{ "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). Backwards compatibility will be maintained (after 1.0 release)", "title": "cBioPortal web Public API [Beta]", "contact": { "name": "cBioPortal", "url": "https://www.cbioportal.org", "email": "cbioportal@googlegroups.com" }, "license": { "name": "License", "url": "https://github.com/cBioPortal/cbioportal/blob/master/LICENSE" } }, "tags": [ { "name": "Cancer Types" }, { "name": "Studies" }, { "name": "Patients" }, { "name": "Samples" }, { "name": "Sample Lists" }, { "name": "Clinical Attributes" }, { "name": "Clinical Data" }, { "name": "Molecular Data" }, { "name": "Molecular Profiles" }, { "name": "Mutations" }, { "name": "Discrete Copy Number Alterations" }, { "name": "Copy Number Segments" }, { "name": "Genes" }, { "name": "Gene Panels" }, { "name": "Generic Assays" }, { "name": "Generic Assay Data" }, { "name": "Info" }, { "name": "Gene Panel Data", "description": " " }, { "name": "Server running status", "description": "This end point does not require authentication" }, { "name": "Treatments", "description": " " } ], "paths": { "/cancer-types": { "get": { "tags": [ "Cancer Types" ], "summary": "Get all cancer types", "operationId": "getAllCancerTypesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "cancerTypeId", "dedicatedColor", "name", "parent", "shortName" ] } ], "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": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "clinicalAttributeId", "datatype", "description", "displayName", "patientAttribute", "priority", "studyId" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalAttribute" } } } } } }, "/clinical-attributes/fetch": { "post": { "tags": [ "Clinical Attributes" ], "summary": "Fetch clinical attributes", "operationId": "fetchClinicalAttributesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "in": "body", "name": "studyIds", "description": "List of Study IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/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": [ { "in": "body", "name": "clinicalDataMultiStudyFilter", "description": "List of patient or sample identifiers and attribute IDs", "required": true, "schema": { "$ref": "#/definitions/ClinicalDataMultiStudyFilter" } }, { "name": "clinicalDataType", "in": "query", "description": "Type of the clinical data", "required": false, "type": "string", "default": "SAMPLE", "enum": [ "PATIENT", "SAMPLE" ] }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$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": [ { "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": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "in": "body", "name": "sampleIdentifiers", "description": "List of sample identifiers", "required": true, "schema": { "type": "array", "items": { "$ref": "#/definitions/SampleIdentifier" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CopyNumberSeg" } } } } } }, "/gene-panel-data/fetch": { "post": { "tags": [ "Gene Panel Data" ], "summary": "Fetch gene panel data", "operationId": "fetchGenePanelDataInMultipleMolecularProfilesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genePanelDataMultipleStudyFilter", "description": "Gene panel data filter object", "required": true, "schema": { "$ref": "#/definitions/GenePanelDataMultipleStudyFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenePanelData" } } } } } }, "/gene-panels": { "get": { "tags": [ "Gene Panels" ], "summary": "Get all gene panels", "operationId": "getAllGenePanelsUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "description", "genePanelId" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenePanel" } } } } } }, "/gene-panels/fetch": { "post": { "tags": [ "Gene Panels" ], "summary": "Get gene panel", "operationId": "fetchGenePanelsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genePanelIds", "description": "List of Gene Panel IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$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": { "$ref": "#/definitions/GenePanel" } } } } }, "/generic-assay-data/{molecularProfileId}/generic-assay/{genericAssayStableId}": { "get": { "tags": [ "Generic Assay Data" ], "summary": "Get generic_assay_data in a molecular profile", "operationId": "getGenericAssayDataInMolecularProfileUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "genericAssayStableId", "in": "path", "description": "Generic Assay stable ID", "required": true, "type": "string" }, { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayData" } } } } } }, "/generic-assay-meta/generic-assay/{genericAssayStableId}": { "get": { "tags": [ "Generic Assays" ], "summary": "Fetch meta data for generic-assay by ID", "operationId": "getGenericAssayMeta_gaUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "genericAssayStableId", "in": "path", "description": "Generic Assay stable ID", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayMeta" } } } } } }, "/generic-assay-meta/{molecularProfileId}": { "get": { "tags": [ "Generic Assays" ], "summary": "Fetch meta data for generic-assay by ID", "operationId": "getGenericAssayMetaUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayMeta" } } } } } }, "/generic_assay_data/fetch": { "post": { "tags": [ "Generic Assay Data" ], "summary": "Fetch generic_assay_data", "operationId": "fetchGenericAssayDataInMultipleMolecularProfilesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genericAssayDataMultipleStudyFilter", "description": "List of Molecular Profile ID and Sample ID pairs or List of MolecularProfile IDs and Generic Assay IDs", "required": true, "schema": { "$ref": "#/definitions/GenericAssayDataMultipleStudyFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayData" } } } } } }, "/generic_assay_data/{molecularProfileId}/fetch": { "post": { "tags": [ "Generic Assay Data" ], "summary": "fetch generic_assay_data in a molecular profile", "operationId": "fetchGenericAssayDataInMolecularProfileUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genericAssayDataFilter", "description": "List of Sample IDs/Sample List ID and Generic Assay IDs", "required": true, "schema": { "$ref": "#/definitions/GenericAssayFilter" } }, { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayData" } } } } } }, "/generic_assay_meta/fetch": { "post": { "tags": [ "Generic Assays" ], "summary": "Fetch meta data for generic-assay by ID", "operationId": "fetchGenericAssayMetaUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genericAssayMetaFilter", "description": "List of Molecular Profile ID or List of Stable ID", "required": true, "schema": { "$ref": "#/definitions/GenericAssayMetaFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayMeta" } } } } } }, "/genes": { "get": { "tags": [ "Genes" ], "summary": "Get all genes", "operationId": "getAllGenesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "alias", "in": "query", "description": "Alias of the gene", "required": false, "type": "string" }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "keyword", "in": "query", "description": "Search keyword that applies to hugo gene symbol of the genes", "required": false, "type": "string" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "cytoband", "entrezGeneId", "hugoGeneSymbol", "length", "type" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Gene" } } } } } }, "/genes/fetch": { "post": { "tags": [ "Genes" ], "summary": "Fetch genes by ID", "operationId": "fetchGenesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "geneIds", "description": "List of Entrez Gene IDs or Hugo Gene Symbols", "required": true, "schema": { "type": "array", "items": { "type": "string" } } }, { "name": "geneIdType", "in": "query", "description": "Type of gene ID", "required": false, "type": "string", "default": "ENTREZ_GENE_ID", "enum": [ "ENTREZ_GENE_ID", "HUGO_GENE_SYMBOL" ] }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$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": { "$ref": "#/definitions/Gene" } } } } }, "/genes/{geneId}/aliases": { "get": { "tags": [ "Genes" ], "summary": "Get aliases of a gene", "operationId": "getAliasesOfGeneUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "geneId", "in": "path", "description": "Entrez Gene ID or Hugo Gene Symbol e.g. 1 or A1BG", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "type": "string" } } } } } }, "/health": { "get": { "tags": [ "Server running status" ], "summary": "Get the running status of the server", "operationId": "getServerStatusUsingGET", "produces": [ "application/json" ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/ServerStatusMessage" } } } } }, "/info": { "get": { "tags": [ "Info" ], "summary": "Get information about the running instance", "operationId": "getInfoUsingGET", "produces": [ "application/json" ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/Info" } } } } }, "/molecular-data/fetch": { "post": { "tags": [ "Molecular Data" ], "summary": "Fetch molecular data", "operationId": "fetchMolecularDataInMultipleMolecularProfilesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "molecularDataMultipleStudyFilter", "description": "List of Molecular Profile ID and Sample ID pairs or List of MolecularProfile IDs and Entrez Gene IDs", "required": true, "schema": { "$ref": "#/definitions/MolecularDataMultipleStudyFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/NumericGeneMolecularData" } } } } } }, "/molecular-profiles": { "get": { "tags": [ "Molecular Profiles" ], "summary": "Get all molecular profiles", "operationId": "getAllMolecularProfilesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "datatype", "description", "molecularAlterationType", "molecularProfileId", "name", "showProfileInAnalysisTab" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$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": { "$ref": "#/definitions/MolecularProfileFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$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": { "$ref": "#/definitions/MolecularProfile" } } } } }, "/molecular-profiles/{molecularProfileId}/discrete-copy-number": { "get": { "tags": [ "Discrete Copy Number Alterations" ], "summary": "Get discrete copy number alterations in a molecular profile", "operationId": "getDiscreteCopyNumbersInMolecularProfileUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "discreteCopyNumberEventType", "in": "query", "description": "Type of the copy number event", "required": false, "type": "string", "default": "HOMDEL_AND_AMP", "enum": [ "ALL", "AMP", "DIPLOID", "GAIN", "HETLOSS", "HOMDEL", "HOMDEL_AND_AMP" ] }, { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_gistic", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sampleListId", "in": "query", "description": "Sample List ID e.g. acc_tcga_all", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/DiscreteCopyNumberData" } } } } } }, "/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": "discreteCopyNumberEventType", "in": "query", "description": "Type of the copy number event", "required": false, "type": "string", "default": "HOMDEL_AND_AMP", "enum": [ "ALL", "AMP", "DIPLOID", "GAIN", "HETLOSS", "HOMDEL", "HOMDEL_AND_AMP" ] }, { "in": "body", "name": "discreteCopyNumberFilter", "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", "required": true, "schema": { "$ref": "#/definitions/DiscreteCopyNumberFilter" } }, { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_gistic", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/DiscreteCopyNumberData" } } } } } }, "/molecular-profiles/{molecularProfileId}/gene-panel-data/fetch": { "post": { "tags": [ "Gene