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 list to see the local cohort list, study download to install a study into your local root, and study query when you want per-study mutation, CNA, expression, or structural-variant/fusion summaries from local files. If a query names a study outside the local snapshot, BioMCP returns not_in_local_cohorts with a study download <study_id> hint rather than a hollow cohort result.
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|sv> |
Per-study summaries for one gene, including structural variants/fusions from data_sv.txt |
Local analytics workflow over downloaded files |
Example commands¶
Returns a variant section with best-effort cBioPortal cohort frequency context.
Returns a list of downloadable cBioPortal-style study IDs.
Downloads the named study into the configured local study root. biomcp study list documents which cohorts are local in that root.
biomcp study query --study msk_impact_2017 --gene TP53 --type mutations
biomcp study query --study msk_impact_2017 --gene RET --type sv
Returns a per-study mutation summary for TP53 from local study files. Mutation summaries remain mutation-only; if local data_sv.txt is present, BioMCP notes that fusions/SV are excluded and points to --type sv. For a non-local study ID such as an undownloaded melanoma cohort, the query returns not_in_local_cohorts and suggests biomcp study download <study_id>.
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.