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
Tutorial ontology
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. website design professional seo website optimizer logo design realsoft tech