BioThings MCP
Query genes, variants, chemicals, and taxa from BioThings.io (mygene, myvariant, mychem) in your AI client.
Add to your client
Copy the config for your MCP client and paste it into its config file.
uvx biothings-mcpPaste into ~/Library/Application Support/Claude/claude_desktop_config.json
{
"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.
Step-by-step guides: Add to Claude Desktop · Add to Cursor · Add to Windsurf
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
About BioThings MCP
An MCP server that bridges AI assistants and BioThings.io biomedical data services. It exposes typed interfaces for gene annotation (mygene.info), variant annotation (myvariant.info), chemical compound annotation (mychem.info), and taxonomy, plus tools to download data from NCBI Entrez and save sequences/results to local files. Supports stdio, HTTP streamable, and SSE transports, and offers a publicly hosted remote endpoint.
Tools & capabilities (6)
GeneToolsGene interface wrapping GeneClientAsync — query and annotate genes via mygene.info.
VariantToolsVariant interface wrapping VariantClientAsync — query and annotate genetic variants via myvariant.info.
ChemToolsChemical interface wrapping ChemClientAsync — query and annotate chemical compounds via mychem.info.
TaxonToolsTaxon interface wrapping TaxonClientAsync — query and resolve taxonomy data.
download_entrez_dataDownload data from NCBI Entrez databases and return the content as a string.
download_entrez_data_localDownload data from NCBI Entrez databases and save it to a local file (FASTA, GenBank, alignment, JSON, or text).
When to use it
- Look up gene annotations and symbols from mygene.info inside an AI chat
- Annotate and explore genetic variants via myvariant.info
- Retrieve chemical compound information from mychem.info
- Resolve taxonomy data for organisms
- Download gene/sequence data from NCBI Entrez and save it locally as FASTA/GenBank/JSON for downstream analysis
Security notes
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 FAQ
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).
Is it production-ready?
The maintainers describe it as beta-quality. A noted limitation is that LLMs sometimes supply invalid gene/variant symbols; the team plans entity-resolution improvements.
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