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cBioPortal

cBioPortal matters when a single variant or gene question turns into a cohort question. It is the source page to use when you need cancer-study frequencies, downloadable study datasets, or local analytics that operate on a concrete study instead of a live one-record API lookup.

In BioMCP, the variant cbioportal section adds best-effort cohort frequency context, while study is BioMCP's local cBioPortal analytics family for downloaded datasets. Use study download to install a study into your local root and study query when you want per-study mutation, CNA, or expression summaries.

What BioMCP exposes

Command What BioMCP gets from this source Integration note
get variant <id> cbioportal Cohort-frequency context for a variant Best-effort cBioPortal enrichment section
study download --list List of downloadable study IDs Local analytics entry point
study download <study_id> Local installation of one study dataset Downloads into the default study root or BIOMCP_STUDY_DIR
study query --study <id> --gene <symbol> --type <mutations|cna|expression> Per-study summaries for one gene Local analytics workflow over downloaded files

Example commands

biomcp get variant "BRAF V600E" cbioportal

Returns a variant section with best-effort cBioPortal cohort frequency context.

biomcp study download --list

Returns a list of downloadable cBioPortal-style study IDs.

biomcp study download msk_impact_2017

Downloads the named study into the configured local study root.

biomcp study query --study msk_impact_2017 --gene TP53 --type mutations

Returns a per-study mutation summary for TP53 from local study files.

API access

No BioMCP API key required. Local study analytics use downloaded datasets in the default study root or BIOMCP_STUDY_DIR.

Official source

cBioPortal is the official cancer-genomics portal behind BioMCP's cohort-frequency enrichment and study download workflows.