Panel Data" ], "summary": "Get gene panel data", "operationId": "getGenePanelDataUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genePanelDataFilter", "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", "required": true, "schema": { "$ref": "#/definitions/GenePanelDataFilter" } }, { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. nsclc_unito_2016_mutations", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$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": "entrezGeneId", "in": "query", "description": "Entrez Gene ID e.g. 1", "required": true, "type": "integer", "format": "int32" }, { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sampleListId", "in": "query", "description": "Sample List ID e.g. acc_tcga_all", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/NumericGeneMolecularData" } } } } } }, "/molecular-profiles/{molecularProfileId}/molecular-data/fetch": { "post": { "tags": [ "Molecular Data" ], "summary": "Fetch molecular data in a molecular profile", "operationId": "fetchAllMolecularDataInMolecularProfileUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "molecularDataFilter", "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", "required": true, "schema": { "$ref": "#/definitions/MolecularDataFilter" } }, { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "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": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "entrezGeneId", "in": "query", "description": "Entrez Gene ID", "required": false, "type": "integer", "format": "int32" }, { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_mutations", "required": true, "type": "string" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sampleListId", "in": "query", "description": "Sample List ID e.g. acc_tcga_all", "required": true, "type": "string" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "aminoAcidChange", "center", "endPosition", "entrezGeneId", "keyword", "mutationStatus", "mutationType", "ncbiBuild", "normalAltCount", "normalRefCount", "proteinChange", "proteinPosEnd", "proteinPosStart", "referenceAllele", "refseqMrnaId", "startPosition", "tumorAltCount", "tumorRefCount", "validationStatus", "variantAllele", "variantType" ] } ], "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": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "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": { "$ref": "#/definitions/MutationFilter" } }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "aminoAcidChange", "center", "endPosition", "entrezGeneId", "keyword", "mutationStatus", "mutationType", "ncbiBuild", "normalAltCount", "normalRefCount", "proteinChange", "proteinPosEnd", "proteinPosStart", "referenceAllele", "refseqMrnaId", "startPosition", "tumorAltCount", "tumorRefCount", "validationStatus", "variantAllele", "variantType" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Mutation" } } } } } }, "/mutations/fetch": { "post": { "tags": [ "Mutations" ], "summary": "Fetch mutations in multiple molecular profiles by sample IDs", "operationId": "fetchMutationsInMultipleMolecularProfilesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "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": { "$ref": "#/definitions/MutationMultipleStudyFilter" } }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "aminoAcidChange", "center", "endPosition", "entrezGeneId", "keyword", "mutationStatus", "mutationType", "ncbiBuild", "normalAltCount", "normalRefCount", "proteinChange", "proteinPosEnd", "proteinPosStart", "referenceAllele", "refseqMrnaId", "startPosition", "tumorAltCount", "tumorRefCount", "validationStatus", "variantAllele", "variantType" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Mutation" } } } } } }, "/patients": { "get": { "tags": [ "Patients" ], "summary": "Get all patients", "operationId": "getAllPatientsUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "keyword", "in": "query", "description": "Search keyword that applies to ID of the patients", "required": false, "type": "string" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "patientId" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Patient" } } } } } }, "/patients/fetch": { "post": { "tags": [ "Patients" ], "summary": "fetchPatients", "operationId": "fetchPatientsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "patientFilter", "description": "List of patient identifiers", "required": true, "schema": { "$ref": "#/definitions/PatientFilter" } }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Patient" } } } } } }, "/sample-lists": { "get": { "tags": [ "Sample Lists" ], "summary": "Get all sample lists", "operationId": "getAllSampleListsUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "category", "description", "name", "sampleListId", "studyId" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$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": [ { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "in": "body", "name": "sampleListIds", "description": "List of sample list IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } } ], "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": { "get": { "tags": [ "Samples" ], "summary": "Get all samples matching keyword", "operationId": "getSamplesByKeywordUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "keyword", "in": "query", "description": "Search keyword that applies to the study ID", "required": false, "type": "string" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "sampleId", "sampleType" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Sample" } } } } } }, "/samples/fetch": { "post": { "tags": [ "Samples" ], "summary": "Fetch samples by ID", "operationId": "fetchSamplesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "in": "body", "name": "sampleFilter", "description": "List