A practical introduction to OBO-Edit2
Tutorial by David Osumi-Sustherland (FlyBase)
Date: ???
OBO-Edit2, the new version of the popular ontology editing tool, has many powerful new tools for ontology analysis and construction. This tutorial will provide an introduction to the use of OBO-Edit2 to build and maintain OBO ontologies with special emphasis on working with necessary and sufficient definitions.
The following topics will be covered
- OBO basics
- The type/instance distinction [2]
- Theory of OBO relations [2]
- Necessary and sufficient definitions
- Avoiding tangled hierarchies [1]
- OBO-Edit2 basics
- Basic editing with the tree editor and the parent editor
- Basic searching, filtering and rendering
- Necessary and sufficient definitions and use of the reasoner
- Declaring disjunction and finding contradictions
- OBO-Edit2 advanced:
- Advanced searching and rendering
- Using renders to track editing progress
- Selective importation of foreign terms
- Tracking redundancy
- Graphing with OBO-Edit
- Preparing OBO files for release:
- Verification
- Making implied links hard and stripping redundancy.
Faculty
David Osumi-Sutherland is an ontologist and curator at FlyBase, where he is responsible for editing the Drosophila anatomy and development ontologies. He is a member of the OBO-Edit working group and the OBO foundry relations ontology working group.
References
[1] Rector, A., 2003. Modularisation of Domain Ontologies Implemented in Description Logics and related formalisms including OWL. Proc. K-CAP:ACM 2003, 121-129.
[2] Smith B, et al., 2005 "Relations in Biomedical Ontologies", Genome Biology, 2005, 6:R46.
[3] Smith B, wt al., 2007 "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration", Nature Biotechnology 25, 1251 - 1255.