MCP 服务器：biomcp-ts

biomcp-ts（npm 包 biomcp，钉扎 1.4.0）是生物医学数据 MCP 服务器：41 个核心 + 15 个可选工具，stdio JSON-RPC 传输，覆盖文献、临床试验、基因、变异、药物、疾病、专利、组学数据库、GTEx 与 Ensembl/PDB——默认免密钥，服务内建限流。

GitHub ↗ npm ↗

工具目录 (41 + 15)

核心工具 · 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`
可选工具 · 15 (环境变量门控，随服务器启动注册)
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`

接线示例（opencode）

服务器命名 biomcp 时，工具显示为 biomcp_article_search、biomcp_gene_get 等。必须用 -p 精确钉扎版本（裸 npx biomcp 无法解析 peer 依赖）。

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": { "biomcp": { "type": "local",
    "command": ["npx", "-y", "-p", "biomcp@1.4.0", "biomcp"] } }
}

完整接线矩阵（Claude Code、Codex、Cursor 等）

真实调用样本

由确定性 stdio 探针捕获的真实请求/响应对——非手写示例。

`variant_search`

结构化变异检索：gene + 蛋白变化（切勿使用 “BRAF V600E” 这类复合自由文本）。

请求

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

响应（节选，捕获原文）

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

`article_search`

PubMed 联邦检索（Europe PMC / Semantic Scholar / PubTator / LitSense）；1.4.0 响应自带完整引用定位字段（卷/期/页码）。

请求

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

响应（节选，捕获原文）

[{"pmid": "37272060", "doi": "10.1080/15476286.2023.2220210", "title": "Hybrid-seq deciphers the complex transcriptional profile of the human BRCA1 DNA repair associated gene.", "authors": ["Adamopoulos PG", "Athanasopoulou K", "…"], "journal": "RNA Biol", "volume": "20", "issue": "1", "pages": "281-295", "publication_date": "2023-01-01", "cited_by": 4, "source": "europepmc"}]

`gene_get`

按 HGNC 符号查询基因详情，可按 section 裁剪（16 个可选值，含 all）。

请求

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

响应（节选，捕获原文）

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

完整巡览： MCP tool tour — true request/response pairs from 8 core tools · MCP tool tour — the BRAF V600E variant-to-trials chain (zh notes) — 完整服务器文档： MCP 文档