Search and retrieve biomedical data — genes, variants, clinical trials, articles, drugs, diseases, pathways, proteins, adverse events, pharmacogenomics, and phenotype-disease matching. 15 sources including PubMed, ClinicalTrials.gov, ClinVar, OncoKB, Reactome, UniProt, PharmGKB, OpenFDA, Monarch. Use when asked about gene function, variant pathogenicity, trial matching, drug safety, resistance mechanisms, hereditary syndromes, or literature evidence.
Add this skill
npx mdskills install genomoncology/biomcpComprehensive biomedical CLI with clear command grammar, detailed entity guides, and cross-entity pivots across 15+ sources
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.
curl -fsSL https://raw.githubusercontent.com/genomoncology/biomcp/main/install.sh | bash
Install guided investigation workflows into your agent directory:
biomcp skill install ~/.claude --force
{
"mcpServers": {
"biomcp": {
"command": "biomcp",
"args": ["serve"]
}
}
}
cargo build --release --locked
biomcp health --apis-only # verify API connectivity
biomcp list # show all entities and commands
biomcp list gene # show gene-specific filters and examples
search [filters] → discovery
get [sections] → focused detail
→ cross-entity pivots
enrich → gene-set enrichment
batch → parallel gets
| 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" |
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 protein structures P15056
biomcp article entities 22663011
biomcp enrich BRAF,KRAS,NRAS --limit 10
Every get command supports selectable sections for focused output:
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 indications approvals
biomcp get disease "Lynch syndrome" genes phenotypes variants
biomcp get trial NCT02576665 eligibility locations outcomes
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
BioMCP rate limiting is process-local. For many concurrent workers, run one shared
biomcp serve-http endpoint so all workers share a single limiter budget:
biomcp serve-http --host 0.0.0.0 --port 8080
14 guided investigation workflows are built in:
biomcp skill list
biomcp skill show 03
| # | Skill | Focus |
|---|---|---|
| 01 | variant-to-treatment | Variant annotation to treatment options |
| 02 | drug-investigation | Drug mechanism, safety, alternatives |
| 03 | trial-searching | Trial discovery and patient matching |
| 04 | rare-disease | Rare disease evidence and trial strategy |
| 05 | drug-shortages | Shortage monitoring and alternatives |
| 06 | advanced-therapies | CAR-T and checkpoint therapy workflows |
| 07 | hereditary-cancer | Hereditary cancer syndrome workup |
| 08 | resistance | Resistance mechanisms and next-line options |
| 09 | gene-function-lookup | Gene-centric function and context |
| 10 | gene-set-analysis | Enrichment, pathway, and interaction synthesis |
| 11 | literature-synthesis | Evidence synthesis with cross-entity checks |
| 12 | pharmacogenomics | PGx gene-drug interactions and dosing |
| 13 | phenotype-triage | Symptom-first rare disease workup |
| 14 | protein-pathway | Protein structure and pathway deep dive |
biomcp version # show version and build info
biomcp health # check all API connectivity
biomcp update # self-update to latest release
biomcp update --check # check for updates without installing
biomcp uninstall # remove biomcp from ~/.local/bin
Full documentation at biomcp.org.
MIT
Install via CLI
npx mdskills install genomoncology/biomcpBioMCP is a free, open-source AI agent skill. Search and retrieve biomedical data — genes, variants, clinical trials, articles, drugs, diseases, pathways, proteins, adverse events, pharmacogenomics, and phenotype-disease matching. 15 sources including PubMed, ClinicalTrials.gov, ClinVar, OncoKB, Reactome, UniProt, PharmGKB, OpenFDA, Monarch. Use when asked about gene function, variant pathogenicity, trial matching, drug safety, resistance mechanisms, hereditary syndromes, or literature evidence.
Install BioMCP with a single command:
npx mdskills install genomoncology/biomcpThis downloads the skill files into your project and your AI agent picks them up automatically.
BioMCP works with Claude Code, Claude Desktop, Cursor, Vscode Copilot, Windsurf, Continue Dev, Codex, Gemini Cli, Amp, Roo Code, Goose, Opencode, Trae, Qodo, Command Code. Skills use the open SKILL.md format which is compatible with any AI coding agent that reads markdown instructions.