Difference between revisions of "A practical introduction to OBO-Edit2"
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| − | == | + | === Tutorial by David Osumi-Sustherland (FlyBase) === |
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[http://oboedit.org/ 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. | [http://oboedit.org/ 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 | :OBO basics | ||
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:: Making implied links hard and stripping redundancy. | :: Making implied links hard and stripping redundancy. | ||
| − | + | ==== Faculty ==== | |
David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for editing the Drosophila [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_anatomy anatomy] and [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_development development ontologies]. He is a member of the OBO-Edit working group and the OBO foundry relations ontology working group. | David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for editing the Drosophila [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_anatomy anatomy] and [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_development 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. [http://www.cs.man.ac.uk/~rector/papers/rector-modularisation-kcap-2003-distrib.pdf Modularisation of Domain Ontologies Implemented in Description Logics and related formalisms including OWL.] Proc. K-CAP:ACM 2003, 121-129. | [1] Rector, A., 2003. [http://www.cs.man.ac.uk/~rector/papers/rector-modularisation-kcap-2003-distrib.pdf Modularisation of Domain Ontologies Implemented in Description Logics and related formalisms including OWL.] Proc. K-CAP:ACM 2003, 121-129. | ||
Revision as of 03:58, 10 November 2008
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.