{ "openapi": "3.0.1", "info": { "title": "ClinPGx REST API", "description": "This is the RESTful API for accessing data stored in ClinPGx. All responses are in JSON format and can be retrieved as either JSON or JSON-LD linked data format.", "termsOfService": "https://www.clinpgx.org/page/policies", "contact": { "name": "ClinPGx", "url": "https://www.clinpgx.org", "email": "api@clinpgx.org" }, "version": "1.0" }, "servers": [ { "url": "https://api.clinpgx.org/v1" } ], "tags": [ { "name": "data", "description": "How to query specific objects in ClinPGx" }, { "name": "report", "description": "Helper queries for getting connected data in ClinPGx" }, { "name": "services", "description": "ClinPGx implementations of external services" } ], "paths": { "/data/pathway": { "get": { "tags": [ "data" ], "summary": "Query Pathway objects", "parameters": [ { "name": "name", "in": "query", "description": "the name of the Pathway", "schema": { "type": "string" } }, { "name": "accessionId", "in": "query", "description": "the ClinPGx identifier of the Pathway", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/Pathway" } } } } } } } }, "/data/pathway/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve Pathway object using the ClinPGx ID", "parameters": [ { "name": "id", "in": "path", "description": "the Pathway's ClinPGx accession identifier", "required": true, "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Pathway" } } } } } } }, "/data/gene": { "get": { "tags": [ "data" ], "summary": "Query Gene objects", "parameters": [ { "name": "accessionId", "in": "query", "description": "the ClinPGx identifier of the Gene", "schema": { "type": "string" } }, { "name": "symbol", "in": "query", "description": "the HGNC symbol for the gene", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/Gene" } } } } } } } }, "/data/gene/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve a Gene using the ClinPGx ID", "parameters": [ { "name": "id", "in": "path", "description": "the Gene's ClinPGx accession identifier", "required": true, "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Gene" } } } } } } }, "/data/gene/{id}/crossReferences": { "get": { "tags": [ "data" ], "summary": "Retrieve the Cross References for a Gene using the ClinPGx ID", "parameters": [ { "name": "id", "in": "path", "description": "the Gene's ClinPGx accession identifier", "required": true, "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/CrossReference" } } } } } } } }, "/data/gene/{id}/ontologyTerms": { "get": { "tags": [ "data" ], "summary": "Retrieve the Ontology Terms for a Gene using the ClinPGx ID", "parameters": [ { "name": "id", "in": "path", "description": "the Gene's ClinPGx accession identifier", "required": true, "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/OntologyTerm" } } } } } } } }, "/data/chemical": { "get": { "tags": [ "data" ], "summary": "Query Chemical objects", "parameters": [ { "name": "accessionId", "in": "query", "description": "the ClinPGx identifier of the Chemical", "schema": { "type": "string" } }, { "name": "name", "in": "query", "description": "the name of the Chemical", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/Chemical" } } } } } } } }, "/data/chemical/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve a Chemical using the ClinPGx ID", "parameters": [ { "name": "id", "in": "path", "description": "the Chemical's ClinPGx accession identifier", "required": true, "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Chemical" } } } } } } }, "/data/disease": { "get": { "tags": [ "data" ], "summary": "Query Disease objects", "parameters": [ { "name": "accessionId", "in": "query", "description": "the ClinPGx identifier of the Disease", "schema": { "type": "string" } }, { "name": "name", "in": "query", "description": "the name of the Disease", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/Disease" } } } } } } } }, "/data/disease/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve a Disease using the ClinPGx ID", "parameters": [ { "name": "id", "in": "path", "description": "the Chemical's ClinPGx accession identifier", "required": true, "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Disease" } } } } } } }, "/data/variant/": { "get": { "tags": [ "data" ], "summary": "Query a Variant using the ClinPGx ID", "parameters": [ { "name": "symbol", "in": "query", "description": "the Variant's symbol, often the dbSNP RSID", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Variant" } } } } } } }, "/data/variant/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve a Variant using the ClinPGx ID", "parameters": [ { "name": "id", "in": "path", "description": "the Variant's ClinPGx accession identifier", "required": true, "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Variant" } } } } } } }, "/data/literature": { "get": { "tags": [ "data" ], "summary": "Query Literature objects", "parameters": [ { "name": "id", "in": "query", "description": "the ClinPGx identifier of the Literature", "schema": { "type": "string" } }, { "name": "resourceId", "in": "query", "description": "the ID for this Literature in the original resource.", "schema": { "type": "string" } }, { "name": "type", "in": "query", "description": "the type of Literature to find", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/Literature" } } } } } } } }, "/data/literature/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve a Literature object using the ID", "parameters": [ { "name": "id", "in": "path", "description": "The Literature's ID", "required": true, "schema": { "type": "number" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Literature" } } } } } } }, "/data/guidelineAnnotation": { "get": { "tags": [ "data" ], "summary": "Query GuidelineAnnotations", "parameters": [ { "name": "source", "in": "query", "description": "the source of the Guideline Annotation", "schema": { "type": "string", "enum": [ "cpic", "dpwg", "pro" ] } }, { "name": "relatedChemicals.accessionId", "in": "query", "description": "the accession ID of a chemical associated with the Guideline Annotation", "schema": { "type": "string" } }, { "name": "relatedGenes.accessionId", "in": "query", "description": "the accession ID of a gene associated with the Guideline Annotation", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/GuidelineAnnotation" } } } } } } }, "/data/guidelineAnnotation/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve a GuidelineAnnotation using the ClinPGx ID", "parameters": [ { "name": "id", "in": "path", "description": "the Guideline Annotation's ClinPGx accession identifier", "required": true, "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/GuidelineAnnotation" } } } } } } }, "/data/label": { "get": { "tags": [ "data" ], "summary": "Query DrugLabels", "parameters": [ { "name": "source", "in": "query", "description": "the source of the Drug Label", "schema": { "type": "string", "enum": [ "fda", "ema", "pmda", "hcsc" ] } }, { "name": "relatedChemicals.accessionId", "in": "query", "description": "the accession ID of a chemical associated with the Drug Label", "schema": { "type": "string" } }, { "name": "relatedChemicals.name", "in": "query", "description": "the name of a chemical associated with the Drug Label", "schema": { "type": "string" } }, { "name": "relatedGenes.accessionId", "in": "query", "description": "the accession ID of a gene associated with the