Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.
Quick Install
Automated & IDE SetupCopy the AI prompt to install this server into Claude Code, Cursor, or another agent — or use 1-click editor setup below.
Manual Client & Custom JSON ConfigExpand JSON ▾
Client Config & Setup
Choose your client or environment
Target File:
💡 Paste the JSON block into your client's configuration file under mcpServers, then restart the application.
Documentation Overview
BioMCP
Highlights
Democratizing agentic access to bioinformatics and biopharmaceutical databases and analyses.
- Section-based federated access to 50+ bioinformatics, pharmaceutical, and patent databases
- Optional toolboxes for local database curation and dependency-free analysis with Bioconductor and SAM/BED/BCFtools — no R installation, C toolchain, or containers
- Concrete example vignettes, developed fully in the open
Install
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, adverse_events — FDA FAERS reactions ranked by report count) |
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 |
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)
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CategoryDatabases
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