README.md

metadata

title: BioMCP Explorer
emoji: 🧬
colorFrom: blue
colorTo: indigo
sdk: gradio
sdk_version: 6.11.0
app_file: app.py
pinned: false
short_description: Explore genes, variants, drugs, trials & more

BioMCP Explorer — Gradio App

A feature-rich Gradio web interface for exploring all BioMCP tools and features. Search, discover, and analyze biomedical data across 13+ entity types and 30+ upstream APIs.

Quick Start

1. Install BioMCP CLI

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

2. Install Python dependencies

pip install -r requirements.txt

3. Configure API keys (optional)

Copy .env.example to .env and fill in your keys. Or enter them in the Settings tab at runtime.

4. Launch

python app.py

Open http://localhost:7860 in your browser.

Tabs Overview

Tab	Purpose
⚙️ Settings & Health	API keys, health checks, version info
🔍 Discover	Free-text concept resolution
🔎 Search	Entity search across 13 types (gene, variant, article, trial, drug, disease, pathway, protein, adverse-event, pgx, gwas, phenotype, cross-entity)
📋 Get Detail	Focused entity detail with selectable sections
🔗 Cross-Entity Helpers	20 pivot commands between related entities
🧬 Enrichment	g:Profiler gene-set enrichment
📦 Batch	Parallel get calls for up to 10 IDs
📊 Study Analytics	Local cBioPortal study analysis (query, cohort, survival, compare, co-occurrence)

API Keys

All optional — BioMCP works without them at reduced rate/features:

Key	Purpose
NCBI_API_KEY	Better PubMed/PubTator rate limits
S2_API_KEY	Faster Semantic Scholar access
ONCOKB_TOKEN	OncoKB variant therapy evidence
OPENFDA_API_KEY	Better OpenFDA rate limits
NCI_API_KEY	NCI CTS trial search
DISGENET_API_KEY	DisGeNET gene-disease scores
UMLS_API_KEY	Clinical crosswalk in discover
ALPHAGENOME_API_KEY	Variant effect predictions

Requirements

• Python 3.11+
• biomcp CLI on PATH
• Gradio 5.x