Drug Label", "schema": { "type": "string" } }, { "name": "relatedGenes.symbol", "in": "query", "description": "the symbol of a gene associated with the Drug Label", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/LabelAnnotation" } } } } } } }, "/data/label/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve a Drug Label using the ClinPGx ID", "parameters": [ { "name": "id", "in": "path", "description": "the Drug Label's ClinPGx accession identifier", "required": true, "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/LabelAnnotation" } } } } } } }, "/data/summaryAnnotation": { "get": { "tags": [ "data" ], "summary": "Query Clinical Annotations", "parameters": [ { "name": "id", "in": "query", "description": "the ClinPGx identifier of the Clinical Annotation", "schema": { "type": "string" } }, { "name": "relatedChemicals.accessionId", "in": "query", "description": "the accession ID of a chemical associated with the Clinical Annotation", "schema": { "type": "string" } }, { "name": "relatedChemicals.name", "in": "query", "description": "the name of a chemical associated with the Clinical Annotation", "schema": { "type": "string" } }, { "name": "location.genes.symbol", "in": "query", "description": "the symbol of the Gene to get Clinical Annotations for", "schema": { "type": "string" } }, { "name": "location.fingerprint", "in": "query", "description": "the fingerprint (most often RSID) of the Variant to get Clinical Annotations for", "schema": { "type": "string" } }, { "name": "levelOfEvidence.term", "in": "query", "description": "the level of Clinical Annotations to retrieve", "schema": { "type": "string", "enum": [ "1A", "1B", "2A", "2B", "3", "4" ] } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/SummaryAnnotation" } } } } } } } }, "/data/summaryAnnotation/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve a Clinical Annotation using the ID", "parameters": [ { "name": "id", "in": "path", "description": "The annotation's ID", "required": true, "schema": { "type": "number" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SummaryAnnotation" } } } } } } }, "/data/variantAnnotation": { "get": { "tags": [ "data" ], "summary": "Query VariantAnnotations", "parameters": [ { "name": "location.genes.symbol", "in": "query", "description": "the symbol of the Gene to get variant annotations for", "schema": { "type": "string" } }, { "name": "location.fingerprint", "in": "query", "description": "the fingerprint (most often RSID) of the Variant to get variant annotations for", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/VariantDrugAnnotation" } } } } } } } }, "/data/variantAnnotation/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve a VariantAnnotation using the ID", "parameters": [ { "name": "id", "in": "path", "description": "The annotation's ID", "required": true, "schema": { "type": "number" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/VariantDrugAnnotation" } } } } } } }, "/data/vip/{id}": { "get": { "tags": [ "data" ], "summary": "Retrieve a VIP annotation using the ID", "parameters": [ { "name": "id", "in": "path", "description": "The annotation's ID", "required": true, "schema": { "type": "number" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/VipOverviewDisplay" } } } } } } }, "/data/ontologyTerm": { "get": { "tags": [ "data" ], "summary": "Query Ontology Terms", "parameters": [ { "name": "resource", "in": "query", "description": "the ontology resource to get terms for", "schema": { "type": "string", "enum": [ "biomarkerStatus", "alleleFunction", "cpicLevelOfEvidence", "cpicStatus", "geneTestLevel", "guidelineStrength", "levelsOfEvidence" ] } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/OntologyTerm" } } } } } } } }, "/data/dataAnnotation": { "get": { "tags": [ "data" ], "summary": "Query Data Annotations", "parameters": [ { "name": "targets.accessionId", "in": "query", "description": "the Accession ID for the object to find annotations for", "schema": { "type": "string" } }, { "name": "type", "in": "query", "description": "the type of annotation to return", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/DataAnnotation" } } } } } } } }, "/data/connection": { "get": { "tags": [ "data" ], "summary": "Query connections (aka relationships) between two objects, referred to as 'object 1' and 'object2'", "parameters": [ { "name": "object1Id", "in": "query", "description": "the ID of object 1 to find connections for", "schema": { "type": "string" } }, { "name": "object1Name", "in": "query", "description": "the name of object 1 to find connections for", "schema": { "type": "string" } }, { "name": "object1Type", "in": "query", "description": "the type of object 1 to find connections for", "schema": { "type": "string" } }, { "name": "object2Id", "in": "query", "description": "the ID of object 2 to find connections for", "schema": { "type": "string" } }, { "name": "object2Name", "in": "query", "description": "the name of object 2 to find connections for", "schema": { "type": "string" } }, { "name": "object2Type", "in": "query", "description": "the type of object 2 to find connections for", "schema": { "type": "string" } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "$ref": "#/components/schemas/Connection" } } } } } } } }, "/report/variantFrequency": { "get": { "tags": [ "report" ], "summary": "Get all variant frequency data for a given variant fingerprint", "parameters": [ { "name": "fp", "in": "query", "description": "a variant fingerprint to query (e.g. RSID)", "required": true, "schema": { "type": "string" } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/FrequencyResult" } } } } } } }, "/report/stats": { "get": { "tags": [ "report" ], "summary": "Get all the statistics for object counts in ClinPGx", "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/StatsResult" } } } } } } }, "/report/pair/{firstObjId}/{secondObjId}/{resultType}": { "get": { "tags": [ "report" ], "summary": "Retrieve all {type} objects that connect {id1} and {id2}", "parameters": [ { "name": "firstObjId", "in": "path", "description": "an object's unique identifier, either their PA# or numeric ID", "required": true, "schema": { "type": "string" } }, { "name": "secondObjId", "in": "path", "description": "a different object's unique identifier, either their PA# or numeric ID", "required": true, "schema": { "type": "string" } }, { "name": "resultType", "in": "path", "description": "the type of objects that connect the two given IDs. this will also be the type of the returned object", "required": true, "schema": { "type": "string", "enum": [ "variantAnnotation", "summaryAnnotation", "literatureAnnotation", "multilinkAnnotation", "pathway", "guidelineAnnotation", "label", "vip", "vipVariant" ] } }, { "name": "view", "in": "query", "description": "How much data to retrieve on the object", "schema": { "type": "string", "enum": [ "min", "base", "max" ] } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "description": "the returned object schema depends on the requested {type}", "items": { "type": "object", "properties": {}, "description": "The model depends on the resultType parameter" } } } } } } } }, "/report/connectedObjects/{id}/{type}": { "get": { "tags": [ "report" ], "summary": "Query all objects connected to {id} of {type} and list all types of connections between them", "parameters": [ { "name": "id", "in": "path", "description": "an