CAS-ODK Overlay

This repository provides a Copier-based overlay for Ontology Development Kit (ODK) projects.
It extends the standard ODK scaffold with extra files, folders, and patterns that are automatically generated from Cell Annotation Schema (CAS) taxonomy JSON files.

✨ Features

• 📦 ODK-compatible: builds on top of a standard ODK project layout.
• 🧬 CAS-driven: reads CAS taxonomy JSON to generate ontology terms and patterns.
• ⚙️ Templated: uses Copier and Jinja2 to render files/folders.
• 🔁 Re-renderable: changes to your taxonomy or config can be applied repeatedly without breaking your repo.
• 🧪 Extensible: supports custom Python preprocessing (pandas, rdflib, etc.) to derive variables for templates.

🚀 Quickstart

1. Create a base ODK project
   Follow the ODK setup tutorial.
   Example:

   sh seed-via-docker.sh -C my-odk.yaml -c

2. Apply this overlay with Copier

   pip install copier
   copier copy gh:Cellular-Semantics/cas-odk-overlay .

3. Provide inputs

   • src/data/taxonomy.json → your CAS taxonomy file
   • src/data/project.yaml → minimal project metadata (ontology name, publications, species, etc.)

4. Re-render when inputs change

   copier update .

🛠️ Workflow

1. Edit taxonomy.json and project.yaml.

2. Re-render overlay (copier update .).

3. Build ontology with ODK:

   cd src/ontology
   sh run.sh make prepare_release