{ "swagger": "2.0", "info": { "description": "A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.", "version": "1.0 (beta)", "title": "cBioPortal web API [Beta]", "contact": { "name": "cBioPortal", "url": "http://www.cbioportal.org", "email": "cbioportal@googlegroups.com" }, "license": { "name": "License", "url": "https://github.com/cBioPortal/cbioportal/blob/master/LICENSE" } }, "host": "www.cbioportal.org", "basePath": "/api", "tags": [ { "name": "Cancer Types", "description": " " }, { "name": "Clinical Attributes", "description": " " }, { "name": "Clinical Data", "description": " " }, { "name": "Clinical Events", "description": " " }, { "name": "Copy Number Segments", "description": " " }, { "name": "Discrete Copy Number Alterations", "description": " " }, { "name": "Gene Panels", "description": " " }, { "name": "Genes", "description": " " }, { "name": "Molecular Data", "description": " " }, { "name": "Molecular Profiles", "description": " " }, { "name": "Mutations", "description": " " }, { "name": "Patients", "description": " " }, { "name": "Sample Lists", "description": " " }, { "name": "Samples", "description": " " }, { "name": "Studies", "description": " " } ], "schemes": [ "http", "https" ], "paths": { "/cancer-types": { "get": { "tags": [ "Cancer Types" ], "summary": "Get all cancer types", "operationId": "getAllCancerTypesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "cancerTypeId", "name", "clinicalTrialKeywords", "dedicatedColor", "shortName", "parent" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/TypeOfCancer" } } } } } }, "/cancer-types/{cancerTypeId}": { "get": { "tags": [ "Cancer Types" ], "summary": "Get a cancer type", "operationId": "getCancerTypeUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "cancerTypeId", "in": "path", "description": "Cancer Type ID e.g. acc", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/TypeOfCancer" } } } } }, "/clinical-attributes": { "get": { "tags": [ "Clinical Attributes" ], "summary": "Get all clinical attributes", "operationId": "getAllClinicalAttributesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "clinicalAttributeId", "displayName", "description", "datatype", "patientAttribute", "priority", "studyId" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalAttribute" } } } } } }, "/clinical-attributes/counts/fetch": { "post": { "tags": [ "Clinical Attributes" ], "summary": "Get counts for clinical attributes according to their data availability for selected samples/patients", "operationId": "getClinicalAttributeCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "clinicalAttributeCountFilter", "description": "List of SampleIdentifiers or Sample List ID", "required": true, "schema": { "$ref": "#/definitions/ClinicalAttributeCountFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalAttributeCount" } } } } } }, "/clinical-attributes/fetch": { "post": { "tags": [ "Clinical Attributes" ], "summary": "Fetch clinical attributes", "operationId": "fetchClinicalAttributesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyIds", "description": "List of Study IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalAttribute" } } } } } }, "/clinical-data/fetch": { "post": { "tags": [ "Clinical Data" ], "summary": "Fetch clinical data by patient IDs or sample IDs (all studies)", "operationId": "fetchClinicalDataUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "clinicalDataType", "in": "query", "description": "Type of the clinical data", "required": false, "type": "string", "default": "SAMPLE", "enum": [ "SAMPLE", "PATIENT" ] }, { "in": "body", "name": "clinicalDataMultiStudyFilter", "description": "List of patient or sample identifiers and attribute IDs", "required": true, "schema": { "$ref": "#/definitions/ClinicalDataMultiStudyFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalData" } } } } } }, "/copy-number-segments/fetch": { "post": { "tags": [ "Copy Number Segments" ], "summary": "Fetch copy number segments by sample ID", "operationId": "fetchCopyNumberSegmentsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "sampleIdentifiers", "description": "List of sample identifiers", "required": true, "schema": { "type": "array", "items": { "$ref": "#/definitions/SampleIdentifier" } } }, { "name": "chromosome", "in": "query", "description": "Chromosome", "required": false, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CopyNumberSeg" } } } } } }, "/gene-panel-data/fetch": { "post": { "tags": [ "Gene Panels" ], "summary": "Fetch gene panel data", "operationId": "fetchGenePanelDataInMultipleMolecularProfilesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genePanelMultipleStudyFilter", "description": "List of Molecular Profile ID and Sample ID pairs", "required": true, "schema": { "$ref": "#/definitions/GenePanelMultipleStudyFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenePanelData" } } } } } }, "/gene-panels": { "get": { "tags": [ "Gene Panels" ], "summary": "Get all gene panels", "operationId": "getAllGenePanelsUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "genePanelId", "description" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenePanel" } } } } } }, "/gene-panels/fetch": { "post": { "tags": [ "Gene Panels" ], "summary": "Get gene panel", "operationId": "fetchGenePanelsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genePanelIds", "description": "List of Gene Panel IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenePanel" } } } } } }, "/gene-panels/{genePanelId}": { "get": { "tags": [ "Gene Panels" ], "summary": "Get gene panel", "operationId": "getGenePanelUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "genePanelId", "in": "path", "description": "Gene Panel ID e.g. NSCLC_UNITO_2016_PANEL", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/GenePanel" } } } } }, "/genes": { "get": { "tags": [ "Genes" ], "summary": "Get all genes", "operationId": "getAllGenesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "keyword", "in": "query", "description": "Search keyword that applies to hugo gene symbol of the genes", "required": false, "type": "string" }, { "name": "alias", "in": "query", "description": "Alias of the gene", "required": false, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 100000, "maximum": 100000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "entrezGeneId", "hugoGeneSymbol", "type", "cytoband", "length" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Gene" } } } } } }, "/genes/fetch": { "post": { "tags": [ "Genes" ], "summary": "Fetch genes by ID", "operationId": "fetchGenesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "geneIdType", "in": "query", "description": "Type of gene ID", "required": false, "type": "string", "default": "ENTREZ_GENE_ID", "enum": [ "ENTREZ_GENE_ID", "HUGO_GENE_SYMBOL" ] }, { "in": "body", "name": "geneIds", "description": "List of Entrez Gene IDs or Hugo Gene Symbols", "required": true, "schema": { "type": "array", "items": { "type": "string" } } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Gene" } } } } } }, "/genes/{geneId}": { "get": { "tags": [ "Genes" ], "summary": "Get a gene", "operationId": "getGeneUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "geneId", "in": "path", "description": "Entrez Gene ID or Hugo Gene Symbol e.g. 1 or A1BG", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/Gene" } } } } }, "/genes/{geneId}/aliases": { "get": { "tags": [ "Genes" ], "summary": "Get aliases of a gene", "operationId": "getAliasesOfGeneUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "geneId", "in": "path", "description": "Entrez Gene ID or Hugo Gene Symbol e.g. 1 or A1BG", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "type": "string" } } } } } }, "/molecular-data/fetch": { "post": { "tags": [ "Molecular Data" ], "summary": "Fetch molecular data", "operationId": "fetchMolecularDataInMultipleMolecularProfilesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "molecularDataMultipleStudyFilter", "description": "List of Molecular Profile ID and Sample ID pairs or List of MolecularProfile IDs and Entrez Gene IDs", "required": true, "schema": { "$ref": "#/definitions/MolecularDataMultipleStudyFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/NumericGeneMolecularData" } } } } } }, "/molecular-profiles": { "get": { "tags": [ "Molecular Profiles" ], "summary": "Get all molecular profiles", "operationId": "getAllMolecularProfilesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "molecularProfileId", "molecularAlterationType", "datatype", "name", "description", "showProfileInAnalysisTab" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/MolecularProfile" } } } } } }, "/molecular-profiles/fetch": { "post": { "tags": [ "Molecular Profiles" ], "summary": "Fetch molecular profiles", "operationId": "fetchMolecularProfilesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "molecularProfileFilter", "description": "List of Molecular Profile IDs or List of Study IDs", "required": true, "schema": { "$ref": "#/definitions/MolecularProfileFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/MolecularProfile" } } } } } }, "/molecular-profiles/{molecularProfileId}": { "get": { "tags": [ "Molecular Profiles" ], "summary": "Get molecular profile", "operationId": "getMolecularProfileUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_mutations", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/MolecularProfile" } } } } }, "/molecular-profiles/{molecularProfileId}/discrete-copy-number": { "get": { "tags": [ "Discrete Copy Number Alterations" ], "summary": "Get discrete copy number alterations in a molecular profile", "operationId": "getDiscreteCopyNumbersInMolecularProfileUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_gistic", "required": true, "type": "string" }, { "name": "sampleListId", "in": "query", "description": "Sample List ID e.g. acc_tcga_all", "required": true, "type": "string" }, { "name": "discreteCopyNumberEventType", "in": "query", "description": "Type of the copy number event", "required": false, "type": "string", "default": "HOMDEL_AND_AMP", "enum": [ "HOMDEL_AND_AMP", "HOMDEL", "AMP", "GAIN", "HETLOSS", "DIPLOID", "ALL" ] }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/DiscreteCopyNumberData" } } } } } }, "/molecular-profiles/{molecularProfileId}/discrete-copy-number-counts/fetch": { "post": { "tags": [ "Discrete Copy Number Alterations" ], "summary": "Get counts of specific genes and alterations within a CNA molecular profile", "operationId": "fetchCopyNumberCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_gistic", "required": true, "type": "string" }, { "in": "body", "name": "copyNumberCountIdentifiers", "description": "List of copy number count identifiers", "required": true, "schema": { "type": "array", "items": { "$ref": "#/definitions/CopyNumberCountIdentifier" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CopyNumberCount" } } } } } }, "/molecular-profiles/{molecularProfileId}/discrete-copy-number/fetch": { "post": { "tags": [ "Discrete Copy Number Alterations" ], "summary": "Fetch discrete copy number alterations in a molecular profile by sample ID", "operationId": "fetchDiscreteCopyNumbersInMolecularProfileUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_gistic", "required": true, "type": "string" }, { "name": "discreteCopyNumberEventType", "in": "query", "description": "Type of the copy number event", "required": false, "type": "string", "default": "HOMDEL_AND_AMP", "enum": [ "HOMDEL_AND_AMP", "HOMDEL", "AMP", "GAIN", "HETLOSS", "DIPLOID", "ALL" ] }, { "in": "body", "name": "discreteCopyNumberFilter", "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", "required": true, "schema": { "$ref": "#/definitions/DiscreteCopyNumberFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/DiscreteCopyNumberData" } } } } } }, "/molecular-profiles/{molecularProfileId}/gene-panel-data/fetch": { "post": { "tags": [ "Gene Panels" ], "summary": "Get gene panel data", "operationId": "getGenePanelDataUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. nsclc_unito_2016_mutations", "required": true, "type": "string" }, { "in": "body", "name": "genePanelDataFilter", "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", "required": true, "schema": { "$ref": "#/definitions/GenePanelDataFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenePanelData" } } } } } }, "/molecular-profiles/{molecularProfileId}/molecular-data": { "get": { "tags": [ "Molecular Data" ], "summary": "Get all molecular data in a molecular profile", "operationId": "getAllMolecularDataInMolecularProfileUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna", "required": true, "type": "string" }, { "name": "sampleListId", "in": "query", "description": "Sample List ID e.g. acc_tcga_all", "required": true, "type": "string" }, { "name": "entrezGeneId", "in": "query", "description": "Entrez Gene ID e.g. 1", "required": true, "type": "integer", "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/NumericGeneMolecularData" } } } } } }, "/molecular-profiles/{molecularProfileId}/molecular-data/fetch": { "post": { "tags": [ "Molecular Data" ], "summary": "Fetch molecular data in a molecular profile", "operationId": "fetchAllMolecularDataInMolecularProfileUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna", "required": true, "type": "string" }, { "in": "body", "name": "molecularDataFilter", "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", "required": true, "schema": { "$ref": "#/definitions/MolecularDataFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/NumericGeneMolecularData" } } } } } }, "/molecular-profiles/{molecularProfileId}/mutations": { "get": { "tags": [ "Mutations" ], "summary": "Get mutations in a molecular profile by Sample List ID", "operationId": "getMutationsInMolecularProfileBySampleListIdUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_mutations", "required": true, "type": "string" }, { "name": "sampleListId", "in": "query", "description": "Sample List ID e.g. acc_tcga_all", "required": true, "type": "string" }, { "name": "entrezGeneId", "in": "query", "description": "Entrez Gene ID", "required": false, "type": "integer", "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "entrezGeneId", "center", "mutationStatus", "validationStatus", "tumorAltCount", "tumorRefCount", "normalAltCount", "normalRefCount", "aminoAcidChange", "startPosition", "endPosition", "referenceAllele", "variantAllele", "proteinChange", "mutationType", "ncbiBuild", "variantType", "refseqMrnaId", "proteinPosStart", "proteinPosEnd", "keyword" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Mutation" } } } } } }, "/molecular-profiles/{molecularProfileId}/mutations/fetch": { "post": { "tags": [ "Mutations" ], "summary": "Fetch mutations in a molecular profile", "operationId": "fetchMutationsInMolecularProfileUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_mutations", "required": true, "type": "string" }, { "in": "body", "name": "mutationFilter", "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", "required": true, "schema": { "$ref": "#/definitions/MutationFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "entrezGeneId", "center", "mutationStatus", "validationStatus", "tumorAltCount", "tumorRefCount", "normalAltCount", "normalRefCount", "aminoAcidChange", "startPosition", "endPosition", "referenceAllele", "variantAllele", "proteinChange", "mutationType", "ncbiBuild", "variantType", "refseqMrnaId", "proteinPosStart", "proteinPosEnd", "keyword" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Mutation" } } } } } }, "/mutation-counts-by-position/fetch": { "post": { "tags": [ "Mutations" ], "summary": "Fetch mutation counts in all studies by gene and position", "operationId": "fetchMutationCountsByPositionUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "mutationPositionIdentifiers", "description": "List of gene and positions", "required": true, "schema": { "type": "array", "items": { "$ref": "#/definitions/MutationPositionIdentifier" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/MutationCountByPosition" } } } } } }, "/mutations/fetch": { "post": { "tags": [ "Mutations" ], "summary": "Fetch mutations in multiple molecular profiles by sample IDs", "operationId": "fetchMutationsInMultipleMolecularProfilesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "mutationMultipleStudyFilter", "description": "List