object's unique identifier, either their PA# or numeric ID", "required": true, "schema": { "type": "string" } }, { "name": "type", "in": "path", "description": "the type of connected object to search for", "required": true, "schema": { "type": "string" } } ], "responses": { "200": { "description": "success", "content": { "application/json": { "schema": { "type": "array", "items": { "type": "object", "properties": { "connectedObject": { "type": "object", "properties": {}, "description": "the object that's connected to the given ID" }, "connectionTypes": { "type": "array", "description": "the types of objects that connect the 'connectedObject' to the given ID", "items": { "type": "string", "description": "a type of object" } } } } } } } } } } }, "/report/literatureId/{pmid}": { "get": { "tags": [ "report" ], "summary": "Submit a PMID and find the Literature ID for it", "parameters": [ { "name": "pmid", "in": "path", "description": "the PMID to search for", "required": true, "schema": { "type": "string" } } ], "responses": { "200": { "description": "found PMID in a Literature ID, ID in response", "content": { "application/json": { "schema": { "type": "number", "format": "integer" } } } }, "204": { "description": "PMID not stored, no Literature ID to report", "content": {} } } } }, "/infobutton": { "get": { "tags": [ "services" ], "summary": "ClinPGx implementation of InfoButton service", "description": "See [infobutton documentation](/infobutton.html) for more details on the use of request parameters.", "parameters": [ { "name": "mainSearchCriteria.v.c", "in": "query", "description": "The code/identifier for given code system", "schema": { "type": "string" } }, { "name": "mainSearchCriteria.v.cs", "in": "query", "description": "The code system for given identifier", "schema": { "type": "string", "default": "2.16.840.1.113883.6.88" } }, { "name": "mainSearchCriteria.v.dn", "in": "query", "description": "The name of a chemical", "schema": { "type": "string" } }, { "name": "mainSearchCriteria.v.ot", "in": "query", "description": "Text such as a drug name with specific form and/or dose", "schema": { "type": "string" } } ], "responses": { "200": { "description": "A HTML document of ClinPGx data resulting from the query", "content": {} } } }, "post": { "tags": [ "services" ], "summary": "ClinPGx implementation of InfoButton service", "description": "See [infobutton documentation](/infobutton.html) for more details on the use of request parameters.", "requestBody": { "content": { "application/x-www-form-urlencoded": { "schema": { "properties": { "mainSearchCriteria.v.c": { "type": "string", "description": "The code/identifier for given code system" }, "mainSearchCriteria.v.cs": { "type": "string", "description": "The code system for given identifier", "default": "2.16.840.1.113883.6.88" }, "mainSearchCriteria.v.dn": { "type": "string", "description": "The name of a chemical" }, "mainSearchCriteria.v.ot": { "type": "string", "description": "Text such as a drug name with specific form and/or dose" } } } } } }, "responses": { "200": { "description": "A HTML document of ClinPGx data resulting from the query", "content": {} } } } } }, "components": { "schemas": { "JSendSuccess": { "required": [ "data", "status" ], "type": "object", "properties": { "status": { "type": "string", "enum": [ "success" ] }, "data": { "type": "object", "properties": {} } }, "description": "Standard [JSend](https://labs.omniti.com/labs/jsend)-formatted success response." }, "JSendFailure": { "required": [ "data", "status" ], "type": "object", "properties": { "status": { "type": "string", "enum": [ "fail" ] }, "data": { "type": "object", "properties": {} } }, "description": "Standard [JSend](https://labs.omniti.com/labs/jsend)-formatted failure response." }, "JSendError": { "required": [ "message", "status" ], "type": "object", "properties": { "status": { "type": "string", "enum": [ "error" ] }, "data": { "type": "object", "properties": {} }, "code": { "type": "string" }, "message": { "type": "string" } }, "description": "Standard [JSend](https://labs.omniti.com/labs/jsend)-formatted error response." }, "Pathway": { "required": [ "id", "name" ], "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/v1/data/pathway/PA1234" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/jsonld/pathway.jsonld" }, "id": { "type": "string", "description": "The accession identifier for the Pathway", "example": "PA1234" }, "name": { "type": "string", "description": "The name of the pathway", "example": "Abacavir PD Pathway" }, "authors": { "type": "array", "description": "List of all authors of the pathway", "items": { "type": "string", "description": "Author name", "example": "John A. Smith" } }, "chemicals": { "type": "array", "description": "Chemicals related to this pathway", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "gene": { "type": "array", "description": "Genes related to this pathway", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "pathwayComponents": { "type": "array", "description": "Components of the pathway graph", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "citation": { "$ref": "#/components/schemas/Literature" }, "pharmacodynamic": { "type": "boolean", "description": "Is this a pharmacodynamic pathway?" }, "pharmacokinetic": { "type": "boolean", "description": "Is this a pharmacokinetic pathway?" } } }, "Gene": { "required": [ "id", "name", "symbol" ], "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/jsonld/pathway.jsonld" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/v1/data/pathway/PA1234" }, "id": { "type": "string", "description": "the accession identifier for this object", "example": "PA356" }, "name": { "type": "string", "description": "the full name for this gene", "example": "thiopurine S-methyltransferase" }, "symbol": { "type": "string", "description": "The HGNC symbol for this gene", "example": "TPMT" }, "objCls": { "type": "string", "description": "The class of this object", "example": "Gene", "enum": [ "Gene" ] }, "buildVersion": { "type": "string", "description": "The reference genome used to define the location of this gene", "example": "GRCh37.p10" }, "altNames": { "type": "array", "description": "All other names used to identify this gene", "items": { "$ref": "#/components/schemas/AltNames" } }, "cbStart": { "type": "string", "description": "The cytogenetic band this gene starts in", "example": "q12.34" }, "cbStop": { "type": "string", "description": "The cytogenetic band this gene ends in", "example": "q12.35" }, "chr": { "$ref": "#/components/schemas/AccessionIdentifier" }, "chrStart": { "type": "integer", "description": "Chromosomal start position, 1-based", "format": "int32", "example": 100000 }, "chrStop": { "type": "integer", "description": "Chromosomal stop position, 1-based", "format": "int32", "example": 120000 }, "strand": { "type": "string", "description": "The strand the gene appears on, +=plus, -=minus", "example": "+", "enum": [ "+", "-" ] }, "alleleFile": { "type": "string", "description": "the name of the file with allele definitions for this gene", "example": "allelesForGene.xlsx" } }, "description": "A gene object. Gene objects originate from either HGNC or NCBI Gene." }, "Vip": { "type": "object", "properties": { "id": { "type": "number", "description": "the accession identifier for this object", "format": "integer", "example": 