OntoKit API

Collaborative OWL ontology curation API built with FastAPI.

Features

• RESTful API for managing ontologies, classes, properties, and individuals
• Project management with public/private visibility and team collaboration
• Git-based version control with branching, pull requests, and sync from remote (pygit2 bare repos)
• Ontology linting with 20+ semantic validation rules
• Semantic search powered by sentence-transformers
• Authentication via Zitadel (OpenID Connect)
• Real-time collaboration via WebSockets
• Background job queue with ARQ + Redis
• Object storage integration with MinIO for ontology files

Quick Start

Full Docker Mode

# Start all services
docker compose up -d

# Run database migrations
docker compose exec api alembic upgrade head

# Set up Zitadel authentication (creates OIDC apps, updates .env files)
./scripts/setup-zitadel.sh --update-env

# Recreate API/worker containers to pick up the new credentials
docker compose up -d --force-recreate api worker

Hybrid Mode (API on host)

# Start infrastructure
docker compose -f compose.prod.yaml up -d

# Install dependencies and pre-commit hooks (one command)
make setup

# Configure
cp .env.example .env

# Set up Zitadel authentication (creates OIDC apps, updates .env files)
./scripts/setup-zitadel.sh --update-env

# Run database migrations
alembic upgrade head

# Start server
uvicorn ontokit.main:app --reload

Note: make setup requires uv. It installs all dev dependencies and sets up pre-commit hooks (ruff + mypy) so that code quality checks run automatically on every commit.

Documentation

See the wiki for full documentation.

Tech Stack

• Framework: FastAPI (Python 3.13)
• Database: PostgreSQL 17 + SQLAlchemy 2.0 (async)
• Cache/Queue: Redis 7 + ARQ
• Object Storage: MinIO (S3-compatible)
• Authentication: Zitadel (OIDC)
• Git: pygit2 (bare repositories for concurrent access)
• Ontology Processing: RDFLib, OWLReady2
• Semantic Search: sentence-transformers

License

MIT