of Molecular Profile IDs or List of Molecular Profile ID / Sample ID pairs, and List of Entrez Gene IDs", "required": true, "schema": { "$ref": "#/definitions/MutationMultipleStudyFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "entrezGeneId", "center", "mutationStatus", "validationStatus", "tumorAltCount", "tumorRefCount", "normalAltCount", "normalRefCount", "aminoAcidChange", "startPosition", "endPosition", "referenceAllele", "variantAllele", "proteinChange", "mutationType", "ncbiBuild", "variantType", "refseqMrnaId", "proteinPosStart", "proteinPosEnd", "keyword" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Mutation" } } } } } }, "/patients": { "get": { "tags": [ "Patients" ], "summary": "Get all patients", "operationId": "getAllPatientsUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "keyword", "in": "query", "description": "Search keyword that applies to ID of the patients", "required": false, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "patientId" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Patient" } } } } } }, "/patients/fetch": { "post": { "tags": [ "Patients" ], "summary": "Fetch patients by ID", "operationId": "fetchPatientsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "patientFilter", "description": "List of patient identifiers", "required": true, "schema": { "$ref": "#/definitions/PatientFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Patient" } } } } } }, "/sample-lists": { "get": { "tags": [ "Sample Lists" ], "summary": "Get all sample lists", "operationId": "getAllSampleListsUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "sampleListId", "category", "studyId", "name", "description" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/SampleList" } } } } } }, "/sample-lists/fetch": { "post": { "tags": [ "Sample Lists" ], "summary": "Fetch sample lists by ID", "operationId": "fetchSampleListsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "sampleListIds", "description": "List of sample list IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/SampleList" } } } } } }, "/sample-lists/{sampleListId}": { "get": { "tags": [ "Sample Lists" ], "summary": "Get sample list", "operationId": "getSampleListUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "sampleListId", "in": "path", "description": "Sample List ID e.g. acc_tcga_all", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/SampleList" } } } } }, "/sample-lists/{sampleListId}/sample-ids": { "get": { "tags": [ "Sample Lists" ], "summary": "Get all sample IDs in a sample list", "operationId": "getAllSampleIdsInSampleListUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "sampleListId", "in": "path", "description": "Sample List ID e.g. acc_tcga_all", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "type": "string" } } } } } }, "/samples/fetch": { "post": { "tags": [ "Samples" ], "summary": "Fetch samples by ID", "operationId": "fetchSamplesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "sampleFilter", "description": "List of sample identifiers", "required": true, "schema": { "$ref": "#/definitions/SampleFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Sample" } } } } } }, "/studies": { "get": { "tags": [ "Studies" ], "summary": "Get all studies", "operationId": "getAllStudiesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "keyword", "in": "query", "description": "Search keyword that applies to name and cancer type of the studies", "required": false, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "studyId", "cancerTypeId", "name", "shortName", "description", "publicStudy", "pmid", "citation", "groups", "status", "importDate" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CancerStudy" } } } } } }, "/studies/fetch": { "post": { "tags": [ "Studies" ], "summary": "Fetch studies by IDs", "operationId": "fetchStudiesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyIds", "description": "List of Study IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CancerStudy" } } } } } }, "/studies/tags/fetch": { "post": { "tags": [ "Studies" ], "summary": "Get the study tags by IDs", "operationId": "getTagsForMultipleStudiesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyIds", "description": "List of Study IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CancerStudyTags" } } } } } }, "/studies/{studyId}": { "get": { "tags": [ "Studies" ], "summary": "Get a study", "operationId": "getStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/CancerStudy" } } } } }, "/studies/{studyId}/clinical-attributes": { "get": { "tags": [ "Clinical Attributes" ], "summary": "Get all clinical attributes in the specified study", "operationId": "getAllClinicalAttributesInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "clinicalAttributeId", "displayName", "description", "datatype", "patientAttribute", "priority", "studyId" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalAttribute" } } } } } }, "/studies/{studyId}/clinical-attributes/{clinicalAttributeId}": { "get": { "tags": [ "Clinical Attributes" ], "summary": "Get specified clinical attribute", "operationId": "getClinicalAttributeInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "clinicalAttributeId", "in": "path", "description": "Clinical Attribute ID e.g. CANCER_TYPE", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/ClinicalAttribute" } } } } }, "/studies/{studyId}/clinical-data": { "get": { "tags": [ "Clinical Data" ], "summary": "Get all clinical