BioMCP-TS

Install

npx -y [email protected]

5 secret configuration fields are declared. Names and values are omitted here.

Client fit

Inferred for Cursor, Claude, Codex. Basis: stdio. This is not a certification from those products.

Transports: stdio.

Links

• Repository
• Project site
• npm package biomcp
• Registry record

Other

Audit report

Audited by AddonAudit.

Sandbox handshake completed and the published checks passed.

Automated smoke test, not a security guarantee.

Version

1.4.3

Audited

24 Oct 2026

Package

npm biomcp

Advisories

0 critical, 0 high, 0 medium, 0 low

Time to ready

477 ms

Network

Disabled

• Pass Version. Pinned npm [email protected]
• Pass Known vulnerabilities. No critical, high, or medium advisories were returned.
• Pass License. Apache-2.0
• Pass Install scripts. No preinstall, install, postinstall, or prepare script.
• Pass Credential patterns. No credential patterns in the published artifact.
• Pass Package size. 801.7 KB
• Pass Maintainer activity. Active 0 days ago.
• Pass Sandbox. MCP handshake completed. 41 tools listed.

Tools

• gene_search Search for genes by symbol, name, or keyword
• gene_get Get detailed gene information by symbol
• gene_diseases Get diseases associated with a gene. Requires DISGENET_API_KEY environment variable for DisGeNET data; falls back to OpenTargets gene-disease associations when unavailable.
• gene_drugs Find drugs targeting a gene
• gene_trials Find clinical trials for a gene
• gene_articles Find articles about a gene
• gene_enrich Perform pathway enrichment analysis for a gene list
• variant_search Search for variants. Use structured parameters for best results: - rsid: e.g. query="rs113488022" - HGVS: e.g. query="NM_004333.4:c.1799T>A" - Gene filter: e.g. gene="BRAF" with hgvsp="V600E" or consequence="missense" - ClinVar significance
• variant_get Get detailed variant information with optional sections. Core data (id, gene, rsid, significance) is always returned at the top level. Use sections to request additional data.
• variant_oncokb Get OncoKB annotations for a variant in a cancer gene. Requires ONCOKB_TOKEN environment variable.
• variant_trials Find clinical trials for a variant
• drug_search Search for drugs by name, mechanism, or keyword
• drug_get Get detailed drug information by name
• drug_trials Find clinical trials for a drug
• disease_search Search for diseases by name, phenotype, or keyword
• disease_get Get detailed disease information by ID
• disease_drugs Get drugs for a disease via OpenTargets
• disease_trials Get clinical trials for a disease
• article_search Search literature across multiple backends with federated search and deduplication
• article_get Get article by PMID/PMCID/DOI. Citation: fast mode (~4s, 4 providers, auto-fallback to PubMed) or full mode (~15-30s, all 5 providers incl. PubMed). Forward citation lists come from Europe PMC, Semantic Scholar, and OpenCitations; Crossref
• trial_search Search clinical trials by condition, intervention, or keyword
• trial_get Get detailed trial information by NCT ID
• discover Free-text concept resolution - find entities matching a free-text query
• batch_get Get multiple entities in parallel
• pdb Access the Protein Data Bank (RCSB PDB) for macromolecular structure data. SEARCH: Provide "query" to find structures (e.g., "kinase inhibitor", "hemoglobin"). GET: Provide "pdb_id" to retrieve entry metadata with optional detail secti
• patent_search Search patents worldwide (US, EP, WO, JP, and 100+ authorities). Quote exact multi-word concepts (e.g. "mRNA display") to avoid off-topic matches. Backend characters: ppubs = USPTO Public Search full-text conceptual search (US only, keyless
• patent_get Get patent details by publication number (e.g. "US11027025B2", "EP3904939B1", "US20260240819A1"). Sections: abstract, claims (US fulltext via USPTO Public Search; EP/WO via EPO OPS), citations (backward + forward), family, classifications.
• geo_search Search NCBI GEO (Gene Expression Omnibus) for functional genomics studies — expression microarrays, RNA-seq, and other high-throughput sequencing series. Queries accept plain terms ("breast cancer RNA-seq", "melanoma single cell") or NCBI
• geo_get Get the full SOFT record details for a GEO entry: series (GSE...), sample (GSM...), or platform (GPL...). A series detail includes summary, organisms, platform_ids, a sample preview, supplementary file URLs, and cross-references for chaini
• sra_search Search NCBI's Sequence Read Archive (SRA) for sequencing experiments and runs. The query may be free text, an accession (SRP study, SRX experiment, SRR run, SRS sample), or NCBI field syntax ("RNA-SEQ AND Homo sapiens[Organism]"). Results
• sra_get Get full details for an NCBI SRA accession: SRR run (instrument, spots, bases, size), SRX experiment (library design), SRP study (experiment list), or SRS sample. Chain from geo_get (sra field) or sra_search (experiment_accession / first_r
• genbank_search Search NCBI nucleotide records (GenBank/RefSeq/INSDC). Queries may be plain terms, an accession, or NCBI field syntax ("TP53[Gene Name] AND Homo sapiens[Organism]", "BRCA1[Gene Name]"). Results include accession.version, definition, length
• genbank_get Fetch a GenBank/RefSeq nucleotide record as text (GenBank flat file or FASTA). Whole-record fetches are capped at 2,000,000 bp — larger records require a seq_start/seq_stop region (1-based, inclusive, up to 10 Mb span; set strand=2 for a r
• genbank_genes Map a GenBank/RefSeq nucleotide accession to its NCBI Gene IDs (elink nuccore→gene). The returned gene_ids are entrezgene IDs usable directly with MyGene-backed gene tools (gene_get, gene_search). Useful bridge from a sequence record to ge
• gtex_expression Get median gene expression across GTEx tissues (GTEx Analysis v10, 54 tissue sites, TPM, sorted highest first). Accepts an HGNC symbol (TP53) or Ensembl gene ID (ENSG00000141510, versioned or bare). Optionally filter to a single tissue via
• gtex_eqtl Get significant cis-eQTL associations for a gene in a specific GTEx tissue (GTEx Analysis v10): variant_id, p_value, and NES (effect direction/size), sorted by ascending p-value. tissue is a required GTEx tissueSiteDetailId (e.g. Whole_Blo
• ensembl_lookup Resolve a gene in Ensembl terms for ANY Ensembl species (356 available): stable ID (ENSG…), symbol↔ID mapping, versioned identifier, canonical transcript, and coordinates on the current assembly (GRCh38 human, GRCm39 mouse, …). With expand=
• ensembl_homology Find orthologues or paralogues of a gene across species (Ensembl Compara) — the cross-species gene mapping source in biomcp. Returns target stable IDs, species, taxonomy level, and percent identity, sorted by identity. Accepts an HGNC symb
• ensembl_consequence Predict the functional consequence of a variant on demand via Ensembl VEP — works even for NOVEL variants absent from every database, and for non-human species. Input forms: HGVS c./p./g. notation ("NM_004333:c.1799T>A", "ENST00000288602:c
• ensembl_region Query what lives in a genomic interval on the current assembly (GRCh38 for human): genes/transcripts (stable IDs, symbols, biotypes) and known variants (rsIDs, alleles, consequence terms, clinical significance). Ideal for locus triage — "w
• biomcp_configure Inspect and configure biomcp — unified observability and restricted controllability for every parameter. **What it covers:** three optional feature groups (database, analysis_r, analysis_biowasm) whose knobs live in the .biomcp.json projec

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Metadata checks

• Repository activity: Active in the last 180 days
• License: Recognized SPDX id
• Metadata quality: High

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