genomoncology/biomcp

BioMCP

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

Description

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.

Features

• 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 suggest "<question>" routes a biomedical question to a shipped worked example and two starter commands.
• 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.