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PRIDE Ontology

The PRIDE Ontology (PRIDE CV) provides controlled vocabulary terms for proteomics data representation in PRIDE and related resources.

License

PRIDE ontology is licensed under the Creative Commons Attribution 4.0 International License.

Getting Help

For questions, feedback, or support, please contact the PRIDE Helpdesk at the EBI: pride-support@ebi.ac.uk.

We welcome error reports, improvement suggestions, and new feature requests.

Modifying the Ontology

To modify the PRIDE ontology, update the OBO file (pride_cv.obo) and convert it to OWL using the following protocol.

Local Testing of OWL Generation and Validation

To test the ontology conversion and validation process locally, follow these steps:

1. Validate the OBO File

Ensure you have Docker installed and run the following command to validate the OBO file using fastobo-validator:

docker run --rm -v "$PWD:/work" -w /work obolibrary/odkfull \
    fastobo-validator --all pride_cv.obo

2. Convert OBO to OWL and Validate

Use the robot tool to generate the OWL file and validate it:

# Pull the ROBOT container if not already available
docker pull obolibrary/robot

# Convert OBO to OWL
docker run --rm -v "$PWD:/work" -w /work obolibrary/robot \
    robot convert -vvv -i pride_cv.obo -o pride_cv.owl --format owl

# Validate the OWL file
docker run --rm -v "$PWD:/work" -w /work obolibrary/robot \
    robot report -vvv --input pride_cv.owl --output report.tsv

3. Review the Validation Report

After running the above commands, check report.tsv for validation errors.

CI/CD Pipeline

This process is automated in the CI/CD pipeline, which runs on every push and pull request to master and dev branches:

  1. Validate OBO file using fastobo-validator.
  2. Convert OBO to OWL using robot.
  3. Validate OWL file and generate a report (report.tsv).
  4. Upload report as an artifact.

You can check the CI/CD logs and artifacts for additional details.

By following these steps, you can ensure that modifications to the PRIDE ontology maintain consistency and correctness before committing changes.