date_created": "2019-06-10T17:56:55.297135+00:00",
"last_updated": "2021-02-17T07:42:21.884706+00:00",
"url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/indigo/openapi.yml",
"username": "vdancik"
},
"_score": 0.6217669,
"info": {
"contact": {
"email": "translator@broadinstitute.org",
"name": "Broad NCATS translator"
},
"description": "OpenAPI for indigo NCATS Biomedical Translator Reasoner",
"license": {
"name": "Apache 2.0",
"url": "http://www.apache.org/licenses/LICENSE-2.0.html"
},
"termsOfService": "{{url}}",
"title": "OpenAPI for indigo NCATS Biomedical Translator Reasoner",
"version": "0.9.1.1",
"x-reasoner_standard_version": "0.9.1"
},
"paths": {
"/query": {
"post": {
"description": "",
"operationId": "query",
"requestBody": {
"content": {
"application/json": {
"example": {
"query_message": {
"query_graph": {
"edges": [
{
"edge_id": "e00",
"source_id": "n00",
"target_id": "n01",
"type": "targets"
}
],
"nodes": [
{
"curie": "CHEMBL:CHEMBL521",
"node_id": "n00",
"type": "chemical_substance"
},
{
"node_id": "n01",
"type": "protein"
}
]
}
}
},
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "Query information to be submitted",
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Message"
}
}
},
"description": "successful operation"
},
"400": {
"description": "Invalid status value"
}
},
"summary": "Query reasoner via one of several inputs",
"tags": [
"query"
],
"x-swagger-router-controller": "swagger_server.controllers.query_controller"
}
}
},
"servers": [
{
"url": "https://indigo.ncats.io/reasoner/api/v1/"
}
],
"tags": [
{
"description": "Query reasoner using a predefined question type",
"name": "query"
},
{
"name": "translator"
},
{
"name": "reasoner"
}
]
},
{
"_id": "20051e07e2e70ecba18e6bf8f2ca680b",
"_meta": {
"date_created": "2021-01-23T22:44:15.777639+00:00",
"last_updated": "2021-03-29T07:01:49.920221+00:00",
"url": "https://raw.githubusercontent.com/NCATSTranslator/Explanatory-Agent/master/Agent/smart-api.yaml",
"username": "tziomics"
},
"_score": 0.6217669,
"info": {
"contact": {
"email": "rw37@drexel.edu",
"name": "Rosina Weber",
"x-id": "RosinaWeber",
"x-role": "responsible developer"
},
"description": "A Translator Reasoner API for the Explanatory Agent",
"license": {
"name": "To Be Determined",
"url": "TBD"
},
"termsOfService": "TBD",
"title": "Explanatory Agent API",
"version": "1.0",
"x-reasoner_standard_version": "1.0.0",
"x-translator": {
"component": "ARA",
"team": [
"Explanatory Agent"
]
}
},
"paths": {
"/predicates/": {
"get": {
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"additionalProperties": {
"additionalProperties": {
"description": "Array of predicates",
"items": {
"type": "string"
},
"type": "array"
},
"description": "Target map",
"type": "object"
},
"description": "Source map",
"example": {
"biolink:Disease": {
"biolink:Gene": [
"biolink:condition_associated_with_gene"
]
}
},
"type": "object"
}
}
},
"description": "Predicates by source and target"
}
},
"summary": "Get supported relationships by source and target",
"tags": [
"Predicates"
],
"x-accessRestriction": "none"
}
},
"/query/": {
"post": {
"externalDocs": {
"url": "https://github.com/NCATSTranslator/Explanatory-Agent/tree/master/Agent"
},
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "A message with question graph.",
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
}
},
"description": "A message with knowledge graph and answers."
},
"400": {
"description": "The request provided does not conform to the TRAPI standard."
},
"500": {
"description": "An internal server error has occurred."
