foundingGIDE Deliverable D5.1 Updating existing ontologies, and implementing in data resources

A core goal of foundingGIDE was to support participating resources to harmonise their formal descriptions of image data using a shared vocabulary. Ontologies and controlled vocabularies provide much of that vocabulary. This deliverable reports on the work of WP5 to update the ontologies chosen as critical to the project, and to implement them within the participating data resources, so that submissions increasingly describe imaging data using agreed, resolvable terms.

The deliverable takes as its starting point the ontology set recommended in D2.1 (ontology landscaping and recommendations), and the per-component representation specified in D6.1. First it reports the return of the Biological Imaging Methods Ontology (FBbi) to active maintenance, now as a community effort under the FoundingGIDE project. New terms are being added using community-standard tooling, an open contribution process and continuity of its established identifiers. Second, it reports wider GIDE ontologies implementation in the participating resources. The BioImage Archive now uses FBbi identifiers internally within its RO-Crate-based metadata representation, and has published guidance enabling submitters to record ontology terms using its submission system. The corresponding implementation in SSBD, and guidance on future compatibility with the IDR, are reported in the respective sections. Preclinical imaging ontologies are addressed in D4.1 and are outside the scope of this deliverable. The longer-term sustainability of these maintenance arrangements is the subject of D5.2.