{ "swagger": "2.0", "info": { "description": "A web service for supplying JSON formatted data to cBioPortal clients. Please note that interal API is currently in beta and subject to change.", "version": "1.0 (beta). Internal API are prone to change.", "title": "cBioPortal web Internal 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": "Alteration Enrichments", "description": " " }, { "name": "Cache", "description": "Cache Controller" }, { "name": "Clinical Attributes Count", "description": " " }, { "name": "Clinical Data Enrichments", "description": " " }, { "name": "Clinical Events", "description": " " }, { "name": "Co-Expressions", "description": " " }, { "name": "Cosmic Counts", "description": " " }, { "name": "Custom driver annotations", "description": " " }, { "name": "Data Access Tokens", "description": " " }, { "name": "Discrete Copy Number Alteration Counts", "description": " " }, { "name": "Enrichments", "description": " " }, { "name": "Gene Set Correlation", "description": " " }, { "name": "Gene Set Hierarchy", "description": " " }, { "name": "Gene Set Scores", "description": " " }, { "name": "Gene Sets", "description": " " }, { "name": "Mutation Spectrums", "description": " " }, { "name": "Mutations Count", "description": " " }, { "name": "Reference Genome Genes", "description": " " }, { "name": "Resource Data", "description": " " }, { "name": "Resource Definitions", "description": " " }, { "name": "Significant Copy Number Regions", "description": " " }, { "name": "Significantly Mutated Genes", "description": " " }, { "name": "Structural Variants", "description": " " }, { "name": "Study View", "description": " " }, { "name": "Timestamps", "description": " " }, { "name": "Variant Counts", "description": " " }, { "name": "mRNA Percentile", "description": " " } ], "paths": { "/alteration-enrichments/fetch": { "post": { "tags": [ "Alteration Enrichments" ], "summary": "Fetch alteration enrichments in molecular profiles", "operationId": "fetchAlterationEnrichmentsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "enrichmentType", "in": "query", "description": "Type of the enrichment e.g. SAMPLE or PATIENT", "required": false, "type": "string", "default": "SAMPLE", "enum": [ "PATIENT", "SAMPLE" ] }, { "in": "body", "name": "groupsAndAlterationTypes", "description": "List of groups containing sample identifiers and list of Alteration Types", "required": true, "schema": { "$ref": "#/definitions/MolecularProfileCasesGroupAndAlterationTypeFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/AlterationEnrichment" } } } } } }, "/cache": { "delete": { "tags": [ "Cache" ], "summary": "Clear and reinitialize caches", "operationId": "clearAllCachesUsingDELETE", "produces": [ "text/plain" ], "parameters": [ { "name": "springManagedCache", "in": "query", "description": "Clear Spring-managed caches", "required": false, "type": "boolean", "default": true }, { "name": "X-API-KEY", "in": "header", "description": "Secret API key passed in HTTP header. The key is configured in portal.properties of the portal instance.", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "string" } } } } }, "/cache/{studyId}": { "delete": { "tags": [ "Cache" ], "summary": "Clear and reinitialize caches after import/removal/update of a study", "operationId": "clearCachesForStudyUsingDELETE", "produces": [ "text/plain" ], "parameters": [ { "name": "springManagedCache", "in": "query", "description": "Clear Spring-managed caches", "required": false, "type": "boolean", "default": true }, { "name": "studyId", "in": "path", "description": "studyId", "required": true, "type": "string" }, { "name": "X-API-KEY", "in": "header", "description": "Secret API key passed in HTTP header. The key is configured in portal.properties of the portal instance.", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "string" } } } } }, "/clinical-attributes/counts/fetch": { "post": { "tags": [ "Clinical Attributes Count" ], "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-data-bin-counts/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch clinical data bin counts by study view filter", "operationId": "fetchClinicalDataBinCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "clinicalDataBinCountFilter", "description": "Clinical data bin count filter", "required": true, "schema": { "$ref": "#/definitions/ClinicalDataBinCountFilter" } }, { "name": "dataBinMethod", "in": "query", "description": "Method for data binning", "required": false, "type": "string", "default": "DYNAMIC", "enum": [ "DYNAMIC", "STATIC" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataBin" } } } } } }, "/clinical-data-counts/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch clinical data counts by study view filter", "operationId": "fetchClinicalDataCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "clinicalDataCountFilter", "description": "Clinical data count filter", "required": true, "schema": { "$ref": "#/definitions/ClinicalDataCountFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataCountItem" } } } } } }, "/clinical-data-density-plot/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch clinical data density plot bins by study view filter", "operationId": "fetchClinicalDataDensityPlotUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } }, { "name": "xAxisAttributeId", "in": "query", "description": "Clinical Attribute ID of the X axis", "required": true, "type": "string" }, { "name": "xAxisBinCount", "in": "query", "description": "Number of the bins in X axis", "required": false, "type": "integer", "default": 50, "format": "int32" }, { "name": "xAxisEnd", "in": "query", "description": "Starting point of the X axis, if different than largest value", "required": false, "type": "number" }, { "name": "xAxisLogScale", "in": "query", "description": "Use log scale for X axis", "required": false, "type": "boolean", "default": false }, { "name": "xAxisStart", "in": "query", "description": "Starting point of the X axis, if different than smallest value", "required": false, "type": "number" }, { "name": "yAxisAttributeId", "in": "query", "description": "Clinical Attribute ID of the Y axis", "required": true, "type": "string" }, { "name": "yAxisBinCount", "in": "query", "description": "Number of the bins in Y axis", "required": false, "type": "integer", "default": 50, "format": "int32" }, { "name": "yAxisEnd", "in": "query", "description": "Starting point of the Y axis, if different than largest value", "required": false, "type": "number" }, { "name": "yAxisLogScale", "in": "query", "description": "Use log scale for Y axis", "required": false, "type": "boolean", "default": false }, { "name": "yAxisStart", "in": "query", "description": "Starting point of the Y axis, if different than smallest value", "required": false, "type": "number" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/DensityPlotData" } } } } }, "/clinical-data-enrichments/fetch": { "post": { "tags": [ "Clinical Data Enrichments" ], "summary": "Fetch clinical data enrichments for the sample groups", "operationId": "fetchClinicalEnrichmentsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "groupFilter", "description": "List of altered and unaltered Sample/Patient IDs", "required": true, "schema": { "$ref": "#/definitions/GroupFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataEnrichment" } } } } } }, "/clinical-data-table/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch clinical data for the Clinical Tab of Study View", "operationId": "fetchClinicalDataClinicalTableUsingPOST", "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": "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": 0, "maximum": 1000000, "exclusiveMaximum": false, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "searchTerm", "in": "query", "description": "Search term to filter sample rows. Samples are returned with a partial match to the search term for any sample clinical attribute.", "required": false, "type": "string" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "clinicalAttributeId", "value" ] }, { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/ClinicalDataCollection" } } } } }, "/clinical-data-violin-plots/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch