Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.
Connect Runs on your machine
claude mcp add biomcp-ts -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> -e OPENFDA_API_KEY=<OPENFDA_API_KEY> -e ONCOKB_TOKEN=<ONCOKB_TOKEN> -e DISGENET_API_KEY=<DISGENET_API_KEY> -- npx -y [email protected]{
"mcpServers": {
"biomcp-ts": {
"command": "npx",
"args": [
"-y",
"[email protected]"
],
"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>",
"OPENFDA_API_KEY": "<OPENFDA_API_KEY>",
"ONCOKB_TOKEN": "<ONCOKB_TOKEN>",
"DISGENET_API_KEY": "<DISGENET_API_KEY>"
}
}
}
}{
"mcpServers": {
"biomcp-ts": {
"command": "npx",
"args": [
"-y",
"[email protected]"
],
"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>",
"OPENFDA_API_KEY": "<OPENFDA_API_KEY>",
"ONCOKB_TOKEN": "<ONCOKB_TOKEN>",
"DISGENET_API_KEY": "<DISGENET_API_KEY>"
}
}
}
}{
"servers": {
"biomcp-ts": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"[email protected]"
],
"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>",
"OPENFDA_API_KEY": "<OPENFDA_API_KEY>",
"ONCOKB_TOKEN": "<ONCOKB_TOKEN>",
"DISGENET_API_KEY": "<DISGENET_API_KEY>"
}
}
}
}Replace the values in angle brackets with your own. Keys stay on your machine; we never see them.
Tools
This server runs locally, so its tools are listed by your MCP client once it starts.
Environment variables
| Name | Description |
|---|---|
ANALYSIS_BIOWASMOptional | Set to 1 to enable the samtools/bedtools/bcftools biowasm analysis tools |
ANALYSIS_ROptional | Set to 1 to enable the R/Bioconductor analysis tools (requires the webr peer dependency; use the pinned one-shot client command) |
DB_TYPEOptional | Set to mysql or sqlite to enable the read-only SQL database tools |
NCBI_API_KEYOptional, secret | Higher NCBI E-utilities rate limits (3 -> 10 req/s) |
S2_API_KEYOptional, secret | Higher Semantic Scholar rate limits |
OPENFDA_API_KEYOptional, secret | Higher OpenFDA rate limits |
ONCOKB_TOKENOptional, secret | Required by the variant_oncokb tool (OncoKB annotations) |
DISGENET_API_KEYOptional, secret | Required for DisGeNET disease-gene associations |
Details
| Package | [email protected] (NPM, stdio) |
| First published | 14 Sep 2026 |
| Last updated | 14 Sep 2026 |
| Registry name | io.github.yeyuan98/biomcp-ts |
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