How do I install Biomcp Ts?

Biomcp Ts is a local plugin. Install it using npm package: biomcp and add the generated configuration snippet to your AI app's MCP config file. Then restart your AI app.

Is Biomcp Ts safe to use?

Biomcp Ts scored 6/10 (moderate risk) in MCP Marketplace's automated security scan. It has 1 high or critical finding to review. It's listed, but review the security report on this page before installing.

What credentials does Biomcp Ts need?

Biomcp Ts requires the following credentials or environment variables: ANALYSIS_BIOWASM, ANALYSIS_R, DB_TYPE, NCBI_API_KEY, S2_API_KEY, OPENFDA_API_KEY, ONCOKB_TOKEN, DISGENET_API_KEY. You can find setup instructions on the server detail page.

What AI apps work with Biomcp Ts?

Biomcp Ts uses the Model Context Protocol (MCP) and works with any MCP-compatible AI app, including Claude, ChatGPT / Codex, Gemini, Copilot, Cursor, and more.

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Biomcp Ts MCP Server

by Yeyuan98

Developer ToolsModerate6.0MCP RegistryLocal

Free

Server data from the Official MCP Registry

Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.

About

Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.

Security Report

6.0

Moderate6.0Moderate Risk

BioMCP is a well-engineered TypeScript MCP server for biomedical data access with comprehensive test coverage and generally sound authentication practices. However, the server has moderate-severity findings around overly broad environment variable access, some input validation gaps in optional features, and potential credential exposure vectors in the R analysis module. Permissions are appropriate for the stated purpose of federated biomedical API access, but the optional analysis features require careful security consideration. Supply chain analysis found 2 known vulnerabilities in dependencies (0 critical, 1 high severity). Package verification found 1 issue.

3 files analyzed · 11 issues found

Security scores are indicators to help you make informed decisions, not guarantees. Always review permissions before connecting any MCP server.

Permissions Required

This plugin requests these system permissions. Most are normal for its category.

env_vars

Check that this permission is expected for this type of plugin.

HTTP Network Access

Connects to external APIs or services over the internet.

File System Read

Reads files on your machine. Normal for tools that analyze or process local data.

File System Write

Writes or modifies files on your machine. Check that this is expected for the tool.

database

Check that this permission is expected for this type of plugin.

process_spawn

Check that this permission is expected for this type of plugin.

What You'll Need

Set these up before or after installing:

Set to 1 to enable the samtools/bedtools/bcftools biowasm analysis toolsOptional

Environment variable: ANALYSIS_BIOWASM

Set to 1 to enable the R/Bioconductor analysis tools (requires the webr peer dependency; use the pinned one-shot client command)Optional

Environment variable: ANALYSIS_R

Set to mysql or sqlite to enable the read-only SQL database toolsOptional

Environment variable: DB_TYPE

Higher NCBI E-utilities rate limits (3 -> 10 req/s)Required

Environment variable: NCBI_API_KEY

Higher Semantic Scholar rate limitsRequired

Environment variable: S2_API_KEY

Higher OpenFDA rate limitsRequired

Environment variable: OPENFDA_API_KEY

Required by the variant_oncokb tool (OncoKB annotations)Required

Environment variable: ONCOKB_TOKEN

Required for DisGeNET disease-gene associationsRequired

Environment variable: DISGENET_API_KEY

How to Install

Add this to your MCP configuration file:

{
  "mcpServers": {
    "io-github-yeyuan98-biomcp-ts": {
      "env": {
        "DB_TYPE": "your-db-type-here",
        "ANALYSIS_R": "your-analysis-r-here",
        "S2_API_KEY": "your-s2-api-key-here",
        "NCBI_API_KEY": "your-ncbi-api-key-here",
        "ONCOKB_TOKEN": "your-oncokb-token-here",
        "OPENFDA_API_KEY": "your-openfda-api-key-here",
        "ANALYSIS_BIOWASM": "your-analysis-biowasm-here",
        "DISGENET_API_KEY": "your-disgenet-api-key-here"
      },
      "args": [
        "-y",
        "biomcp"
      ],
      "command": "npx"
    }
  }
}

Documentation

View on GitHub

From the project's GitHub README.