violin plot curves per categorical clinical data value, filtered by study view filter", "operationId": "fetchClinicalDataViolinPlotsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "axisEnd", "in": "query", "description": "Ending point of the violin plot axis, if different than largest value", "required": false, "type": "number" }, { "name": "axisStart", "in": "query", "description": "Starting point of the violin plot axis, if different than smallest value", "required": false, "type": "number" }, { "name": "categoricalAttributeId", "in": "query", "description": "Clinical Attribute ID of the categorical attribute", "required": true, "type": "string" }, { "name": "logScale", "in": "query", "description": "Use log scale for the numerical attribute", "required": false, "type": "boolean", "default": false }, { "name": "numCurvePoints", "in": "query", "description": "Number of points in the curve", "required": false, "type": "number", "default": 100 }, { "name": "numericalAttributeId", "in": "query", "description": "Clinical Attribute ID of the numerical attribute", "required": true, "type": "string" }, { "name": "sigmaMultiplier", "in": "query", "description": "Sigma stepsize multiplier", "required": false, "type": "number", "default": 1 }, { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/ClinicalViolinPlotData" } } } } }, "/cna-genes/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch CNA genes by study view filter", "operationId": "fetchCNAGenesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CopyNumberCountByGene" } } } } } }, "/cosmic-counts/fetch": { "post": { "tags": [ "Cosmic Counts" ], "summary": "Get counts within the COSMIC database by keywords", "operationId": "fetchCosmicCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "keywords", "description": "List of keywords", "required": true, "schema": { "type": "array", "items": { "type": "string" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CosmicMutation" } } } } } }, "/custom-data-counts/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch custom data counts by study view filter", "operationId": "fetchCustomDataCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "clinicalDataCountFilter", "description": "Custom data count filter", "required": true, "schema": { "$ref": "#/definitions/ClinicalDataCountFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataCountItem" } } } } } }, "/custom-driver-annotation-report/fetch": { "post": { "tags": [ "Custom driver annotations" ], "summary": "Return availability of custom driver annotations for molecular profiles", "operationId": "fetchAlterationDriverAnnotationReportUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "molecularProfileIds", "description": "molecularProfileIds", "required": true, "schema": { "type": "array", "items": { "type": "string" } } } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/CustomDriverAnnotationReport" } } } } }, "/data-access-token": { "get": { "tags": [ "Data Access Tokens" ], "summary": "Create a new data access token", "operationId": "downloadDataAccessTokenUsingGET", "produces": [ "*/*" ], "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": "principal", "in": "query", "required": false, "type": "object" } ], "responses": { "200": { "description": "OK", "schema": { "type": "string" } } } } }, "/data-access-tokens": { "get": { "tags": [ "Data Access Tokens" ], "summary": "Retrieve all data access tokens", "operationId": "getAllDataAccessTokensUsingGET", "produces": [ "*/*" ], "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": "principal", "in": "query", "required": false, "type": "object" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/DataAccessToken" } } } } }, "post": { "tags": [ "Data Access Tokens" ], "summary": "Get all data access tokens", "operationId": "createDataAccessTokenUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "authenticated", "in": "query", "required": false, "type": "boolean" }, { "name": "authorities[0].authority", "in": "query", "required": false, "type": "string" }, { "name": "credentials", "in": "query", "required": false, "type": "object" }, { "name": "details", "in": "query", "required": false, "type": "object" }, { "name": "principal", "in": "query", "required": false, "type": "object" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/DataAccessToken" } } } }, "delete": { "tags": [ "Data Access Tokens" ], "summary": "Delete all data access tokens", "operationId": "revokeAllDataAccessTokensUsingDELETE", "produces": [ "*/*" ], "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": "principal", "in": "query", "required": false, "type": "object" } ], "responses": { "200": { "description": "OK" } } } }, "/data-access-tokens/{token}": { "get": { "tags": [ "Data Access Tokens" ], "summary": "Retrieve an existing data access token", "operationId": "getDataAccessTokenUsingGET", "produces": [ "*/*" ], "parameters": [ { "name": "token", "in": "path", "description": "token", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/DataAccessToken" } } } }, "delete": { "tags": [ "Data Access Tokens" ], "summary": "Delete a data access token", "operationId": "revokeDataAccessTokenUsingDELETE", "produces": [ "*/*" ], "parameters": [ { "name": "token", "in": "path", "description": "token", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK" } } } }, "/expression-enrichments/fetch": { "post": { "tags": [ "Enrichments" ], "summary": "Fetch genomic enrichments in a molecular profile", "operationId": "fetchGenomicEnrichmentsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "enrichmentType", "in": "query", "description": "Type of the enrichment e.g. SAMPLE or PATIENT", "required": false, "type": "string", "default": "SAMPLE", "enum": [ "PATIENT", "SAMPLE" ] }, { "in": "body", "name": "groups", "description": "List of groups containing sample and molecular profile identifiers", "required": true, "schema": { "type": "array", "items": { "$ref": "#/definitions/MolecularProfileCasesGroupFilter" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenomicEnrichment" } } } } } }, "/filtered-samples/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch sample IDs by study view filter", "operationId": "fetchFilteredSamplesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "negateFilters", "in": "query", "description": "Whether to negate the study view filters", "required": false, "type": "boolean", "default": false }, { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Sample" } } } } } }, "/generic-assay-data-bin-counts/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch generic assay data bin counts by study view filter", "operationId": "fetchGenericAssayDataBinCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "dataBinMethod", "in": "query", "description": "Method for data binning", "required": false, "type": "string", "default": "DYNAMIC", "enum": [ "DYNAMIC", "STATIC" ] }, { "in": "body", "name": "genericAssayDataBinCountFilter", "description": "Generic assay data bin count filter", "required": true, "schema": { "$ref": "#/definitions/GenericAssayDataBinCountFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayDataBin" } } } } } }, "/generic-assay-data-counts/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch generic assay data counts by study view filter", "operationId": "fetchGenericAssayDataCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genericAssayDataCountFilter", "description": "Generic assay data count filter", "required": true, "schema": { "$ref": "#/definitions/GenericAssayDataCountFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayDataCountItem" } } } } } }, "/generic-assay-enrichments/fetch": { "post": { "tags": [ "Enrichments" ], "summary": "Fetch generic assay enrichments in a molecular profile", "operationId": "fetchGenericAssayEnrichmentsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "enrichmentType", "in": "query", "description": "Type of the enrichment e.g. SAMPLE