biomcp

Overview

BioMCP cuts through the biomedical data maze by providing a single command grammar to search, focus, and pivot across various biomedical sources that normally live behind different APIs and search interfaces. It supports 13 different entity types including genes, variants, articles, trials, drugs, diseases, pathways, proteins, and more. The server can be run as a local binary, through PyPI, or as an HTTP server, and integrates with Claude Desktop as an extension. BioMCP provides features like literature search across PubTator3 and Europe PMC, entity pivoting, study analysis, and enrichment capabilities.

Try asking AI

After installing, here are 5 things you can ask your AI assistant:

• searchsearch <entity> [filters]

  Discovery search across biomedical entities

  Try:Search articles about BRAF and melanomaTry:Find clinical trials for melanoma
• suggestsuggest <question>

  Route biomedical questions to worked examples and starter commands

  Try:What drugs treat melanoma?Try:How to analyze variant rs113488022?
• getget <entity> <id> [sections]

  Get detailed information about a specific biomedical entity

  Try:Get details for gene BRAFTry:Get information about variant BRAF V600E
• enrichenrich <GENE1,GENE2,...>

  Perform gene-set enrichment analysis using g:Profiler

  Try:Enrich genes BRAF, KRAS, NRASTry:Analyze enrichment for TP53 and BRCA1
• batchbatch <entity> <id1,id2,...>

  Get details for multiple entities in parallel

  Try:Batch get genes BRAF, KRAS, NRASTry:Get details for variants BRAF V600E, BRAF V600E_K601E
• discoverdiscover <query>

  Resolve biomedical concepts before entity selection

  Try:Discover genes related to melanomaTry:Resolve drug names for targeted therapy
• studystudy <command>

  Local study analytics for cBioPortal-style datasets

  Try:Query study msk_impact_2017 for TP53 mutationsTry:Analyze survival in study cohort
• listlist <entity>

  List available options for an entity type

  Try:List all available genesTry:Show diseases in the database
• healthhealth

  Check API connectivity and status

  Try:Check API healthTry:Verify all services are available
• skillskill <command>

  Manage BioMCP agent skills and workflows

  Try:Install BioMCP skillsTry:List available skills
• drug interactionsdrug interactions <drug>

  Find drug interactions for a specific medication

  Try:Find interactions for warfarinTry:Check interactions with pembrolizumab
• article entitiesarticle entities <article_id>

  Extract entities from a specific article

  Try:Find entities in article 22663011Try:Get entities from PMID:12345678

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Installation

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

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

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

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

FAQ

What biomedical sources does BioMCP integrate with?

BioMCP integrates with 13+ biomedical data sources including PubTator3, Europe PMC, MyGene.info, UniProt, Reactome, ClinicalTrials.gov, and many others depending on the entity type.

Does BioMCP require API keys to function?

Most commands work without credentials, but optional API keys can improve rate limits or unlock additional features like Semantic Scholar access, OncoKB variant data, and DisGeNET associations.

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