BioContextAI Knowledgebase MCP

A single MCP server that fronts 14+ biomedical APIs as a unified retrieval layer — antibody and protein identifier resolution, pathway and interaction lookups, predicted structures, drug and clinical trial cross-references.

   
Type MCP server
Supplier BioContextAI (Heidelberg-led OSS initiative)
Availability GA — v0.2.1 (May 2026)
Pricing Free / OSS (Apache-2.0). Underlying data sources keep their own licenses; KEGG restricts commercial remote hosting.
Capabilities Read-only
Verified works · 2026-07-20
Security cleared · 2026-07-20 — provenance matches biocontext-ai, PyPI biocontext_kb 0.2.1, Apache-2.0, no advisories

The server is published as the biocontext_kb package and is most easily run with uv (which handles its own Python). To verify it starts:

uvx biocontext_kb@latest

Then register it as an MCP server (Claude Code launches the process itself — don’t keep the verification command running):

  • Claude Code (stdio, recommended): 
    claude mcp add --transport stdio biocontext_kb -- uvx biocontext_kb@latest
  • Claude Desktop (stdio) — add to claude_desktop_config.json: 
    {
  "mcpServers": {
    "biocontext_kb": {
      "command": "uvx",
      "args": ["biocontext_kb@latest"],
      "env": { "UV_PYTHON": "3.12" }
    }
  }
}
  • Docker (HTTP) — no image is published to a registry, so you must build it from a clone first. The container is a long-lived service: leave it running in its own terminal. 
    git clone https://github.com/biocontext-ai/knowledgebase-mcp
cd knowledgebase-mcp
docker build -t biocontext_kb:latest .
docker run -p 127.0.0.1:8000:8000 biocontext_kb:latest

    Then, in a second terminal:

    claude mcp add --transport http biocontext_kb http://127.0.0.1:8000/mcp
  • Remote test endpoint (no install): 
    claude mcp add --transport http biocontext_kb https://biocontext-kb.fastmcp.app/mcp

What it does

Unified access to:

  • Antibody / immunology: Antibody Registry, PRIDE
  • Protein / structure: UniProt, InterPro, AlphaFold DB, Human Protein Atlas
  • Interactions / pathways: STRING, Reactome, KEGG
  • Targets / drugs: Open Targets, Drugs@openFDA
  • Single-cell context: PanglaoDB
  • Genomes / literature: Ensembl, EuropePMC, bioRxiv
  • Ontologies: OLS
  • Trials: ClinicalTrials.gov

Primary use cases: Antibody and reagent identifier resolution; immune protein and pathway context; pulling AlphaFold structures for antigen-binding analysis; building integrated knowledge graphs for a target list.

Notes

stdio (dev) and HTTP/uvicorn (prod) transports. No auth for the server itself, but it respects upstream rate limits. IEDB is not yet integrated.

The hosted biocontext-kb.fastmcp.app endpoint is published by the project for testing only and is subject to fair use — self-host for anything you depend on.

Sources

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