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---
title: MCP Res
emoji: 📊
colorFrom: red
colorTo: gray
sdk: docker
sdk_version: 1.46.0
app_file: app.py
pinned: false
short_description: Research
---
MedGenesis AI
MedGenesis AI is a biomedical literature discovery workbench that unifies live data from PubMed, arXiv, MyGene.info, ClinicalTrials.gov v2, DisGeNET, openFDA, Open Targets, DrugCentral, UMLS and more—then lets you explore the evidence in a rich Streamlit interface powered by OpenAI or Gemini LLMs.
┌────────────────────────────────────────────┐
│ Streamlit UI (app.py) │
│ • Results / Genes / Trials / Graph tabs │
│ • PDF / CSV export & follow-up Q&A │
└──────────────┬─────────────────────────────┘
│ async calls
┌──────────────▼─────────────────────────────┐
│ Orchestrator (mcp/orchestrator.py) │
│ • pulls PubMed, arXiv │
│ • keyword extraction (spaCy) │
│ • fans-out to MyGene, CT.gov v2, UMLS… │
│ • merges & summarises with LLM │
└──────────────┬─────────────────────────────┘
│ helpers (mcp/*.py)
▼
┌────────────────────────────────────────────┐
│ External APIs + local TSV (DrugBank) │
└────────────────────────────────────────────┘
🔑 Features
Domain Source / API What you get
Literature PubMed + arXiv titles, abstracts, authors, year
Gene info MyGene.info + NCBI Gene symbol, name, GO, ClinVar, MeSH definitions
Trials ClinicalTrials.gov v2 NCT ID, phase, status, start date
Disease ↔ gene DisGeNET top associations & scores
Drug safety openFDA, DrugCentral adverse events, approvals, MoA
Graph edges Open Targets GraphQL gene–disease-drug links (+ OT score)
Ontology UMLS, HPO, Wikidata concept CUI, phenotype look-ups
🚀 Quick start
bash
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# clone repo
git clone https://github.com/your-org/medgenesis.git
cd medgenesis
# build & run locally
python -m venv .venv && source .venv/bin/activate
pip install -r requirements.txt
python -m spacy download en_core_web_sm
streamlit run app.py
app.py starts a Streamlit server on localhost:8501.
Enter a biomedical question (e.g. “CRISPR glioblastoma therapy”) and press Run Search 🚀.
🐳 Docker / Hugging Face Space
The included Dockerfile is CPU-only and downloads the spaCy model at build time:
bash
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docker build -t medgenesis .
docker run -p 7860:7860 -e OPENAI_API_KEY=sk-... medgenesis
HF Spaces: push the repo, set the environment secrets below, and Spaces will pick up Dockerfile.
🔐 Environment variables
Variable Description
OPENAI_API_KEY OpenAI account key (GPT-4o, GPT-4o-mini …)
GEMINI_KEY Google Generative AI key (Gemini 1.5 Flash)
UMLS_KEY UMLS Licensing key (ticket auth)
DISGENET_KEY DisGeNET Bearer token (optional)
PUB_KEY NCBI E-utils key (optional, boosts quota)
BIO_KEY NCBI E-utils key for Gene/MeSH (optional)
Set them in .env, your shell, or HF Secrets.
🗃️ Local data
mcp/data/drugbank_open_structured_drug_links.tsv – DrugBank Open Data
Download from the DrugBank Open-Data page and place it here.
The file is lazy-loaded and cached; the app still works without it.
🧪 Tests
bash
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pytest tests/
Unit tests mock external APIs and verify parsing, caching and orchestrator merges.
🛠️ Contributing
Fork & create a feature branch.
Follow Conventional Commits for PR titles.
Run pre-commit install to auto-format with black & ruff.
Submit a PR; GitHub Actions will run lint + tests.
📄 License
Apache 2.0 – free for research and commercial use.
API terms of each external provider still apply.
Happy discovering! |