BioMCP

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Connects AI assistants to authoritative biomedical data sources like PubMed and ClinicalTrials.gov, enabling natural language queries.

Install

How to run this server

[ { "cmd": "pip install biomcp-cli", "imports": [] } ]

server path: biomcp

Tools

What this server exposes

Search for entities (article, gene, variant, drug, disease, etc.) with filters for discovery

suggest

Route a biomedical question to a shipped worked example and two starter commands

discover

Concept resolution before entity selection

get

Focused detail on an entity by ID with optional sections

enrich

Gene-set enrichment analysis via g:Profiler

batch

Parallel gets for up to 10 focused calls in one command

study

Analyze local datasets with query, cohort, survival, compare, and co-occurrence workflows

article citations

Get citations for a known article

article references

Get references for a known article

article recommendations

Get recommendations for a known article

article entities

Get entities mentioned in a known article

Configuration

Environment & auth

authnone

envS2_API_KEY

envNCBI_API_KEY

envOPENFDA_API_KEY

envNCI_API_KEY

envONCOKB_TOKEN

envALPHAGENOME_API_KEY

envDISGENET_API_KEY

Resources