BioMCP

BioMCP is a 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 | | | drug | MyChem.info, ChEMBL, OpenTargets, Drugs@FDA, CIViC | | | disease | Monarch Initiative, MONDO, CIViC, OpenTargets | | | pathway | Reactome, g:Profiler | | | protein | UniProt, InterPro, STRING, PDB/AlphaFold | | | adverse-event | OpenFDA (FAERS, MAUDE, Recalls) | | | pgx | CPIC, PharmGKB | | | gwas | GWAS Catalog | | | phenotype | Monarch Initiative (HPO) | |