1234 } }, "description": "A VIP annotation on a gene" }, "VipOverviewDisplay": { "type": "object", "properties": { "vip": { "$ref": "#/components/schemas/VipDisplay" }, "citation": { "$ref": "#/components/schemas/Literature" }, "spliceVips": { "type": "array", "items": { "$ref": "#/components/schemas/VipDisplay" } }, "variantVips": { "type": "array", "items": { "$ref": "#/components/schemas/VipDisplay" } }, "haplotypeVips": { "type": "array", "items": { "$ref": "#/components/schemas/VipDisplay" } }, "submitted": { "type": "string", "description": "text describing the submission history" }, "updated": { "type": "string", "description": "text describing the update history" }, "reviewed": { "type": "string", "description": "text describing the review history" } }, "description": "A simplified and enhanced VIP annotation suitable for display" }, "VipDisplay": { "type": "object", "properties": { "id": { "type": "number", "description": "the ID for this specific VIP", "format": "integer" }, "title": { "type": "string", "description": "the title of this VIP" }, "text": { "type": "string", "description": "the main body text of this VIP, in HTML" }, "appendix": { "type": "string", "description": "the appendix text of this VIP, in HTML" }, "related": { "type": "array", "description": "objects related to this VIP", "items": { "type": "object", "properties": { "typeName": { "type": "string", "description": "The name of the types of objects described here" }, "objects": { "type": "array", "description": "The related objects", "items": { "type": "object", "properties": { "text": { "type": "string", "description": "The text name of this object and what the link text should be" }, "url": { "type": "string", "description": "The url to this object, may be null" } } } } }, "description": "a group of objects related to this VIP" } } }, "description": "" }, "VipGene": { "type": "object", "properties": { "id": { "type": "string", "description": "the accession identifier for this VIP", "example": "PA123456" }, "target": { "$ref": "#/components/schemas/AccessionIdentifier" }, "citation": { "$ref": "#/components/schemas/Literature" }, "summary": { "$ref": "#/components/schemas/Markdown" }, "sections": { "$ref": "#/components/schemas/DataAnnotation" }, "relationships": { "$ref": "#/components/schemas/MultilinkAnnotation" }, "keyLiterature": { "type": "array", "description": "important literature to this VIP (is the set of all literature from each section)", "items": { "$ref": "#/components/schemas/Literature" } } }, "description": "A representation of a VIP object" }, "Markdown": { "type": "object", "properties": { "markdown": { "type": "string", "description": "Markdown formatted text", "example": "Some __markdown__ formatted text" }, "html": { "type": "string", "description": "Rendered HTML of markdown property", "example": "Some markdown formatted text" }, "rsids": { "type": "array", "description": "Array of RSIDs extracted from the markdown text", "items": { "type": "string", "example": "rs12345" } }, "relatedObjects": { "type": "array", "description": "Array of Accession Ids of Accession Objects extracted from the markdown text", "items": { "type": "string", "example": "PA12345" } }, "internalLinks": { "type": "array", "description": "Array of links to webpages on the ClinPGx domain extracted from the markdown text", "items": { "type": "string", "example": "/gene/PA123" } } }, "description": "Represents a piece of text in markdown format" }, "AccessionIdentifier": { "required": [ "id", "name" ], "type": "object", "properties": { "id": { "type": "string", "description": "the accession identifier for this object", "example": "PA356" }, "name": { "type": "string", "description": "the full name for this object", "example": "thiopurine S-methyltransferase" }, "symbol": { "type": "string", "description": "A short symbolic representation of this object", "example": "TPMT" }, "objCls": { "type": "string", "description": "The class of this object. Any accession object type can appear here, so this is deliberately not constrained to a fixed list - the concrete schemas pin their own value instead.", "example": "Gene" } }, "description": "A basic representation of an accession object. These are major domain objects and retain a durable identifier (in the form of 'PA####' that does not change over time." }, "AltNames": { "type": "object", "properties": { "symbols": { "type": "array", "description": "Other symbols that can be used to identify this object", "items": { "type": "string" } }, "synonyms": { "type": "array", "description": "Other names that can be used to identify this object", "items": { "type": "string" } }, "generic": { "type": "array", "description": "Generic names, usually from a naming standards body like USN or INN (only applicable to chemicals)", "items": { "type": "string" } }, "trade": { "type": "array", "description": "Trade names used by manufacturers for a drug (only applicable to chemicals)", "items": { "type": "string" } } } }, "VariantLocation": { "type": "object", "properties": { "id": { "type": "integer", "description": "System-generated identifier for this location, (more than one ID can exist for the same position", "format": "int32" }, "name": { "type": "string", "description": "A name to identify this variant. This will be used if type=undefined", "example": "Splice acceptor site" }, "chromosomeName": { "type": "string", "description": "name of the chromosome this variant location is on", "example": "chr12" }, "copyNumber": { "type": "integer", "description": "the number of copies of this variation", "format": "int32", "example": 2 }, "displayName": { "type": "string", "description": "a human-readable name for this variant that varies depending on type", "example": "rs12345, GENEA *1" }, "genes": { "type": "array", "description": "genes that this variant is associated with", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "gpPosition": { "type": "integer", "description": "Chromosomal position of this variant, 1-based, on the plus strand", "format": "int32" }, "refSeqCrossReference": { "type": "object", "properties": {}, "description": "The reference sequence this variant appears on, should be either NCBI RefSeq or GenBank" }, "refSeqPosition": { "type": "integer", "description": "Position of this variant on the reference sequence specified in refSeqCrossReference", "format": "int32" }, "rsid": { "type": "string", "description": "The dbSNP identifier for this variant", "example": "rs12345" }, "haplotypes": { "type": "array", "description": "The haplotype(s) this variant represents. This will only be used if type=haplotype", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "diplotypes": { "type": "array", "description": "The diplotype(s) this variant represents", "items": { "$ref": "#/components/schemas/Diplotype" } }, "genePhenotype": { "$ref": "#/components/schemas/OntologyTerm" }, "tagGene": { "type": "boolean", "description": "Indicates that genes has been overridden from the default set for this location (and there will only be one gene)" }, "type": { "type": "string", "description": "The type of this variant: snp = single location SNP, haplotype = one or more haplotypes, cnv = copy number variation, undefinedSnp = variation with an undefined location", "enum": [ "snp", "haplotype", "cnv", "undefinedSnp" ] }, "variant": { "$ref": "#/components/schemas/AccessionIdentifier" }, "linkedObjects": { "type": "array", "description": "A