Build Process¶

This page describes the build process for PBPKO, including how to generate the ontology from templates and manage releases.

Overview¶

The PBPKO build process uses ROBOT to: 1. Generate ontology from TSV templates 2. Merge with imported ontologies 3. Validate the resulting ontology 4. Generate release files

Build Steps¶

1. Template Processing¶

Generate edit.owl from templates:

robot template --template Robot/templates/vocab.tsv \
               --template Robot/templates/properties.tsv \
               --output Robot/ontologies/edit.owl

2. Import Management¶

Update imported modules:

robot extract --input Robot/ontologies/imported_modules.owl \
              --term-file Robot/extracted_terms/imported_modules/go_terms.txt \
              --output Robot/ontologies/go_module.owl

3. Ontology Merging¶

Merge edit.owl with imports:

robot merge --input Robot/ontologies/edit.owl \
           --input Robot/ontologies/imported_modules.owl \
           --output Robot/ontologies/pbpko.owl

4. Validation¶

Validate the ontology:

robot validate --input Robot/ontologies/pbpko.owl

Check for errors:

robot report --input Robot/ontologies/pbpko.owl \
             --output reports/pbpko-report.html

Build Scripts¶

Complete Build¶

Run full build process:

./scripts/build.sh

Windows:

scripts\build.bat

Individual Steps¶

Template only:

./scripts/template.sh

Merge only:

./scripts/merge.sh

Validate only:

./scripts/validate.sh

Build Configuration¶

ROBOT Configuration¶

robot-config.yaml:

build:
  inputs:
    - edit.owl
    - imported_modules.owl
  outputs:
    - pbpko.owl
  reports:
    - pbpko-report.html

Template Configuration¶

Template settings in TSV files: - Column headers must match ROBOT expectations - IDs must follow PBPKO format - Required columns must be filled

Release Process¶

1. Pre-release Checks¶

[ ] All templates validated
[ ] Imports updated
[ ] Tests passing
[ ] Documentation updated

2. Version Management¶

Update version in: - Robot/ontologies/catalog-v001.xml - Release notes - Documentation

3. Release Generation¶

Generate release files:

robot convert --input Robot/ontologies/pbpko.owl \
              --format owl \
              --output releases/pbpko.owl

Generate different formats:

# OBO format
robot convert --input Robot/ontologies/pbpko.owl \
              --format obo \
              --output releases/pbpko.obo

# JSON-LD format
robot convert --input Robot/ontologies/pbpko.owl \
              --format json \
              --output releases/pbpko.json

Continuous Integration¶

GitHub Actions¶

Build on every push:

name: Build PBPKO
on: [push, pull_request]
jobs:
  build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - name: Setup ROBOT
        run: |
          wget https://github.com/ontodev/robot/releases/download/v1.8.1/robot.jar
      - name: Build ontology
        run: ./scripts/build.sh

Automated Testing¶

Run tests:

robot test --input Robot/ontologies/pbpko.owl \
           --test all

Troubleshooting¶

Common Build Errors¶

Template errors: - Check TSV format - Verify column headers - Ensure required fields are filled

Import errors: - Verify import URLs - Check network connectivity - Update import versions

Merge conflicts: - Resolve duplicate terms - Check logical consistency - Validate relationships

Debug Mode¶

Enable verbose output:

robot --verbose template --template Robot/templates/vocab.tsv

Check intermediate files:

ls -la Robot/ontologies/