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>.

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 skill [list|install|<name>]
biomcp mcp
biomcp serve
biomcp serve-http [--host 127.0.0.1] [--port 8080]
biomcp update [--check]
biomcp uninstall
biomcp version

Search command families¶

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

Organization (NCI CTS)¶

biomcp search organization -q "MD Anderson" --city Houston --state TX --limit 5 --offset 0

Intervention (NCI CTS)¶

biomcp search intervention -q pembrolizumab --type drug --limit 5 --offset 0

Biomarker (NCI CTS)¶

biomcp search biomarker -q "PD-L1" --type reference_gene --limit 5 --offset 0

NCI vocabulary search commands require NCI_API_KEY.

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
biomcp get gene BRAF diseases

Disease¶

biomcp get disease melanoma
biomcp get disease MONDO:0005105 genes phenotypes
biomcp get disease MONDO:0005105 variants models
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

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 MCP over HTTP/SSE.

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

Helper command families¶

biomcp variant trials "BRAF V600E"
biomcp variant oncokb "BRAF V600E"
biomcp drug adverse-events pembrolizumab
biomcp disease drugs melanoma
biomcp gene pathways BRAF
biomcp pathway drugs R-HSA-5673001
biomcp protein structures P15056

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