collection of both the 'haplotypes' and 'variant' fields. This is a definitive set of what this object is about", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } } } }, "HaplotypeAllele": { "type": "object", "properties": { "id": { "type": "number", "description": "the identifier for this allele", "format": "integer", "example": 1234 }, "allele": { "type": "string", "description": "the allele at this location", "example": "G" }, "location": { "$ref": "#/components/schemas/VariantLocation" } } }, "Haplotype": { "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/jsonld/pathway.jsonld" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/v1/data/pathway/PA1234" }, "id": { "type": "string", "description": "the accession identifier for this object", "example": "PA1234" }, "name": { "type": "string", "description": "the full name for this haplotype", "example": "*1" }, "objCls": { "type": "string", "description": "The class of this object", "example": "Haplotype", "enum": [ "Haplotype" ] }, "alleles": { "type": "array", "description": "the alleles and their location that constitute this haplotype", "items": { "$ref": "#/components/schemas/HaplotypeAllele" } }, "copyNumber": { "type": "string", "description": "", "example": "1" }, "gene": { "$ref": "#/components/schemas/AccessionIdentifier" } } }, "Diplotype": { "required": [ "allele1" ], "type": "object", "properties": { "allele1": { "type": "string", "description": "The first allele in the Diplotype, will be an allele of a SNP or a Haplotype name", "example": "*1" }, "allele2": { "type": "string", "description": "The second allele in the Diplotype, will be an allele of a SNP or a Haplotype name. This can be null if on a sex chromosome or is mitochondrial.", "example": "*3" } } }, "CrossReference": { "required": [ "id" ], "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/v1/data/pathway/PA1234" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/jsonld/pathway.jsonld" }, "id": { "type": "integer", "description": "System-generated identifier for this crossReference", "format": "int32" }, "name": { "type": "string", "description": "The name to display in the cross reference link (optional)" }, "_url": { "type": "string", "description": "URL to the other resource" }, "resource": { "type": "string", "description": "The name of the other resource" }, "resourceId": { "type": "string", "description": "The identifier for this object in the other resource" } }, "description": "Cross reference to this object in another resource" }, "LinkOut": { "required": [ "id" ], "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/v1/data/pathway/PA1234" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/jsonld/pathway.jsonld" }, "id": { "type": "integer", "description": "System-generated identifier", "format": "int32" }, "name": { "type": "string", "description": "The descriptive name assigned to this link (optional)" }, "_url": { "type": "string", "description": "URL to the other resource" }, "resource": { "type": "string", "description": "The name of the resource linked to" }, "resourceId": { "type": "string", "description": "The identifier for this object in the other resource" } }, "description": "A link from this object to another equivalent entry at another resource" }, "OntologyTerm": { "required": [ "src", "term", "termId" ], "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/v1/data/ontologyTerm/ATC/A01AB" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/jsonld/pathway.jsonld" }, "id": { "type": "number", "description": "The accession identifier for the Ontology Term", "example": 12345 }, "resource": { "type": "string", "description": "The resource this ontology term comes from", "example": "ATC" }, "term": { "type": "string", "description": "The resource-specific term of this ontology term", "example": "Antiinfectives and antiseptics for local oral treatment" }, "termId": { "type": "string", "description": "The resource-specific ID of this ontology term", "example": "A01AB" }, "description": { "type": "string", "description": "More information about this term, optional" } } }, "VariantDrugAnnotation": { "required": [ "id" ], "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/v1/data/variantAnnotation/12345" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/jsonld/pathway.jsonld" }, "id": { "type": "integer", "description": "The identifier for this annotation", "format": "int32" }, "objCls": { "type": "string", "description": "The class of this object", "example": "VariantAnnotation", "enum": [ "VariantAnnotation", "VariantDrugAnnotation", "VariantPhenotypeAnnotation", "VariantFunctionalAssayAnnotation" ] }, "alleleGenotype": { "type": "string", "description": "The allele/genotype that is being annotated", "example": "T" }, "comparison": { "type": "string", "description": "The allele/genotype to compare against", "example": "G" }, "connWords1": { "$ref": "#/components/schemas/OntologyTerm" }, "description": { "type": "string", "description": "An optional further description of this annotation" }, "drugsConnWord": { "$ref": "#/components/schemas/OntologyTerm" }, "isAssociated": { "type": "boolean", "description": "Whether this is a positive association (true) or a negative association (false)" }, "isPlural": { "type": "boolean", "description": "Whether alleleGenotype is single (false) or plural (true), used when generating the sentence" }, "literature": { "$ref": "#/components/schemas/Literature" }, "location": { "$ref": "#/components/schemas/VariantLocation" }, "phenotypeCategories": { "type": "array", "description": "", "items": { "$ref": "#/components/schemas/OntologyTerm" } }, "relatedChemicals": { "type": "array", "description": "The chemicals used in this annotation", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "sentence": { "type": "string", "description": "The annotation. This is generated from most of the other properties in this object." }, "significance": { "$ref": "#/components/schemas/OntologyTerm" }, "studyParameters": { "type": "array", "description": "The statistical parameters found in the literature that support this annotation.", "items": { "$ref": "#/components/schemas/StudyParameters" } } } }, "StudyParameters": { "required": [ "id", "ratioStatType" ], "type": "object", "properties": { "id": { "type": "integer", "description": "The identifier for this annotation", "format": "int32" }, "alleleOfFreqInCases": { "type": "string" }, "alleleOfFreqInControls": { "type": "string" }, "characteristics": { "type": "string" }, "characteristicsType": { "type": "string" }, "confidenceIntervalStart": { "type": "number", "format": "float" }, "confidenceIntervalStop": { "type": "number", "format": "float" }, "frequencyInCases": { "type": "number", "format": "float" }, "frequencyInControls": { "type": "number", "format": "float" }, "mixedPopulation": { "type": "boolean" }, "populationTypes": { "type": "array", "items": { "$ref": "#/components/schemas/OntologyTerm" } }, "pvalue": { "type": "number", "format": "float" }, "pvalueOp": { "$ref": "#/components/schemas/OntologyTerm" }, "pvalueString": { "type": "string" }, "ratioStat": { "type": "number", "format": "float" }, "ratioStatType": { "$ref": "#/components/schemas/OntologyTerm" }, "statTests": { "type": "array", "items": { "$ref": "#/components/schemas/OntologyTerm" } }, "studyCases": { "type": "number", "format": "int32" }, "studyControls": { "type": "number", "format": "int32" }, "studyType": { "type": "string", "description": "A