Repository File Structure

This document describes the file structure of the MIECO ODK repository.

Directory Structure

MIECO/
├── .github/
│   └── workflows/
│       ├── qc.yml          # CI quality control workflow
│       └── docs.yml        # Documentation build & commit workflow
├── docs/                   # Generated HTML documentation (served by GitHub Pages)
├── docs_src/               # Documentation source files (Markdown, edit these)
│   ├── index.md            # Documentation home page
│   └── odk-workflows/      # ODK workflow documentation
├── mkdocs.yaml             # MkDocs configuration (docs_dir: docs_src, site_dir: docs)
├── ontology/               # Legacy ontology files (backward compatibility)
│   ├── MIECO.owl           # Original OWL file
│   └── MIECO.obo           # OBO format version
├── src/
│   └── ontology/
│       ├── mieco-edit.owl      # Source ontology file (edit this!)
│       ├── mieco-odk.yaml      # ODK project configuration
│       ├── Makefile            # ODK Makefile (DO NOT EDIT)
│       ├── mieco.Makefile      # Custom Makefile overrides
│       ├── run.sh              # Docker wrapper script
│       ├── catalog-v001.xml    # OWL catalog for imports
│       └── README-editors.md   # Editor instructions
└── README.md               # Repository README

Key Files

• src/ontology/mieco-edit.owl: This is the source file that editors should modify.
• src/ontology/run.sh: Use this to run make commands inside the ODK Docker container.
• src/ontology/Makefile: The main build file generated by ODK. Do not edit this directly.
• src/ontology/mieco.Makefile: Add custom make rules here.
• src/ontology/mieco-odk.yaml: ODK project configuration.

Release Files

After running make prepare_release, the following files are generated at the repository root: - mieco.owl - Primary release file - mieco-base.owl - Base release (without imported axioms)