Development

Protégé

The Xenopus Anatomy Ontology is maintained in Web Ontology Language (OWL) and Open Biomedical Ontologies (OBO) file formats. OWL files use standard RDF/XML syntax. The open-source OWL ontology editor Protégé is the preferred tool for XAO development.

Before creating new terms (OWL classes) in Protégé, configure it to generate proper IRIs (Internationalized Resource Identifiers). Use the dictionary utility to find the most recently used XAO anatomy ID. Then in Protégé do the following:

• Open Preferences and select the New Entities tab.
• Set the Entity IRI to end with Auto-generated ID.
• Set the Auto-generated ID to be Numeric (iterative).
  • Prefix: XAO_
  • Suffix: (leave blank)
  • Digit count: 7
  • Start: one number greater than the XAO ID you found above.

After creating each new class, add the following annotations:

• has_obo_namespace: xenopus_anatomy
• id: XAO:<number>

If the IRI of the new class is, for example, http://purl.obolibrary.org/obo/XAO_0005328, then the id annotation value should be XAO:0005328.

Workflow

Ontology updates should be made in one or more Git branches.

Keep the xenopus_anatomy OWL and OBO files in sync within your current branch, as the Python utilities rely on the latter. Install and use the ROBOT tool to convert from OWL to OBO. Open a terminal, change to the root directory of the repository, and run:

$ robot convert --input xenopus_anatomy.owl --format obo --output xenopus_anatomy.obo

Making a release

Merge any changes that should be included in the release with the master branch. Sync the OWL and OBO versions of the ontology if necessary and commit the changes.

Run the checkup utility to ensure that the ontology has a complete is_a structure and all terms have definitions and valid stage ranges. Fix and commit any outstanding issues.

In Protégé, modify the Ontology Version IRI so it contains the date of the release in the following style:

http://purl.obolibrary.org/obo/xao/releases/YYYY-MM-DD/xao.owl

Update the ontology header annotations with a new Xenbase-assigned XAO version number, e.g.:

Version: 9

Add or update any other comments as needed.

Sync the OWL and OBO files one more time, commit, and push the changes to the server.

Go to the releases page and draft a new release with the same version number specified in the ontology header. Set a Git tag formatted as the release date with the prefix 'v', e.g.:

v2020-06-26

External sites such as the EBI Ontology Lookup Service and Ontobee should load the new version automatically within a few days.

If any of the ontology metadata on OBO Foundry needs to be updated, submit an issue request.