BioMCP

A high-performance MCP server that gives LLMs access to 40 biomedical tools federated across 50+ upstream APIs — genes, variants, drugs, diseases, literature, clinical trials, structural biology, and functional genomics in a single integration.

Note: this is BioMCP-TS, the TypeScript server published as npm package biomcp. It is distinct from the Python/Rust BioMCP by genomoncology — CLI flags like biomcp run / --biowasm do not exist here; optional features are enabled with environment variables or the .biomcp.json config file.

Highlights

41 tools across 15 registration modules — search, retrieve, and cross-reference biomedical entities, plus the biomcp_configure meta tool for configuration observability (+3 optional database tools, +4 optional R analysis tools, +8 optional biowasm analysis tools)
50+ upstream sources — MyGene, MyVariant, MyChem, MyDisease, ClinVar, gnomAD, UniProt, Reactome, OpenTargets, CIViC, OncoKB, DisGeNET, GTEx, STRING, DGIdb, ClinicalTrials.gov, PubMed, EuropePMC, Semantic Scholar, PubTator, LitSense, Monarch Initiative, OpenFDA, NIH Reporter, NCBI GEO, SRA, GenBank, Ensembl, and more
Functional genomics & sequences — GEO series/sample search with SOFT detail parsing, SRA experiment/run metadata, GenBank/RefSeq records with region slices, and GTEx v10 median expression + cis-eQTLs
Section-based fetching — entityGet(id, sections) fans out to multiple sources with per-section timeouts and graceful degradation (failed sections return { _error } instead of crashing)
Federated article search — queries 5 literature backends simultaneously with PMID/PMCID/DOI deduplication
Patent access — worldwide patent search and detail via keyed EPO OPS / USPTO ODP; keyless USPTO Public Search and Google Patents (+Wayback archive) fallbacks
Zero-config startup — works out of the box; optional API keys unlock higher rate limits and premium data
1234 unit tests (mocked, 74 suites) + integration tests across 19 files (live APIs via in-process MCP client, gated skips)

Install

npx -y biomcp doctor   # diagnose a machine: Node gate, config health, feature gates, peer deps
npx biomcp             # zero-config stdio MCP server (this is what MCP clients run); Node >= 22.13

Setup is guided in docs/AGENT-INSTALL.md — a one-minute start, copy-paste config entries for Claude Desktop, Claude Code, Codex, and OpenCode (one canonical pinned command covering every feature), biomcp doctor as the single troubleshooting entry point, and agent-friendly paths for API keys and optional features.

Available Tools

Full tool schemas (params, enums, defaults) live in src/server/README.md.

Gene (7)

Tool	Description
`gene_search`	Search genes by symbol, name, or keyword with chromosome filter
`gene_get`	Get detailed gene info by HGNC symbol with optional sections (core, pathways, protein, ontology, go, interactions, expression, protein_atlas, constraint, druggability, dosage_sensitivity, clinical_evidence, disease_associations, diseases, funding). Set `smart=true` to auto-resolve gene aliases (e.g., "HER2" → "ERBB2")
`gene_diseases`	Get diseases associated with a gene (DisGeNET / OpenTargets)
`gene_drugs`	Find drugs targeting a gene (OpenTargets)
`gene_trials`	Find clinical trials for a gene
`gene_articles`	Find articles about a gene
`gene_enrich`	Pathway enrichment analysis for a gene list (Reactome)

Variant (4)

Tool	Description
`variant_search`	Search variants by rsid, HGVS, gene, ClinVar significance, frequency, CADD
`variant_get`	Get detailed variant info with optional sections (frequency, predictions, clinical; `alphagenome_scores` currently returns an unavailability error pending reimplementation)
`variant_oncokb`	Get OncoKB cancer variant annotations (requires `ONCOKB_TOKEN`)
`variant_trials`	Find clinical trials for a variant

Drug (3)

Tool	Description
`drug_search`	Search drugs by name, mechanism, or keyword
`drug_get`	Get detailed drug info with optional sections (us_regulatory, eu_regulatory, who_regulatory, safety, targets, indications)
`drug_trials`	Find clinical trials for a drug

Disease (4)

