| --- |
| 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. |
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| ┌────────────────────────────────────────────┐ |
| │ 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) │ |
| └────────────────────────────────────────────┘ |
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| 🔑 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 |
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| 🚀 Quick start |
| bash |
| Copy |
| Edit |
| # clone repo |
| git clone https://github.com/your-org/medgenesis.git |
| cd medgenesis |
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| # 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 🚀. |
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| 🐳 Docker / Hugging Face Space |
| The included Dockerfile is CPU-only and downloads the spaCy model at build time: |
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| bash |
| Copy |
| Edit |
| 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. |
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| 🔐 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) |
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| Set them in .env, your shell, or HF Secrets. |
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| 🗃️ Local data |
| mcp/data/drugbank_open_structured_drug_links.tsv – DrugBank Open Data |
| Download from the DrugBank Open-Data page and place it here. |
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| The file is lazy-loaded and cached; the app still works without it. |
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| 🧪 Tests |
| bash |
| Copy |
| Edit |
| pytest tests/ |
| Unit tests mock external APIs and verify parsing, caching and orchestrator merges. |
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| 🛠️ Contributing |
| Fork & create a feature branch. |
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| Follow Conventional Commits for PR titles. |
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| Run pre-commit install to auto-format with black & ruff. |
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| Submit a PR; GitHub Actions will run lint + tests. |
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| 📄 License |
| Apache 2.0 – free for research and commercial use. |
| API terms of each external provider still apply. |
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| Happy discovering! |
