BioMCP (Biomedical Database Integration)

One binary. One grammar. Evidence from the biomedical sources you already trust.

BioMCP is one CLI binary over a single command grammar that reaches ~30 trusted biomedical sources (PubMed, ClinVar, ClinicalTrials.gov, OncoKB, Reactome, and more). It is also an MCP (Model Context Protocol) server, so the same tools are available to AI agents such as Claude Code, Codex, and Claude Desktop.

BioMCP cuts through the usual biomedical data maze: one query reaches the sources that normally live behind different APIs, identifiers, and search habits. Researchers, clinicians, and agents use the same command grammar to search, focus, and pivot without rebuilding the workflow for each source. You get compact, evidence-oriented results across live public data plus local study analytics.

- Search the literature:search articlefans out across PubTator3 and Europe PMC, deduplicates PMID/PMCID/DOI identifiers, and can add a Semantic Scholar leg when your filters support it.
- Pivot without rework:move from a gene, variant, drug, disease, pathway, protein, or article straight into the next built-in view instead of rebuilding filters by hand.
- Choose a playbook:biomcp skill listshows shipped worked examples so you can open the matchingbiomcp skill <slug>workflow.
- Analyze studies locally:studycommands cover local query, cohort, survival, compare, and co-occurrence workflows with native terminal, SVG, and PNG charts for downloaded cBioPortal-style datasets.
- Follow the paper trail:article citations,article references,article recommendations, andarticle entitiesturn one known paper into a broader evidence map.
- Enrich and batch:usebiomcp enrichfor top-level g:Profiler enrichment andbiomcp batchfor up to 10 focusedgetcalls in one command.

uv tool install biomcp-cli biomcp health --apis-only biomcp skill list biomcp list gene biomcp search all --gene BRAF --disease melanoma # unified cross-entity discovery biomcp get gene BRAF pathways hpa

curl -fsSL https://biomcp.org/install.sh | bash

uv tool install biomcp-cli # or: pip install biomcp-cli

PyPI package warning:installbiomcp-cli, notbiomcp. ThebiomcpPyPI package is unrelated to this project.

MCP Registry ownership marker:mcp-name: io.github.genomoncology/biomcp.

This installs thebiomcpbinary in~/.local/bin. If that directory is not already onPATH, the installer prints one command to add it; it never edits your shell startup files.

brew tap genomoncology/biomcp brew install biomcp

The separategenomoncology/homebrew-biomcptap repository must exist before these commands can work.

docker run --rm ghcr.io/genomoncology/biomcp --version docker run --rm ghcr.io/genomoncology/biomcp list docker run --rm -i ghcr.io/genomoncology/biomcp serve

Use the GHCR image for quick CLI checks or stdio MCP clients without a local install.

Install thebiomcpbinary first, then add the hosted plugin marketplace and install the BioMCP plugin in Claude Code:

/plugin marketplace add genomoncology/biomcp /plugin install biomcp@biomcp

The plugin wires Claude Code to the local stdio MCP server withbiomcp serve. For guided BioMCP workflows, also install the skill assets below.

Install thebiomcpbinary first, then register the same stdio MCP server with Codex:

Install BioMCP from the Anthropic Directory in Claude Desktop when that path is available for your environment. For local/manual setups, use the JSON MCP config below.

Install guided investigation workflows into your agent directory:

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

biomcp serve-http --host 127.0.0.1 --port 8080

Remote clients connect tohttp://127.0.0.1:8080/mcp. Probe routes areGET /health,GET /readyz, andGET /.

uv run --script examples/streamable-http/streamable_http_client.py

SeeRemote HTTP Serverfor the newcomer guide.

make install "$HOME/.local/bin/biomcp" --version

search <entity> [filters] → discovery skill list → playbook catalog for how-to questions discover <query> → concept resolution before entity selection get <entity> <id> [sections] → focused detail <entity> <helper> <id> → cross-entity pivots enrich <GENE1,GENE2,...> → gene-set enrichment batch <entity> <id1,id2,...> → parallel gets search all [slot filters] → counts-first cross-entity orientation

The tables below distinguish detail-card entities from search-only surfaces so agents do not synthesize unsupportedgetcommands.

Pivot between related entities without rebuilding filters.

See the[cross-entity pivot guidefor when to use a helper versus a fresh search.

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 trials BRAF biomcp gene drugs BRAF biomcp gene articles BRCA1 biomcp gene pathways BRAF biomcp pathway drugs R-HSA-5673001 biomcp pathway drugs hsa05200 biomcp pathway articles R-HSA-5673001 biomcp pathway trials R-HSA-5673001 biomcp protein structures P15056 biomcp article entities 22663011 biomcp article citations 22663011 --limit 3 biomcp article references 22663011 --limit 3 biomcp article recommendations 22663011 --limit 3

Top-levelbiomcp enrichusesg:Profiler. Gene enrichment sections inside other entity views still referenceEnrichrwhere that is the backing source.

Everygetcommand supports selectable sections for focused output:

biomcp get gene BRAF # summary card biomcp get gene BRAF pathways # add pathway section biomcp get gene BRCA1 diagnostics # diagnostic-test pivot from GTR biomcp get gene BRAF hpa # protein tissue expression + localization biomcp get gene BRAF civic interactions # multiple sections biomcp get gene BRAF all # standard sections; diagnostics/funding stay opt-in biomcp get variant "BRAF V600E" clinvar population conservation biomcp get article 22663011 tldr biomcp get drug pembrolizumab label targets civic approvals biomcp get drug trastuzumab regulatory --region who biomcp get disease "Lynch syndrome" genes phenotypes variants biomcp get disease tuberculosis diagnostics biomcp get diagnostic GTR000006692.3 regulatory biomcp get trial NCT02576665 eligibility locations outcomes

In JSON mode,getresponses expose_meta.next_commandsfor the next likely follow-ups and_meta.section_sourcesfor section-level provenance.batch ... --jsonreturns per-entity objects with the same metadata shape.

Most commands work without credentials. Optional keys improve rate limits or unlock optional enrichments:

export NCBI_API_KEY="..." # PubTator, PubMed/efetch, PMC OA, NCBI ID converter export S2_API_KEY="..." # Optional Semantic Scholar auth; dedicated quota at 1 req/sec 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

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