of sample identifiers", "required": true, "schema": { "$ref": "#/definitions/SampleFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Sample" } } } } } }, "/studies": { "get": { "tags": [ "Studies" ], "summary": "Get all studies", "operationId": "getAllStudiesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "authenticated", "in": "query", "required": false, "type": "boolean" }, { "name": "authorities[0].authority", "in": "query", "required": false, "type": "string" }, { "name": "credentials", "in": "query", "required": false, "type": "object" }, { "name": "details", "in": "query", "required": false, "type": "object" }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "keyword", "in": "query", "description": "Search keyword that applies to name and cancer type of the studies", "required": false, "type": "string" }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "principal", "in": "query", "required": false, "type": "object" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "cancerTypeId", "citation", "description", "groups", "importDate", "name", "pmid", "publicStudy", "status", "studyId" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CancerStudy" } } } } } }, "/studies/fetch": { "post": { "tags": [ "Studies" ], "summary": "Fetch studies by IDs", "operationId": "fetchStudiesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "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": { "$ref": "#/definitions/CancerStudy" } } } } } }, "/studies/tags/fetch": { "post": { "tags": [ "Studies" ], "summary": "Get the study tags by IDs", "operationId": "getTagsForMultipleStudiesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyIds", "description": "List of Study IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$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": { "$ref": "#/definitions/CancerStudy" } } } } }, "/studies/{studyId}/clinical-attributes": { "get": { "tags": [ "Clinical Attributes" ], "summary": "Get all clinical attributes in the specified study", "operationId": "getAllClinicalAttributesInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "clinicalAttributeId", "datatype", "description", "displayName", "patientAttribute", "priority", "studyId" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalAttribute" } } } } } }, "/studies/{studyId}/clinical-attributes/{clinicalAttributeId}": { "get": { "tags": [ "Clinical Attributes" ], "summary": "Get specified clinical attribute", "operationId": "getClinicalAttributeInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "clinicalAttributeId", "in": "path", "description": "Clinical Attribute ID e.g. CANCER_TYPE", "required": true, "type": "string" }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/ClinicalAttribute" } } } } }, "/studies/{studyId}/clinical-data": { "get": { "tags": [ "Clinical Data" ], "summary": "Get all clinical data in a study", "operationId": "getAllClinicalDataInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "attributeId", "in": "query", "description": "Attribute ID e.g. CANCER_TYPE", "required": false, "type": "string" }, { "name": "clinicalDataType", "in": "query", "description": "Type of the clinical data", "required": false, "type": "string", "default": "SAMPLE", "enum": [ "PATIENT", "SAMPLE" ] }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "clinicalAttributeId", "value" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$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": [ { "in": "body", "name": "clinicalDataSingleStudyFilter", "description": "List of patient or sample IDs and attribute IDs", "required": true, "schema": { "$ref": "#/definitions/ClinicalDataSingleStudyFilter" } }, { "name": "clinicalDataType", "in": "query", "description": "Type of the clinical data", "required": false, "type": "string", 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"OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/MolecularProfile" } } } } } }, "/studies/{studyId}/patients": { "get": { "tags": [ "Patients" ], "summary": "Get all patients in a study", "operationId": "getAllPatientsInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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": "projection", "in": "query", "description": "Level of detail of 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"SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "sampleId", "sampleType" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "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": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": 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} } } }, "/studies/{studyId}/samples": { "get": { "tags": [ "Samples" ], "summary": "Get all samples in a study", "operationId": "getAllSamplesInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", 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} }, "/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": "attributeId", "in": "query", "description": "Attribute ID e.g. CANCER_TYPE", "required": false, "type": "string" }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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, 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"getCopyNumberSegmentsInSampleInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "chromosome", "in": "query", "description": "Chromosome", "required": false, "type": "string" }, { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "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": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sampleId", "in": "path", "description": "Sample ID e.g. TCGA-OR-A5J2-01", "required": true, "type": "string" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "chromosome", "end", "numberOfProbes", "segmentMean", "start" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "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" } } } } }, "/treatments/display-patient": { "post": { "tags": [ "Treatments" ], "summary": "Should patient level treatments be displayed", "operationId": "getContainsTreatmentDataUsingPOST", "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": "tier", "in": "query", "description": "tier", "required": false, "type": "string", "default": "Treatment", "enum": [ "Agent", "AgentClass", "AgentTarget" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "boolean" } } } } }, "/treatments/display-sample": { "post": { "tags": [ "Treatments" ], "summary": "Should sample level treatments be displayed", "operationId": "getContainsSampleTreatmentDataUsingPOST", "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": "tier", "in": "query", "description": "tier", "required": false, "type": "string", "default": "Treatment", "enum": [ "Agent", "AgentClass", "AgentTarget" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "boolean" } } } } }, "/treatments/patient": { "post": { "tags": [ "Treatments" ], "summary": "Get all patient level treatments", "operationId": "getAllPatientTreatmentsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } }, { "name": "tier", "in": "query", "description": "tier", "required": false, "type": "string", "default": "Treatment", "enum": [ "Agent", "AgentClass", "AgentTarget" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/PatientTreatmentRow" } } } } } }, "/treatments/sample": { "post": { "tags": [ "Treatments" ], "summary": "Get all sample level treatments", "operationId": "getAllSampleTreatmentsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } }, { "name": "tier", "in": "query", "description": "tier", "required": false, "type": "string", "default": "Treatment", "enum": [ "Agent", "AgentClass", "AgentTarget" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/SampleTreatmentRow" } } } } } } }, "definitions": { "AlleleSpecificCopyNumber": { "type": "object", "properties": { "ascnIntegerCopyNumber": { "type": "integer", "format": "int32" }, "ascnMethod": { "type": "string" }, "ccfExpectedCopies": { "type": "number", "format": "float" }, "ccfExpectedCopiesUpper": { "type": "number", "format": "float" }, "clonal": { "type": "string" }, "expectedAltCopies": { "type": "integer", "format": "int32" }, "minorCopyNumber": { "type": "integer", "format": "int32" }, "totalCopyNumber": { "type": "integer", "format": "int32" } }, "title": "AlleleSpecificCopyNumber" }, "AlterationFilter": { "type": "object", "properties": { "copyNumberAlterationEventTypes": { "type": "object", "additionalProperties": { "type": "boolean" } }, "includeDriver": { "type": "boolean" }, "includeGermline": { "type": "boolean" }, "includeSomatic": { "type": "boolean" }, "includeUnknownOncogenicity": { "type": "boolean" }, "includeUnknownStatus": { "type": "boolean" }, "includeUnknownTier": { "type": "boolean" }, "includeVUS": { "type": "boolean" }, "mutationEventTypes": { "type": "object", "additionalProperties": { "type": "boolean" } }, "structuralVariants": { "type": "boolean" }, "tiersBooleanMap": { "type": "object", "additionalProperties": { "type": "boolean" } } }, "title": "AlterationFilter" }, "AndedPatientTreatmentFilters": { "type": "object", "properties": { "filters": { "type": "array", "items": { "$ref": "#/definitions/OredPatientTreatmentFilters" } } }, "title": "AndedPatientTreatmentFilters" }, "AndedSampleTreatmentFilters": { "type": "object", "properties": { "filters": { "type": "array", "items": { "$ref": "#/definitions/OredSampleTreatmentFilters" } } }, "title": "AndedSampleTreatmentFilters" }, "CancerStudy": { "type": "object", "required": [ "studyId" ], "properties": { "allSampleCount": { "type": "integer", "format": "int32" }, "cancerType": { "$ref": "#/definitions/TypeOfCancer" }, "cancerTypeId": { "type": "string" }, "citation": { "type": "string" }, "cnaSampleCount": { "type": "integer", "format": "int32" }, "completeSampleCount": { "type": "integer", "format": "int32" }, "description": { "type": "string" }, "groups": { "type": "string" }, "importDate": { "type": "string", "example": "yyyy-MM-dd HH:mm:ss" }, "massSpectrometrySampleCount": { "type": "integer", "format": "int32" }, "methylationHm27SampleCount": { "type": "integer", "format": "int32" }, "miRnaSampleCount": { "type": "integer", "format": "int32" }, "mrnaMicroarraySampleCount": { "type": "integer", "format": "int32" }, "mrnaRnaSeqSampleCount": { "type": "integer", "format": "int32" }, "mrnaRnaSeqV2SampleCount": { "type": "integer", "format": "int32" }, "name": { "type": "string" }, "pmid": { "type": "string" }, "publicStudy": { "type": "boolean" }, "readPermission": { "type": "boolean" }, "referenceGenome": { "type": "string" }, "rppaSampleCount": { "type": "integer", "format": "int32" }, "sequencedSampleCount": { "type": "integer", "format": "int32" }, "status": { "type": "integer", "format": "int32" }, "studyId": { "type": "string" } }, "title": "CancerStudy" }, "CancerStudyTags": { "type": "object", "properties": { "cancerStudyId": { "type": "integer", "format": "int32" }, "tags": { "type": "string" } }, "title": "CancerStudyTags" }, "ClinicalAttribute": { "type": "object", "required": [ "clinicalAttributeId", "displayName", "patientAttribute", "studyId" ], "properties": { "clinicalAttributeId": { "type": "string" }, "datatype": { "type": "string" }, "description": { "type": "string" }, "displayName": { "type": "string" }, "patientAttribute": { "type": "boolean" }, "priority": { "type": "string" }, "studyId": { "type": "string" } }, "title": "ClinicalAttribute" }, "ClinicalData": { "type": "object", "required": [ "clinicalAttributeId", "patientId", "studyId" ], "properties": { "clinicalAttribute": { "$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" }, "ClinicalDataFilter": { "type": "object", "properties": { "attributeId": { "type": "string" }, "values": { "type": "array", "items": { "$ref": "#/definitions/DataFilterValue" } } }, "title": "ClinicalDataFilter" }, "ClinicalDataIdentifier": { "type": "object", "properties": { "entityId": { "type": "string" }, "studyId": { "type": "string" } }, "title": "ClinicalDataIdentifier" }, "ClinicalDataMultiStudyFilter": { "type": "object", "properties": { "attributeIds": { "type": "array", "items": { "type": "string" } }, "identifiers": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataIdentifier" } } }, "title": "ClinicalDataMultiStudyFilter" }, "ClinicalDataSingleStudyFilter": { "type": "object", "properties": { "attributeIds": { "type": "array", "items": { "type": "string" } }, "ids": { "type": "array", "items": { "type": "string" } } }, "title": "ClinicalDataSingleStudyFilter" }, "ClinicalEventSample": { "type": "object", "properties": { "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "timeTaken": { "type": "integer", "format": "int32" } }, "title": "ClinicalEventSample" }, "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" }, "DataFilterValue": { "type": "object", "properties": { "end": { "type": "number" }, "start": { "type": "number" }, "value": { "type": "string" } }, "title": "DataFilterValue" }, "DiscreteCopyNumberData": { "type": "object", "required": [ "alteration", "entrezGeneId", "molecularProfileId", "patientId", "sampleId", "studyId" ], "properties": { "alteration": { "type": "integer", "format": "int32" }, "driverFilter": { "type": "string" }, "driverFilterAnnotation": { "type": "string" }, "driverTiersFilter": { "type": "string" }, "driverTiersFilterAnnotation": { "type": "string" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "gene": { "$ref": "#/definitions/Gene" }, "molecularProfileId": { "type": "string" }, "namespaceColumns": { "type": "object", "additionalProperties": { "type": "object" } }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" } }, "title": "DiscreteCopyNumberData" }, "DiscreteCopyNumberFilter": { "type": "object", "properties": { "entrezGeneIds": { "type": "array", "items": { "type": "integer", "format": "int32" } }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "DiscreteCopyNumberFilter" }, "Gene": { "type": "object", "required": [ "entrezGeneId", "geneticEntityId", "hugoGeneSymbol" ], "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "geneticEntityId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" }, "type": { "type": "string" } }, "title": "Gene" }, "GeneFilter": { "type": "object", "properties": { "geneQueries": { "type": "array", "items": { "type": "array", "items": { "$ref": "#/definitions/GeneFilterQuery" } } }, "molecularProfileIds": { "type": "array", "uniqueItems": true, "items": { "type": "string" } } }, "title": "GeneFilter" }, "GeneFilterQuery": { "type": "object", "properties": { "alterations": { "type": "array", "items": { "type": "string", "enum": [ "AMP", "DIPLOID", "GAIN", "HETLOSS", "HOMDEL" ] } }, "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" }, "includeDriver": { "type": "boolean" }, "includeGermline": { "type": "boolean" }, "includeSomatic": { "type": "boolean" }, "includeUnknownOncogenicity": { "type": "boolean" }, "includeUnknownStatus": { "type": "boolean" }, "includeUnknownTier": { "type": "boolean" }, "includeVUS": { "type": "boolean" }, "tiersBooleanMap": { "type": "object", "additionalProperties": { "type": "boolean" } } }, "title": "GeneFilterQuery" }, "GenePanel": { "type": "object", "required": [ "genePanelId" ], "properties": { "description": { "type": "string" }, "genePanelId": { "type": "string" }, "genes": { "type": "array", "items": { "$ref": "#/definitions/GenePanelToGene" } } }, "title": "GenePanel" }, "GenePanelData": { "type": "object", "required": [ "molecularProfileId", "patientId", "profiled", "sampleId", "studyId" ], "properties": { "genePanelId": { "type": "string" }, "molecularProfileId": { "type": "string" }, "patientId": { "type": "string" }, "profiled": { "type": "boolean" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" } }, "title": "GenePanelData" }, "GenePanelDataFilter": { "type": "object", "properties": { "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "GenePanelDataFilter" }, "GenePanelDataMultipleStudyFilter": { "type": "object", "properties": { "molecularProfileIds": { "type": "array", "items": { "type": "string" } }, "sampleMolecularIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleMolecularIdentifier" } } }, "title": "GenePanelDataMultipleStudyFilter" }, "GenePanelToGene": { "type": "object", "required": [ "entrezGeneId", "hugoGeneSymbol" ], "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" } }, "title": "GenePanelToGene" }, "GenericAssayData": { "type": "object", "required": [ "genericAssayStableId", "molecularProfileId", "patientId", "sampleId", "studyId", "value" ], "properties": { "genericAssayStableId": { "type": "string" }, "molecularProfileId": { "type": "string" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "stableId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "value": { "type": "string" } }, "title": "GenericAssayData" }, "GenericAssayDataFilter": { "type": "object", "properties": { "profileType": { "type": "string" }, "stableId": { "type": "string" }, "values": { "type": "array", "items": { "$ref": "#/definitions/DataFilterValue" } } }, "title": "GenericAssayDataFilter" }, "GenericAssayDataMultipleStudyFilter": { "type": "object", "properties": { "genericAssayStableIds": { "type": "array", "items": { "type": "string" } }, "molecularProfileIds": { "type": "array", "items": { "type": "string" } }, "sampleMolecularIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleMolecularIdentifier" } } }, "title": "GenericAssayDataMultipleStudyFilter" }, "GenericAssayFilter": { "type": "object", "properties": { "genericAssayStableIds": { "type": "array", "items": { "type": "string" } }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "GenericAssayFilter" }, "GenericAssayMeta": { "type": "object", "properties": { "entityType": { "type": "string" }, "genericEntityMetaProperties": { "type": "object", "additionalProperties": { "type": "string" } }, "stableId": { "type": "string" } }, "title": "GenericAssayMeta" }, "GenericAssayMetaFilter": { "type": "object", "properties": { "genericAssayStableIds": { "type": "array", "items": { "type": "string" } }, "molecularProfileIds": { "type": "array", "items": { "type": "string" } } }, "title": "GenericAssayMetaFilter" }, "GenomicDataFilter": { "type": "object", "properties": { "hugoGeneSymbol": { "type": "string" }, "profileType": { "type": "string" }, "values": { "type": "array", "items": { "$ref": "#/definitions/DataFilterValue" } } }, "title": "GenomicDataFilter" }, "Info": { "type": "object", "required": [ "dbVersion", "gitBranch", "gitCommitId", "gitCommitIdAbbrev", "gitCommitIdDescribe", "gitCommitIdDescribeShort", "gitCommitMessageFull", "gitCommitMessageShort", "gitCommitMessageUserEmail", "gitCommitMessageUserName", "gitDirty", "portalVersion" ], "properties": { "dbVersion": { "type": "string" }, "gitBranch": { "type": "string" }, "gitCommitId": { "type": "string" }, "gitCommitIdAbbrev": { "type": "string" }, "gitCommitIdDescribe": { "type": "string" }, "gitCommitIdDescribeShort": { "type": "string" }, "gitCommitMessageFull": { "type": "string" }, "gitCommitMessageShort": { "type": "string" }, "gitCommitMessageUserEmail": { "type": "string" }, "gitCommitMessageUserName": { "type": "string" }, "gitDirty": { "type": "boolean" }, "portalVersion": { "type": "string" } }, "title": "Info" }, "MolecularDataFilter": { "type": "object", "properties": { "entrezGeneIds": { "type": "array", "items": { "type": "integer", "format": "int32" } }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "MolecularDataFilter" }, "MolecularDataMultipleStudyFilter": { "type": "object", "properties": { "entrezGeneIds": { "type": "array", "items": { "type": "integer", "format": "int32" } }, "molecularProfileIds": { "type": "array", "items": { "type": "string" } }, "sampleMolecularIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleMolecularIdentifier" } } }, "title": "MolecularDataMultipleStudyFilter" }, "MolecularProfile": { "type": "object", "required": [ "molecularProfileId", "patientLevel", "studyId" ], "properties": { "datatype": { "type": "string" }, "description": { "type": "string" }, "genericAssayType": { "type": "string" }, "molecularAlterationType": { "type": "string", "enum": [ "COPY_NUMBER_ALTERATION", "GENERIC_ASSAY", "GENESET_SCORE", "METHYLATION", "METHYLATION_BINARY", "MICRO_RNA_EXPRESSION", "MRNA_EXPRESSION", "MRNA_EXPRESSION_NORMALS", "MUTATION_EXTENDED", "MUTATION_UNCALLED", "PHOSPHORYLATION", "PROTEIN_ARRAY_PHOSPHORYLATION", "PROTEIN_ARRAY_PROTEIN_LEVEL", "PROTEIN_LEVEL", "RNA_EXPRESSION", "STRUCTURAL_VARIANT" ] }, "molecularProfileId": { "type": "string" }, "name": { "type": "string" }, "patientLevel": { "type": "boolean" }, "pivotThreshold": { "type": "number", "format": "float" }, "showProfileInAnalysisTab": { "type": "boolean" }, "sortOrder": { "type": "string" }, "study": { "$ref": "#/definitions/CancerStudy" }, "studyId": { "type": "string" } }, "title": "MolecularProfile" }, "MolecularProfileFilter": { "type": "object", "properties": { "molecularProfileIds": { "type": "array", "uniqueItems": true, "items": { "type": "string" } }, "studyIds": { "type": "array", "items": { "type": "string" } } }, "title": "MolecularProfileFilter" }, "Mutation": { "type": "object", "required": [ "entrezGeneId", "molecularProfileId", "patientId", "sampleId", "studyId" ], "properties": { "alleleSpecificCopyNumber": { "$ref": "#/definitions/AlleleSpecificCopyNumber" }, "aminoAcidChange": { "type": "string" }, "center": { "type": "string" }, "chr": { "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": { "$ref": "#/definitions/Gene" }, "keyword": { "type": "string" }, "linkMsa": { "type": "string" }, "linkPdb": { "type": "string" }, "linkXvar": { "type": "string" }, "molecularProfileId": { "type": "string" }, "mutationStatus": { "type": "string" }, "mutationType": { "type": "string" }, "namespaceColumns": { "type": "object", "additionalProperties": { "type": "object" } }, "ncbiBuild": { "type": "string" }, "normalAltCount": { "type": "integer", "format": "int32" }, "normalRefCount": { "type": "integer", "format": "int32" }, "patientId": { "type": "string" }, "proteinChange": { "type": "string" }, "proteinPosEnd": { "type": "integer", "format": "int32" }, "proteinPosStart": { "type": "integer", "format": "int32" }, "referenceAllele": { "type": "string" }, "refseqMrnaId": { "type": "string" }, "sampleId": { "type": "string" }, "startPosition": { "type": "integer", "format": "int64" }, "studyId": { "type": "string" }, "tumorAltCount": { "type": "integer", "format": "int32" }, "tumorRefCount": { "type": "integer", "format": "int32" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "validationStatus": { "type": "string" }, "variantAllele": { "type": "string" }, "variantType": { "type": "string" } }, "title": "Mutation" }, "MutationFilter": { "type": "object", "properties": { "entrezGeneIds": { "type": "array", "items": { "type": "integer", "format": "int32" } }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "MutationFilter" }, "MutationMultipleStudyFilter": { "type": "object", "properties": { "entrezGeneIds": { "type": "array", "items": { "type": "integer", "format": "int32" } }, "molecularProfileIds": { "type": "array", "items": { "type": "string" } }, "sampleMolecularIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleMolecularIdentifier" } } }, "title": "MutationMultipleStudyFilter" }, "NumericGeneMolecularData": { "type": "object", "required": [ "entrezGeneId", "molecularProfileId", "patientId", "sampleId", "studyId", "value" ], "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "gene": { "$ref": "#/definitions/Gene" }, "molecularProfileId": { "type": "string" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "value": { "type": "number" } }, "title": "NumericGeneMolecularData" }, "OredPatientTreatmentFilters": { "type": "object", "properties": { "filters": { "type": "array", "items": { "$ref": "#/definitions/PatientTreatmentFilter" } } }, "title": "OredPatientTreatmentFilters" }, "OredSampleTreatmentFilters": { "type": "object", "properties": { "filters": { "type": "array", "items": { "$ref": "#/definitions/SampleTreatmentFilter" } } }, "title": "OredSampleTreatmentFilters" }, "Patient": { "type": "object", "required": [ "patientId", "studyId" ], "properties": { "cancerStudy": { "$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": { "$ref": "#/definitions/PatientIdentifier" } }, "uniquePatientKeys": { "type": "array", "items": { "type": "string" } } }, "title": "PatientFilter" }, "PatientIdentifier": { "type": "object", "properties": { "patientId": { "type": "string" }, "studyId": { "type": "string" } }, "title": "PatientIdentifier" }, "PatientTreatmentFilter": { "type": "object", "properties": { "treatment": { "type": "string" } }, "title": "PatientTreatmentFilter" }, "PatientTreatmentRow": { "type": "object", "properties": { "count": { "type": "integer", "format": "int32" }, "samples": { "type": "array", "uniqueItems": true, "items": { "$ref": "#/definitions/ClinicalEventSample" } }, "treatment": { "type": "string" } }, "title": "PatientTreatmentRow" }, "Sample": { "type": "object", "required": [ "patientId", "sampleId", "studyId" ], "properties": { "copyNumberSegmentPresent": { "type": "boolean" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "sampleType": { "type": "string", "enum": [ "BLOOD_NORMAL", "METASTATIC", "PRIMARY_BLOOD_TUMOR", "PRIMARY_SOLID_TUMOR", "RECURRENT_BLOOD_TUMOR", "RECURRENT_SOLID_TUMOR", "SOLID_NORMAL" ] }, "sequenced": { "type": "boolean" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" } }, "title": "Sample" }, "SampleFilter": { "type": "object", "properties": { "sampleIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleIdentifier" } }, "sampleListIds": { "type": "array", "items": { "type": "string" } }, "uniqueSampleKeys": { "type": "array", "items": { "type": "string" } } }, "title": "SampleFilter" }, "SampleIdentifier": { "type": "object", "properties": { "sampleId": { "type": "string" }, "studyId": { "type": "string" } }, "title": "SampleIdentifier" }, "SampleList": { "type": "object", "required": [ "sampleListId" ], "properties": { "category": { "type": "string" }, "description": { "type": "string" }, "name": { "type": "string" }, "sampleCount": { "type": "integer", "format": "int32" }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" }, "studyId": { "type": "string" } }, "title": "SampleList" }, "SampleMolecularIdentifier": { "type": "object", "properties": { "molecularProfileId": { "type": "string" }, "sampleId": { "type": "string" } }, "title": "SampleMolecularIdentifier" }, "SampleTreatmentFilter": { "type": "object", "properties": { "time": { "type": "string", "enum": [ "Post", "Pre" ] }, "treatment": { "type": "string" } }, "title": "SampleTreatmentFilter" }, "SampleTreatmentRow": { "type": "object", "properties": { "count": { "type": "integer", "format": "int32" }, "samples": { "type": "array", "uniqueItems": true, "items": { "$ref": "#/definitions/ClinicalEventSample" } }, "time": { "type": "string", "enum": [ "Post", "Pre" ] }, "treatment": { "type": "string" } }, "title": "SampleTreatmentRow" }, "ServerStatusMessage": { "type": "object", "properties": { "status": { "type": "string" } }, "title": "ServerStatusMessage" }, "StudyViewFilter": { "type": "object", "properties": { "alterationFilter": { "$ref": "#/definitions/AlterationFilter" }, "caseLists": { "type": "array", "items": { "type": "array", "items": { "type": "string" } } }, "clinicalDataFilters": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataFilter" } }, "customDataFilters": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataFilter" } }, "geneFilters": { "type": "array", "items": { "$ref": "#/definitions/GeneFilter" } }, "genericAssayDataFilters": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayDataFilter" } }, "genomicDataFilters": { "type": "array", "items": { "$ref": "#/definitions/GenomicDataFilter" } }, "genomicProfiles": { "type": "array", "items": { "type": "array", "items": { "type": "string" } } }, "patientTreatmentFilters": { "$ref": "#/definitions/AndedPatientTreatmentFilters" }, "patientTreatmentGroupFilters": { "$ref": "#/definitions/AndedPatientTreatmentFilters" }, "patientTreatmentTargetFilters": { "$ref": "#/definitions/AndedPatientTreatmentFilters" }, "sampleIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleIdentifier" } }, "sampleTreatmentFilters": { "$ref": "#/definitions/AndedSampleTreatmentFilters" }, "sampleTreatmentGroupFilters": { "$ref": "#/definitions/AndedSampleTreatmentFilters" }, "sampleTreatmentTargetFilters": { "$ref": "#/definitions/AndedSampleTreatmentFilters" }, "studyIds": { "type": "array", "items": { "type": "string" } } }, "title": "StudyViewFilter" }, "TypeOfCancer": { "type": "object", "required": [ "cancerTypeId" ], "properties": { "cancerTypeId": { "type": "string" }, "dedicatedColor": { "type": "string" }, "name": { "type": "string" }, "parent": { "type": "string" }, "shortName": { "type": "string" } }, "title": "TypeOfCancer" } } }