FireBrowse Beta API API

by firebrowse.org

Overview

A simple and elegant way to explore cancer data

FireBrowse Beta API is an open data API from firebrowse.org. It needs no API key. It is served over HTTPS. Its OpenAPI description documents 30 endpoints.

At a glance

Authentication: No auth
HTTPS: Yes
CORS: Unknown
Category: Open Data
Base URL: http://firebrowse.org/api/v1
Version: 1.1.38 (2018-02-26 11:01:29 484103261f6ef681a05cf163)
Endpoints: 30
OpenAPI: Specification ↗
Spec updated: 2019-07-25

Make a first request

Replace the placeholders; the documentation says exactly where credentials go.

cURL

curl -X GET "http://firebrowse.org/api/v1/Analyses/CopyNumber/Genes/All" \
  -H "Accept: application/json"

JavaScript

const response = await fetch("http://firebrowse.org/api/v1/Analyses/CopyNumber/Genes/All", {
  method: "GET",
  headers: {
    "Accept": "application/json",
  },
});
const data = await response.json();
console.log(data);

Python

import requests

response = requests.request(
    "GET",
    "http://firebrowse.org/api/v1/Analyses/CopyNumber/Genes/All",
    headers={
    "Accept": "application/json",
    },
    timeout=30,
)
print(response.json())

Endpoints

Method	Path	What it does
GET	`/Analyses/CopyNumber/Genes/All`	Retrieve all data by genes Gistic2 results.
GET	`/Analyses/CopyNumber/Genes/Amplified`	Retrieve Gistic2 significantly amplified genes results.
GET	`/Analyses/CopyNumber/Genes/Deleted`	Retrieve Gistic2 significantly deleted genes results.
GET	`/Analyses/CopyNumber/Genes/Focal`	Retrieve focal data by genes Gistic2 results.
GET	`/Analyses/CopyNumber/Genes/Thresholded`	Retrieve all thresholded by genes Gistic2 results.
GET	`/Analyses/FeatureTable`	Retrieve aggregated analysis features table.
GET	`/Analyses/Mutation/MAF`	Retrieve MutSig final analysis MAF.
GET	`/Analyses/Mutation/SMG`	Retrieve Significantly Mutated Genes (SMG).
GET	`/Analyses/Reports`	Retrieve links to summary reports from Firehose analysis runs.
GET	`/Analyses/mRNASeq/Quartiles`	Returns RNASeq expression quartiles, e.g. suitable for drawing a boxplot.
GET	`/Archives/StandardData`	Retrieve standard data archives.
GET	`/Metadata/Centers`	Obtain identities of TCGA consortium member centers.
GET	`/Metadata/ClinicalNames`	Retrieve names of all TCGA clinical data elements (CDEs).
GET	`/Metadata/ClinicalNames_FH`	Retrieve names of CDEs normalized by Firehose and selected for analyses.
GET	`/Metadata/Cohorts`	Translate TCGA cohort abbreviations to full disease names.
GET	`/Metadata/Counts`	Retrieve sample counts.
GET	`/Metadata/Dates`	Retrieve dates of all GDAC Firehose stddata & analyses runs that have been ingested into FireBrowse.
GET	`/Metadata/HeartBeat`	Simple way to discern whether API server is up and running
GET	`/Metadata/MAFColNames`	Retrieve names of all columns in the mutation annotation files (MAFs) served by FireBrowse.
GET	`/Metadata/Patients`	Retrieve list of all TCGA patients.
GET	`/Metadata/Platforms`	Translate TCGA platform codes to full platform names.
GET	`/Metadata/SampleType/Barcode/{TCGA_Barcode}`	Given a TCGA barcode, return its short letter sample type code.
GET	`/Metadata/SampleType/Code/{code}`	Translate from numeric to symbolic TCGA sample codes.
GET	`/Metadata/SampleType/ShortLetterCode/{short_letter_code}`	Translate from symbolic to numeric TCGA sample codes.
GET	`/Metadata/SampleTypes`	Return all TCGA sample type codes, both numeric and symbolic.
GET	`/Metadata/TSSites`	Obtain identities of tissue source sites in TCGA.
GET	`/Samples/Clinical`	Retrieve TCGA CDEs verbatim, i.e. not normalized by Firehose.
GET	`/Samples/Clinical_FH`	Retrieve CDEs normalized by Firehose and selected for analyses.
GET	`/Samples/mRNASeq`	Retrieve mRNASeq data.
GET	`/Samples/miRSeq`	Retrieve miRSeq data.