Introduction to Protege and OWL for the Planteome project

As a part of the Planteome project, we develop common reference ontologies and applications for plant biology.

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As an initial phase of this work, we are transitioning from editing standalone ontologies in OBO-Edit to integrated ontologies using increased OWL axiomatization and reasoning. In November we held a workshop that brought together plant trait experts from across the world, and developed a plan for integrating multiple species-specific ontologies with a reference trait ontology.

As part of the workshop, we took a tour of some of the fundamentals of OWL, hybrid obo/owl editing using Protege 5, and using reasoners and template-based systems to automate large portions of ontology development.

I based the material on an earlier tutorial prepared for the Gene Ontology editors, it’s available on the Planteome GitHub Repository at:

https://github.com/Planteome/protege-tutorial