description of the type of study being quantified" }, "unknownRace": { "type": "boolean", "description": "Was race description missing in this study? yes = true, no = false" } } }, "Literature": { "required": [ "id", "resourceId", "title", "type" ], "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/v1/data/literature/12920170" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/v1/data/literature.jsonld" }, "id": { "type": "integer", "description": "The ClinPGx identifier for this literature", "format": "int32" }, "resourceId": { "type": "string", "description": "The unique external identifier for this literature: PubMed ID for type=pubmed; URL for type=url; ISBN for type=book", "example": "12345678" }, "title": { "type": "string", "description": "The full title of this literature" }, "authors": { "type": "array", "description": "The list of author names for this literature", "items": { "type": "string", "description": "Author name", "example": "Jane Q. Doe" } }, "journal": { "type": "string", "description": "The name of the journal this literature was published in" }, "month": { "type": "integer", "description": "The month of publication", "format": "int32", "example": 5 }, "page": { "type": "string", "description": "The pages where this literature can be found in the journal" }, "pubDate": { "type": "string", "description": "The date of publication (no time-of-day component)", "format": "date" }, "type": { "type": "string", "description": "The type of this piece of literature", "enum": [ "article", "book", "url" ] }, "volume": { "type": "string", "description": "The volume where this literature can be found in the journal" }, "year": { "type": "integer", "description": "The year of publication", "format": "int32", "example": 2009 } } }, "Chemical": { "required": [ "id", "name" ], "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/jsonld/chemical.jsonld" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/v1/data/pathway/PA1234" }, "id": { "type": "string", "description": "the accession identifier for this object", "example": "PA452632" }, "name": { "type": "string", "description": "the full name for this chemical", "example": "non-existium" }, "objCls": { "type": "string", "description": "The class of this object", "example": "Chemical", "enum": [ "Chemical" ] }, "altNames": { "type": "array", "description": "All other names used to identify this Chemical", "items": { "$ref": "#/components/schemas/AltNames" } }, "types": { "type": "array", "description": "What types this Chemical could be categorized as", "items": { "type": "string", "description": "A Chemical type as defined by ClinPGx", "enum": [ "drug", "smallmolecule", "prodrug", "metabolite" ] } }, "linkOuts": { "type": "array", "description": "The links from this Chemical to other systems", "items": { "$ref": "#/components/schemas/LinkOut" } } }, "description": "A chemical object. Chemical objects are some compound of small molecules, a subset of which can be used for therapeutic purposes." }, "Disease": { "required": [ "id", "name" ], "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/jsonld/chemical.jsonld" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/v1/data/pathway/PA1234" }, "id": { "type": "string", "description": "the accession identifier for this object", "example": "PA452632" }, "name": { "type": "string", "description": "the full name for this disease", "example": "non-existium" }, "objCls": { "type": "string", "description": "The class of this object", "example": "Phenotype", "enum": [ "Phenotype" ] }, "altNames": { "type": "array", "description": "All other names used to identify this Disease", "items": { "$ref": "#/components/schemas/AltNames" } }, "terms": { "type": "array", "description": "The ontology terms this Disease is equivalent to", "items": { "$ref": "#/components/schemas/OntologyTerm" } } }, "description": "A Disease object. This also includes other phenotypes that may not technically be diseases" }, "SummaryAnnotation": { "required": [ "id" ], "type": "object", "properties": { "id": { "type": "integer", "description": "The identifier for this annotation", "format": "int32" }, "levelOfEvidence": { "$ref": "#/components/schemas/OntologyTerm" }, "location": { "$ref": "#/components/schemas/VariantLocation" }, "relatedChemicals": { "type": "array", "description": "The chemicals described in this annotation", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "relatedChemicalsLogic": { "type": "string", "description": "Describes the logic that links all the Chemicals in relatedChemicals. A value of AND means a combination of all those chemicals, a value of OR means any one of the listed chemicals", "example": "OR", "enum": [ "AND", "OR" ] }, "allelePhenotypes": { "$ref": "#/components/schemas/AllelePhenotype" } }, "description": "" }, "AllelePhenotype": { "type": "object", "properties": { "allele": { "type": "string", "description": "The genotype allele at the annotation's location that the phenotype applies to", "example": "AT" }, "phenotype": { "type": "string", "description": "The phenotype description for the associated allele", "example": "Patients with the AT genotype are more likely to understand this API" } }, "description": "" }, "StatsResult": { "type": "object", "properties": { "statName": { "type": "object", "properties": { "count": { "type": "number", "description": "the count for this statistic", "format": "integer", "example": 12345 }, "comment": { "type": "string", "description": "an explanatory comment for this statistic", "example": "the number of annotated kittens in ClinPGx" }, "category": { "type": "string", "description": "the category of this statistic", "example": "DbStat" } }, "description": "The statistic payload, the key for this property will change per statistic type" } }, "description": "An object to hold all the counts keyed by the count type" }, "PublicationsResult": { "type": "object", "properties": { "pathways": { "type": "array", "description": "A list of literature with their associated pathways", "items": { "type": "object", "properties": { "literature": { "$ref": "#/components/schemas/Literature" }, "pathways": { "type": "array", "items": { "$ref": "#/components/schemas/LinkObject" } } } } }, "dosingGuidelines": { "type": "array", "description": "A list of literature with their associated Guideline Annotations", "items": { "type": "object", "properties": { "literature": { "$ref": "#/components/schemas/Literature" }, "guidelines": { "type": "array", "items": { "$ref": "#/components/schemas/LinkObject" } } } } }, "vips": { "type": "array", "description": "A list of literature with their associated Guideline Annotations", "items": { "type": "object", "properties": { "literature": { "$ref": "#/components/schemas/Literature" }, "vips": { "type": "array", "items": { "$ref": "#/components/schemas/LinkObject" } } } } }, "other": { "type": "array", "description": "A list of other literature objects to link to", "items": { "$ref": "#/components/schemas/Literature" } } }, "description": "An object to hold all the publications by ClinPGx grouped by annotation" }, "FrequencyResult": { "type": "object", "properties": { "frequencyMap": { "$ref": "#/components/schemas/FrequencyMap" }, "refBases": { "type": "array", "description": "The