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{"openapi":"3.0.0","info":{"description":"A simple and elegant way to explore cancer data","title":"FireBrowse Beta API","version":"1.1.38 (2018-02-26 11:01:29 484103261f6ef681a05cf163)","x-apisguru-categories":["open_data"],"x-logo":{"url":"http://firebrowse.org/img/firebrowse.png"},"x-origin":[{"converter":{"url":"https://github.com/lucybot/api-spec-converter","version":"2.7.11"},"format":"swagger","url":"http://firebrowse.org/api/api-docs","version":"1.2"}],"x-providerName":"firebrowse.org"},"tags":[{"description":"Fine grained retrieval of analysis pipeline results","name":"Analyses"},{"description":"Bulk retrieval of data or analysis pipeline results","name":"Archives"},{"description":"Retrieve disease, sample, and datatype descriptions, sample counts, and more","name":"Metadata"},{"description":"Fine grained retrieval of sample-level data","name":"Samples"}],"paths":{"/Analyses/CopyNumber/Genes/All":{"get":{"description":"This service provides access to the Gistic2 all_data_by_genes.txt output data. This data is a gene-level table of copy number values for all samples. The returned copy number values are in units (copy number - 2) so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers. 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Results may be filtered by date or cohort, but at least 1 cohort must be specified here. For more details please visit the <a href=https://confluence.broadinstitute.org/display/GDAC/Documentation\\#Documentation-FeatureTable>online documentation</a>. 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Specifying 'all' in this parameter is a convenient way to return every column of the respective MAF, and has precedence over any any other column selection expression. The complete list of column names that may be specified is <a href='http://firebrowse.org/api-docs/#!/Metadata/MAFColNames'>given here</a>. 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","in":"query","name":"page","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"default":1,"format":"int32","minimum":1,"type":"integer"}}},{"description":"Number of records per page of results. Max is 2000.","in":"query","name":"page_size","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"default":250,"format":"int32","maximum":2000,"minimum":1,"type":"integer"}}},{"description":"Which column in the results should be used for sorting paginated results?","in":"query","name":"sort_by","required":false,"schema":{"type":"string","enum":["tcga_participant_barcode","cohort","tool","gene"],"default":"cohort"}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Retrieve MutSig final analysis MAF.","tags":["Analyses"]}},"/Analyses/Mutation/SMG":{"get":{"description":"This service provides a list of significantly mutated genes, as scored by MutSig. 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","in":"query","name":"page","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"default":1,"format":"int32","minimum":1,"type":"integer"}}},{"description":"Number of records per page of results. Max is 2000.","in":"query","name":"page_size","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"default":250,"format":"int32","maximum":2000,"minimum":1,"type":"integer"}}},{"description":"Which column in the results should be used for sorting paginated results?","in":"query","name":"sort_by","required":false,"schema":{"type":"string","enum":["date","cohort","type","name"],"default":"date"}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Retrieve links to summary reports from Firehose analysis runs.","tags":["Analyses"]}},"/Analyses/mRNASeq/Quartiles":{"get":{"description":"For a given gene compute quartiles and extrema, suitable e.g. for drawing a boxplot (Tukey 1977). 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Note that samples for which no expression value was recorded (e.g. <a href=\"http://firebrowse.org/api/v1/Samples/mRNASeq?&gene=egfr&cohort=SKCM&tcga_participant_barcode=TCGA-GN-A262\">the melanoma sample TCGA-GN-262</a>) are removed prior to calculation.","operationId":"mRNASeq/Quartiles","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"type":"string","enum":["json","tsv","csv"],"default":"json"}},{"description":"Enter a single gene name.","in":"query","name":"gene","required":true,"schema":{"type":"string"}},{"description":"Narrow search to one or more TCGA disease cohorts from the scrollable list.","in":"query","name":"cohort","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":["ACC","BLCA","BRCA","CESC","CHOL","COAD","COADREAD","DLBC","ESCA","FPPP","GBM","GBMLGG","HNSC","KICH","KIPAN","KIRC","KIRP","LAML","LGG","LIHC","LUAD","LUSC","MESO","OV","PAAD","PCPG","PRAD","READ","SARC","SKCM","STAD","STES","TGCT","THCA","THYM","UCEC","UCS","UVM"],"type":"string"}}},{"description":"Narrow search to one or more sample characterization protocols from the scrollable list.","in":"query","name":"protocol","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"default":"RSEM","enum":["RPKM","RSEM"],"type":"string"}}},{"description":"For which type of sample(s) should quartiles be computed?","in":"query","name":"sample_type","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"default":"tumors","enum":["tumors","normals","TP","TB","TAM","TBM","NBC","TRB","TR","TRBM","TAP","TM","THOC","NB","NT","NEBV","NBM"],"type":"string"}}},{"description":"Comma separated list of TCGA participants, identified by barcodes such as TCGA-GF-A4EO, denoting samples to exclude from computation.","in":"query","name":"Exclude","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"type":"string"}}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Returns RNASeq expression quartiles, e.g. suitable for drawing a boxplot.","tags":["Analyses"]}},"/Archives/StandardData":{"get":{"description":"This service returns the archive URLs for our Firehose standard data runs, providing a RESTful interface similar in spirit to the command line <a href=\"https://confluence.broadinstitute.org/display/GDAC/Download\">firehose_get</a> tool. 