biomcp

Search genes, variants, trials, and articles across biomedical data sources.

581|113|Updated Apr 1, 2025
One-click install
npx skills add https://github.com/genomoncology/biomcp --skill biomcp
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: biomcp
Source: https://github.com/genomoncology/biomcp/tree/main/skills
Command: npx skills add https://github.com/genomoncology/biomcp --skill biomcp

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Solves multisource biomedical data discovery by enabling unified search and retrieval.

Core Features & Use Cases

  • Unified command grammar for cross-source discovery and retrieval across genes, variants, trials, articles, drugs, diseases, and more.
  • Cross-entity pivots and study analytics enable integrated workflows from discovery to evidence, with compact markdown outputs.
  • Use Case: researchers can perform a gene-level query across literature, trials, and databases and compile results into concise, evidence-oriented outputs.

Quick Start

Install biomcp CLI and run a simple cross-entity search, e.g., biomcp search gene BRAF.

Frequently Asked Questions about biomcp

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search for biomedical literature and clinical trials across multiple sources at once?

Cross-source biomedical data discovery allows you to query genes, variants, trials, and articles simultaneously. BioMCP applies a unified command grammar to retrieve and integrate these diverse data types into concise, evidence-oriented markdown outputs.

What is cross-entity pivoting in biomedical data integration?

Cross-entity pivoting connects genes, variants, trials, and articles to enable evidence-backed workflows. BioMCP executes these pivots to help researchers transition from initial discovery to literature and trial analytics, generating compact markdown outputs.

How do I retrieve gene, variant, and disease data using a CLI?

Retrieving gene, variant, and disease data via CLI requires a unified command grammar like BioMCP. You run simple search commands, such as querying a specific gene, to retrieve machine-readable JSON outputs compiled from diverse biomedical databases.

Can I use a single command grammar for both bioinformatics literature search and clinical trial retrieval?

Yes, a single command grammar can handle both literature search and clinical trial retrieval. BioMCP applies a unified CLI syntax to query diverse sources, enabling researchers and clinicians to obtain evidence-backed results and machine-readable JSON outputs.

Do I need to install dependencies to run biomedical data discovery queries?

No external dependencies are required to run biomedical data discovery queries with BioMCP. The Skill operates independently, requiring only a YAML frontmatter in the SKILL.md file to define its name and description before executing searches.

What format are biomedical search results output in for integration workflows?

Biomedical search results are output in machine-readable JSON format for integration workflows. BioMCP utilizes schemas and examples to structure these results, also providing compact markdown outputs to support human-readable cross-entity pivots and study analytics.