BioMCP

One binary. One grammar. Evidence from the biomedical sources you already trust.

Description

BioMCP cuts through the usual biomedical data maze: one query reaches the sources that normally live behind different APIs, identifiers, and search habits. Researchers, clinicians, and agents use the same command grammar to search, focus, and pivot without rebuilding the workflow for each source. You get compact, evidence-oriented results across live public data plus local study analytics.

Features

• Search the literature: search article fans out across PubTator3 and Europe PMC, deduplicates PMID/PMCID/DOI identifiers, and can add a Semantic Scholar leg when your filters support it.
• Pivot without rework: move from a gene, variant, drug, disease, pathway, protein, or article straight into the next built-in view instead of rebuilding filters by hand.
• Analyze studies locally: study commands cover local query, cohort, survival, compare, and co-occurrence workflows with native terminal, SVG, and PNG charts for downloaded cBioPortal-style datasets.
• Follow the paper trail: article citations, article references, article recommendations, and article entities turn one known paper into a broader evidence map.
• Enrich and batch: use biomcp enrich for top-level g:Profiler enrichment and biomcp batch for up to 10 focused get calls in one command.

Installation

PyPI tool install

uv tool install biomcp-cli
# or: pip install biomcp-cli

This installs the biomcp binary on your PATH.

Binary install

curl -fsSL https://biomcp.org/install.sh | bash

Claude Desktop extension (.mcpb)

Install BioMCP from the Anthropic Directory in Claude Desktop when that path is available for your environment. For local/manual setups, use the JSON MCP config below.

Install skills

Install guided investigation workflows into your agent directory:

biomcp skill install ~/.claude --force

MCP clients

{
  "mcpServers": {
    "biomcp": {
      "command": "biomcp",
      "args": ["serve"]
    }
  }
}

Remote HTTP server

For shared or remote deployments:

biomcp serve-http --host 127.0.0.1 --port 8080

Remote clients connect to http://127.0.0.1:8080/mcp. Probe routes are GET /health, GET /readyz, and GET /.

Runnable demo:

uv run --script examples/streamable-http/streamable_http_client.py

See Remote HTTP Server for the newcomer guide.

From source

make install
"$HOME/.local/bin/biomcp" --version

Quick start

First useful query in under 30 seconds:

uv tool install biomcp-cli
biomcp health --apis-only
biomcp list gene
biomcp search all --gene BRAF --disease melanoma  # unified cross-entity discovery
biomcp get gene BRAF pathways hpa

Command grammar

search <entity> [filters]    → discovery
discover <query>             → concept resolution before entity selection
get <entity> <id> [sections] → focused detail
<entity> <helper> <id>       → cross-entity pivots
enrich <GENE1,GENE2,...>     → gene-set enrichment
batch <entity> <id1,id2,...> → parallel gets
search all [slot filters]    → counts-first cross-entity orientation

Entities and sources

| Entity | Upstream providers used by BioMCP | Example | |--------|-----------------------------------|---------| | gene | MyGene.info, UniProt, Reactome, QuickGO, STRING, GTEx, Human Protein Atlas, DGIdb, ClinGen | biomcp get gene BRAF pathways hpa | | variant | MyVariant.info, ClinVar, gnomAD fields via MyVariant, CIViC, Cancer Genome Interpreter, OncoKB, cBioPortal, GWAS Catalog, AlphaGenome | biomcp get variant "BRAF V600E" clinvar | | article | PubMed, PubTator3, Europe PMC, PMC OA, NCBI ID Converter, Semantic Scholar (optional auth; S2_API_KEY recommended) | biomcp search article -g BRAF --limit 5 | | trial | ClinicalTrials.gov API v2, NCI CTS API | biomcp search trial -c melanoma -s recruiting | | drug | MyChem.info, EMA local batch, ChEMBL, OpenTargets, Drugs@FDA, OpenFDA, CIViC | biomcp get drug Keytruda regulatory --region eu | | disease | MyDisease.info, Monarch Initiative, MONDO, OpenTargets, Reactome, CIViC | biomcp get disease "Lynch syndrome" genes | | pathway | Reactome, KEGG, g:Profiler, Enrichr-backed enrichment sections | biomcp get pathway hsa05200 genes | | protein | UniProt, InterPro, STRING, ComplexPortal, PDB, AlphaFold | biomcp get protein P15056 complexes | | adverse-event | OpenFDA FAERS, MAUDE, Recalls | biomcp search adverse-event --drug pembrolizumab | | pgx | CPIC, PharmGKB | biomcp get pgx CYP2D6 recommendations | | gwas | GWAS Catalog | biomcp search gwas --trait "type 2 diabetes" | | phenotype | Monarch Initiative (HPO semantic similarity) | biomcp search phenotype "HP:0001250" |

Cross-entity helpers

Pivot between related entities without rebuilding filters.