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search to one or more TCGA centers from the scrollable list.","in":"query","name":"center","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":["bcgsc.ca","broad.mit.edu","broadinstitute.org","genome.wustl.edu","hgsc.bcm.edu","hms.harvard.edu","hudsonalpha.org","intgen.org","jhu-usc.edu","jhu.edu","lbl.gov","mdanderson.org","mskcc.org","nationwidechildrens.org","pnl.gov","rubicongenomics.com","sanger.ac.uk","systemsbiology.org","ucsc.edu","unc.edu","vanderbilt.edu"],"type":"string"}}},{"description":"Narrow search to one or more TCGA data levels.","in":"query","name":"level","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":[1,2,3,4],"format":"int32","type":"integer"}}},{"description":"Narrow search to one or more sample characterization protocols from the scrollable list.","in":"query","name":"protocol","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":["birdseed_genotype","exon_expression","exon_quantification","gene_expression","gene_rma","junction_quantification","miR_gene_expression","miR_isoform_expression","probeset_rma","protein_normalization","quantile_normalization_exon","quantile_normalization_gene","RSEM_genes","RSEM_genes_normalized","RSEM_isoforms","RSEM_isoforms_normalized","segmentation","segmentation_data_computation","segmented_as_firma","segmented_cna","segmented_cnv","segmented_loh","segmented_scna_hg18","segmented_scna_hg19","segmented_scna_minus_germline_cnv_hg18","segmented_scna_minus_germline_cnv_hg19","splice_junction_expression","unc_DWD_Batch_adjusted","unc_lowess_normalization_gene_level","unc_lowess_normalization_probe_level","within_bioassay_data_set_function"],"type":"string"}}},{"description":"Which page (slice) of entire results set should be returned. ","in":"query","name":"page","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"default":1,"format":"int32","minimum":1,"type":"integer"}}},{"description":"Number of records per page of results. Max is 2000.","in":"query","name":"page_size","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"default":250,"format":"int32","maximum":2000,"minimum":1,"type":"integer"}}},{"description":"Which column in the results should be used for sorting paginated results?","in":"query","name":"sort_by","required":false,"schema":{"type":"string","enum":["cohort","protocol","center","data_type","level","tool","platform","date"],"default":"cohort"}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Retrieve standard data archives.","tags":["Archives"]}},"/Metadata/Centers":{"get":{"description":"By default this function returns a table of all consortium members in TCGA, aka centers; it provides both the HTTP domain and full organizational name of each center. A subset of this table may be obtained by explicitly specifying one or more domain names.","operationId":"Centers","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"type":"string","enum":["json","tsv","csv"],"default":"json"}},{"description":"Narrow search to one or more TCGA centers from the scrollable list.","in":"query","name":"center","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":["bcgsc.ca","broad.mit.edu","broadinstitute.org","genome.wustl.edu","hgsc.bcm.edu","hms.harvard.edu","hudsonalpha.org","intgen.org","jhu-usc.edu","jhu.edu","lbl.gov","mdanderson.org","mskcc.org","nationwidechildrens.org","pnl.gov","rubicongenomics.com","sanger.ac.uk","systemsbiology.org","ucsc.edu","unc.edu","vanderbilt.edu"],"type":"string"}}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Obtain identities of TCGA consortium member centers.","tags":["Metadata"]}},"/Metadata/ClinicalNames":{"get":{"description":"Retrieve names of all patient-level clinical data elements (CDES) available in TCGA, unioned across all disease cohorts. A CDE will be listed here only when it has a value other than NA for at least 1 patient case in any disease cohort. For more information on how these CDEs are processed see our <a href=\"https://confluence.broadinstitute.org/display/GDAC/Documentation\">pipeline documentation</a>.","operationId":"ClinicalNames","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"type":"string","enum":["json","tsv","csv"],"default":"json"}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Retrieve names of all TCGA clinical data elements (CDEs).","tags":["Metadata"]}},"/Metadata/ClinicalNames_FH":{"get":{"description":"This service returns the names of patient-level clinical data elements (CDEs) that have been normalized by Firehose for use in analyses, unioned across all disease cohorts. For more information on how these CDEs are processed, see our <a href=\"https://confluence.broadinstitute.org/display/GDAC/Documentation\">pipeline documentation</a>.","operationId":"ClinicalNames_FH","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"type":"string","enum":["json","tsv","csv"],"default":"json"}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Retrieve names of CDEs normalized by Firehose and selected for