Biomedical Relation Annotation Platform

A full-stack web application with two annotation modes for biomedical knowledge graph curation.

Mode	Route	Purpose
RELATE	/relate-triples	Predicate annotation of PubMed abstracts
TMKP Verification	/tmkp-triples	Fact-checking text-mined knowledge graph edges

Quick Start

Backend

cd backend
pip install -r requirements.txt
python main.py

Frontend

cd frontend
npm install
npm run dev

Backend runs on http://localhost:8000, frontend on http://localhost:5173.

Architecture

Backend: FastAPI + SQLAlchemy + SQLite Frontend: React + TypeScript + Tailwind CSS + Framer Motion Deployment: Kubernetes (Helm) or Docker Compose

Annotator Login

Both modes use the same login: first name + last name, creating a firstname.lastname identifier. Name collisions are detected automatically and resolved with a middle initial.

Project Structure

annotation-ui/
├── backend/
│   ├── main.py              # FastAPI app + RELATE endpoints
│   ├── tmkp_routes.py       # TMKP API router
│   ├── models.py            # SQLAlchemy models (RELATE + TMKP)
│   ├── schemas.py           # Pydantic schemas
│   ├── database.py          # Database config (SQLite)
│   ├── load_corpus.py       # RELATE corpus loader
│   ├── load_tmkp.py         # TMKP JSONL loader (filters, sampling, streaming)
│   ├── node_norm.py         # Node Normalizer CURIE name resolution
│   ├── assign_dual.py       # Dual-annotator assignment utility
│   └── requirements.txt
├── frontend/src/
│   ├── components/
│   │   ├── LandingPage.tsx       # Home — choose RELATE or TMKP
│   │   ├── RelateApp.tsx         # RELATE annotation interface
│   │   ├── TmkpApp.tsx           # TMKP verification interface
│   │   ├── Login.tsx             # Shared login with collision detection
│   │   ├── AbstractView.tsx      # Entity highlighting in abstracts
│   │   ├── AnnotationPanel.tsx   # Predicate selection & controls
│   │   ├── AdminDashboard.tsx    # RELATE admin interface
│   │   ├── CompletionModal.tsx   # Article completion popup
│   │   └── ProgressBar.tsx       # Progress visualization
│   ├── api.ts / types.ts        # API client + TypeScript types
│   └── App.tsx                   # Router
├── docs/
│   ├── RELATE.md
│   └── TMKP.md
├── helm/                         # Kubernetes Helm chart
└── annotations.db                # SQLite database (auto-created)

Deployment

Kubernetes + Helm

helm install annotation-ui ./helm/annotation-ui -n <namespace> --create-namespace

Upgrade / restart:

helm upgrade annotation-ui ./helm/annotation-ui -n <namespace>
kubectl rollout restart deployment/annotation-backend -n <namespace>
kubectl rollout restart deployment/annotation-frontend -n <namespace>

Docker Compose (Local)

docker-compose up -d

License

MIT License — see LICENSE for details.