MCP Directory

How to add BioThings MCP to Claude Desktop

Query genes, variants, chemicals, and taxa from BioThings.io (mygene, myvariant, mychem) in your AI client. Paste the config into ~/Library/Application Support/Claude/claude_desktop_config.json and restart Claude Desktop.

Last updated June 14, 2026 · 32★ · stdio · no auth

Claude Desktop config for BioThings MCP

uvx biothings-mcp
{
  "mcpServers": {
    "biothings-mcp": {
      "command": "uvx",
      "args": [
        "--from",
        "biothings-mcp",
        "stdio"
      ]
    }
  }
}

Requires `uv` (the Python package runner). Install it from https://docs.astral.sh/uv/ if `uvx` is not found.

Setup steps

  1. 1Open Claude Desktop → Settings → Developer → Edit Config (this opens ~/Library/Application Support/Claude/claude_desktop_config.json).
  2. 2Paste the BioThings MCP config below under the top-level "mcpServers" key.
  3. 3Fill in any placeholder secrets (API keys, paths) in the snippet.
  4. 4Save the file, then fully quit and reopen Claude Desktop.
  5. 5Open a chat and confirm BioThings MCP's tools appear under the 🔌 tools menu.

Before you start

  • uv / uvx (Astral) installed to run the server, OR Python with the biothings-mcp PyPI package
  • Node.js + npx only if you want to use the MCP Inspector or the remote proxy config

What BioThings MCP can do in Claude Desktop

GeneTools

Gene interface wrapping GeneClientAsync — query and annotate genes via mygene.info.

VariantTools

Variant interface wrapping VariantClientAsync — query and annotate genetic variants via myvariant.info.

ChemTools

Chemical interface wrapping ChemClientAsync — query and annotate chemical compounds via mychem.info.

TaxonTools

Taxon interface wrapping TaxonClientAsync — query and resolve taxonomy data.

download_entrez_data

Download data from NCBI Entrez databases and return the content as a string.

download_entrez_data_local

Download data from NCBI Entrez databases and save it to a local file (FASTA, GenBank, alignment, JSON, or text).

Security

The publicly hosted and HTTP/streamable configs reference an API_ACCESS_TOKEN env value, but the default stdio mode runs locally with no authentication. The download tools write files to the local filesystem (default ./biothings_output/), so be mindful of the output directory when granting the server access. The maintainers describe the library as beta-quality.

BioThings MCP + Claude Desktop FAQ

Where is the Claude Desktop config file?

Claude Desktop reads MCP servers from ~/Library/Application Support/Claude/claude_desktop_config.json. Paste the BioThings MCP config there under the "mcpServers" key and restart the client.

Is BioThings MCP safe to use with Claude Desktop?

The publicly hosted and HTTP/streamable configs reference an API_ACCESS_TOKEN env value, but the default stdio mode runs locally with no authentication. The download tools write files to the local filesystem (default ./biothings_output/), so be mindful of the output directory when granting the server access. The maintainers describe the library as beta-quality.

Do I need to clone the repo to run it?

No. You can run it directly with uvx (e.g. `uvx biothings-mcp` for stdio, or `uvx --from biothings-mcp server run` for HTTP) without cloning.

Is there a hosted version?

Yes. A publicly hosted server is available at https://biothings.longevity-genie.info/mcp via the mcp-config-remote.json configuration, so you don't need to run anything locally.

What transports are supported?

stdio (default), HTTP streamable (default port 3001 at /mcp), and SSE (Server-Sent Events).

View repo Full BioThings MCP page