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 article`fans 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 list`shows shipped worked examples so you can open the matching`biomcp skill <slug>`workflow. - **Analyze studies locally:**`study`commands 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`, and`article entities`turn one known paper into a broader evidence map. - **Enrich and batch:**use`biomcp enrich`for top-level g:Profiler enrichment and`biomcp batch`for up to 10 focused`get`calls 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:**install`biomcp-cli`, not`biomcp`. The`biomcp`PyPI package is unrelated to this project. MCP Registry ownership marker:`mcp-name: io.github.genomoncology/biomcp`. This installs the`biomcp`binary in`~/.local/bin`. If that directory is not already on`PATH`, the installer prints one command to add it; it never edits your shell startup files. ``` `brew tap genomoncology/biomcp brew install biomcp` ``` The separate`genomoncology/homebrew-biomcp`tap 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 the`biomcp`binary 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 with`biomcp serve`. For guided BioMCP workflows, also install the skill assets below. Install the`biomcp`binary 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 to`http://127.0.0.1:8080/mcp`. Probe routes are`GET /health`,`GET /readyz`, and`GET /`. ``` `uv run --script examples/streamable-http/streamable_http_client.py` ``` See[Remote HTTP Serverfor the newcomer guide. ``` `make install "$HOME/.local/bin/biomcp" --version` ``` For repo-local verification, run the standard gates directly:`make lint`,`make test`, and`make spec`.`make test`includes both Rust nextest and the Python/docs contract lane, while`make release-gate`adds the named full-feature proof and runs specs against the all-feature release binary. There is no supported`make check`command. Use`make verify`only for opt-in live public-upstream confidence;`make release-live-smoke`remains a compatibility alias. ``` `search <entity> ](https://biomcp.org/getting-started/remote-http/)[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 unsupported`get`commands. 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-level`biomcp enrich`uses**g:Profiler**. Gene enrichment sections inside other entity views still reference**Enrichr**where that is the backing source. 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 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,`get`responses expose`_meta.next_commands`for the next likely follow-ups and`_meta.section_sources`for section-level provenance.`batch ... --json`returns 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` ``` `search article`,`get article`,`article batch`,`get article ... tldr`, and the explicit Semantic Scholar helpers all work without`S2_API_KEY`. With the key, BioMCP sends authenticated requests and uses a dedicated rate limit at 1 req/sec. Without it, BioMCP uses the shared unauthenticated pool at 1 req/2sec.`search article --source`supports`all`,`pubtator`,`europepmc`,`pubmed`,`semanticscholar`, and`litsense2`. The default compatible article federation uses PubTator3, Europe PMC, PubMed, and automatic Semantic Scholar; use`--source semanticscholar`or`--source litsense2`explicitly when you want one of those sources alone. Explicit source selection also disables cross-provider row enrichment. References and recommendations can be empty for paywalled papers because of publisher elision in Semantic Scholar upstream coverage. The directory bundle exposes only the optional settings needed for the first reviewer-facing build: The first directory build exposes only those three optional settings. Advanced CLI-only env vars remain documented in](https://github.com/genomoncology/biomcp/blob/HEAD/docs/how-to/cross-entity-pivots.md)[API Keysfor the general BioMCP CLI path. **User prompt:**Give me a low-noise overview of BRAF in melanoma. **Expected tool call:**`biomcp search all --gene BRAF --disease melanoma --counts-only` **Expected behavior:**Returns a cross-entity counts summary that orients the next command instead of dumping long detail tables. **Expected output:**Counts-first summary with suggested next commands for the highest-yield entity follow-ups. **User prompt:**Summarize ClinVar significance and population frequency for BRAF V600E. **Expected tool call:**`biomcp get variant "BRAF V600E" clinvar population` **Expected behavior:**Retrieves the focused variant card, ClinVar section, and population-frequency data in one read-only call. **Expected output:**Variant summary, ClinVar significance details, and gnomAD population frequencies. **User prompt:**Show OncoKB therapy evidence for BRAF V600E. **Expected tool call:**`biomcp variant oncokb "BRAF V600E"` **Expected behavior:**Uses`ONCOKB_TOKEN`when configured and otherwise returns helpful guidance about the missing credential. **Expected output:**Therapy and level evidence when`ONCOKB_TOKEN`is set, or a clear setup hint when it is not. **User prompt:**Show scored DisGeNET associations for TP53. **Expected tool call:**`biomcp get gene TP53 disgenet` **Expected behavior:**Uses`DISGENET_API_KEY`to retrieve the scored gene-disease association section. **Expected output:**Ranked disease-association table with evidence counts and scores when`DISGENET_API_KEY`is configured. BioMCP does not add telemetry, analytics, or remote log upload. Review the full privacy statement