BioMCP-TS — Claude Code MCP server: genes, trials and papers
Gives an agent tools for genes, variants, clinical trials, literature and patents. Useful when a medical lookup has to happen inside the editor.
claude mcp add biomcp-ts -e NCBI_API_KEY=<NCBI_API_KEY> -e S2_API_KEY=<S2_API_KEY> -e OPENFDA_API_KEY=<OPENFDA_API_KEY> -e ONCOKB_TOKEN=<ONCOKB_TOKEN> -e DISGENET_API_KEY=<DISGENET_API_KEY> -- npx -y biomcpWhat BioMCP-TS does
BioMCP-TS is a single stdio MCP server that queries many bioinformatics and pharmaceutical sources in a federated way. The toolset splits into genes, variants, drugs and diseases. Genes get search, a detail card with optional sections, linked diseases and compounds, trials, articles and Reactome enrichment. Variants cover rsid or HGVS lookup, frequencies, predictions and OncoKB annotations. Each drug and disease tool connects to its own trial search. Literature runs across several backends at once, and a preprint-only mode narrows results to bioRxiv and medRxiv. Replies arrive as a results / warnings / errors envelope, so a failing source shows up instead of an empty list.
The server starts with npx -y biomcp and needs Node 22.13 or newer. Some tools stay dark until you supply credentials: variant annotations want ONCOKB_TOKEN, while keys such as NCBI_API_KEY or S2_API_KEY go in as environment variables when the server is registered. npx -y biomcp doctor checks the Node version, config health and optional features. Toolboxes for local database curation, R analysis and biowasm analysis are switched on through the ANALYSIS_R, ANALYSIS_BIOWASM and DB_TYPE variables.
Run several agents on one machine and each process enforces the arXiv limit of 1 request / 3 s on its own, so the limit is not shared. The README suggests a single biomcp serve daemon for that setup. Apache-2.0.
What it helps with
- find clinical trials for a given gene
- pull OncoKB annotations for a variant
- collect recent preprints on a topic
- check which drugs target a gene
- see disease links to genes and pathways
Example prompts for the agent
- Find clinical trials for ERBB2 and summarise the phases.
- Look up variant rs113488022: frequencies and clinical significance.
- Search CRISPR papers from the last year, preprints only.
How to install BioMCP-TS
Platform CLI
claude mcp add biomcp-ts -e NCBI_API_KEY=<NCBI_API_KEY> -e S2_API_KEY=<S2_API_KEY> -e OPENFDA_API_KEY=<OPENFDA_API_KEY> -e ONCOKB_TOKEN=<ONCOKB_TOKEN> -e DISGENET_API_KEY=<DISGENET_API_KEY> -- npx -y biomcpReplace <…> with your own values. 3 more environment variables are in the server README
Platform CLI
codex mcp add biomcp-ts --env ANALYSIS_BIOWASM=<ANALYSIS_BIOWASM> --env ANALYSIS_R=<ANALYSIS_R> --env DB_TYPE=<DB_TYPE> --env NCBI_API_KEY=<NCBI_API_KEY> --env S2_API_KEY=<S2_API_KEY> -- npx -y biomcpReplace <…> with your own values. 3 more environment variables are in the server README
Config file
{
"mcpServers": {
"biomcp-ts": {
"command": "npx",
"args": [
"-y",
"biomcp"
],
"env": {
"ANALYSIS_BIOWASM": "<ANALYSIS_BIOWASM>",
"ANALYSIS_R": "<ANALYSIS_R>",
"DB_TYPE": "<DB_TYPE>",
"NCBI_API_KEY": "<NCBI_API_KEY>",
"S2_API_KEY": "<S2_API_KEY>"
}
}
}
}Replace <…> with your own values. 3 more environment variables are in the server README
Config file
{
"servers": {
"biomcp-ts": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"biomcp"
],
"env": {
"ANALYSIS_BIOWASM": "<ANALYSIS_BIOWASM>",
"ANALYSIS_R": "<ANALYSIS_R>",
"DB_TYPE": "<DB_TYPE>",
"NCBI_API_KEY": "<NCBI_API_KEY>",
"S2_API_KEY": "<S2_API_KEY>"
}
}
}
}Replace <…> with your own values. 3 more environment variables are in the server README
Platform CLI
gemini mcp add -e ANALYSIS_BIOWASM=<ANALYSIS_BIOWASM> -e ANALYSIS_R=<ANALYSIS_R> -e DB_TYPE=<DB_TYPE> -e NCBI_API_KEY=<NCBI_API_KEY> -e S2_API_KEY=<S2_API_KEY> biomcp-ts npx -y biomcpReplace <…> with your own values. 3 more environment variables are in the server README
Step by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about BioMCP-TS
How do I install BioMCP-TS in Claude Code?
Run `claude mcp add biomcp-ts -e NCBI_API_KEY=<NCBI_API_KEY> -e S2_API_KEY=<S2_API_KEY> -e OPENFDA_API_KEY=<OPENFDA_API_KEY> -e ONCOKB_TOKEN=<ONCOKB_TOKEN> -e DISGENET_API_KEY=<DISGENET_API_KEY> -- npx -y biomcp`.
What is BioMCP-TS for?
It hands the agent lookup tools for genes, variants, drugs, diseases, clinical trials, articles and preprints, backed by a federation of many databases.
Does it need API keys?
For some tools, yes. OncoKB annotation requires ONCOKB_TOKEN; other keys are passed as environment variables when you register the server.
