CLI Reference¶

BioMCP provides one command family with entity-oriented subcommands.

Global options¶

--json: return structured JSON output
--no-cache: bypass HTTP cache for the current command

Core command patterns¶

biomcp search <entity> [filters]
biomcp get <entity> <id> [section...]

Section names are positional trailing arguments after <id>.

Evidence metadata¶

get responses include outbound evidence links in markdown output where available. In JSON mode, links are exposed under _meta.evidence_urls and can include Ensembl, OMIM, NCBI Gene, and UniProt URLs.

Top-level commands¶

biomcp search ...
biomcp get ...
biomcp enrich <GENE1,GENE2,...> [--limit N]
biomcp batch <entity> <id1,id2,...> [--sections ...] [--source ...]
biomcp health [--apis-only]
biomcp list [entity]
biomcp study list
biomcp study download [--list] [<study_id>]
biomcp study filter --study <id> [--mutated <symbol>] [--amplified <symbol>] [--deleted <symbol>] [--expression-above <gene:threshold>] [--expression-below <gene:threshold>] [--cancer-type <type>]
biomcp study query --study <id> --gene <symbol> --type <mutations|cna|expression>
biomcp study cohort --study <id> --gene <symbol>
biomcp study survival --study <id> --gene <symbol> [--endpoint <os|dfs|pfs|dss>]
biomcp study compare --study <id> --gene <symbol> --type <expression|mutations> --target <symbol>
biomcp study co-occurrence --study <id> --genes <g1,g2,...>
biomcp skill
biomcp skill install [dir]
biomcp skill list                 # legacy compatibility alias
biomcp mcp
biomcp serve
biomcp serve-http [--host 127.0.0.1] [--port 8080]
biomcp serve-sse                  # removed compatibility command; use serve-http
biomcp update [--check]
biomcp uninstall
biomcp version

Numeric and slug skill lookups remain compatibility behavior, but they are not part of the recommended command synopsis because current builds do not ship a browsable embedded catalog.

Search command families¶

All (cross-entity)¶

biomcp search all --gene BRAF --disease melanoma
biomcp search all --gene BRAF --counts-only
biomcp search all --keyword "immunotherapy resistance" --since 2024-01-01

Gene¶

biomcp search gene -q BRAF --limit 10 --offset 0

Disease¶

biomcp search disease -q melanoma --source mondo --limit 10 --offset 0

PGx¶

biomcp search pgx -g CYP2D6 --limit 10
biomcp search pgx -d warfarin --limit 10

Phenotype (Monarch semsim)¶

biomcp search phenotype "HP:0001250 HP:0001263" --limit 10

GWAS¶

biomcp search gwas -g TCF7L2 --limit 10
biomcp search gwas --trait "type 2 diabetes" --limit 10

Article¶

biomcp search article -g BRAF -d melanoma --since 2024-01-01 --limit 5 --offset 0

Trial¶

biomcp search trial -c melanoma --status recruiting --source ctgov --limit 5 --offset 0

Variant¶

biomcp search variant -g BRAF --hgvsp V600E --limit 5 --offset 0

Drug¶

biomcp search drug -q "kinase inhibitor" --limit 5 --offset 0

Pathway¶

biomcp search pathway -q "MAPK signaling" --limit 5 --offset 0

Protein¶

biomcp search protein -q kinase --limit 5 --offset 0
biomcp search protein -q kinase --all-species --limit 5

Adverse event¶

biomcp search adverse-event --drug pembrolizumab --serious --limit 5 --offset 0
biomcp search adverse-event --type device --manufacturer Medtronic --limit 5
biomcp search adverse-event --type device --product-code PQP --limit 5

Get command families¶

Gene¶

biomcp get gene BRAF
biomcp get gene BRAF pathways ontology diseases protein
biomcp get gene BRAF go interactions civic expression druggability clingen
biomcp get gene BRAF all

Disease¶

biomcp get disease melanoma
biomcp get disease MONDO:0005105 genes phenotypes
biomcp get disease MONDO:0005105 variants models
biomcp get disease MONDO:0005105 pathways prevalence civic
biomcp get disease MONDO:0005105 all

PGx¶

biomcp get pgx CYP2D6
biomcp get pgx codeine recommendations frequencies
biomcp get pgx warfarin annotations