at](https://github.com/genomoncology/biomcp/blob/HEAD/docs/getting-started/api-keys.md)[https://biomcp.org/policies/. BioMCP rate limiting is process-local. For many concurrent workers, run one shared Streamable HTTP`biomcp serve-http`endpoint so all workers share a single limiter budget: ``` `biomcp serve-http --host 0.0.0.0 --port 8080 \ --allowed-hosts biomcp.example.org` ``` Loopback servers accept only local`Host`values by default. A non-loopback bind requires`--allowed-hosts`. The explicit`--unsafe-allow-any-host`escape hatch disables only this Host check; it does not add authentication, TLS, or encryption. Put remote deployments behind a trusted authenticated TLS proxy or inside a private network. Remote clients should connect to`http://<host>:8080/mcp`. Lightweight process probes are available at`GET /health`,`GET /readyz`, and`GET /`. BioMCP ships an embedded agent guide and a worked-example catalog. Use`biomcp skill list`when you need the right worked example, then use`biomcp skill`to read the embedded BioMCP guide or install it into your agent directory when you want local copies of the workflow references: ``` `biomcp skill list biomcp skill biomcp skill install ~/.claude --force` ``` See](https://biomcp.org/policies/)[Skillsfor supported install targets, installed files, and legacy compatibility notes. `study`is BioMCP's local analysis family for downloaded cBioPortal-style datasets. The public entity surface handles API-backed, local-runtime, and hybrid discovery/detail;`study`commands work on local datasets when you need per-study query, cohort, survival, comparison, or co-occurrence workflows. Per-gene queries include mutations, CNA, expression, and structural variants/fusions from local`data_sv.txt`files. Mutation summaries stay mutation-only and note when fusions/SV need`--type sv`. Use`study download`to fetch a dataset into your local study root. Set`BIOMCP_STUDY_DIR`when you want an explicit dataset location for reproducible scripts and demos; if it is unset, BioMCP falls back to its default study root. ``` `export BIOMCP_STUDY_DIR="$HOME/.local/share/biomcp/studies" biomcp study download msk_impact_2017 biomcp study query --study msk_impact_2017 --gene TP53 --type mutations --chart bar --theme dark --palette wong -o docs/blog/images/tp53-mutation-bar.svg biomcp study query --study msk_impact_2017 --gene RET --type sv` ``` See the](https://github.com/genomoncology/biomcp/blob/HEAD/docs/getting-started/skills.md)[CLI referencefor the full`study`command family and dataset prerequisites. ``` `biomcp version # show version and build info biomcp health # inspect API connectivity plus local DDInter/EMA/cache readiness biomcp update # self-update with release SHA256 checksum verification biomcp update --check # check for updates without installing biomcp uninstall # remove biomcp from ~/.local/bin` ``` - GitHub issues:](https://github.com/genomoncology/biomcp/blob/HEAD/docs/user-guide/cli-reference.md#local-study-analytics)[https://github.com/genomoncology/biomcp/issues - Troubleshooting:](https://github.com/genomoncology/biomcp/issues)[docs/troubleshooting.md - Full documentation:](https://github.com/genomoncology/biomcp/blob/HEAD/docs/troubleshooting.md)[https://biomcp.org/ - ](https://biomcp.org/)[Getting Started - ](https://github.com/genomoncology/biomcp/blob/HEAD/docs/getting-started/installation.md)[Search All Workflow - ](https://github.com/genomoncology/biomcp/blob/HEAD/docs/how-to/search-all-workflow.md)[BioASQ Benchmark - ](https://github.com/genomoncology/biomcp/blob/HEAD/docs/reference/bioasq-benchmark.md)[Cross-Entity Pivot Guide - ](https://github.com/genomoncology/biomcp/blob/HEAD/docs/how-to/cross-entity-pivots.md)[Privacy Policy - ](https://github.com/genomoncology/biomcp/blob/HEAD/docs/policies.md)[Source Licensing and Terms - ](https://github.com/genomoncology/biomcp/blob/HEAD/docs/reference/source-licensing.md)[Data Sources - ](https://github.com/genomoncology/biomcp/blob/HEAD/docs/reference/data-sources.md)[Quick Reference - ](https://github.com/genomoncology/biomcp/blob/HEAD/docs/reference/quick-reference.md)[Troubleshooting If you use BioMCP in research, cite it via](https://github.com/genomoncology/biomcp/blob/HEAD/docs/troubleshooting.md)[`CITATION.cff`. GitHub also exposes`Cite this repository`in the repository sidebar when that file is present. BioMCP is MIT-licensed. It performs on-demand queries against upstream providers instead of vendoring or mirroring their datasets, but upstream terms govern reuse of retrieved results. Some providers are fully open, some BioMCP features require registration or API keys, and some queryable sources still impose notable reuse limits. The two biggest cautions are KEGG, which distinguishes academic and non-academic use, and COSMIC, which BioMCP keeps indirect-only because its licensing model is incompatible with a direct open integration. Use](https://github.com/genomoncology/biomcp/blob/HEAD/CITATION.cff)[Source Licensing and Termsfor the per-source breakdown and](https://github.com/genomoncology/biomcp/blob/HEAD/docs/reference/source-licensing.md)[API Keysfor setup steps and registration links. Official Airtable MCP server and skills for working with bases, records, workflows, and business operations from AI agents. MCP Server For Apache Doris, an MPP-based real-time data warehouse. Official MCP Server from Atlan which enables you to bring the power of metadata to your AI tools](https://github.com/genomoncology/biomcp/blob/HEAD/docs/getting-started/api-keys.md)