Human Protein Atlas MCP Server

Community MCP server wrapping the Human Protein Atlas, exposing protein expression, subcellular localization, cancer pathology, and antibody validation/staining data to Claude.

   
Type MCP server
Supplier Augmented Nature (Moudather Chelbi)
Availability GA
Pricing Free / OSS (MIT). No API key required — queries the public proteinatlas.org.
Capabilities Read-only — Human Protein Atlas queries

How to install

This server is not published to npm; install from source.

  • Prerequisite — Node.js 18+ and git.

  • Clone and build:

    git clone https://github.com/Augmented-Nature/ProteinAtlas-MCP-Server/
cd ProteinAtlas-MCP-Server/proteinatlas-server
npm install
npm run build

    (The upstream README writes cd proteinatlas-server; the server lives in the proteinatlas-server/ subdirectory of the cloned ProteinAtlas-MCP-Server repo — cd into that path. Confirm build/index.js exists after npm run build.)

  • Claude Code — register the built server (replace /path/to with the absolute path of your clone — e.g., $(pwd)/build/index.js if you’re still in proteinatlas-server from the previous step):

    claude mcp add --transport stdio proteinatlas -- node /path/to/ProteinAtlas-MCP-Server/proteinatlas-server/build/index.js

  • Claude Desktop — add to claude_desktop_config.json (same absolute path):

    {
  "mcpServers": {
    "proteinatlas": {
      "command": "node",
      "args": ["/path/to/ProteinAtlas-MCP-Server/proteinatlas-server/build/index.js"]
    }
  }
}

    Both Claude Code and Claude Desktop launch the process themselves over stdio — you do not keep a server running in a separate terminal.

What it does

Fourteen read-only tools over the Human Protein Atlas:

  • Search/retrieval — search_proteins, get_protein_info (by gene symbol), get_protein_by_ensembl.
  • Expression — get_tissue_expression, search_by_tissue, get_blood_expression, get_brain_expression.
  • Subcellular localization — get_subcellular_location, search_by_subcellular_location.
  • Pathology/cancer — get_pathology_data, search_cancer_markers.
  • Advanced — advanced_search (multi-filter), batch_protein_lookup (up to 100 proteins), compare_expression_profiles (2–10 proteins).

Antibody validation and immunostaining data are returned through the protein-info and tissue-expression tools.

Primary use cases: Antibody validation lookup, tissue/single-cell expression profiling, cancer prognostic-marker discovery.

Notes

License is MIT. No API key or account required. The server queries the public Human Protein Atlas; respect HPA’s data-usage terms for downstream redistribution. Tool list and install steps verified against the upstream README 2026-06-13.

Sources

Installed this tool?

Share feedback — install path, OS, errors, workarounds. The form opens with this tool pre-selected and a link back to this page.