A practical introduction to OBO-Edit2

An 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.