BioThings

This MCP server exposes the BioThings.io ecosystem via MCP endpoints, enabling you to query MyGene.info and MyVariant.info through a unified context protocol. You can retrieve gene and variant annotations, run batch operations, and leverage advanced search tools for genes and variants (such as pathway-based gene searches, GO term queries, orthologs, and drug-target queries). The server is designed to work with MCP tooling and Claude/Desktop workflows, so you can integrate it into your existing pipelines to enrich biological data with minimal friction. Typical use cases include retrieving gene annotations by Entrez/Ensembl IDs, querying variants by HGVS or rsID, and performing batch queries for high-throughput annotation tasks.

To use the tools, configure your MCP client to connect to the biothings MCP server and call the available actions such as get_gene_annotation, query_genes, batch_gene_query, get_variant_annotation, query_variants, batch_variant_query, as well as the advanced and utility tools like search_genes_by_pathway, search_genes_by_go_term, get_gene_metadata, and get_variant_metadata. The server will translate MCP requests into BioThings.io API calls under the hood and return structured results suitable for downstream analysis and visualization.

Prerequisites:

• Node.js (LTS version) installed on your system
• Access to a shell/terminal
• (Optional) MCP tooling or a client to send MCP requests

Installation steps:

1. Clone or download the BioThings MCP server repository to your machine.
2. Install dependencies (if a package.json exists):

npm install

3. Ensure you have a running Node.js environment and that the server can access BioThings APIs (no API keys required per the project).
4. Start the MCP server using the node entry point specified in your environment. Example (from the README):

node /path/to/biothings-server/build/index.js

5. Verify the server is reachable through your MCP client by sending a basic get_gene_annotation request (or the equivalent MCP call) and inspecting the response.

Notes and tips:

• No API keys are required for BioThings APIs in this setup, but ensure your network allows outbound requests to BioThings endpoints.
• The server supports batch operations (up to 1000 items per request) for both genes and variants to improve throughput.
• If you run into connectivity or rate-limit issues, check your network firewall, ensure DNS resolution works, and consider adding basic retry logic in your client.
• Environment variables can be used to customize endpoints, timeouts, and logging levels (e.g., BIOOTHINGS_API_BASE, REQUEST_TIMEOUT, LOG_LEVEL).