or PATIENT", "required": false, "type": "string", "default": "SAMPLE", "enum": [ "PATIENT", "SAMPLE" ] }, { "in": "body", "name": "groups", "description": "List of groups containing sample and molecular profile identifiers", "required": true, "schema": { "type": "array", "items": { "$ref": "#/definitions/MolecularProfileCasesGroupFilter" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayEnrichment" } } } } } }, "/geneset-hierarchy/fetch": { "post": { "tags": [ "Gene Set Hierarchy" ], "summary": "Get gene set hierarchical organization information. I.e. how different gene sets relate to other gene sets, in a hierarchy", "operationId": "fetchGenesetHierarchyInfoUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "geneticProfileId", "in": "query", "description": "Genetic Profile ID e.g. gbm_tcga_gsva_scores. The final hierarchy will only include gene sets scored in the specified profile.", "required": true, "type": "string" }, { "name": "percentile", "in": "query", "description": "Percentile (for score calculation). Which percentile to use when determining the *representative score*", "required": false, "type": "integer", "default": 75, "maximum": 100, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "pvalueThreshold", "in": "query", "description": "p-value threshold. Filters out gene sets for which the score p-value is higher than this threshold.", "required": false, "type": "number", "default": 0.05, "maximum": 1, "exclusiveMaximum": false, "minimum": 0, "exclusiveMinimum": false, "format": "double" }, { "in": "body", "name": "sampleIds", "description": "Fill this one if you want to specify a subset of samples: sampleIds: custom list of samples or patients to query, e.g. [\"TCGA-A1-A0SD-01\", \"TCGA-A1-A0SE-01\"]", "required": false, "schema": { "type": "array", "items": { "type": "string" } } }, { "name": "sampleListId", "in": "query", "description": "Identifier of pre-defined sample list with samples to query, e.g. brca_tcga_all", "required": false, "type": "string" }, { "name": "scoreThreshold", "in": "query", "description": "Gene set score threshold (for absolute score value). Filters out gene sets where the GSVA(like) *representative score* is under this threshold.", "required": false, "type": "number", "default": 0.4, "maximum": 1, "exclusiveMaximum": false, "minimum": 0, "exclusiveMinimum": false, "format": "double" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenesetHierarchyInfo" } } } } } }, "/genesets": { "get": { "tags": [ "Gene Sets" ], "summary": "Get all gene sets", "operationId": "getAllGenesetsUsingGET", "produces": [ "application/json" ], "parameters": [ { "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": 2147483647, "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" ] } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Geneset" } } } } } }, "/genesets/fetch": { "post": { "tags": [ "Gene Sets" ], "summary": "Fetch gene sets by ID", "operationId": "fetchGenesetsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genesetIds", "description": "List of Gene set IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Geneset" } } } } } }, "/genesets/version": { "get": { "tags": [ "Gene Sets" ], "summary": "Get the geneset version", "operationId": "getGenesetVersionUsingGET", "produces": [ "application/json" ], "responses": { "200": { "description": "OK", "schema": { "type": "string" } } } } }, "/genesets/{genesetId}": { "get": { "tags": [ "Gene Sets" ], "summary": "Get a gene set", "operationId": "getGenesetUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "genesetId", "in": "path", "description": "Gene set ID e.g. GNF2_ZAP70", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/Geneset" } } } } }, "/genesets/{genesetId}/expression-correlation/fetch": { "post": { "tags": [ "Gene Set Correlation" ], "summary": "Get the genes in a gene set that have expression correlated to the gene set scores (calculated using Spearman's correlation)", "operationId": "fetchCorrelatedGenesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "correlationThreshold", "in": "query", "description": "Correlation threshold (for absolute correlation value, Spearman correlation)", "required": false, "type": "number", "default": 0.3, "maximum": 1, "exclusiveMaximum": false, "minimum": 0, "exclusiveMinimum": false, "format": "double" }, { "name": "genesetId", "in": "path", "description": "Gene set ID, e.g. HINATA_NFKB_MATRIX.", "required": true, "type": "string" }, { "name": "geneticProfileId", "in": "query", "description": "Genetic Profile ID e.g. gbm_tcga_gsva_scores", "required": true, "type": "string" }, { "in": "body", "name": "sampleIds", "description": "Fill this one if you want to specify a subset of samples: sampleIds: custom list of samples or patients to query, e.g. [\"TCGA-A1-A0SD-01\", \"TCGA-A1-A0SE-01\"]", "required": false, "schema": { "type": "array", "items": { "type": "string" } } }, { "name": "sampleListId", "in": "query", "description": "Identifier of pre-defined sample list with samples to query, e.g. brca_tcga_all", "required": false, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenesetCorrelation" } } } } } }, "/genetic-profiles/{geneticProfileId}/geneset-genetic-data/fetch": { "post": { "tags": [ "Gene Set Scores" ], "summary": "Fetch gene set \"genetic data\" items (gene set scores) by profile Id, gene set ids and sample ids", "operationId": "fetchGeneticDataItemsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "genesetDataFilterCriteria", "description": "Search criteria to return the values for a given set of samples and gene set items. genesetIds: The list of identifiers for the gene sets of interest, e.g. HINATA_NFKB_MATRIX. Use one of these if you want to specify a subset of samples:(1) sampleListId: Identifier of pre-defined sample list with samples to query, e.g. brca_tcga_all or (2) sampleIds: custom list of samples or patients to query, e.g. TCGA-BH-A1EO-01, TCGA-AR-A1AR-01", "required": true, "schema": { "$ref": "#/definitions/GenesetDataFilterCriteria" } }, { "name": "geneticProfileId", "in": "path", "description": "Genetic profile ID, e.g. gbm_tcga_gsva_scores", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenesetMolecularData" } } } } } }, "/genomic-data-bin-counts/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch genomic data bin counts by study view filter", "operationId": "fetchGenomicDataBinCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "dataBinMethod", "in": "query", "description": "Method for data binning", "required": false, "type": "string", "default": "DYNAMIC", "enum": [ "DYNAMIC", "STATIC" ] }, { "in": "body", "name": "genomicDataBinCountFilter", "description": "Genomic data bin count filter", "required": true, "schema": { "$ref": "#/definitions/GenomicDataBinCountFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenomicDataBin" } } } } } }, "/molecular-profile-sample-counts/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch sample counts by study view filter", "operationId": "fetchMolecularProfileSampleCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/GenomicDataCount" } } } } } }, "/molecular-profiles/co-expressions/fetch": { "post": { "tags": [ "Co-Expressions" ], "summary": "Calculates correlations between a genetic entity from a specific profile and another profile from the same study", "operationId": "fetchCoExpressionsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "coExpressionFilter", "description": "List of Sample IDs/Sample List ID and Entrez Gene ID/Gene set ID", "required": true, "schema": { "$ref": "#/definitions/CoExpressionFilter" } }, { "name": "molecularProfileIdA", "in": "query", "description": "Molecular Profile ID from the Genetic Entity referenced in the co-expression filter e.g. acc_tcga_rna_seq_v2_mrna", "required": true, "type": "string" }, { "name": "molecularProfileIdB", "in": "query", "description": "Molecular Profile ID (can be the same as molecularProfileIdA) e.g. acc_tcga_rna_seq_v2_mrna", "required": true, "type": "string" }, { "name": "threshold", "in": "query", "description": "Threshold", "required": false, "type": "number", "default": 