biomcp MCP — Cas d'usage, Installer & Démo en direct

Pourquoi l'utiliser

Fonctionnalités clés

11+ entity types covering genes, variants, articles, trials, drugs, diseases, pathways, proteins, adverse events, pharmacogenomics, GWAS
Deduplication across overlapping sources (PubTator3)
Optional API keys unlock higher rate limits and premium data (NCBI, OncoKB, Semantic Scholar, NCI, OpenFDA)
Install via curl script, PyPI (biomcp-cli), or remote HTTP
Zero-key operation possible — unauthenticated public APIs work by default

Démo en direct

Aperçu en pratique

biomcp.replay ▶ prêt

0/0

Installer

Choisissez votre client

~/Library/Application Support/Claude/claude_desktop_config.json · Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "biomcp": {
      "command": "TODO",
      "args": [
        "See README: https://github.com/genomoncology/biomcp"
      ],
      "_inferred": true
    }
  }
}

Ouvrez Claude Desktop → Settings → Developer → Edit Config. Redémarrez après avoir enregistré.

~/.cursor/mcp.json · .cursor/mcp.json

{
  "mcpServers": {
    "biomcp": {
      "command": "TODO",
      "args": [
        "See README: https://github.com/genomoncology/biomcp"
      ],
      "_inferred": true
    }
  }
}

Cursor utilise le même schéma mcpServers que Claude Desktop. La config projet l'emporte sur la globale.

VS Code → Cline → MCP Servers → Edit

{
  "mcpServers": {
    "biomcp": {
      "command": "TODO",
      "args": [
        "See README: https://github.com/genomoncology/biomcp"
      ],
      "_inferred": true
    }
  }
}

Cliquez sur l'icône MCP Servers dans la barre latérale Cline, puis "Edit Configuration".

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "biomcp": {
      "command": "TODO",
      "args": [
        "See README: https://github.com/genomoncology/biomcp"
      ],
      "_inferred": true
    }
  }
}

Même format que Claude Desktop. Redémarrez Windsurf pour appliquer.

~/.continue/config.json

{
  "mcpServers": [
    {
      "name": "biomcp",
      "command": "TODO",
      "args": [
        "See README: https://github.com/genomoncology/biomcp"
      ]
    }
  ]
}

Continue utilise un tableau d'objets serveur plutôt qu'une map.

~/.config/zed/settings.json

{
  "context_servers": {
    "biomcp": {
      "command": {
        "path": "TODO",
        "args": [
          "See README: https://github.com/genomoncology/biomcp"
        ]
      }
    }
  }
}

Ajoutez dans context_servers. Zed recharge à chaud à la sauvegarde.

claude mcp add biomcp -- TODO 'See README: https://github.com/genomoncology/biomcp'

Une seule ligne. Vérifiez avec claude mcp list. Supprimez avec claude mcp remove.

Cas d'usage

Usages concrets : biomcp

Triage a patient's gene variant for clinical relevance

👤 Genetic counselors, clinical researchers ⏱ ~15 min advanced

Quand l'utiliser : A VCF annotation returned a variant you've never seen — is it actionable?

Prérequis

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

Déroulement

Look up the variant

Look up BRCA2 c.7934del. ClinVar significance, gnomAD frequency, and any CIViC evidence.✓ Copié

→ Consolidated card from multiple sources
Pull supporting papers

Find the 3 most cited PubMed articles on this variant.✓ Copié

→ Paper list with PMIDs
Check for trials

Any open clinical trials recruiting for BRCA2 mutation carriers?✓ Copié

→ Trial list from ClinicalTrials.gov

Résultat : A multi-source picture of a variant with evidence pointers.

Pièges

Not a substitute for clinical review — Always have a qualified clinician review — this is research aid, not diagnosis
Some sources disagree on variant classification — Surface disagreements explicitly; don't average them

Conduct a targeted literature review

👤 PhD students, MDs, industry researchers ⏱ ~20 min intermediate

Quand l'utiliser : You need a bibliography on a specific gene-disease-drug angle.

