The MCP server: biomcp-ts

biomcp-ts (npm package biomcp, pinned 1.1.1) is an MCP server for biomedical data: 41 core + 15 optional tools over stdio JSON-RPC, spanning articles, trials, genes, variants, drugs, diseases, patents, omics databases, GTEx and Ensembl/PDB — keyless by default, rate-limited in-process.

GitHub ↗ npm ↗

Tool catalog (41 + 15)

Core tools · 41
articles	`article_search` `article_get`
genes	`gene_search` `gene_get` `gene_diseases` `gene_drugs` `gene_trials` `gene_articles` `gene_enrich`
variants	`variant_search` `variant_get` `variant_oncokb` `variant_trials`
drugs	`drug_search` `drug_get` `drug_trials`
diseases	`disease_search` `disease_get` `disease_drugs` `disease_trials`
clinical trials	`trial_search` `trial_get`
patents	`patent_search` `patent_get`
omics databases	`geo_search` `geo_get` `sra_search` `sra_get` `genbank_search` `genbank_get` `genbank_genes`
GTEx	`gtex_expression` `gtex_eqtl`
Ensembl/PDB	`ensembl_lookup` `ensembl_homology` `ensembl_consequence` `ensembl_region` `pdb`
utility	`discover` `batch_get` `biomcp_configure`
Optional tools · 15 (env-gated, register at server start)
SQL database (mysql2)	`db_query` `db_list_tables` `db_describe_table`
R analysis (webR)	`analysis_r_deseq2` `analysis_r_edger` `analysis_r_limma` `analysis_r_session_info`
Biowasm (SAM/BCF/BED)	`analysis_bam_summary` `analysis_bam_view_region` `analysis_bcf_summary` `analysis_bcf_view_region` `analysis_bed_op` `analysis_biowasm_convert` `analysis_biowasm_session_info` `analysis_biowasm_cli`

Wiring (opencode)

With the server named biomcp, tools surface as biomcp_article_search, biomcp_gene_get, … Exact version pinning via -p is mandatory (bare npx biomcp cannot resolve peer deps).

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": { "biomcp": { "type": "local",
    "command": ["npx", "-y", "-p", "biomcp@1.1.1", "biomcp"] } }
}

Full wiring matrix (Claude Code, Codex, Cursor, …)

True captures

Real request/response pairs captured by a deterministic stdio probe — not hand-written examples.

`variant_search`

Structured variant query: gene + protein change (never compound free text like "BRAF V600E").

Request

{
  "gene": "BRAF",
  "hgvsp": "V600E",
  "limit": 3
}

Response (excerpt, as captured)

[{"id":"rs113488022","gene":"BRAF","hgvs_p":"V600E","hgvs_c":"c.1799T>A","significance":"Pathogenic","gnomad_af":0.00000397994}]

`article_search`

Federated PubMed search (Europe PMC / Semantic Scholar / PubTator / LitSense); returns PMIDs + titles.

Request

{
  "query": "BRCA1 DNA repair",
  "limit": 3
}

Response (excerpt, as captured)

[{"doi": "10.1042/BJ20141077", "title": "Protein stability versus function: effects of destabilizing missense mutations on BRCA1 DNA repair activity.", "authors": ["David C. A. Gaboriau", "P. Rowling", "C. Morrison", "L. Itzhaki"], "journal": "Biochemical Journa…

`gene_get`

Gene detail by HGNC symbol with section filtering (16 section values incl. all).

Request

{
  "symbol": "BRCA1",
  "sections": [
    "core"
  ]
}

Response (excerpt, as captured)

{"symbol": "BRCA1", "name": "BRCA1 DNA repair associated", "summary": "This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability…

Full tours: MCP tool tour — true request/response pairs from 8 core tools · MCP tool tour — the BRAF V600E variant-to-trials chain (zh notes) — complete server documentation: MCP doc