Tool	Description
`disease_search`	Search diseases by name, phenotype, or keyword
`disease_get`	Get detailed disease info by ID (DOID, MONDO, OMIM, etc.) with optional sections (gene_associations, phenotypes, pathways)
`disease_drugs`	Get drugs for a disease (OpenTargets)
`disease_trials`	Get clinical trials for a disease (ClinicalTrials.gov)

Article (2)

Tool	Description
`article_search`	Federated literature search across PubMed, EuropePMC, Semantic Scholar, PubTator, and LitSense with optional date range filtering
`article_get`	Get detailed article info by identifier (PMID, PMCID, or DOI) with optional sections: `oa` (open access / license info), `annotations`, `graph` (citation graph), `citation` (fast/full citation data)

Trial (2)

Tool	Description
`trial_search`	Search clinical trials by condition, intervention, status, or phase. Cursor-based pagination via `page_token`
`trial_get`	Get detailed trial info by NCT ID with optional sections (eligibility, locations, outcomes)

Utility (2)

Tool	Description
`discover`	Free-text concept resolution across all entity types
`batch_get`	Retrieve multiple entities in parallel

Structural Biology (1)

Tool	Description
`pdb`	Search PDB structures, get entry metadata with optional sections (polymer entities, ligands, assembly, experiment, citation), and download structure files (mmCIF/PDB)

Patents (2)

Tool Description

patent_search Search patents worldwide (US, EP, WO, JP, 100+ authorities) with assignee/inventor/CPC/status/date filters and relevance ranking (sort_by). Quote exact multi-word concepts (e.g. "mRNA display"). Foundational prior art is auto-discovered via co-citation mining (seminal_prior_art; disable with seminal: false). Default backends: USPTO Public Search full-text (US, keyless, relevance-ranked) + EPO OPS (worldwide, keyed); uspto_odp (US bibliographic metadata) and google_patents (best-effort) available via source

patent_get Get patent details by publication number with sections: abstract, claims (US fulltext via USPTO Public Search; EP/WO via EPO OPS), citations (forward + backward), family, classifications

Tool	Description
`patent_search`	Search patents worldwide (US, EP, WO, JP, 100+ authorities) with assignee/inventor/CPC/status/date filters and relevance ranking (`sort_by`). Quote exact multi-word concepts (e.g. "mRNA display"). Foundational prior art is auto-discovered via co-citation mining (`seminal_prior_art`; disable with `seminal: false`). Default backends: USPTO Public Search full-text (US, keyless, relevance-ranked) + EPO OPS (worldwide, keyed); uspto_odp (US bibliographic metadata) and google_patents (best-effort) available via `source`
`patent_get`	Get patent details by publication number with sections: abstract, claims (US fulltext via USPTO Public Search; EP/WO via EPO OPS), citations (forward + backward), family, classifications

GEO (2)

Tool	Description
`geo_search`	Search NCBI GEO for functional genomics studies (expression microarrays, RNA-seq, single-cell series) by entry type (GSE/GSM/GPL/GDS) and organism; results carry cross-links (sra_project, bioproject, pubmed_ids) for chaining
`geo_get`	Get the full SOFT record for a GEO series/sample/platform: summary, organisms, sample preview (≤20), supplementary file URLs, and cross-references; optionally download the first supplementary file

SRA (2)

Tool	Description
`sra_search`	Search NCBI's Sequence Read Archive for sequencing experiments and runs by free text, accession, or field syntax; returns experiment/study/sample accessions with library strategy and run counts
`sra_get`	Get full details for an SRA accession: SRR run (instrument, spots, bases, size), SRX experiment (library design), SRP study (experiment list), or SRS sample; ENA/DDBJ accessions rejected with an ENA pointer

GenBank (3)

Tool	Description
`genbank_search`	Search NCBI nucleotide records (GenBank/RefSeq/INSDC) by plain terms, accession, or field syntax; results include accession.version, definition, length, organism, topology
`genbank_get`	Fetch a GenBank/RefSeq record as GenBank flat file or FASTA; whole records capped at 2 Mb — larger records require a `seq_start`/`seq_stop` region (up to 10 Mb, reverse-strand via `strand=2`)
`genbank_genes`	Map a GenBank/RefSeq accession to its NCBI Gene IDs (elink nuccore→gene) for bridging into gene tools

GTEx (2)