Article¶

biomcp get article 22663011
biomcp get article 22663011 fulltext

Trial¶

biomcp get trial NCT02576665
biomcp get trial NCT02576665 eligibility

Variant¶

biomcp get variant "BRAF V600E"
biomcp get variant "BRAF V600E" predict
biomcp get variant rs7903146 gwas

Drug¶

biomcp get drug pembrolizumab
biomcp get drug carboplatin shortage

Pathway¶

biomcp get pathway R-HSA-5673001
biomcp get pathway R-HSA-5673001 genes

Protein¶

biomcp get protein P15056
biomcp get protein P15056 domains interactions

Adverse event¶

biomcp get adverse-event 10222779
biomcp get adverse-event 10222779 reactions outcomes
biomcp get adverse-event 10222779 concomitant guidance all

Enrichment¶

biomcp enrich BRAF,KRAS,NRAS --limit 10
biomcp enrich BRAF,KRAS,NRAS --limit 10 --json

MCP mode¶

biomcp serve runs the stdio MCP server.
biomcp serve-http runs the MCP Streamable HTTP server.
Streamable HTTP clients connect to /mcp.
Probe routes: /health, /readyz, and /.
biomcp serve-sse remains visible only as a removed compatibility command that points back to biomcp serve-http.

See also: docs/reference/mcp-server.md.

Helper command families¶

biomcp variant trials "BRAF V600E"
biomcp variant articles "BRAF V600E"
biomcp variant oncokb "BRAF V600E"
biomcp drug adverse-events pembrolizumab
biomcp drug trials pembrolizumab
biomcp disease trials melanoma
biomcp disease drugs melanoma
biomcp disease articles "Lynch syndrome"
biomcp gene trials BRAF
biomcp gene drugs BRAF
biomcp gene articles BRCA1
biomcp gene pathways BRAF
biomcp pathway drugs R-HSA-5673001
biomcp pathway articles R-HSA-5673001
biomcp pathway trials R-HSA-5673001
biomcp protein structures P15056
biomcp article entities 22663011

Local study analytics¶

study is BioMCP's local cBioPortal analytics family for downloaded cBioPortal-style datasets. Unlike the 12 remote entity commands, study operates on files in your local study root instead of querying remote APIs for each request.

Use BIOMCP_STUDY_DIR when you want an explicit study root for reproducible downloads and examples; if it is unset, BioMCP falls back to its default study root. biomcp study download --list shows downloadable IDs, and biomcp study download <study_id> installs a study into that local root.

Use this	When
`biomcp search/get/<entity>`	You want live API-backed discovery or detail across the 12 remote entity commands
`biomcp study download`	You need to fetch a cBioPortal-style study dataset into your local study root
`biomcp study ...` analytics commands	You already have local study files and want cohort, query, survival, compare, or co-occurrence analysis

Study command examples¶

biomcp study list
biomcp study download --list
biomcp study download msk_impact_2017
biomcp study query --study msk_impact_2017 --gene TP53 --type mutations
biomcp study filter --study brca_tcga_pan_can_atlas_2018 --mutated TP53 --amplified ERBB2 --expression-above ERBB2:1.5
biomcp study cohort --study brca_tcga_pan_can_atlas_2018 --gene TP53
biomcp study survival --study brca_tcga_pan_can_atlas_2018 --gene TP53 --endpoint os
biomcp study compare --study brca_tcga_pan_can_atlas_2018 --gene TP53 --type expression --target ERBB2
biomcp study compare --study brca_tcga_pan_can_atlas_2018 --gene TP53 --type mutations --target PIK3CA
biomcp study co-occurrence --study msk_impact_2017 --genes TP53,KRAS

Dataset requirements¶

study list shows locally available studies.
study download fetches remote datasets into the local study root.
study filter intersects mutation, CNA, expression, and clinical filters.
study query supports mutations, cna, and expression per-gene summaries.
study cohort, study survival, and study compare require data_mutations.txt and data_clinical_sample.txt.
study survival also requires data_clinical_patient.txt with canonical {ENDPOINT}_STATUS and {ENDPOINT}_MONTHS columns.
Expression workflows require a supported expression matrix file.

Batch mode¶

biomcp batch gene BRAF,TP53
biomcp batch gene BRAF,TP53 --sections pathways,interactions
biomcp batch trial NCT02576665,NCT03715933 --source nci
biomcp batch variant "BRAF V600E","KRAS G12D" --json