A practical introduction to OBO-Edit2

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Tutorial by David Osumi-Sutherland (FlyBase)

Date: ???

OBO-Edit2, the new version of the popular ontology editing software, 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 use
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 development of 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.

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