0.3, "format": "double" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CoExpression" } } } } } }, "/molecular-profiles/{molecularProfileId}/discrete-copy-number-counts/fetch": { "post": { "tags": [ "Discrete Copy Number Alteration Counts" ], "summary": "Get counts of specific genes and alterations within a CNA molecular profile", "operationId": "fetchCopyNumberCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "copyNumberCountIdentifiers", "description": "List of copy number count identifiers", "required": true, "schema": { "type": "array", "items": { "$ref": "#/definitions/CopyNumberCountIdentifier" } } }, { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_gistic", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CopyNumberCount" } } } } } }, "/molecular-profiles/{molecularProfileId}/mrna-percentile/fetch": { "post": { "tags": [ "mRNA Percentile" ], "summary": "Get mRNA expression percentiles for list of genes for a sample", "operationId": "fetchMrnaPercentileUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "entrezGeneIds", "description": "List of Entrez Gene IDs", "required": true, "schema": { "type": "array", "items": { "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": "sampleId", "in": "query", "description": "Sample ID e.g. TCGA-OR-A5J2-01", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/MrnaPercentile" } } } } } }, "/molecular-profiles/{molecularProfileId}/mutation-spectrums/fetch": { "post": { "tags": [ "Mutation Spectrums" ], "summary": "Fetch mutation spectrums in a molecular profile", "operationId": "fetchMutationSpectrumsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_mutations", "required": true, "type": "string" }, { "in": "body", "name": "mutationSpectrumFilter", "description": "List of Sample IDs/Sample List ID", "required": true, "schema": { "$ref": "#/definitions/MutationSpectrumFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/MutationSpectrum" } } } } } }, "/molecular-profiles/{molecularProfileId}/variant-counts/fetch": { "post": { "tags": [ "Variant Counts" ], "summary": "Get counts of specific variants within a mutation molecular profile", "operationId": "fetchVariantCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "molecularProfileId", "in": "path", "description": "Molecular Profile ID e.g. acc_tcga_mutations", "required": true, "type": "string" }, { "in": "body", "name": "variantCountIdentifiers", "description": "List of variant count identifiers", "required": true, "schema": { "type": "array", "items": { "$ref": "#/definitions/VariantCountIdentifier" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/VariantCount" } } } } } }, "/mutated-genes/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch mutated genes by study view filter", "operationId": "fetchMutatedGenesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/AlterationCountByGene" } } } } } }, "/mutation-counts-by-position/fetch": { "post": { "tags": [ "Mutations Count" ], "summary": "Fetch mutation counts in all studies by gene and position", "operationId": "fetchMutationCountsByPositionUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "mutationPositionIdentifiers", "description": "List of gene and positions", "required": true, "schema": { "type": "array", "items": { "$ref": "#/definitions/MutationPositionIdentifier" } } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/MutationCountByPosition" } } } } } }, "/reference-genome-genes/{genomeName}": { "get": { "tags": [ "Reference Genome Genes" ], "summary": "Get all reference genes", "operationId": "getAllReferenceGenomeGenesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "genomeName", "in": "path", "description": "Name of Reference Genome hg19", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ReferenceGenomeGene" } } } } } }, "/reference-genome-genes/{genomeName}/fetch": { "post": { "tags": [ "Reference Genome Genes" ], "summary": "Fetch genes of reference genome of interest", "operationId": "fetchReferenceGenomeGenesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "geneIds", "description": "List of Entrez Gene IDs", "required": true, "schema": { "type": "array", "items": { "type": "string" } } }, { "name": "genomeName", "in": "path", "description": "Name of Reference Genome hg19", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ReferenceGenomeGene" } } } } } }, "/reference-genome-genes/{genomeName}/{geneId}": { "get": { "tags": [ "Reference Genome Genes" ], "summary": "Get a gene of a reference genome of interest", "operationId": "getReferenceGenomeGeneUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "geneId", "in": "path", "description": "Entrez Gene ID 207", "required": true, "type": "integer", "format": "int32" }, { "name": "genomeName", "in": "path", "description": "Name of Reference Genome hg19", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/ReferenceGenomeGene" } } } } }, "/resource-definitions/fetch": { "post": { "tags": [ "Resource Definitions" ], "summary": "Get all resource definitions for specified studies", "operationId": "fetchResourceDefinitionsUsingPOST", "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": { "$ref": "#/definitions/ResourceDefinition" } } } } } }, "/sample-lists-counts/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch case list sample counts by study view filter", "operationId": "fetchCaseListCountsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/CaseListDataCount" } } } } } }, "/structural-variant/fetch": { "post": { "tags": [ "Structural Variants" ], "summary": "Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers", "operationId": "fetchStructuralVariantsUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "name": "entrezGeneIds", "in": "query", "required": false, "type": "array", "items": { "type": "integer", "format": "int32" }, "collectionFormat": "multi" }, { "name": "molecularProfileIds", "in": "query", "required": false, "type": "array", "items": { "type": "string" }, "collectionFormat": "multi" }, { "name": "sampleMolecularIdentifiers[0].molecularProfileId", "in": "query", "required": false, "type": "string" }, { "name": "sampleMolecularIdentifiers[0].sampleId", "in": "query", "required": false, "type": "string" }, { "in": "body", "name": "structuralVariantFilter", "description": "List of entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers", "required": true, "schema": { "$ref": "#/definitions/StructuralVariantFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/StructuralVariant" } } } } } }, "/structuralvariant-genes/fetch": { "post": { "tags": [ "Study View" ], "summary": "Fetch structural variant genes by study view filter", "operationId": "fetchStructuralVariantGenesUsingPOST", "consumes": [ "application/json" ], "produces": [ "application/json" ], "parameters": [ { "in": "body", "name": "studyViewFilter", "description": "Study view filter", "required": true, "schema": { "$ref": "#/definitions/StudyViewFilter" } } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/AlterationCountByGene" } } } } } }, "/studies/{studyId}/clinical-events": { "get": { "tags": [ "Clinical Events" ], "summary": "Get all clinical events in a study", "operationId": "getAllClinicalEventsInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "endNumberOfDaysSinceDiagnosis", "eventType", "startNumberOfDaysSinceDiagnosis" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. lgg_ucsf_2014", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalEvent" } } } } } }, "/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": "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": "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": [ "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": [ "endNumberOfDaysSinceDiagnosis", "eventType", "startNumberOfDaysSinceDiagnosis" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. lgg_ucsf_2014", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ClinicalEvent" } } } } } }, "/studies/{studyId}/patients/{patientId}/resource-data": { "get": { "tags": [ "Resource Data" ], "summary": "Get all resource data of a patient in