Automate FireBrowse Beta

What FireBrowse Beta is

A simple and elegant way to explore cancer data

API host: firebrowse.org

What HumDay can read from FireBrowse Beta

These are the operations a schedule or a trigger can watch.

• GETRetrieve list of all TCGA patients./Metadata/Patients
• GETRetrieve names of all columns in the mutation annotation files (MAFs) served by FireBrowse./Metadata/MAFColNames
• GETRetrieve dates of all GDAC Firehose stddata & analyses runs that have been ingested into FireBrowse./Metadata/Dates
• GETRetrieve miRSeq data./Samples/miRSeq
• GETRetrieve sample counts./Metadata/Counts
• GETRetrieve mRNASeq data./Samples/mRNASeq
• GETRetrieve links to summary reports from Firehose analysis runs./Analyses/Reports
• GETObtain identities of TCGA consortium member centers./Metadata/Centers
• GETTranslate TCGA cohort abbreviations to full disease names./Metadata/Cohorts
• GETObtain identities of tissue source sites in TCGA./Metadata/TSSites
• GETRetrieve TCGA CDEs verbatim, i.e./Samples/Clinical
• GETSimple way to discern whether API server is up and running/Metadata/HeartBeat
• GETTranslate TCGA platform codes to full platform names./Metadata/Platforms
• GETRetrieve CDEs normalized by Firehose and selected for analyses./Samples/Clinical_FH
• GETReturn all TCGA sample type codes, both numeric and symbolic./Metadata/SampleTypes
• GETRetrieve aggregated analysis features table./Analyses/FeatureTable
• GETRetrieve standard data archives./Archives/StandardData
• GETRetrieve names of all TCGA clinical data elements (CDEs)./Metadata/ClinicalNames
• GETRetrieve names of CDEs normalized by Firehose and selected for analyses./Metadata/ClinicalNames_FH
• GETRetrieve MutSig final analysis MAF./Analyses/Mutation/MAF
• GETRetrieve Significantly Mutated Genes (SMG)./Analyses/Mutation/SMG
• GETReturns RNASeq expression quartiles, e.g./Analyses/mRNASeq/Quartiles
• GETRetrieve all data by genes Gistic2 results./Analyses/CopyNumber/Genes/All
• GETRetrieve focal data by genes Gistic2 results./Analyses/CopyNumber/Genes/Focal
• GETRetrieve Gistic2 significantly deleted genes results./Analyses/CopyNumber/Genes/Deleted
• GETRetrieve Gistic2 significantly amplified genes results./Analyses/CopyNumber/Genes/Amplified
• GETRetrieve all thresholded by genes Gistic2 results./Analyses/CopyNumber/Genes/Thresholded
• GETTranslate from numeric to symbolic TCGA sample codes./Metadata/SampleType/Code/{code}
• GETGiven a TCGA barcode, return its short letter sample type code./Metadata/SampleType/Barcode/{TCGA_Barcode}
• GETTranslate from symbolic to numeric TCGA sample codes./Metadata/SampleType/ShortLetterCode/{short_letter_code}

How automating FireBrowse Beta works

1. Describe the outcome. Say what you want to happen, in your own words. No node graphs, no field mapping.
2. Approve the contract. HumDay writes down exactly what it will do, what it will touch, and what it will never do. You approve it before anything is built.
3. See it proven. The program runs and shows you the result before it is allowed near your live FireBrowse Beta account.
4. Grant access, then go live. You approve the specific FireBrowse Beta operations it may use — and only those.

Automate FireBrowse Beta with these

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• UniCourt Enterprise158 operations
• OSF APIv2 Documentation156 operations
• IllumiDesk143 operations
• Figshare136 operations
• MCW Rat Genome Database100 operations
• U.S. EPA Enforcement and Compliance History Online (ECHO) Detailed Facility Report (DFR)94 operations
• OpenFEC91 operations
• NBA Stats83 operations
• Thebluealliance The Blue Alliance65 operations
• eDRV57 operations
• Collegefootballdata College Football Data51 operations

Categories

• Open data

Questions about FireBrowse Beta automation

Can HumDay connect to FireBrowse Beta?

Yes. HumDay reads FireBrowse Beta's own published API description and derives the operations from it, so there is no hand-built connector to wait for. 30 operations are documented.

Do I need to write code to automate FireBrowse Beta?

No. You describe the outcome you want in plain words. HumDay agrees a contract with you, writes the program, and shows you a test run before anything touches your FireBrowse Beta account.

What can HumDay do in FireBrowse Beta?

0 of the 30 documented operations change something in FireBrowse Beta, and 30 read from it. HumDay only ever uses the specific operations your approved contract needs.

Is my FireBrowse Beta account safe?

Your credentials are stored encrypted and are never shown in chat, code, or logs. Every run is limited to the operations you explicitly approved, and anything that writes to FireBrowse Beta is held behind that approval.

Where this came from

The operations above are read from a published API description for FireBrowse Beta at firebrowse.org/api/api-docs. Descriptions are the provider’s own words, not ours. Last published 2019-07-25.