OBO-Edit

The OBO-Edit Ontology Developer's Environment: A Practical Introduction

Tutorial by David Osumi-Sutherland (FlyBase / Gene Ontology Consortium) organized in conjunction with the International Conference on Biomedical Ontology.

Date: July 23, 2009 (Afternoon)

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 using OBO-Edit2 to build and maintain ontologies, with special emphasis on working with computable 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

Instantiating implied links and eliminating 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.

Slides and example ontology presentation:OE2-tutorial.ppt ontology:tutorial.obo

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, et al., 2007 The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Nature Biotechnology 25, 1251 - 1255.