a study", "operationId": "getAllResourceDataOfPatientInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "patientId", "in": "path", "description": "Patient ID e.g. TCGA-OR-A5J2", "required": true, "type": "string" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "resourceId", "in": "query", "description": "Resource ID", "required": false, "type": "string" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "ResourceId", "url" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ResourceData" } } } } } }, "/studies/{studyId}/resource-data": { "get": { "tags": [ "Resource Data" ], "summary": "Get all resource data for a study", "operationId": "getAllStudyResourceDataInStudyUsingGET", "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": "resourceId", "in": "query", "description": "Resource ID", "required": false, "type": "string" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "ResourceId", "url" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ResourceData" } } } } } }, "/studies/{studyId}/resource-definitions": { "get": { "tags": [ "Resource Definitions" ], "summary": "Get all resource definitions in the specified study", "operationId": "getAllResourceDefinitionsInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "description", "displayName", "openByDefault", "priority", "resourceId", "resourceType", "studyId" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ResourceDefinition" } } } } } }, "/studies/{studyId}/resource-definitions/{resourceId}": { "get": { "tags": [ "Resource Definitions" ], "summary": "Get specified resource definition", "operationId": "getResourceDefinitionInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "resourceId", "in": "path", "description": "Resource ID", "required": true, "type": "string" }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "$ref": "#/definitions/ResourceDefinition" } } } } }, "/studies/{studyId}/samples/{sampleId}/resource-data": { "get": { "tags": [ "Resource Data" ], "summary": "Get all resource data of a sample in a study", "operationId": "getAllResourceDataOfSampleInStudyUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "resourceId", "in": "query", "description": "Resource ID", "required": false, "type": "string" }, { "name": "sampleId", "in": "path", "description": "Sample ID e.g. TCGA-OR-A5J2-01", "required": true, "type": "string" }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "ResourceId", "url" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/ResourceData" } } } } } }, "/studies/{studyId}/significant-copy-number-regions": { "get": { "tags": [ "Significant Copy Number Regions" ], "summary": "Get significant copy number alteration regions in a study", "operationId": "getSignificantCopyNumberRegionsUsingGET", "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": [ "amp", "chromosome", "cytoband", "qValue", "widePeakEnd", "widePeakStart" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/Gistic" } } } } } }, "/studies/{studyId}/significantly-mutated-genes": { "get": { "tags": [ "Significantly Mutated Genes" ], "summary": "Get significantly mutated genes in a study", "operationId": "getSignificantlyMutatedGenesUsingGET", "produces": [ "application/json" ], "parameters": [ { "name": "direction", "in": "query", "description": "Direction of the sort", "required": false, "type": "string", "default": "ASC", "enum": [ "ASC", "DESC" ] }, { "name": "pageNumber", "in": "query", "description": "Page number of the result list", "required": false, "type": "integer", "default": 0, "minimum": 0, "exclusiveMinimum": false, "format": "int32" }, { "name": "pageSize", "in": "query", "description": "Page size of the result list", "required": false, "type": "integer", "default": 10000000, "maximum": 10000000, "exclusiveMaximum": false, "minimum": 1, "exclusiveMinimum": false, "format": "int32" }, { "name": "projection", "in": "query", "description": "Level of detail of the response", "required": false, "type": "string", "default": "SUMMARY", "enum": [ "DETAILED", "ID", "META", "SUMMARY" ] }, { "name": "sortBy", "in": "query", "description": "Name of the property that the result list is sorted by", "required": false, "type": "string", "enum": [ "entrezGeneId", "hugoGeneSymbol", "numberOfMutations", "pValue", "qValue", "rank" ] }, { "name": "studyId", "in": "path", "description": "Study ID e.g. acc_tcga", "required": true, "type": "string" } ], "responses": { "200": { "description": "OK", "schema": { "type": "array", "items": { "$ref": "#/definitions/MutSig" } } } } } }, "/timestamps": { "get": { "tags": [ "Timestamps" ], "summary": "Get the last time each static resource was updated", "operationId": "getAllTimestampsUsingGET", "produces": [ "application/json" ], "responses": { "200": { "description": "OK", "schema": { "type": "object", "additionalProperties": { "type": "string" } } } } } } }, "definitions": { "AlterationCountByGene": { "type": "object", "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" }, "matchingGenePanelIds": { "type": "array", "uniqueItems": true, "items": { "type": "string" } }, "numberOfAlteredCases": { "type": "integer", "format": "int32" }, "numberOfProfiledCases": { "type": "integer", "format": "int32" }, "qValue": { "type": "number" }, "totalCount": { "type": "integer", "format": "int32" } }, "title": "AlterationCountByGene" }, "AlterationEnrichment": { "type": "object", "required": [ "counts", "entrezGeneId", "hugoGeneSymbol" ], "properties": { "counts": { "type": "array", "items": { "$ref": "#/definitions/CountSummary" } }, "cytoband": { "type": "string" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" }, "pValue": { "type": "number" } }, "title": "AlterationEnrichment" }, "AlterationFilter": { "type": "object", "properties": { "copyNumberAlterationEventTypes": { "type": "object", "additionalProperties": { "type": "boolean" } }, "includeDriver": { "type": "boolean" }, "includeGermline": { "type": "boolean" }, "includeSomatic": { "type": "boolean" }, "includeUnknownOncogenicity": { "type": "boolean" }, "includeUnknownStatus": { "type": "boolean" }, "includeUnknownTier": { "type": "boolean" }, "includeVUS": { "type": "boolean" }, "mutationEventTypes": { "type": "object", "additionalProperties": { "type": "boolean" } }, "structuralVariants": { "type": "boolean" }, "tiersBooleanMap": { "type": "object", "additionalProperties": { "type": "boolean" } } }, "title": "AlterationFilter" }, "AndedPatientTreatmentFilters": { "type": "object", "properties": { "filters": { "type": "array", "items": { "$ref": "#/definitions/OredPatientTreatmentFilters" } } }, "title": "AndedPatientTreatmentFilters" }, "AndedSampleTreatmentFilters": { "type": "object", "properties": { "filters": { "type": "array", "items": { "$ref": "#/definitions/OredSampleTreatmentFilters" } } }, "title": "AndedSampleTreatmentFilters" }, "BinsGeneratorConfig": { "type": "object", "properties": { "anchorValue": { "type": "number" }, "binSize": { "type": "number" } }, "title": "BinsGeneratorConfig" }, "CaseListDataCount": { "type": "object", "properties": { "count": { "type": "integer", "format": "int32" }, "label": { "type": "string" }, "value": { "type": "string" } }, "title": "CaseListDataCount" }, "ClinicalAttribute": { "type": "object", "required": [ "clinicalAttributeId", "displayName", "patientAttribute", "studyId" ], "properties": { "clinicalAttributeId": { "type": "string" }, "datatype": { "type": "string" }, "description": { "type": "string" }, "displayName": { "type": "string" }, "patientAttribute": { "type": "boolean" }, "priority": { "type": "string" }, "studyId": { "type": "string" } }, "title": "ClinicalAttribute" }, "ClinicalAttributeCount": { "type": "object", "properties": { "clinicalAttributeId": { "type": "string" }, "count": { "type": "integer", "format": "int32" } }, "title": "ClinicalAttributeCount" }, "ClinicalAttributeCountFilter": { "type": "object", "properties": { "sampleIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleIdentifier" } }, "sampleListId": { "type": "string" } }, "title": "ClinicalAttributeCountFilter" }, "ClinicalData": { "type": "object", "required": [ "clinicalAttributeId", "patientId", "studyId" ], "properties": { "clinicalAttribute": { "$ref": "#/definitions/ClinicalAttribute" }, "clinicalAttributeId": { "type": "string" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "value": { "type": "string" } }, "title": "ClinicalData" }, "ClinicalDataBin": { "type": "object", "properties": { "attributeId": { "type": "string" }, "count": { "type": "integer", "format": "int32" }, "end": { "type": "number" }, "specialValue": { "type": "string" }, "start": { "type": "number" } }, "title": "ClinicalDataBin" }, "ClinicalDataBinCountFilter": { "type": "object", "properties": { "attributes": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataBinFilter" } }, "studyViewFilter": { "$ref": "#/definitions/StudyViewFilter" } }, "title": "ClinicalDataBinCountFilter" }, "ClinicalDataBinFilter": { "type": "object", "properties": { "attributeId": { "type": "string" }, "binMethod": { "type": "string", "enum": [ "CUSTOM", "GENERATE", "MEDIAN", "QUARTILE" ] }, "binsGeneratorConfig": { "$ref": "#/definitions/BinsGeneratorConfig" }, "customBins": { "type": "array", "items": { "type": "number" } }, "disableLogScale": { "type": "boolean" }, "end": { "type": "number" }, "start": { "type": "number" } }, "title": "ClinicalDataBinFilter" }, "ClinicalDataCollection": { "type": "object", "properties": { "patientClinicalData": { "type": "array", "items": { "$ref": "#/definitions/ClinicalData" } }, "sampleClinicalData": { "type": "array", "items": { "$ref": "#/definitions/ClinicalData" } } }, "title": "ClinicalDataCollection" }, "ClinicalDataCount": { "type": "object", "properties": { "count": { "type": "integer", "format": "int32" }, "value": { "type": "string" } }, "title": "ClinicalDataCount" }, "ClinicalDataCountFilter": { "type": "object", "properties": { "attributes": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataFilter" } }, "studyViewFilter": { "$ref": "#/definitions/StudyViewFilter" } }, "title": "ClinicalDataCountFilter" }, "ClinicalDataCountItem": { "type": "object", "properties": { "attributeId": { "type": "string" }, "counts": { "type": "array", "items": { "$ref": "#/definitions/ClinicalDataCount" } } }, "title": "ClinicalDataCountItem" }, "ClinicalDataEnrichment": { "type": "object", "required": [ "clinicalAttribute", "method", "pValue", "score" ], "properties": { "clinicalAttribute": { "$ref": "#/definitions/ClinicalAttribute" }, "method": { "type": "string" }, "pValue": { "type": "number" }, "score": { "type": "number" } }, "title": "ClinicalDataEnrichment" }, "ClinicalDataFilter": { "type": "object", "properties": { "attributeId": { "type": "string" }, "values": { "type": "array", "items": { "$ref": "#/definitions/DataFilterValue" } } }, "title": "ClinicalDataFilter" }, "ClinicalEvent": { "type": "object", "required": [ "eventType", "patientId", "studyId" ], "properties": { "attributes": { "type": "array", "items": { "$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" }, "ClinicalViolinPlotBoxData": { "type": "object", "properties": { "median": { "type": "number", "format": "double" }, "q1": { "type": "number", "format": "double" }, "q3": { "type": "number", "format": "double" }, "whiskerLower": { "type": "number", "format": "double" }, "whiskerUpper": { "type": "number", "format": "double" } }, "title": "ClinicalViolinPlotBoxData" }, "ClinicalViolinPlotData": { "type": "object", "properties": { "axisEnd": { "type": "number", "format": "double" }, "axisStart": { "type": "number", "format": "double" }, "rows": { "type": "array", "items": { "$ref": "#/definitions/ClinicalViolinPlotRowData" } } }, "title": "ClinicalViolinPlotData" }, "ClinicalViolinPlotIndividualPoint": { "type": "object", "properties": { "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "value": { "type": "number", "format": "double" } }, "title": "ClinicalViolinPlotIndividualPoint" }, "ClinicalViolinPlotRowData": { "type": "object", "properties": { "boxData": { "$ref": "#/definitions/ClinicalViolinPlotBoxData" }, "category": { "type": "string" }, "curveData": { "type": "array", "items": { "type": "number", "format": "double" } }, "individualPoints": { "type": "array", "items": { "$ref": "#/definitions/ClinicalViolinPlotIndividualPoint" } }, "numSamples": { "type": "integer", "format": "int32" } }, "title": "ClinicalViolinPlotRowData" }, "CoExpression": { "type": "object", "required": [ "geneticEntityId", "geneticEntityType", "pValue", "spearmansCorrelation" ], "properties": { "geneticEntityId": { "type": "string" }, "geneticEntityType": { "type": "string", "enum": [ "GENE", "GENERIC_ASSAY", "GENESET", "PHOSPHOPROTEIN" ] }, "pValue": { "type": "number" }, "spearmansCorrelation": { "type": "number" } }, "title": "CoExpression" }, "CoExpressionFilter": { "type": "object", "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "genesetId": { "type": "string" }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "CoExpressionFilter" }, "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" }, "CopyNumberCountByGene": { "type": "object", "properties": { "alteration": { "type": "integer", "format": "int32" }, "cytoband": { "type": "string" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" }, "matchingGenePanelIds": { "type": "array", "uniqueItems": true, "items": { "type": "string" } }, "numberOfAlteredCases": { "type": "integer", "format": "int32" }, "numberOfProfiledCases": { "type": "integer", "format": "int32" }, "qValue": { "type": "number" }, "totalCount": { "type": "integer", "format": "int32" } }, "title": "CopyNumberCountByGene" }, "CopyNumberCountIdentifier": { "type": "object", "properties": { "alteration": { "type": "integer", "format": "int32" }, "entrezGeneId": { "type": "integer", "format": "int32" } }, "title": "CopyNumberCountIdentifier" }, "CosmicMutation": { "type": "object", "required": [ "cosmicMutationId", "count", "proteinChange" ], "properties": { "cosmicMutationId": { "type": "string" }, "count": { "type": "integer", "format": "int32" }, "keyword": { "type": "string" }, "proteinChange": { "type": "string" } }, "title": "CosmicMutation" }, "CountSummary": { "type": "object", "required": [ "alteredCount", "name", "profiledCount" ], "properties": { "alteredCount": { "type": "integer", "format": "int32" }, "name": { "type": "string" }, "profiledCount": { "type": "integer", "format": "int32" } }, "title": "CountSummary" }, "CustomDriverAnnotationReport": { "type": "object", "properties": { "hasBinary": { "type": "boolean" }, "tiers": { "type": "array", "uniqueItems": true, "items": { "type": "string" } } }, "title": "CustomDriverAnnotationReport" }, "DataAccessToken": { "type": "object", "properties": { "creation": { "type": "string", "example": "yyyy-MM-dd HH:mm:ss" }, "expiration": { "type": "string", "example": "yyyy-MM-dd HH:mm:ss" }, "token": { "type": "string" }, "username": { "type": "string" } }, "title": "DataAccessToken" }, "DataFilterValue": { "type": "object", "properties": { "end": { "type": "number" }, "start": { "type": "number" }, "value": { "type": "string" } }, "title": "DataFilterValue" }, "DensityPlotBin": { "type": "object", "properties": { "binX": { "type": "number" }, "binY": { "type": "number" }, "count": { "type": "integer", "format": "int32" }, "maxX": { "type": "number" }, "maxY": { "type": "number" }, "minX": { "type": "number" }, "minY": { "type": "number" } }, "title": "DensityPlotBin" }, "DensityPlotData": { "type": "object", "required": [ "bins" ], "properties": { "bins": { "type": "array", "items": { "$ref": "#/definitions/DensityPlotBin" } }, "pearsonCorr": { "type": "number", "format": "double" }, "spearmanCorr": { "type": "number", "format": "double" } }, "title": "DensityPlotData" }, "GeneFilter": { "type": "object", "properties": { "geneQueries": { "type": "array", "items": { "type": "array", "items": { "$ref": "#/definitions/GeneFilterQuery" } } }, "molecularProfileIds": { "type": "array", "uniqueItems": true, "items": { "type": "string" } } }, "title": "GeneFilter" }, "GeneFilterQuery": { "type": "object", "properties": { "alterations": { "type": "array", "items": { "type": "string", "enum": [ "AMP", "DIPLOID", "GAIN", "HETLOSS", "HOMDEL" ] } }, "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" }, "includeDriver": { "type": "boolean" }, "includeGermline": { "type": "boolean" }, "includeSomatic": { "type": "boolean" }, "includeUnknownOncogenicity": { "type": "boolean" }, "includeUnknownStatus": { "type": "boolean" }, "includeUnknownTier": { "type": "boolean" }, "includeVUS": { "type": "boolean" }, "tiersBooleanMap": { "type": "object", "additionalProperties": { "type": "boolean" } } }, "title": "GeneFilterQuery" }, "GenericAssayDataBin": { "type": "object", "properties": { "count": { "type": "integer", "format": "int32" }, "end": { "type": "number" }, "profileType": { "type": "string" }, "specialValue": { "type": "string" }, "stableId": { "type": "string" }, "start": { "type": "number" } }, "title": "GenericAssayDataBin" }, "GenericAssayDataBinCountFilter": { "type": "object", "properties": { "genericAssayDataBinFilters": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayDataBinFilter" } }, "studyViewFilter": { "$ref": "#/definitions/StudyViewFilter" } }, "title": "GenericAssayDataBinCountFilter" }, "GenericAssayDataBinFilter": { "type": "object", "properties": { "binMethod": { "type": "string", "enum": [ "CUSTOM", "GENERATE", "MEDIAN", "QUARTILE" ] }, "binsGeneratorConfig": { "$ref": "#/definitions/BinsGeneratorConfig" }, "customBins": { "type": "array", "items": { "type": "number" } }, "disableLogScale": { "type": "boolean" }, "end": { "type": "number" }, "profileType": { "type": "string" }, "stableId": { "type": "string" }, "start": { "type": "number" } }, "title": "GenericAssayDataBinFilter" }, "GenericAssayDataCount": { "type": "object", "properties": { "count": { "type": "integer", "format": "int32" }, "value": { "type": "string" } }, "title": "GenericAssayDataCount" }, "GenericAssayDataCountFilter": { "type": "object", "properties": { "genericAssayDataFilters": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayDataFilter" } }, "studyViewFilter": { "$ref": "#/definitions/StudyViewFilter" } }, "title": "GenericAssayDataCountFilter" }, "GenericAssayDataCountItem": { "type": "object", "properties": { "counts": { "type": "array", "items": { "$ref": "#/definitions/GenericAssayDataCount" } }, "stableId": { "type": "string" } }, "title": "GenericAssayDataCountItem" }, "GenericAssayDataFilter": { "type": "object", "properties": { "profileType": { "type": "string" }, "stableId": { "type": "string" }, "values": { "type": "array", "items": { "$ref": "#/definitions/DataFilterValue" } } }, "title": "GenericAssayDataFilter" }, "GenericAssayEnrichment": { "type": "object", "required": [ "genericEntityMetaProperties", "groupsStatistics", "name", "pValue", "stableId" ], "properties": { "genericEntityMetaProperties": { "type": "object", "additionalProperties": { "type": "string" } }, "groupsStatistics": { "type": "array", "items": { "$ref": "#/definitions/GroupStatistics" } }, "name": { "type": "string" }, "pValue": { "type": "number" }, "stableId": { "type": "string" } }, "title": "GenericAssayEnrichment" }, "Geneset": { "type": "object", "properties": { "description": { "type": "string" }, "genesetId": { "type": "string" }, "name": { "type": "string" }, "refLink": { "type": "string" }, "representativePvalue": { "type": "number", "format": "double" }, "representativeScore": { "type": "number", "format": "double" } }, "title": "Geneset" }, "GenesetCorrelation": { "type": "object", "properties": { "correlationValue": { "type": "number", "format": "double" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "expressionGeneticProfileId": { "type": "string" }, "hugoGeneSymbol": { "type": "string" }, "zScoreGeneticProfileId": { "type": "string" } }, "title": "GenesetCorrelation" }, "GenesetDataFilterCriteria": { "type": "object", "properties": { "genesetIds": { "type": "array", "items": { "type": "string" } }, "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "GenesetDataFilterCriteria" }, "GenesetHierarchyInfo": { "type": "object", "properties": { "genesets": { "type": "array", "items": { "$ref": "#/definitions/Geneset" } }, "nodeId": { "type": "integer", "format": "int32" }, "nodeName": { "type": "string" }, "parentId": { "type": "integer", "format": "int32" }, "parentNodeName": { "type": "string" } }, "title": "GenesetHierarchyInfo" }, "GenesetMolecularData": { "type": "object", "required": [ "geneticProfileId", "patientId", "sampleId", "studyId", "value" ], "properties": { "geneset": { "$ref": "#/definitions/Geneset" }, "genesetId": { "type": "string" }, "geneticProfileId": { "type": "string" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "stableId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "value": { "type": "string" } }, "title": "GenesetMolecularData" }, "GenomicDataBin": { "type": "object", "properties": { "count": { "type": "integer", "format": "int32" }, "end": { "type": "number" }, "hugoGeneSymbol": { "type": "string" }, "profileType": { "type": "string" }, "specialValue": { "type": "string" }, "start": { "type": "number" } }, "title": "GenomicDataBin" }, "GenomicDataBinCountFilter": { "type": "object", "properties": { "genomicDataBinFilters": { "type": "array", "items": { "$ref": "#/definitions/GenomicDataBinFilter" } }, "studyViewFilter": { "$ref": "#/definitions/StudyViewFilter" } }, "title": "GenomicDataBinCountFilter" }, "GenomicDataBinFilter": { "type": "object", "properties": { "binMethod": { "type": "string", "enum": [ "CUSTOM", "GENERATE", "MEDIAN", "QUARTILE" ] }, "binsGeneratorConfig": { "$ref": "#/definitions/BinsGeneratorConfig" }, "customBins": { "type": "array", "items": { "type": "number" } }, "disableLogScale": { "type": "boolean" }, "end": { "type": "number" }, "hugoGeneSymbol": { "type": "string" }, "profileType": { "type": "string" }, "start": { "type": "number" } }, "title": "GenomicDataBinFilter" }, "GenomicDataCount": { "type": "object", "properties": { "count": { "type": "integer", "format": "int32" }, "label": { "type": "string" }, "value": { "type": "string" } }, "title": "GenomicDataCount" }, "GenomicDataFilter": { "type": "object", "properties": { "hugoGeneSymbol": { "type": "string" }, "profileType": { "type": "string" }, "values": { "type": "array", "items": { "$ref": "#/definitions/DataFilterValue" } } }, "title": "GenomicDataFilter" }, "GenomicEnrichment": { "type": "object", "required": [ "entrezGeneId", "groupsStatistics", "hugoGeneSymbol", "pValue" ], "properties": { "cytoband": { "type": "string" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "groupsStatistics": { "type": "array", "items": { "$ref": "#/definitions/GroupStatistics" } }, "hugoGeneSymbol": { "type": "string" }, "pValue": { "type": "number" } }, "title": "GenomicEnrichment" }, "Gistic": { "type": "object", "required": [ "amp", "chromosome", "cytoband", "qValue", "studyId", "widePeakEnd", "widePeakStart" ], "properties": { "amp": { "type": "boolean" }, "chromosome": { "type": "integer", "format": "int32" }, "cytoband": { "type": "string" }, "genes": { "type": "array", "items": { "$ref": "#/definitions/GisticToGene" } }, "qValue": { "type": "number" }, "studyId": { "type": "string" }, "widePeakEnd": { "type": "integer", "format": "int32" }, "widePeakStart": { "type": "integer", "format": "int32" } }, "title": "Gistic" }, "GisticToGene": { "type": "object", "required": [ "entrezGeneId", "hugoGeneSymbol" ], "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" } }, "title": "GisticToGene" }, "Group": { "type": "object", "properties": { "name": { "type": "string" }, "sampleIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/SampleIdentifier" } } }, "title": "Group" }, "GroupFilter": { "type": "object", "properties": { "groups": { "type": "array", "items": { "$ref": "#/definitions/Group" } } }, "title": "GroupFilter" }, "GroupStatistics": { "type": "object", "required": [ "meanExpression", "name", "standardDeviation" ], "properties": { "meanExpression": { "type": "number" }, "name": { "type": "string" }, "standardDeviation": { "type": "number" } }, "title": "GroupStatistics" }, "MolecularProfileCaseIdentifier": { "type": "object", "required": [ "caseId", "molecularProfileId" ], "properties": { "caseId": { "type": "string" }, "molecularProfileId": { "type": "string" } }, "title": "MolecularProfileCaseIdentifier" }, "MolecularProfileCasesGroupAndAlterationTypeFilter": { "type": "object", "required": [ "molecularProfileCasesGroupFilter" ], "properties": { "alterationEventTypes": { "$ref": "#/definitions/AlterationFilter" }, "molecularProfileCasesGroupFilter": { "type": "array", "items": { "$ref": "#/definitions/MolecularProfileCasesGroupFilter" } } }, "title": "MolecularProfileCasesGroupAndAlterationTypeFilter" }, "MolecularProfileCasesGroupFilter": { "type": "object", "properties": { "molecularProfileCaseIdentifiers": { "type": "array", "items": { "$ref": "#/definitions/MolecularProfileCaseIdentifier" } }, "name": { "type": "string" } }, "title": "MolecularProfileCasesGroupFilter" }, "MrnaPercentile": { "type": "object", "required": [ "entrezGeneId", "molecularProfileId", "patientId", "percentile", "sampleId", "studyId", "zScore" ], "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "molecularProfileId": { "type": "string" }, "patientId": { "type": "string" }, "percentile": { "type": "number" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "zScore": { "type": "number" } }, "title": "MrnaPercentile" }, "MutSig": { "type": "object", "required": [ "entrezGeneId", "hugoGeneSymbol", "numberOfMutations", "pValue", "qValue", "rank", "studyId" ], "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" }, "numberOfMutations": { "type": "integer", "format": "int32" }, "pValue": { "type": "number" }, "qValue": { "type": "number" }, "rank": { "type": "integer", "format": "int32" }, "studyId": { "type": "string" } }, "title": "MutSig" }, "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" }, "MutationPositionIdentifier": { "type": "object", "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "proteinPosEnd": { "type": "integer", "format": "int32" }, "proteinPosStart": { "type": "integer", "format": "int32" } }, "title": "MutationPositionIdentifier" }, "MutationSpectrum": { "type": "object", "required": [ "CtoA", "CtoG", "CtoT", "TtoA", "TtoC", "TtoG", "molecularProfileId", "patientId", "sampleId", "studyId" ], "properties": { "CtoA": { "type": "integer", "format": "int32" }, "CtoG": { "type": "integer", "format": "int32" }, "CtoT": { "type": "integer", "format": "int32" }, "TtoA": { "type": "integer", "format": "int32" }, "TtoC": { "type": "integer", "format": "int32" }, "TtoG": { "type": "integer", "format": "int32" }, "molecularProfileId": { "type": "string" }, "patientId": { "type": "string" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" } }, "title": "MutationSpectrum" }, "MutationSpectrumFilter": { "type": "object", "properties": { "sampleIds": { "type": "array", "items": { "type": "string" } }, "sampleListId": { "type": "string" } }, "title": "MutationSpectrumFilter" }, "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" }, "PatientTreatmentFilter": { "type": "object", "properties": { "treatment": { "type": "string" } }, "title": "PatientTreatmentFilter" }, "ReferenceGenomeGene": { "type": "object", "required": [ "entrezGeneId", "referenceGenomeId" ], "properties": { "chromosome": { "type": "string" }, "cytoband": { "type": "string" }, "end": { "type": "integer", "format": "int64" }, "entrezGeneId": { "type": "integer", "format": "int32" }, "hugoGeneSymbol": { "type": "string" }, "referenceGenomeId": { "type": "integer", "format": "int32" }, "start": { "type": "integer", "format": "int64" } }, "title": "ReferenceGenomeGene" }, "ResourceData": { "type": "object", "required": [ "resourceId", "studyId", "url" ], "properties": { "patientId": { "type": "string" }, "resourceDefinition": { "$ref": "#/definitions/ResourceDefinition" }, "resourceId": { "type": "string" }, "sampleId": { "type": "string" }, "studyId": { "type": "string" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "url": { "type": "string" } }, "title": "ResourceData" }, "ResourceDefinition": { "type": "object", "required": [ "displayName", "resourceId", "resourceType", "studyId" ], "properties": { "description": { "type": "string" }, "displayName": { "type": "string" }, "openByDefault": { "type": "boolean" }, "priority": { "type": "string" }, "resourceId": { "type": "string" }, "resourceType": { "type": "string", "enum": [ "PATIENT", "SAMPLE", "STUDY" ] }, "studyId": { "type": "string" } }, "title": "ResourceDefinition" }, "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" }, "SampleIdentifier": { "type": "object", "properties": { "sampleId": { "type": "string" }, "studyId": { "type": "string" } }, "title": "SampleIdentifier" }, "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" }, "StructuralVariant": { "type": "object", "properties": { "annotation": { "type": "string" }, "breakpointType": { "type": "string" }, "comments": { "type": "string" }, "connectionType": { "type": "string" }, "dnaSupport": { "type": "string" }, "driverFilter": { "type": "string" }, "driverFilterAnn": { "type": "string" }, "driverTiersFilter": { "type": "string" }, "driverTiersFilterAnn": { "type": "string" }, "eventInfo": { "type": "string" }, "length": { "type": "integer", "format": "int32" }, "molecularProfileId": { "type": "string" }, "namespaceColumns": { "type": "object", "additionalProperties": { "type": "object" } }, "ncbiBuild": { "type": "string" }, "normalPairedEndReadCount": { "type": "integer", "format": "int32" }, "normalReadCount": { "type": "integer", "format": "int32" }, "normalSplitReadCount": { "type": "integer", "format": "int32" }, "normalVariantCount": { "type": "integer", "format": "int32" }, "patientId": { "type": "string" }, "rnaSupport": { "type": "string" }, "sampleId": { "type": "string" }, "site1Chromosome": { "type": "string" }, "site1Contig": { "type": "string" }, "site1Description": { "type": "string" }, "site1EnsemblTranscriptId": { "type": "string" }, "site1EntrezGeneId": { "type": "integer", "format": "int32" }, "site1HugoSymbol": { "type": "string" }, "site1Position": { "type": "integer", "format": "int32" }, "site1Region": { "type": "string" }, "site1RegionNumber": { "type": "integer", "format": "int32" }, "site2Chromosome": { "type": "string" }, "site2Contig": { "type": "string" }, "site2Description": { "type": "string" }, "site2EffectOnFrame": { "type": "string" }, "site2EnsemblTranscriptId": { "type": "string" }, "site2EntrezGeneId": { "type": "integer", "format": "int32" }, "site2HugoSymbol": { "type": "string" }, "site2Position": { "type": "integer", "format": "int32" }, "site2Region": { "type": "string" }, "site2RegionNumber": { "type": "integer", "format": "int32" }, "studyId": { "type": "string" }, "svStatus": { "type": "string" }, "tumorPairedEndReadCount": { "type": "integer", "format": "int32" }, "tumorReadCount": { "type": "integer", "format": "int32" }, "tumorSplitReadCount": { "type": "integer", "format": "int32" }, "tumorVariantCount": { "type": "integer", "format": "int32" }, "uniquePatientKey": { "type": "string" }, "uniqueSampleKey": { "type": "string" }, "variantClass": { "type": "string" } }, "title": "StructuralVariant" }, "StructuralVariantFilter": { "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": "StructuralVariantFilter" }, "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" }, "VariantCount": { "type": "object", "required": [ "entrezGeneId", "molecularProfileId", "numberOfSamples", "numberOfSamplesWithKeyword", "numberOfSamplesWithMutationInGene" ], "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "keyword": { "type": "string" }, "molecularProfileId": { "type": "string" }, "numberOfSamples": { "type": "integer", "format": "int32" }, "numberOfSamplesWithKeyword": { "type": "integer", "format": "int32" }, "numberOfSamplesWithMutationInGene": { "type": "integer", "format": "int32" } }, "title": "VariantCount" }, "VariantCountIdentifier": { "type": "object", "properties": { "entrezGeneId": { "type": "integer", "format": "int32" }, "keyword": { "type": "string" } }, "title": "VariantCountIdentifier" } } }