Loading...
Biothings MCP server provides a standardized interface for accessing and manipulating biomedical data via the Model Context Protocol.
Boost this tool
Subscribe to listing upgrades or segmented pushes.
Biothings MCP server provides a standardized interface for accessing and manipulating biomedical data via the Model Context Protocol.
The Biothings MCP server is generally safe for read-only operations. The risk increases when using the download tools due to potential write access and the lack of authentication. Exercise caution when using the file saving features and consider implementing additional security measures in production environments.
Performance depends on the underlying BioThings API and network latency. Large downloads can take significant time.
The server itself is free to run, but the underlying BioThings APIs may have usage limits or associated costs.
npx @modelcontextprotocol/inspector --config mcp-config.json --server biothings-mcpGeneToolsProvides access to gene annotation and query services.
Read-only access to gene information.
VariantToolsProvides access to variant annotation and query services.
Read-only access to variant information.
ChemToolsProvides access to chemical compound annotation and query services.
Read-only access to chemical information.
TaxonToolsProvides access to taxonomic information.
Read-only access to taxonomic data.
DownloadToolsProvides file download and sequence analysis capabilities.
Allows writing files to the local file system.
None
hybrid
The Biothings MCP server is generally safe for read-only operations. The risk increases when using the download tools due to potential write access and the lack of authentication. Exercise caution when using the file saving features and consider implementing additional security measures in production environments.
The server allows file downloads to a local directory, which can be configured. Ensure the output directory has appropriate permissions to prevent unauthorized access.
Production Tip
Monitor disk usage and network traffic when using the download tools to prevent resource exhaustion.
MCP is a protocol that bridges the gap between AI systems and specialized domain knowledge, enabling structured access to authoritative data sources.
The server supports mygene.info, myvariant.info, and mychem.info.
Use the `--output-dir` parameter when running the server.
FASTA, GenBank, Alignment, JSON, and Text.
Use the command `uvx --from biothings-mcp server run`.
Use the MCP Inspector with the appropriate configuration file (mcp-config.json or mcp-config-stdio.json).
No, authentication is not required for basic usage.