Tool	Description
`gtex_expression`	Get median gene expression across GTEx tissues (Analysis v10, 54 tissue sites, TPM, highest first); accepts HGNC symbol or Ensembl gene ID, with optional single-tissue filter
`gtex_eqtl`	Get significant cis-eQTL associations for a gene in a specific GTEx tissue (v10): variant_id, p_value, NES, slope, sorted by ascending p-value

Ensembl (4)

Tool	Description
`ensembl_lookup`	Resolve a gene in Ensembl terms for any of ~356 species: stable ID (+version), symbol, coordinates on the current assembly, canonical transcript; `expand=true` adds transcripts with translation/protein IDs
`ensembl_homology`	Find orthologues/paralogues across species via Ensembl Compara — target stable IDs, taxonomy level, percent identity, sorted by identity; filter with `target_species`/`target_taxon`
`ensembl_consequence`	Compute variant consequences on demand via Ensembl VEP for NOVEL variants and non-human species: most severe consequence, per-transcript effects (SIFT/PolyPhen), co-located ClinVar/COSMIC/gnomAD data. Known human variants get deeper pre-computed scores via `variant_get`; prefer HGVS input over rsIDs for precision
`ensembl_region`	Query genes/transcripts/known variants in a genomic interval (`chr:start-end`) on the current assembly — locus triage

R Analysis (4, optional — `ANALYSIS_R=1`)

Tool	Description
`analysis_r_deseq2`	Differential expression for RNA-seq counts with Bioconductor DESeq2 (negative binomial, independent filtering, optional LFC shrinkage) in sandboxed WebAssembly R. Inputs: integer count matrix + sample metadata + design formula; output: markdown table of top genes by adjusted p-value with summary (`format="json"`, `include_full=true` for full base64(gzip(TSV)) table)
`analysis_r_edger`	Differential expression with edgeR — TMM normalization, empirical-Bayes dispersion, quasi-likelihood F-test (`test="qlm"`) or 2-group exact test; same input/output contract
`analysis_r_limma`	Differential expression with limma-voom — precision-weighted linear models with empirical-Bayes moderation; same input/output contract
`analysis_r_session_info`	R runtime report: R/webR versions, installed package versions, memory, mirror endpoint — for diagnosing analysis issues

First use starts a ~1 GB WebAssembly R worker and downloads the wasm package bundle (~62 MB) from GitHub releases (cached). Requires webr installed next to biomcp. Guide: docs/R-ANALYSIS.md.

Biowasm Analysis (8, optional — `ANALYSIS_BIOWASM=1`)

Tool	Description
`analysis_bam_summary`	Inspect an alignment (SAM/BAM/CRAM): header contigs, sample/read groups, flagstat mapping metrics, per-contig counts via idxstats when indexed — "what's in this BAM?" before region work
`analysis_bam_view_region`	Reads, depth, pileup, or read extraction in a genomic region (samtools view/depth/mpileup); indexed sources use fast positional retrieval, indexless sources stream a BED filter (depth requires coordinate-sorted input and detects order violations), returning counts, coverage tables, SAM rows, or a BAM artifact
`analysis_bcf_summary`	Inspect a VCF/BCF: contigs, sample count and names, INFO/FORMAT field inventory from the header
`analysis_bcf_view_region`	Variants in a region as a narrow field projection (bcftools query): chosen columns, sample subsets, expression filters, variant types — or a sliced VCF.gz artifact
`analysis_bed_op`	Interval algebra on BED tracks (bedtools intersect/merge/subtract/coverage/jaccard/sort) with the streaming `-sorted` algorithm for sorted inputs
`analysis_biowasm_convert`	Format plumbing: SAM/BAM/CRAM via samtools view, VCF/BCF via bcftools view, VCF/BCF → TSV via bcftools query; results are artifact handles reusable as `artifact_id`
`analysis_biowasm_session_info`	Biowasm runtime report: pinned tool versions, asset cache state, engine status, retained artifacts, memory
`analysis_biowasm_cli`	Constrained escape hatch: an allowlisted samtools/bedtools/bcftools subcommand with schema-validated args (no shell, paths under /shared only)

First use downloads checksum-verified wasm assets (~4.5 MB, cached); no extra npm packages. Indexed sources answer region queries with fast positional retrieval (~0.2 % of file read); indexless sources fall back to streaming BED filters. Guide: docs/BIOWASM-ANALYSIS.md.

