biomcp MCP — Сценарии использования, Установка & Живое демо

Зачем использовать

Ключевые функции

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

Живое демо

Как выглядит на практике

biomcp.replay ▶ готово

0/0

Установка

Выберите клиент

~/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
    }
  }
}

Откройте Claude Desktop → Settings → Developer → Edit Config. Перезапустите после сохранения.

~/.cursor/mcp.json · .cursor/mcp.json

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

Cursor использует ту же схему mcpServers, что и Claude Desktop. Конфиг проекта приоритетнее глобального.

VS Code → Cline → MCP Servers → Edit

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

Щёлкните значок MCP Servers на боковой панели Cline, затем "Edit Configuration".

~/.codeium/windsurf/mcp_config.json

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

Тот же формат, что и Claude Desktop. Перезапустите Windsurf для применения.

~/.continue/config.json

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

Continue использует массив объектов серверов, а не map.

~/.config/zed/settings.json

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

Добавьте в context_servers. Zed перезагружается автоматически.

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

Однострочная команда. Проверить: claude mcp list. Удалить: claude mcp remove.

Сценарии использования

Реальные сценарии: biomcp

Triage a patient's gene variant for clinical relevance

👤 Genetic counselors, clinical researchers ⏱ ~15 min advanced

Когда использовать: A VCF annotation returned a variant you've never seen — is it actionable?

Предварительные требования

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

Поток

Look up the variant

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

→ Consolidated card from multiple sources
Pull supporting papers

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

→ Paper list with PMIDs
Check for trials

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

→ Trial list from ClinicalTrials.gov

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

Подводные камни

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

Когда использовать: You need a bibliography on a specific gene-disease-drug angle.

Поток

Search articles

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

→ Deduplicated paper list
Summarize

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

→ Annotated bibliography

Итог: A defensible starting bibliography.

Сочетать с: filesystem

Check adverse-event profile for a drug

👤 Pharmacy, safety teams ⏱ ~20 min intermediate

Когда использовать: Before recommending a drug, check OpenFDA / Drugs@FDA signals.

Поток

Query drug

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

→ Ranked AE table
Context

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

→ Label vs real-world comparison

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

Find clinical trials matching a patient profile

👤 Clinicians, patient advocates ⏱ ~25 min advanced

Когда использовать: A patient exhausted standard options and you want to scan for trial matches.

Поток

Match trials

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

→ Trial list with NCT IDs
Summarize eligibility

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

→ Per-trial eligibility card

Итог: A prioritized trial match list for clinical discussion.

Комбинации

Сочетайте с другими MCP — эффект 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.✓ Скопировано

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.✓ Скопировано

Инструменты

Что предоставляет этот MCP

Инструмент	Входные данные	Когда вызывать	Стоимость
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

Стоимость и лимиты

Во что обходится

Квота API: Public APIs default. Optional keys raise limits: NCBI_API_KEY, S2_API_KEY, ONCOKB_TOKEN, OPENFDA_API_KEY, NCI_API_KEY
Токенов на вызов: Consolidated entity responses 1-5k tokens
Деньги: Free; some premium sources (OncoKB clinical) require license even with key
Совет: For heavy literature work, get NCBI_API_KEY (free) — triples PubMed rate.

Безопасность

Права, секреты, радиус поражения

Хранение учётных данных: Env vars per provider key

Исходящий трафик: 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.

Устранение неполадок

Частые ошибки и исправления

Rate limited on PubMed

Set NCBI_API_KEY for higher limits.

Проверить: Check NCBI API Key page

OncoKB returns 403

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

Проверить: 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).

Проверить: Search on genecards.org

Альтернативы

biomcp в сравнении

Альтернатива	Когда использовать	Компромисс
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

Ещё

Ресурсы

📖 Читать официальный README на GitHub

🐙 Открытые задачи

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