}
},
"summary": "Get answers to a question",
"tags": [
"Query"
],
"x-accessRestriction": "none"
}
}
},
"servers": [
{
"description": "Production Server",
"url": "https://explanatory-agent.azurewebsites.net/v1.0/"
}
],
"tags": [
{
"name": "explanatory"
},
{
"name": "translator"
},
{
"name": "1.0.0"
}
]
},
{
"_id": "0a29abdf1b63a762ee93d29f29a8db67",
"_meta": {
"date_created": "2021-01-22T18:08:13.583794+00:00",
"last_updated": "2021-03-29T07:01:50.562624+00:00",
"url": "https://aragorn-ranker.renci.org/openapi.json",
"username": "PhillipsOwen"
},
"_score": 0.6217669,
"info": {
"contact": {
"email": "patrick@covar.com",
"name": "Patrick Wang",
"x-id": "https://github.com/patrickkwang",
"x-role": "responsible developer"
},
"description": "ARAGORN Ranker: The ranker used by the ARAGORN ARA, which takes a TRAPI 1.0 message containing answers, and calculates numerical scores for each answer.",
"termsOfService": "http://robokop.renci.org:7055/tos?service_long=ARAGORN Ranker&provider_long=RENCI",
"title": "ARAGORN Ranker",
"version": "2.2.2",
"x-translator": {
"component": "ARA",
"team": [
"Ranking Agent"
]
}
},
"paths": {
"/omnicorp_overlay": {
"post": {
"description": "Add support to message.\n\nAdd support edges to knowledge_graph and bindings to results.",
"operationId": "query_omnicorp_overlay_post",
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Query",
"tags": [
"ARAGORN-Ranker"
]
}
},
"/score": {
"post": {
"description": "Score answers.\n\nThis is mostly glue around the heavy lifting in ranker_obj.Ranker",
"operationId": "query_score_post",
"parameters": [
{
"in": "query",
"name": "jaccard_like",
"required": false,
"schema": {
"default": false,
"title": "Jaccard Like",
"type": "boolean"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Query",
"tags": [
"ARAGORN-Ranker"
]
}
},
"/weight_correctness": {
"post": {
"description": "Weight kgraph edges based on metadata.\n\n\"19 pubs from CTD is a 1, and 2 should at least be 0.5\"\n - cbizon",
"operationId": "query_weight_correctness_post",
"parameters": [
{
"description": "Portion of cooccurrence publications relevant to a question",
"in": "query",
"name": "relevance",
"required": false,
"schema": {
"default": 0.0025,
"description": "Portion of cooccurrence publications relevant to a question",
"title": "Relevance",
"type": "number"
}
},
{
"description": "Minimum weight (at 0 publications)",
"in": "query",
"name": "wt_min",
"required": false,
"schema": {
"default": 0,
"description": "Minimum weight (at 0 publications)",
"title": "Wt Min",
"type": "number"
}
},
{
"description": "Maximum weight (at inf publications)",
"in": "query",
"name": "wt_max",
"required": false,
"schema": {
"default": 1,
"description": "Maximum weight (at inf publications)",
"title": "Wt Max",
"type": "number"
}
},
{
"description": "Publications at 50% of wt_max",
"in": "query",
"name": "p50",
"required": false,
"schema": {
"default": 2,
"description": "Publications at 50% of wt_max",
"title": "P50",
"type": "number"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
}
},
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Response"
}
}
},
"description": "Successful Response"
},
"422": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/HTTPValidationError"
}
}
},
"description": "Validation Error"
}
},
"summary": "Query",
"tags": [
"ARAGORN-Ranker"
]
}
}
},
"servers": [
{
"description": "Default server",
"url": "https://aragorn-ranker.renci.org"
}
],
"tags": [
{
"name": "translator"
},
{
"name": "ARAGORN"
},
{
"name": "ARA"
}
]
},
{
"_id": "a85f096bd4120ba065b2f25ffb68dcb0",
"_meta": {
"date_created": "2019-10-05T04:28:54.585739+00:00",
"last_updated": "2021-02-17T07:42:19.595885+00:00",
"slug": "robokop",
"url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/robokop/openapi.yml",
"username": "patrickkwang"
},
"_score": 0.6217669,
"info": {
"contact": {
"email": "patrick@covar.com",
"name": "Patrick Wang",
"url": "robokop.renci.org"
},
"description": "An API for answering biomedical questions",
"termsOfService": "https://robokop.renci.org/termsofservice/",
"title": "ROBOKOP Ranker",
"version": "0.0.1",
"x-reasoner_standard_version": "0.9.1"
},
"paths": {
"/query/": {
"post": {
"parameters": [
{
"description": "Maximum number of results to return. Provide -1 to indicate no maximum.",
"in": "query",
"name": "max_results",
"schema": {
"default": -1,
"type": "integer"
}
},
{
"description": "Requested output format. DENSE, MESSAGE, CSV or ANSWERS",
"in": "query",
"name": "output_format",
"schema": {
"default": "MESSAGE",
"type": "string"
}
},
{
"description": "Max connectivity of nodes considered in the answers, Use -1 for no restriction",
"in": "query",
"name": "max_connectivity",
"schema": {
"default": -1,
"type": "integer"
}
}
],
"requestBody": {
"content": {
"application/json": {
"example": {
"message": {
"query_graph": {
"edges": [
{
"id": "e00",
"source_id": "n00",
"target_id": "n01"
},
{
"id": "e01",
"source_id": "n01",
"target_id": "n02"
}
],
"nodes": [
{
"curie": "MONDO:0005737",
"id": "n00",
"type": "disease"
},
{
"id": "n01",
"set": true,
"type": "gene"
},
{
"id": "n02",
"type": "genetic_condition"
}
]
}
}
},
"schema": {
"$ref": "#/components/schemas/Query"
}
}
},
"description": "A message with question graph.",
"required": true
},
"responses": {
"200": {
"content": {
"application/json": {
"schema": {
"$ref": "#/components/schemas/Message"
}
}
},
"description": "A message with knowledge graph and answers."
}
},
"summary": "Get answers to a question",
"tags": [
"0.9.2"
]
}
}
},
"servers": [
{
"url": "https://robokop.renci.org/ranker/api/"
}
],
"tags": [
{
"name": "0.9.2"
},
{
"name": "translator"
},
{
"name": "reasoner"
}
]
},
{
"_id": "9df83f691d5fa0d8eb9c9f5f6b6ebb39",
"_meta": {
"date_created": "2021-01-30T21:31:39.801826+00:00",
"last_updated": "2021-03-29T07:03:29.076512+00:00",
"url": "https://bl-lookup-sri.renci.org/apidocs/openapi.yml",
"username": "kshefchek"
},
"_score": 0.6217669,
"info": {
"contact": {
"email": "bizon@renci.org",
"name": "Chris Bizon",
"x-id": "https://github.com/cbizon",
"x-role": "responsible developer"
},
"description": "The