biomcp

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

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.

Multiple agents on one machine: biomcp enforces arXiv's Terms-of-Use rate limit (1 request / 3 s) per process. When running multiple biomcp MCP instances on one machine (e.g., one stdio instance per agent), rate limits are not coordinated across processes, and arXiv's TOU applies to all your machines in aggregate. For multi-agent single-machine deployments, run a single shared biomcp serve daemon (see docs/SELF-HOSTING.md) so all agents share one process and one global rate limiter.

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, arXiv, PubTator, and LitSense with optional date range filtering; source: "preprint_only" switches to bioRxiv+medRxiv preprints only (abstracts, citation counts, date filtering)
article_get	Get detailed article info by identifier (PMID, PMCID, DOI, or bioRxiv/medRxiv preprint DOI) with optional sections: oa (open access / license info), annotations, graph (citation graph), citation (fast/full citation data; Europe PMC citations for preprints). Preprint records include all versions, license, category, funders, JATS full-text URL, and published-version mapping

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)

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; slow links: asset_timeout_ms or a self-fetched mirror_url)	Set ANALYSIS_R=1; needs the webr peer dep — use the pinned one-shot client command ["npx","-y","-p","biomcp@1.5","-p","webr@0.6","biomcp"] (all-features variant adds -p mysql2@3); 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.