Déroulement

Search articles

Search PubMed + Europe PMC for 'KRAS G12C AND adagrasib' 2022-2026. Dedupe across sources.✓ Copié

→ Deduplicated paper list
Summarize

For the top 10 by citation count, give me title + one-line take-home.✓ Copié

→ Annotated bibliography

Résultat : A defensible starting bibliography.

Combiner avec : filesystem

Check adverse-event profile for a drug

👤 Pharmacy, safety teams ⏱ ~20 min intermediate

Quand l'utiliser : Before recommending a drug, check OpenFDA / Drugs@FDA signals.

Déroulement

Query drug

For pembrolizumab: top adverse events per OpenFDA FAERS, last 5 years, broken down by seriousness.✓ Copié

→ Ranked AE table
Context

What's the expected AE profile per the FDA label vs FAERS real-world?✓ Copié

→ Label vs real-world comparison

Résultat : Grounded safety picture combining label and post-market data.

Find clinical trials matching a patient profile

👤 Clinicians, patient advocates ⏱ ~25 min advanced

Quand l'utiliser : A patient exhausted standard options and you want to scan for trial matches.

Déroulement

Match trials

Find Phase 2/3 recruiting trials for stage IV NSCLC with EGFR exon 20 insertion, US sites.✓ Copié

→ Trial list with NCT IDs
Summarize eligibility

For the top 5, summarize key inclusion/exclusion criteria.✓ Copié

→ Per-trial eligibility card

Résultat : A prioritized trial match list for clinical discussion.

Combinaisons

Associez-le à d'autres MCPs pour un effet X10

biomcp + filesystem

Save evidence memos as local markdown

For variant BRCA2 c.7934del, generate a one-page evidence memo and save to ~/research/brca2-7934.md.✓ Copié

biomcp + documentation-server

Build a personal literature library across biomcp queries

Every paper I star via biomcp, also ingest into documentation-server for future RAG queries.✓ Copié

Outils

Ce que ce MCP expose

Outil	Entrées	Quand appeler	Coût
gene	symbol or id, sources?: str[]	Gene-level lookup	multiple upstream calls
variant	hgvs\|rsid\|position	Variant interpretation	multiple upstream calls
article	query or pmid	Literature search	PubMed/Europe PMC/S2 calls
trial	query/condition/phase/status	Clinical trial match	CT.gov + NCI CTS calls
drug	name or id	Drug profile	multiple calls
disease	name or MONDO id	Disease context	multiple calls
adverse_event	drug or reaction	Safety analysis	OpenFDA calls

Coût et limites

Coût d'exécution

Quota d'API: Public APIs default. Optional keys raise limits: NCBI_API_KEY, S2_API_KEY, ONCOKB_TOKEN, OPENFDA_API_KEY, NCI_API_KEY
Tokens par appel: Consolidated entity responses 1-5k tokens
Monétaire: Free; some premium sources (OncoKB clinical) require license even with key
Astuce: For heavy literature work, get NCBI_API_KEY (free) — triples PubMed rate.

Sécurité

Permissions, secrets, portée

Stockage des identifiants : Env vars per provider key

Sortie de données : Calls to biomedical public APIs; queries themselves can be sensitive (patient variants etc.)

Queries can include PHI-adjacent data — confirm your deployment's data handling before running on real patient info.
Not a medical device; outputs are research aids only.

Dépannage

Erreurs courantes et correctifs

Rate limited on PubMed

Set NCBI_API_KEY for higher limits.

Vérifier : Check NCBI API Key page

OncoKB returns 403

OncoKB requires a token; register at oncokb.org and set ONCOKB_TOKEN.

Vérifier : curl -H 'Authorization: Bearer $ONCOKB_TOKEN' https://www.oncokb.org/api/v1/utils/numbers

No results for a known gene symbol

Some symbols have aliases; try both (e.g. ERBB2 vs HER2).

Vérifier : Search on genecards.org

Alternatives

biomcp vs autres

Alternative	Quand l'utiliser	Compromis
Individual databases via direct REST	You only need one source	No deduplication or cross-linking
OpenTargets Platform directly	You primarily care about target-disease evidence	Narrower coverage

Plus

Ressources

📖 Lire le README officiel sur GitHub

🐙 Voir les issues ouvertes

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