analyses.","tags":["Metadata"]}},"/Metadata/Cohorts":{"get":{"description":"By default this function returns a table containing all TCGA cohort abbreviations and their corresponding disease names. A subset of that table may be obtained by explicitly specifying one or more cohort abbreviations.","operationId":"Cohorts","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"type":"string","enum":["json","tsv","csv"],"default":"json"}},{"description":"Narrow search to one or more TCGA disease cohorts from the scrollable list.","in":"query","name":"cohort","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":["ACC","BLCA","BRCA","CESC","CHOL","COAD","COADREAD","DLBC","ESCA","FPPP","GBM","GBMLGG","HNSC","KICH","KIPAN","KIRC","KIRP","LAML","LGG","LIHC","LUAD","LUSC","MESO","OV","PAAD","PCPG","PRAD","READ","SARC","SKCM","STAD","STES","TGCT","THCA","THYM","UCEC","UCS","UVM"],"type":"string"}}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Translate TCGA cohort abbreviations to full disease names.","tags":["Metadata"]}},"/Metadata/Counts":{"get":{"description":"Returns the aliquot counts for each disease cohort, per sample\ntype and data type. The sample type designation of \"Tumor\"\nmay be used to aggregate the count of all tumor aliquots into\na single number per disease and data type. See the SampleTypes\nfunction for a complete description of sample types.","operationId":"Counts","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"type":"string","enum":["json","tsv","csv"],"default":"json"}},{"description":"Select one or more date stamps.","in":"query","name":"date","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":[20160128,20151101,20150821,20150601,20150402,20150204,20141206,20141017,20140902,20140715,20140518,20140416,20140316],"format":"date","type":"string"}}},{"description":"Narrow search to one or more TCGA disease cohorts from the scrollable list.","in":"query","name":"cohort","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":["ACC","BLCA","BRCA","CESC","CHOL","COAD","COADREAD","DLBC","ESCA","FPPP","GBM","GBMLGG","HNSC","KICH","KIPAN","KIRC","KIRP","LAML","LGG","LIHC","LUAD","LUSC","MESO","OV","PAAD","PCPG","PRAD","READ","SARC","SKCM","STAD","STES","TGCT","THCA","THYM","UCEC","UCS","UVM"],"type":"string"}}},{"description":"Narrow search to one or more TCGA sample types from the scrollable list.","in":"query","name":"sample_type","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":["FFPE","NB","NBC","NBM","NT","TAM","TAP","TB","TM","TP","TR","Tumor"],"type":"string"}}},{"description":"Narrow search to one or more TCGA data types from the scrollable list.","in":"query","name":"data_type","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":["bcr","clinical","cn","lowp","methylation","mrna","mrnaseq","mir","mirseq","rppa","maf","rawmaf"],"type":"string"}}},{"description":"Output an entry providing the totals for each data type.","in":"query","name":"totals","required":false,"schema":{"type":"boolean","default":true}},{"description":"Which column in the results should be used for sorting paginated results?","in":"query","name":"sort_by","required":false,"schema":{"type":"string","enum":["cohort"],"default":"cohort"}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Retrieve sample counts.","tags":["Metadata"]}},"/Metadata/Dates":{"get":{"operationId":"Dates","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"type":"string","enum":["json","tsv","csv"],"default":"json"}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Retrieve dates of all GDAC Firehose stddata & analyses runs that have been ingested into FireBrowse.","tags":["Metadata"]}},"/Metadata/HeartBeat":{"get":{"description":"Returns a message to indicate that API (server) is up and running, or times out if not.","operationId":"HeartBeat","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"type":"string","enum":["json","tsv","csv"],"default":"json"}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Simple way to discern whether API server is up and running","tags":["Metadata"]}},"/Metadata/MAFColNames":{"get":{"description":"Retrieve the names of all columns in the mutation annotation files (MAFs) hosted by FireBrowse. For more information on the mutation data, and how it is processed by Firehose, please consult the <a href=\"https://confluence.broadinstitute.org/display/GDAC/Documentation#Documentation-MutationPipelines\">pipeline documentation</a>.","operationId":"MAFColNames","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"type":"string","enum":["json","tsv","csv"],"default":"json"}}],"responses":{"200":{"description":"No response was specified"}},"summary":"Retrieve names of all columns in the mutation annotation files (MAFs) served by FireBrowse.","tags":["Metadata"]}},"/Metadata/Patients":{"get":{"description":"This service returns a list of all TCGA patient barcodes in FireBrowse, optionally filtered by disease cohort. The barcodes are obtained directy from the clinical data.","operationId":"Patients","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"type":"string","enum":["json","tsv","csv"],"default":"json"}},{"description":"Narrow search to one or more TCGA disease cohorts from the scrollable list.","in":"query","name":"cohort","required":false,"style":"form","explode":false,"schema":{"type":"array","items":{"enum":["ACC","BLCA","BRCA","CESC","CHOL","COAD","COADREAD","DLBC","ESCA","FPPP","GBM","GBMLGG","HNSC","KICH","KIPAN","KIRC","KIRP","LAML","LGG","LIHC","LUAD","LUSC","MESO","OV","PAAD","PCPG","PRAD","READ","SARC","SKCM","STAD","STES","TGCT","THCA","THYM","UCEC","UCS","U