cBioPortal Cancer Genomics Extractor

Point at any cBioPortal instance and pull structured cancer-genomics metadata — studies, the OncoTree cancer-type taxonomy, molecular profiles, and genes — as clean, tabular JSON. One actor speaks to every cBioPortal deployment, because they all expose the identical Swagger-generated REST API.

cBioPortal is the open-source standard for exploring multidimensional cancer-genomics data. The public MSKCC flagship (www.cbioportal.org) hosts 500+ published studies; the BC Genome Sciences Centre mirror (cbioportal.bcgsc.ca), GENIE, and dozens of institutional deployments run the same API. This actor turns any of them into a dataset — no per-portal scraper, no HTML parsing, no host guessing.

What you can extract

Pick a mode:

Mode	Endpoint	One row per…
studies (default)	/api/studies	cancer study (id, cancer type, sample count, reference genome, PMID, import date)
cancerTypes	/api/cancer-types	OncoTree cancer-type node (name, short name, parent, color)
study-detail	/api/studies/{id}	the full DETAILED record for one study — every per-datatype sample count
molecular-profiles	/api/molecular-profiles	molecular profile — portal-wide, or for one study
genes	/api/genes	gene in the portal's gene table (Entrez ID + HUGO symbol)

Every row carries the mapped, human-friendly fields plus a lossless _raw object with the complete original API record, so nothing is ever dropped.

Example input

{
  "servers": ["https://www.cbioportal.org", "https://cbioportal.bcgsc.ca"],
  "mode": "studies",
  "pageSize": 500,
  "maxRecords": 1000
}

Full-study detail for one study:

{
  "server": "https://www.cbioportal.org",
  "mode": "study-detail",
  "studyId": "brca_tcga_pan_can_atlas_2018"
}

Input reference

• server / servers — one cBioPortal base URL, or a list to query several instances at once. Accepts a bare host, an https:// URL, a proxied path prefix, or a URL ending in /api (all normalised). At least one is required.
• mode — what to extract (see the table above). Default studies.
• studyId — required for study-detail; optional filter for molecular-profiles.
• pageSize — records requested per API page (default 500).
• maxRecords — global cap on rows emitted across all servers (each row is one billable event). Leave empty to emit everything.
• userAgent, timeoutSecs, bearer, extraHeaders — optional request tuning and auth for gated deployments.

Behaviour & robustness

• Instance-agnostic pagination. cBioPortal honours pageSize everywhere but its pageNumber handling varies by endpoint (the studies list ignores it; genes/cancer-types honour it). The actor paginates defensively — de-duplicates by natural key, stops on a short page, and escalates to a single large pull when a server ignores pageNumber — so the whole collection is captured on any instance.
• Auth-gated instances are skipped, not fatal. GENIE / triage / pediatric deployments return 401/403; those servers are skipped with a warning and the batch continues. If every server is skipped, the run fails fast rather than emitting an empty dataset silently.
• A reachable server with zero public studies is a real zero — never fabricated data.

Pricing

Pay-per-event: one event per record (row) emitted. Set maxRecords to bound the cost of a run.

Notes

This actor reads public metadata from cBioPortal's documented REST API. It does not download raw genomic/sample-level patient data. Respect each instance's terms of use.