Difference between revisions of "A practical introduction to OBO-Edit2"
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==== The following topics will be covered ==== | ==== The following topics will be covered ==== | ||
| − | :OBO basics | + | :''OBO basics'' |
:: The type/instance distinction [2] | :: The type/instance distinction [2] | ||
:: Theory of OBO relations [2] | :: Theory of OBO relations [2] | ||
:: Necessary and sufficient definitions | :: Necessary and sufficient definitions | ||
:: Avoiding tangled hierarchies [1] | :: Avoiding tangled hierarchies [1] | ||
| − | :OBO-Edit2 basics | + | :''OBO-Edit2 basics'' |
:: Basic editing with the tree editor and the parent editor | :: Basic editing with the tree editor and the parent editor | ||
:: Basic searching, filtering and rendering | :: Basic searching, filtering and rendering | ||
:: Necessary and sufficient definitions and use of the reasoner | :: Necessary and sufficient definitions and use of the reasoner | ||
:: Declaring disjunction and finding contradictions | :: Declaring disjunction and finding contradictions | ||
| − | :OBO-Edit2 advanced | + | :''OBO-Edit2 advanced use'' |
:: Advanced searching and rendering | :: Advanced searching and rendering | ||
:: Using renders to track editing progress | :: Using renders to track editing progress | ||
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:: Tracking redundancy | :: Tracking redundancy | ||
:: Graphing with OBO-Edit | :: Graphing with OBO-Edit | ||
| − | :Preparing OBO files for release | + | :''Preparing OBO files for release'' |
:: Verification | :: Verification | ||
:: Making implied links hard and stripping redundancy. | :: Making implied links hard and stripping redundancy. | ||
Revision as of 05:01, 10 November 2008
Tutorial by David Osumi-Sustherland (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 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.