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genomoncology/biomcp

BioMCP¶

Single-binary CLI and MCP server for querying biomedical databases. One command grammar, compact markdown output, 12 entities across 15+ data sources.

Install¶

Binary install (recommended)¶

curl -fsSL https://raw.githubusercontent.com/genomoncology/biomcp/main/install.sh | bash

Install skills¶

Install guided investigation workflows into your agent directory:

biomcp skill install ~/.claude --force

For Claude Desktop / Cursor / MCP clients¶

{
  "mcpServers": {
    "biomcp": {
      "command": "biomcp",
      "args": ["serve"]
    }
  }
}

From source¶

cargo build --release --locked

Quick start¶

biomcp health --apis-only            # verify API connectivity
biomcp list                          # show all entities and commands
biomcp list gene                     # show gene-specific filters and examples

Command grammar¶

search <entity> [filters]    → discovery
get <entity> <id> [sections] → focused detail
<entity> <helper> <id>       → cross-entity pivots
enrich <GENE1,GENE2,...>     → gene-set enrichment
batch <entity> <id1,id2,...> → parallel gets

Entities and sources¶

Entity	Sources	Example
gene	MyGene.info, UniProt, Reactome, QuickGO, STRING, CIViC	`biomcp get gene BRAF pathways`
variant	MyVariant.info, ClinVar, gnomAD, CIViC, OncoKB, cBioPortal, GWAS Catalog, AlphaGenome	`biomcp get variant "BRAF V600E" clinvar`
article	PubMed, PubTator3, Europe PMC	`biomcp search article -g BRAF --limit 5`
trial	ClinicalTrials.gov, NCI CTS API	`biomcp search trial -c melanoma -s recruiting`
drug	MyChem.info, ChEMBL, OpenTargets, Drugs\@FDA, CIViC	`biomcp get drug pembrolizumab targets`
disease	Monarch Initiative, MONDO, CIViC, OpenTargets	`biomcp get disease "Lynch syndrome" genes`
pathway	Reactome, g:Profiler	`biomcp get pathway R-HSA-5673001 genes`
protein	UniProt, InterPro, STRING, PDB/AlphaFold	`biomcp get protein P15056 domains`
adverse-event	OpenFDA (FAERS, MAUDE, Recalls)	`biomcp search adverse-event -d pembrolizumab`
pgx	CPIC, PharmGKB	`biomcp get pgx CYP2D6 recommendations`
gwas	GWAS Catalog	`biomcp search gwas --trait "type 2 diabetes"`
phenotype	Monarch Initiative (HPO)	`biomcp search phenotype "HP:0001250"`

Cross-entity helpers¶

Pivot between related entities without rebuilding filters:

biomcp variant trials "BRAF V600E" --limit 5
biomcp variant articles "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 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

Gene-set enrichment¶

biomcp enrich BRAF,KRAS,NRAS --limit 10

Sections and progressive disclosure¶

Every get command supports selectable sections:

biomcp get gene BRAF                    # summary card
biomcp get gene BRAF pathways           # add pathway section
biomcp get gene BRAF civic interactions # multiple sections
biomcp get gene BRAF all                # everything

biomcp get variant "BRAF V600E" clinvar population conservation
biomcp get drug pembrolizumab label shortage targets approvals
biomcp get disease "Lynch syndrome" genes phenotypes variants
biomcp get trial NCT02576665 eligibility locations outcomes

API keys¶

Most commands work without credentials. Optional keys improve rate limits:

export NCBI_API_KEY="..."        # PubTator, PMC OA, NCBI ID converter
export OPENFDA_API_KEY="..."     # OpenFDA rate limits
export NCI_API_KEY="..."         # NCI CTS trial search (--source nci)
export ONCOKB_TOKEN="..."        # OncoKB variant helper
export ALPHAGENOME_API_KEY="..." # AlphaGenome variant effect prediction

Skills¶

14 guided investigation workflows are built in. See Skills for details.

Documentation¶

License¶

MIT