data in a study", "operationId": "getAllClinicalDataInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "attributeId", "in": "query", "description": "Attribute ID e.g. CANCER_TYPE", "required": false, "type": "string" }, { "name": "clinicalDataType", "in": "query", "description": "Type of the clinical data", "required": false, "type": "string", "default": "SAMPLE", "enum": [ "SAMPLE", "PATIENT" ] }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "clinicalAttributeId", "value" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalData" } } } } } }, "/studies/{studyId}/clinical-data/fetch": { "post": { "tags": [ "Clinical Data" ], "summary": "Fetch clinical data by patient IDs or sample IDs (specific study)", "operationId": "fetchAllClinicalDataInStudyUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "clinicalDataType", "in": "query", "description": "Type of the clinical data", "required": false, "type": "string", "default": "SAMPLE", "enum": [ "SAMPLE", "PATIENT" ] }, { "in": "body", "name": "clinicalDataSingleStudyFilter", "description": "List of patient or sample IDs and attribute IDs", "required": true, "schema": { "$ref": "#/definitions/ClinicalDataSingleStudyFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalData" } } } } } }, "/studies/{studyId}/molecular-profiles": { "get": { "tags": [ "Molecular Profiles" ], "summary": "Get all molecular profiles in a study", "operationId": "getAllMolecularProfilesInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "molecularProfileId", "molecularAlterationType", "datatype", "name", "description", "showProfileInAnalysisTab" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/MolecularProfile" } } } } } }, "/studies/{studyId}/patients": { "get": { "tags": [ "Patients" ], "summary": "Get all patients in a study", "operationId": "getAllPatientsInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "patientId" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Patient" } } } } } }, "/studies/{studyId}/patients/{patientId}": { "get": { "tags": [ "Patients" ], "summary": "Get a patient in a study", "operationId": "getPatientInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "patientId", "in": "path", "description": "Patient ID e.g. TCGA-OR-A5J2", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/Patient" } } } } }, "/studies/{studyId}/patients/{patientId}/clinical-data": { "get": { "tags": [ "Clinical Data" ], "summary": "Get all clinical data of a patient in a study", "operationId": "getAllClinicalDataOfPatientInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "patientId", "in": "path", "description": "Patient ID e.g. TCGA-OR-A5J2", "required": true, "type": "string" }, { "name": "attributeId", "in": "query", "description": "Attribute ID e.g. AGE", "required": false, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "clinicalAttributeId", "value" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalData" } } } } } }, "/studies/{studyId}/patients/{patientId}/clinical-events": { "get": { "tags": [ "Clinical Events" ], "summary": "Get all clinical events of a patient in a study", "operationId": "getAllClinicalEventsOfPatientInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. lgg_ucsf_2014", "required": true, "type": "string" }, { "name": "patientId", "in": "path", "description": "Patient ID e.g. P01", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "eventType", "startNumberOfDaysSinceDiagnosis", "endNumberOfDaysSinceDiagnosis" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalEvent" } } } } } }, "/studies/{studyId}/patients/{patientId}/samples": { "get": { "tags": [ "Samples" ], "summary": "Get all samples of a patient in a study", "operationId": "getAllSamplesOfPatientInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "patientId", "in": "path", "description": "Patient ID e.g. TCGA-OR-A5J2", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "sampleId", "sampleType" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Sample" } } } } } }, "/studies/{studyId}/sample-lists": { "get": { "tags": [ "Sample Lists" ], "summary": "Get all sample lists in a study", "operationId": "getAllSampleListsInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "sampleListId", "category", "studyId", "name", "description" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/SampleList" } } } } } }, "/studies/{studyId}/samples": { "get": { "tags": [ "Samples" ], "summary": "Get all samples in a study", "operationId": "getAllSamplesInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "sampleId", "sampleType" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Sample" } } } } } }, "/studies/{studyId}/samples/{sampleId}": { "get": { "tags": [ "Samples" ], "summary": "Get a sample in a study", "operationId": "getSampleInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "sampleId", "in": "path", "description": "Sample ID e.g. TCGA-OR-A5J2-01", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/Sample" } } } } }, "/studies/{studyId}/samples/{sampleId}/clinical-data": { "get": { "tags": [ "Clinical Data" ], "summary": "Get all clinical data of a sample in a study", "operationId": "getAllClinicalDataOfSampleInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "sampleId", "in": "path", "description": "Sample ID e.g. TCGA-OR-A5J2-01", "required": true, "type": "string" }, { "name": "attributeId", "in": "query", "description": "Attribute ID