See the cross-entity pivot guide for when to use a helper versus a fresh search.

biomcp variant trials "BRAF V600E" --limit 5
biomcp variant articles "BRAF V600E"
biomcp drug adverse-events pembrolizumab
biomcp drug trials pembrolizumab
biomcp disease trials melanoma
biomcp disease drugs melanoma
biomcp disease articles "Lynch syndrome"
biomcp gene trials BRAF
biomcp gene drugs BRAF
biomcp gene articles BRCA1
biomcp gene pathways BRAF
biomcp pathway drugs R-HSA-5673001
biomcp pathway drugs hsa05200
biomcp pathway articles R-HSA-5673001
biomcp pathway trials R-HSA-5673001
biomcp protein structures P15056
biomcp article entities 22663011
biomcp article citations 22663011 --limit 3
biomcp article references 22663011 --limit 3
biomcp article recommendations 22663011 --limit 3

Gene-set enrichment

biomcp enrich BRAF,KRAS,NRAS --limit 10

Top-level biomcp enrich uses g:Profiler. Gene enrichment sections inside other entity views still reference Enrichr where that is the backing source.

Sections and progressive disclosure

Every get command supports selectable sections for focused output:

biomcp get gene BRAF                    # summary card
biomcp get gene BRAF pathways           # add pathway section
biomcp get gene BRAF hpa                # protein tissue expression + localization
biomcp get gene BRAF civic interactions # multiple sections
biomcp get gene BRAF all                # everything

biomcp get variant "BRAF V600E" clinvar population conservation
biomcp get article 22663011 tldr
biomcp get drug pembrolizumab label targets civic approvals
biomcp get drug Keytruda regulatory --region eu
biomcp get disease "Lynch syndrome" genes phenotypes variants
biomcp get trial NCT02576665 eligibility locations outcomes

In JSON mode, get responses expose _meta.next_commands for the next likely follow-ups and _meta.section_sources for section-level provenance. batch ... --json returns per-entity objects with the same metadata shape.

API keys

Most commands work without credentials. Optional keys improve rate limits or unlock optional enrichments:

export NCBI_API_KEY="..."        # PubTator, PMC OA, NCBI ID converter
export S2_API_KEY="..."          # Optional Semantic Scholar auth; dedicated quota at 1 req/sec
export OPENFDA_API_KEY="..."     # OpenFDA rate limits
export NCI_API_KEY="..."         # NCI CTS trial search (--source nci)
export ONCOKB_TOKEN="..."        # OncoKB variant helper
export ALPHAGENOME_API_KEY="..." # AlphaGenome variant effect prediction

search article, get article, article batch, get article ... tldr, and the explicit Semantic Scholar helpers all work without S2_API_KEY. With the key, BioMCP sends authenticated requests and uses a dedicated rate limit at 1 req/sec. Without it, BioMCP uses the shared unauthenticated pool at 1 req/2sec. search article --source supports all, pubtator, europepmc, and pubmed. The default compatible article federation uses PubTator3, Europe PMC, and PubMed, while the S2 leg remains automatic rather than directly selectable. References and recommendations can be empty for paywalled papers because of publisher elision in Semantic Scholar upstream coverage.

Configuration

Claude Desktop extension settings

The directory bundle exposes only the optional settings needed for the first reviewer-facing build:

| Claude Desktop field | Runtime env var | Purpose | |----------------------|-----------------|---------| | OncoKB Token | ONCOKB_TOKEN | Enables biomcp variant oncokb "<gene> <variant>" therapy and level evidence | | DisGeNET API Key | DISGENET_API_KEY | Enables scored DisGeNET sections on gene and disease lookups | | Semantic Scholar API Key | S2_API_KEY | Improves reliability for article TLDR, citation, reference, and recommendation helpers |

The first directory build exposes only those three optional settings. Advanced CLI-only env vars remain documented in API Keys for the general BioMCP CLI path.

Usage Examples

Public cross-entity overview

User prompt: Give me a low-noise overview of BRAF in melanoma.

Expected tool call: biomcp search all --gene BRAF --disease melanoma --counts-only

Expected behavior: Returns a cross-entity counts summary that orients the next command instead of dumping long detail tables.

Expected output: Counts-first summary with suggested next commands for the highest-yield entity follow-ups.

Public variant evidence

User prompt: Summarize ClinVar significance and population frequency for BRAF V600E.

Expected tool call: biomcp get variant "BRAF V600E" clinvar population

Expected behavior: Retrieves the focused variant card, ClinVar section, and population-frequency data in one read-only call.

Expected output: Variant summary, ClinVar significance details, and gnomAD population frequencies.

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