reference alleles", "items": { "type": "string", "example": "A" } }, "varBases": { "type": "array", "description": "The variant alleles", "items": { "type": "string", "example": "G" } }, "dbSnpId": { "type": "string", "description": "The dbSNP identifier (RSID) for this variant", "example": "rs2228001" } }, "description": "An object that holds variant frequency information for a given variant in multiple populations" }, "FrequencyMap": { "type": "object", "properties": { "popCode": { "type": "object", "properties": { "baseFrequencies": { "type": "object", "properties": { "allele": { "type": "number", "format": "double", "example": 0.825 } }, "description": "the frequency of all samples in this population with this allele" }, "baseSize": { "type": "object", "properties": { "allele": { "type": "number", "format": "integer", "example": 124 } }, "description": "the number of samples with this allele" } }, "description": "a collection of samples from a particular HapMap population (defined by HapMap)" } }, "description": "a mapping of population codes to objects describing that population's frequencies" }, "GuidelineAnnotation": { "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/jsonld/chemical.jsonld" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/v1/data/pathway/PA1234" }, "id": { "type": "string", "description": "the accession identifier for this object", "example": "PA452632" }, "name": { "type": "string", "description": "the full name for this guideline" }, "objCls": { "type": "string", "description": "The class of this object", "example": "GuidelineAnnotation", "enum": [ "GuidelineAnnotation" ] }, "relatedChemicals": { "type": "array", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "relatedGenes": { "type": "array", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "source": { "type": "string", "description": "the group that authored this guideline", "enum": [ "cpic", "dpwg", "pro" ] }, "summaryMarkdown": { "$ref": "#/components/schemas/Markdown" }, "textMarkdown": { "$ref": "#/components/schemas/Markdown" } } }, "LabelAnnotation": { "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/jsonld/chemical.jsonld" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/v1/data/pathway/PA1234" }, "id": { "type": "string", "description": "the accession identifier for this object", "example": "PA452632" }, "name": { "type": "string", "description": "the full name for this guideline" }, "objCls": { "type": "string", "description": "The class of this object", "example": "LabelAnnotation", "enum": [ "LabelAnnotation" ] }, "relatedChemicals": { "type": "array", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "relatedGenes": { "type": "array", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "source": { "type": "string", "description": "the group that authored this label", "enum": [ "fda", "hcsc", "ema" ] }, "summaryMarkdown": { "$ref": "#/components/schemas/Markdown" }, "textMarkdown": { "$ref": "#/components/schemas/Markdown" }, "biomarkerStatus": { "$ref": "#/components/schemas/OntologyTerm" }, "labelXref": { "$ref": "#/components/schemas/CrossReference" }, "testing": { "$ref": "#/components/schemas/OntologyTerm" } } }, "SequenceLocation": { "type": "object", "properties": { "id": { "type": "number", "description": "The ClinPGx-assigned identifier for this", "format": "integer", "example": 12345 }, "name": { "type": "string", "description": "the name of this sequence location", "example": "[GRCh37]chrN:########" }, "begin": { "type": "number", "description": "the beginning index of the sequence location of this variant, 1-based", "format": "integer", "example": 98765 }, "end": { "type": "number", "description": "the ending index of the sequence location of this variant, 1-based (can be same as begin if only 1bp long)", "format": "integer", "example": 98766 }, "reference": { "type": "string", "description": "the reference allele for this variant", "example": "A" }, "sequence": { "$ref": "#/components/schemas/CrossReference" }, "source": { "type": "string", "description": "the source of this location data", "example": "dbSNP" }, "type": { "type": "string", "description": "the type of sequence this is", "enum": [ "g", "c", "m", "n", "r", "p" ] }, "variants": { "type": "array", "description": "the variant alleles for this variant", "items": { "type": "string", "description": "a variant allele", "example": "G" } } } }, "Variant": { "type": "object", "properties": { "@id": { "type": "string", "description": "JSON-LD property used to uniquely identify things that are being described in the document with IRIs or blank node identifiers", "example": "https://api.clinpgx.org/jsonld/chemical.jsonld" }, "@context": { "type": "string", "description": "JSON-LD property used to define the short-hand names that are used throughout a JSON-LD document.", "example": "https://api.clinpgx.org/v1/data/pathway/PA1234" }, "id": { "type": "string", "description": "the accession identifier for this object", "example": "PA452632" }, "name": { "type": "string", "description": "the full name for this variant" }, "symbol": { "type": "string", "description": "the symbol for this variant, optional, often a dbSNP identifier" }, "objCls": { "type": "string", "description": "The class of this object", "example": "Variant", "enum": [ "Variant" ] }, "altNames": { "type": "array", "description": "All other names used to identify this gene", "items": { "$ref": "#/components/schemas/AltNames" } }, "alternateLocations": { "type": "array", "description": "All other locations this variant has been mapped to", "items": { "$ref": "#/components/schemas/SequenceLocation" } }, "location": { "$ref": "#/components/schemas/SequenceLocation" }, "changeClassification": { "type": "string", "description": "the type of change this variation may produce or where it falls in relation to the gene" }, "clinicalSignificance": { "type": "string", "description": "the clinical significance of this variation as report by dbSNP" }, "relatedGenes": { "type": "array", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "type": { "type": "string", "description": "the type of variant this is" } } }, "DataAnnotation": { "type": "object", "properties": { "id": { "type": "number", "description": "The ClinPGx-assigned identifier for this annotation", "format": "integer", "example": 12345 }, "text": { "type": "string", "description": "The plain text of the annotation - non-null if the annotation's source is not ClinPGx or its DataAnnotationType does not support markdown text", "example": "Will turn your hair purple and your teeth green" }, "markdown": { "$ref": "#/components/schemas/Markdown" }, "sources": { "type": "array", "description": "the sources this information comes from", "items": { "type": "string", "description": "The name of the source of this information", "example": "drugBank" } }, "targets": { "type": "array", "description": "the things this annotation should be displayed on, what this annotation is about", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "type": { "type": "string", "description": "the type of annotation that this is", "example": "description" }, "userId": { "type": "string", "description": "who entered this annotation", "example": "joeblow" } } }, "MultilinkAnnotation": { "type": "object", "properties": { "id": { "type": "number", "description": "The