Citation Module

Citations federate 5 providers in fast (~4s) or full (~15-30s) mode. Forward citation lists come from Europe PMC, OpenCitations, and Semantic Scholar; Crossref supplies counts and backward references. Provider matrix and schema details: src/server/README.md.

Optional Features

Capabilities that ship with the package but stay inactive until enabled. Each links to its own guide:

Feature	Enable	Guide
Database access — read-only SQL tools (`db_query`, `db_list_tables`, `db_describe_table`) for MySQL and local-file SQLite	Set `DB_TYPE` (+ connection env vars); MySQL needs the `mysql2` peer dep — use the pinned one-shot client command (see docs/DATABASE.md)	docs/DATABASE.md
R analysis — Bioconductor differential expression (`analysis_r_deseq2`, `analysis_r_edger`, `analysis_r_limma`, `analysis_r_session_info`) running DESeq2/edgeR/limma in sandboxed WebAssembly R; wasm packages download from GitHub releases at first use (~62 MB, cached)	Set `ANALYSIS_R=1`; needs the `webr` peer dep — use the pinned one-shot client command `["npx","-y","-p","biomcp@0.9","-p","webr@0.6","biomcp"]`; expect ~1 GB RSS	docs/R-ANALYSIS.md
Biowasm analysis — samtools/bedtools/bcftools (BAM/BED/VCF) in sandboxed WebAssembly; streams/indexes real human-scale datasets (~300 MB BAM scans, region queries touch ~0.2 % of the file); assets ~4.5 MB cached at first use; no extra npm packages	Set `ANALYSIS_BIOWASM=1`	docs/BIOWASM-ANALYSIS.md

Instead of hand-editing env blocks, agents (and users) can self-serve through the always-available biomcp_configure tool: it reports every parameter's status/provenance, writes the .biomcp.json project config file for the optional features above (env vars keep precedence; env-only parameters are query-only and value-masked), validates changes, detects conflicts, checks peer-dependency prerequisites, and spells out the restart/verify steps. Details: docs/ENV-VARS.md → Project config file.

Documentation

Doc	Contents
docs/AGENT-INSTALL.md	Guided installation & client configuration (Claude Desktop, Claude Code, Codex, OpenCode)
docs/ENV-VARS.md	Single source of truth for every environment variable
docs/DATABASE.md	Database access feature guide
docs/R-ANALYSIS.md	R analysis feature guide (Bioconductor in WebAssembly)
docs/BIOWASM-ANALYSIS.md	Biowasm analysis feature guide (samtools/bedtools/bcftools in WebAssembly)
docs/DEVELOPMENT.md	Build, test, publish workflow
docs/development/CI.md	CI pipeline, Dependabot automation, auto-merge safety model
src/server/README.md	Full tool schemas (params, enums, defaults)
agent-test/README.md	User-agent E2E tests for the analysis tools

License

Licensed under the Apache License, Version 2.0. See NOTICE for attributions.

BioMCP-TS is adapted from the upstream BioMCP Rust project (MIT) with an agent-first development approach and enhancements — kudos to the original authors.

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Biomcp Ts MCP Server

About

Security Report

Findings (11)Action required

Permissions Required

What You'll Need

How to Install

Documentation

BioMCP

Highlights

Install

Available Tools

Gene (7)

Variant (4)

Drug (3)

Disease (4)

Article (2)

Trial (2)

Utility (2)

Structural Biology (1)

Patents (2)

GEO (2)

SRA (2)

GenBank (3)

GTEx (2)

Ensembl (4)

R Analysis (4, optional — ANALYSIS_R=1)

Biowasm Analysis (8, optional — ANALYSIS_BIOWASM=1)

Citation Module

Optional Features

Documentation

License

Reviews

No reviews yet

More Developer Tools MCP Servers

Git

Fetch

Toleno

mcp-creator-python

MCP Marketplace

MarkItDown

R Analysis (4, optional — `ANALYSIS_R=1`)

Biowasm Analysis (8, optional — `ANALYSIS_BIOWASM=1`)