BioMCP is a server implementation that provides structured access to key biomedical databases through a unified interface. Developed by GenomOncology, it connects to ClinicalTrials.gov, PubMed (via PubTator3), and MyVariant.info to enable searching and retrieving information about clinical trials, research articles, and genetic variants. The server exposes these capabilities as MCP tools that can be used by AI assistants to access up-to-date biomedical data, overcoming knowledge cutoff limitations. BioMCP handles entity normalization, intelligent rendering of complex data as Markdown, and transparent attribution of sources, making it valuable for biomedical research, clinical decision support, and literature review workflows.
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Highlight AISearch for articles in PubTator3 and Europe PMC, deduplicating PMID/PMCID/DOI identifiers, with optional Semantic Scholar integration.
Show shipped worked examples for workflows that can be executed with biomcp.
Execute local query, cohort, survival, comparison, and co-occurrence workflows on downloaded datasets, generating charts in SVG and PNG formats.
Retrieve citations for a specified article, providing a broader evidence map.
Get references for a specified article, helping to explore related literature.
Obtain recommendations based on a specified article, expanding the evidence base.
Extract entities from a specified article to understand its content better.
Perform gene-set enrichment analysis using g:Profiler for specified genes.
Execute up to 10 focused 'get' calls in one command for efficiency.
Retrieve detailed information for a specified entity (e.g., gene, variant, drug) with optional sections for focused output.
Inspect API connectivity and readiness of local services.
Self-update the biomcp tool with verification of release SHA256 checksums.
Show the version and build information for the biomcp tool.
Remove the biomcp tool from the system.