ClinPGx-assigned identifier for this annotation", "format": "integer", "example": 12345 }, "literature": { "type": "array", "description": "Literature supporting this annotation", "items": { "$ref": "#/components/schemas/Literature" } }, "object1s": { "type": "array", "description": "Objects making up one side of the relationship", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "object2s": { "type": "array", "description": "Objects making up the second side of the relationship", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "operator1": { "type": "boolean", "description": "The operator for how the objects in object1s property are associated" }, "operator2": { "type": "boolean", "description": "The operator for how the objects in object2s property are associated" }, "related": { "type": "boolean", "description": "Whether the object1s group is (or is not) related to the object2s group" }, "terms": { "type": "array", "description": "An array of ontology terms that describe the relationship between the object1s group and object2s group", "items": { "$ref": "#/components/schemas/OntologyTerm" } } } }, "LiteratureAnnotation": { "type": "object", "properties": { "id": { "type": "number", "description": "The ClinPGx-assigned identifier for this annotation", "format": "integer", "example": 12345 } } }, "LinkObject": { "type": "object", "properties": { "linkText": { "type": "string", "description": "Text to display for the link", "example": "hi, I'm link text" }, "url": { "type": "string", "description": "The partial URL for this link", "example": "/class/PA1234" } } }, "Page": { "type": "object", "properties": { "id": { "type": "number", "description": "a unique integer identifier", "format": "integer" }, "key": { "type": "string", "description": "a unique short String for this page, camel-cased", "example": "pageKey" }, "title": { "type": "string", "description": "a title to be displayed as the main heading for this page", "example": "I have a HAM radio" }, "markdown": { "$ref": "#/components/schemas/Markdown" }, "version": { "type": "number", "description": "the version number of this page, iterates on edits", "format": "integer" } }, "description": "Full or partial page content generated from markdown text" }, "DosingGuidelineAnnotation": { "type": "object", "properties": { "id": { "type": "integer", "format": "int32" }, "markdown": { "$ref": "#/components/schemas/Markdown" }, "type": { "$ref": "#/components/schemas/OntologyTerm" } } }, "VersionResponse": { "type": "array", "items": { "type": "object", "properties": { "name": { "type": "string", "description": "the name of the property", "example": "dbSNP" }, "version": { "type": "string", "description": "the description of the version, could be build, date, or any textual descriptor", "example": "build 146" } }, "description": "Version information for a data source" } }, "UserResponse": { "type": "object", "properties": { "userId": { "type": "string" }, "email": { "type": "string" }, "displayName": { "type": "string" }, "fullName": { "type": "string" }, "position": { "type": "string" }, "dept": { "type": "string" }, "institution": { "type": "string" }, "country": { "type": "string" } } }, "LabelSummary": { "type": "object", "properties": { "url": { "type": "string", "description": "a partial URL for this label" }, "status": { "type": "string", "description": "what does this label say about genetic testing" }, "biomarker": { "type": "boolean", "description": "is this label part of the FDA biomarker list" }, "dosingInfo": { "type": "boolean", "description": "does this label include information on dosing" } } }, "GuidelineSummary": { "type": "object", "properties": { "url": { "type": "string", "description": "a partial URL for this guideline" }, "genes": { "type": "string", "description": "a comma-delimited list of gene symbols for this guideline" }, "updatedDate": { "type": "string", "description": "the date of the last published change to this guideline, may be null", "format": "date-time" } } }, "DisplayLiteratureResponse": { "required": [ "publication" ], "type": "object", "properties": { "publication": { "$ref": "#/components/schemas/Literature" }, "variantAnnotations": { "type": "array", "items": { "$ref": "#/components/schemas/VariantDrugAnnotation" } }, "literatureAnnotation": { "$ref": "#/components/schemas/LiteratureAnnotation" }, "relationships": { "type": "array", "items": { "type": "object", "properties": {}, "description": "A multilink annotation" } }, "pathways": { "type": "array", "items": { "$ref": "#/components/schemas/Pathway" } }, "dosingInfo": { "type": "array", "items": { "$ref": "#/components/schemas/DataAnnotation" } }, "dosingGuidelines": { "type": "array", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } } } }, "VariantAnnotationDisplay": { "type": "object", "properties": { "id": { "type": "number", "format": "integer" }, "variants": { "type": "array", "items": { "type": "object", "properties": { "name": { "type": "string" }, "id": { "type": "string" }, "url": { "type": "string" } } } }, "literature": { "type": "string", "description": "the PMID of the annotated literature" }, "literatureUrl": { "type": "string", "description": "the URL for the annotated literature" }, "significance": { "type": "string", "description": "was the annotation significant? yes or no" }, "chemicals": { "type": "array", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "genes": { "type": "array", "items": { "$ref": "#/components/schemas/AccessionIdentifier" } }, "phenotypeCategories": { "type": "string" }, "sentence": { "type": "string" }, "notes": { "type": "string" }, "cases": { "type": "number", "format": "integer" }, "controls": { "type": "number", "format": "integer" }, "pvalue": { "type": "string" }, "race": { "type": "string" } }, "description": "a simplified version of a variant annotation model for display on the site" }, "Connection": { "type": "object", "description": "a simple record derived from an existing annotation that relates one object (object 1) to another (object 2)", "properties": { "object1Id": { "type": "string" }, "object1Name": { "type": "string" }, "object1Type": { "type": "string" }, "object2Id": { "type": "string" }, "object2Name": { "type": "string" }, "object2Type": { "type": "string" }, "relId": { "type": "string" }, "relType": { "type": "string" }, "associated": { "type": "boolean" }, "pd": { "type": "boolean" }, "pk": { "type": "boolean" }, "pmid": { "type": "array", "description": "the PMIDs for annotations this connection comes from", "items": { "type": "string", "description": "A PubMed identifier" } } } } }, "responses": { "400": { "description": "Bad request.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/JSendFailure" } } } }, "401": { "description": "Not authorized.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/JSendFailure" } } } }, "403": { "description": "Forbidden.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/JSendFailure" } } } }, "404": { "description": "Not found.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/JSendFailure" } } } } }, "requestBodies": { "authForm": { "content": { "*/*": { "schema": { "required": [ "email", "password" ], "type": "object", "properties": { "email": { "type": "string" }, "password": { "type": "string", "format": "password" } } } } }, "required": false } } } }