e.g. CANCER_TYPE", "required": false, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "clinicalAttributeId", "value" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalData" } } } } } }, "/studies/{studyId}/samples/{sampleId}/copy-number-segments": { "get": { "tags": [ "Copy Number Segments" ], "summary": "Get copy number segments in a sample in a study", "operationId": "getCopyNumberSegmentsInSampleInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" }, { "name": "sampleId", "in": "path", "description": "Sample ID e.g. TCGA-OR-A5J2-01", "required": true, "type": "string" }, { "name": "chromosome", "in": "query", "description": "Chromosome", "required": false, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "ID", "SUMMARY", "DETAILED", "META" ] }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 20000, "maximum": 20000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "chromosome", "start", "end", "numberOfProbes", "segmentMean" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CopyNumberSeg" } } } } } }, "/studies/{studyId}/tags": { "get": { "tags": [ "Studies" ], "summary": "Get the tags of a study", "operationId": "getTagsUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "object" } } } } } }, "definitions": { "CancerStudy": { "type": "object", "required": [ "studyId" ], "properties": { "allSampleCount": { "type": "integer", "format": "int32" }, "cancerType": { "$ref": "#/definitions/TypeOfCancer" }, "cancerTypeId": { "type": "string" }, "citation": { "type": "string" }, "cnaSampleCount": { "type": "integer", "format": "int32" }, "completeSampleCount": { "type": "integer", "format": "int32" }, "description": { "type": "string" }, "groups": { "type": "string" }, "importDate": { "type": "string", "example": "yyyy-MM-dd HH:mm:ss" }, "methylationHm27SampleCount": { "type": "integer", "format": "int32" }, "miRnaSampleCount": { "type": "integer", "format": "int32" }, "mrnaMicroarraySampleCount": { "type": "integer", "format": "int32" }, "mrnaRnaSeqSampleCount": { "type": "integer", "format": "int32" }, "mrnaRnaSeqV2SampleCount": { "type": "integer", "format": "int32" }, "name": { "type": "string" }, "pmid": { "type": "string" }, "publicStudy": { "type": "boolean" }, "rppaSampleCount": { "type": "integer", "format": "int32" }, "sequencedSampleCount": { "type": "integer", "format": "int32" }, "shortName": { "type": "string" }, "status": { "type": "integer", "format": "int32" }, "studyId": { "type": "string" } }, "title": "CancerStudy" }, "CancerStudyTags": { "type": "object", "properties": { "cancerStudyId": { "type": "integer", "format": "int32" }, "tags": { "type": "string" } }, "title": "CancerStudyTags" }, "ClinicalAttribute": { "type": "object", "required": [ "clinicalAttributeId", "displayName", "patientAttribute", "studyId" ], "properties": { "clinicalAttributeId": { "type": "string" }, "datatype": { "type": "string" }, "description": { "type": "string" }, "displayName": { "type": "string" }, "patientAttribute": { "type": "boolean" }, "priority": { "type": "string" }, "studyId": { "type": "string" } }, "title": "ClinicalAttribute" }, "ClinicalAttributeCount": { "type": "object", "properties": { "clinicalAttributeId": { "type": "string" }, "count": { "type": "integer", "format": "int32" } }, "title": "ClinicalAttributeCount" }, "ClinicalAttributeCountFilter": { "type": "object", "properties": { "sampleIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleIdentifier" } }, "sampleListId": { "type": "string" } }, "title": "ClinicalAttributeCountFilter" }, "ClinicalData": { "type": "object", "required": [ "clinicalAttributeId", "patientId", "studyId" ], "properties": { "clinicalAttribute": { "$ref": "#/definitions/ClinicalAttribute" }, "clinicalAttributeId": { "type": "string" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "value": { "type": "string" } }, "title": "ClinicalData" }, "ClinicalDataIdentifier": { "type": "object", "properties": { "entityId": { "type": "string" }, "studyId": { "type": "string" } }, "title": "ClinicalDataIdentifier" }, "ClinicalDataMultiStudyFilter": { "type": "object", "properties": { "attributeIds": { "type": "array", "items": { "type": "string" } }, "identifiers": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataIdentifier" } } }, "title": "ClinicalDataMultiStudyFilter" }, "ClinicalDataSingleStudyFilter": { "type": "object", "properties": { "attributeIds": { "type": "array", "items": { "type": "string" } }, "ids": { "type": "array", "items": { "type": "string" } } }, "title": "ClinicalDataSingleStudyFilter" }, "ClinicalEvent": { "type": "object", "required": [ "eventType", "patientId", "studyId" ], "properties": { "attributes": { "type": "array", "items": { "$ref": "#/definitions/ClinicalEventData" } }, "endNumberOfDaysSinceDiagnosis": { "type": "integer", "format": "int32" }, "eventType": { "type": "string" }, "patientId": { "type": "string" }, "startNumberOfDaysSinceDiagnosis": { "type": "integer", "format": "int32" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" } }, "title": "ClinicalEvent" }, "ClinicalEventData": { "type": "object", "required": [ "key", "value" ], "properties": { "key": { "type": "string" }, "value": { "type": "string" } }, "title": "ClinicalEventData" }, "CopyNumberCount": { "type": "object", "required": [ "alteration", "entrezGeneId", "molecularProfileId", "numberOfSamples", "numberOfSamplesWithAlterationInGene" ], "properties": { "alteration": { "type": "integer", "format": "int32" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "molecularProfileId": { "type": "string" }, "numberOfSamples": { "type": "integer", "format": "int32" }, "numberOfSamplesWithAlterationInGene": { "type": "integer", "format": "int32" } }, "title": "CopyNumberCount" }, "CopyNumberCountIdentifier": { "type": "object", "properties": { "alteration": { "type": "integer", "format": "int32" }, "entrezGeneId": { "type": "integer", "format": "int32" } }, "title": "CopyNumberCountIdentifier" }, "CopyNumberSeg": { "type": "object", "required": [ "chromosome", "end", "numberOfProbes", "patientId", "sampleId", "segmentMean", "start", "studyId" ], "properties": { "chromosome": { "type": "string" }, "end": { "type": "integer", "format": "int32" }, "numberOfProbes": { "type": "integer", "format": "int32" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "segmentMean": { "type": "number" }, "start": { "type": "integer", "format": "int32" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" } }, "title": "CopyNumberSeg" }, "DiscreteCopyNumberData": { "type": "object", "required": [ "alteration", "entrezGeneId", "molecularProfileId", "patientId", "sampleId", "studyId" ], "properties": { "alteration": { "type": "integer", "format": "int32" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "gene": { "$ref": "#/definitions/Gene" }, "molecularProfileId": { "type": "string" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" } }, "title": "DiscreteCopyNumberData" }, "DiscreteCopyNumberFilter": { "type": "object", "properties": { "entrezGeneIds": { "type": "array", "items": { "type": "integer", "format": "int32", "minimum": 1, "maximum": 50000 } }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "DiscreteCopyNumberFilter" }, "Gene": { "type": "object", "required": [ "entrezGeneId", "hugoGeneSymbol" ], "properties": { "chromosome": { "type": "string" }, "cytoband": { "type": "string" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" }, "length": { "type": "integer", "format": "int32" }, "type": { "type": "string" } }, "title": "Gene" }, "GenePanel": { "type": "object", "required": [ "genePanelId" ], "properties": { "description": { "type": "string" }, "genePanelId": { "type": "string" }, "genes": { "type": "array", "items": { "$ref": "#/definitions/GenePanelToGene" } } }, "title": "GenePanel" }, "GenePanelData": { "type": "object", "required": [ "molecularProfileId", "patientId", "profiled", "sampleId", "studyId" ], "properties": { "genePanelId": { "type": "string" }, "molecularProfileId": { "type": "string" }, "patientId": { "type": "string" }, "profiled": { "type": "boolean" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" } }, "title": "GenePanelData" }, "GenePanelDataFilter": { "type": "object", "properties": { "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "GenePanelDataFilter" }, "GenePanelMultipleStudyFilter": { "type": "object", "required": [ "sampleMolecularIdentifiers" ], "properties": { "sampleMolecularIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleMolecularIdentifier" } } }, "title": "GenePanelMultipleStudyFilter" }, "GenePanelToGene": { "type": "object", "required": [ "entrezGeneId", "hugoGeneSymbol" ], "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" } }, "title": "GenePanelToGene" }, "MolecularDataFilter": { "type": "object", "properties": { "entrezGeneIds": { "type": "array", "items": { "type": "integer", "format": "int32", "minimum": 1, "maximum": 10000000 } }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "MolecularDataFilter" }, "MolecularDataMultipleStudyFilter": { "type": "object", "properties": { "entrezGeneIds": { "type": "array", "items": { "type": "integer", "format": "int32", "minimum": 1, "maximum": 10000000 } }, "molecularProfileIds": { "type": "array", "items": { "type": "string" } }, "sampleMolecularIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleMolecularIdentifier" } } }, "title": "MolecularDataMultipleStudyFilter" }, "MolecularProfile": { "type": "object", "required": [ "molecularProfileId", "studyId" ], "properties": { "datatype": { "type": "string" }, "description": { "type": "string" }, "molecularAlterationType": { "type": "string", "enum": [ "MUTATION_EXTENDED", "MUTATION_UNCALLED", "FUSION", "STRUCTURAL_VARIANT", "COPY_NUMBER_ALTERATION", "MICRO_RNA_EXPRESSION", "MRNA_EXPRESSION", "MRNA_EXPRESSION_NORMALS", "RNA_EXPRESSION", "METHYLATION", "METHYLATION_BINARY", "PHOSPHORYLATION", "PROTEIN_LEVEL", "PROTEIN_ARRAY_PROTEIN_LEVEL", "PROTEIN_ARRAY_PHOSPHORYLATION", "GENESET_SCORE" ] }, "molecularProfileId": { "type": "string" }, "name": { "type": "string" }, "showProfileInAnalysisTab": { "type": "boolean" }, "study": { "$ref": "#/definitions/CancerStudy" }, "studyId": { "type": "string" } }, "title": "MolecularProfile" }, "MolecularProfileFilter": { "type": "object", "properties": { "molecularProfileIds": { "type": "array", "items": { "type": "string" } }, "studyIds": { "type": "array", "items": { "type": "string" } } }, "title": "MolecularProfileFilter" }, "Mutation": { "type": "object", "required": [ "entrezGeneId", "molecularProfileId", "patientId", "sampleId", "studyId" ], "properties": { "aminoAcidChange": { "type": "string" }, "center": { "type": "string" }, "driverFilter": { "type": "string" }, "driverFilterAnnotation": { "type": "string" }, "driverTiersFilter": { "type": "string" }, "driverTiersFilterAnnotation": { "type": "string" }, "endPosition": { "type": "integer", "format": "int64" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "fisValue": { "type": "number" }, "functionalImpactScore": { "type": "string" }, "gene": { "$ref": "#/definitions/Gene" }, "keyword": { "type": "string" }, "linkMsa": { "type": "string" }, "linkPdb": { "type": "string" }, "linkXvar": { "type": "string" }, "molecularProfileId": { "type": "string" }, "mutationStatus": { "type": "string" }, "mutationType": { "type": "string" }, "ncbiBuild": { "type": "string" }, "normalAltCount": { "type": "integer", "format": "int32" }, "normalRefCount": { "type": "integer", "format": "int32" }, "patientId": { "type": "string" }, "proteinChange": { "type": "string" }, "proteinPosEnd": { "type": "integer", "format": "int32" }, "proteinPosStart": { "type": "integer", "format": "int32" }, "referenceAllele": { "type": "string" }, "refseqMrnaId": { "type": "string" }, "sampleId": { "type": "string" }, "startPosition": { "type": "integer", "format": "int64" }, "studyId": { "type": "string" }, "tumorAltCount": { "type": "integer", "format": "int32" }, "tumorRefCount": { "type": "integer", "format": "int32" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "validationStatus": { "type": "string" }, "variantAllele": { "type": "string" }, "variantType": { "type": "string" } }, "title": "Mutation" }, "MutationCountByPosition": { "type": "object", "required": [ "count", "entrezGeneId", "proteinPosEnd", "proteinPosStart" ], "properties": { "count": { "type": "integer", "format": "int32" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "proteinPosEnd": { "type": "integer", "format": "int32" }, "proteinPosStart": { "type": "integer", "format": "int32" } }, "title": "MutationCountByPosition" }, "MutationFilter": { "type": "object", "properties": { "entrezGeneIds": { "type": "array", "items": { "type": "integer", "format": "int32", "minimum": 1, "maximum": 10000000 } }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "MutationFilter" }, "MutationMultipleStudyFilter": { "type": "object", "properties": { "entrezGeneIds": { "type": "array", "items": { "type": "integer", "format": "int32", "minimum": 1, "maximum": 10000000 } }, "molecularProfileIds": { "type": "array", "items": { "type": "string" } }, "sampleMolecularIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleMolecularIdentifier" } } }, "title": "MutationMultipleStudyFilter" }, "MutationPositionIdentifier": { "type": "object", "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "proteinPosEnd": { "type": "integer", "format": "int32" }, "proteinPosStart": { "type": "integer", "format": "int32" } }, "title": "MutationPositionIdentifier" }, "NumericGeneMolecularData": { "type": "object", "required": [ "entrezGeneId", "molecularProfileId", "patientId", "sampleId", "studyId", "value" ], "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "gene": { "$ref": "#/definitions/Gene" }, "molecularProfileId": { "type": "string" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "value": { "type": "number" } }, "title": "NumericGeneMolecularData" }, "Patient": { "type": "object", "required": [ "patientId", "studyId" ], "properties": { "cancerStudy": { "$ref": "#/definitions/CancerStudy" }, "patientId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" } }, "title": "Patient" }, "PatientFilter": { "type": "object", "properties": { "patientIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/PatientIdentifier" } }, "uniquePatientKeys": { "type": "array", "items": { "type": "string" } } }, "title": "PatientFilter" }, "PatientIdentifier": { "type": "object", "properties": { "patientId": { "type": "string" }, "studyId": { "type": "string" } }, "title": "PatientIdentifier" }, "Sample": { "type": "object", "required": [ "patientId", "sampleId", "studyId" ], "properties": { "copyNumberSegmentPresent": { "type": "boolean" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "sampleType": { "type": "string", "enum": [ "Primary Solid Tumor", "Recurrent Solid Tumor", "Primary Blood Tumor", "Recurrent Blood Tumor", "Metastatic", "Blood Derived Normal", "Solid Tissues Normal" ] }, "sequenced": { "type": "boolean" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" } }, "title": "Sample" }, "SampleFilter": { "type": "object", "properties": { "sampleIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleIdentifier" } }, "sampleListIds": { "type": "array", "items": { "type": "string" } }, "uniqueSampleKeys": { "type": "array", "items": { "type": "string" } } }, "title": "SampleFilter" }, "SampleIdentifier": { "type": "object", "properties": { "sampleId": { "type": "string" }, "studyId": { "type": "string" } }, "title": "SampleIdentifier" }, "SampleList": { "type": "object", "required": [ "sampleListId" ], "properties": { "category": { "type": "string" }, "description": { "type": "string" }, "name": { "type": "string" }, "sampleCount": { "type": "integer", "format": "int32" }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" }, "studyId": { "type": "string" } }, "title": "SampleList" }, "SampleMolecularIdentifier": { "type": "object", "properties": { "molecularProfileId": { "type": "string" }, "sampleId": { "type": "string" } }, "title": "SampleMolecularIdentifier" }, "TypeOfCancer": { "type": "object", "required": [ "cancerTypeId" ], "properties": { "cancerTypeId": { "type": "string" }, "clinicalTrialKeywords": { "type": "string" }, "dedicatedColor": { "type": "string" }, "name": { "type": "string" }, "parent": { "type": "string" }, "shortName": { "type": "string" } }, "title": "TypeOfCancer" } } }