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--- |
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title: MCP Res |
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emoji: 📊 |
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colorFrom: red |
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colorTo: gray |
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sdk: docker |
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sdk_version: 1.46.0 |
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app_file: app.py |
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pinned: false |
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short_description: Research |
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--- |
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MedGenesis AI |
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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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┌────────────────────────────────────────────┐ |
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│ Streamlit UI (app.py) │ |
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│ • Results / Genes / Trials / Graph tabs │ |
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│ • PDF / CSV export & follow-up Q&A │ |
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└──────────────┬─────────────────────────────┘ |
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│ async calls |
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┌──────────────▼─────────────────────────────┐ |
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│ Orchestrator (mcp/orchestrator.py) │ |
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│ • pulls PubMed, arXiv │ |
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│ • keyword extraction (spaCy) │ |
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│ • fans-out to MyGene, CT.gov v2, UMLS… │ |
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│ • merges & summarises with LLM │ |
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└──────────────┬─────────────────────────────┘ |
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│ helpers (mcp/*.py) |
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▼ |
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┌────────────────────────────────────────────┐ |
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│ External APIs + local TSV (DrugBank) │ |
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└────────────────────────────────────────────┘ |
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🔑 Features |
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Domain Source / API What you get |
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Literature PubMed + arXiv titles, abstracts, authors, year |
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Gene info MyGene.info + NCBI Gene symbol, name, GO, ClinVar, MeSH definitions |
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Trials ClinicalTrials.gov v2 NCT ID, phase, status, start date |
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Disease ↔ gene DisGeNET top associations & scores |
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Drug safety openFDA, DrugCentral adverse events, approvals, MoA |
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Graph edges Open Targets GraphQL gene–disease-drug links (+ OT score) |
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Ontology UMLS, HPO, Wikidata concept CUI, phenotype look-ups |
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🚀 Quick start |
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bash |
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Copy |
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Edit |
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# clone repo |
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git clone https://github.com/your-org/medgenesis.git |
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cd medgenesis |
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# build & run locally |
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python -m venv .venv && source .venv/bin/activate |
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pip install -r requirements.txt |
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python -m spacy download en_core_web_sm |
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streamlit run app.py |
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app.py starts a Streamlit server on localhost:8501. |
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Enter a biomedical question (e.g. “CRISPR glioblastoma therapy”) and press Run Search 🚀. |
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🐳 Docker / Hugging Face Space |
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The included Dockerfile is CPU-only and downloads the spaCy model at build time: |
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bash |
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Copy |
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docker build -t medgenesis . |
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docker run -p 7860:7860 -e OPENAI_API_KEY=sk-... medgenesis |
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HF Spaces: push the repo, set the environment secrets below, and Spaces will pick up Dockerfile. |
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🔐 Environment variables |
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Variable Description |
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OPENAI_API_KEY OpenAI account key (GPT-4o, GPT-4o-mini …) |
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GEMINI_KEY Google Generative AI key (Gemini 1.5 Flash) |
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UMLS_KEY UMLS Licensing key (ticket auth) |
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DISGENET_KEY DisGeNET Bearer token (optional) |
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PUB_KEY NCBI E-utils key (optional, boosts quota) |
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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 |
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mcp/data/drugbank_open_structured_drug_links.tsv – DrugBank Open Data |
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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 |
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bash |
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Edit |
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pytest tests/ |
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Unit tests mock external APIs and verify parsing, caching and orchestrator merges. |
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🛠️ Contributing |
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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 |
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Apache 2.0 – free for research and commercial use. |
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API terms of each external provider still apply. |
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Happy discovering! |
