Difference between revisions of "OBO-Edit"
m (New page: '''The OBO-Edit Ontology Developer's Environment: A Practical Introduction''' '''Tutorial by David Osumi-Sutherland (FlyBase / Gene Ontology Consortium)''' '''Date: July 23, 2009 (Aftern...) |
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'''The OBO-Edit Ontology Developer's Environment: A Practical Introduction''' | '''The OBO-Edit Ontology Developer's Environment: A Practical Introduction''' | ||
| − | + | Tutorial by David Osumi-Sutherland (FlyBase / Gene Ontology Consortium) organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology.] | |
| − | + | Date: July 23, 2009 (Afternoon) | |
| − | [http://oboedit.org/ 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 | + | [http://oboedit.org/ 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''' | ''''The following topics will be covered''' | ||
| Line 27: | Line 27: | ||
:''Preparing OBO files for release'' | :''Preparing OBO files for release'' | ||
:: Verification | :: Verification | ||
| − | :: | + | :: Instantiating implied links and eliminating redundancy. |
'''Faculty''' | '''Faculty''' | ||
| − | David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for development of 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 | + | David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for development of 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. |
| + | |||
| + | '''Slides''' | ||
| + | : [[media:OE2-tutorial.ppt]] | ||
| + | |||
| + | '''Tutorial ontology''' | ||
| + | |||
| + | [http://oboedit.org/ICBOtutorialData/tutorial.obo tutorial.obo] | ||
'''References''' | '''References''' | ||
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[2] Smith B, et al., 2005 [http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies], Genome Biology, 2005, 6:R46. | [2] Smith B, et al., 2005 [http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies], Genome Biology, 2005, 6:R46. | ||
| − | [3] Smith B, | + | [3] Smith B, et al., 2007 [http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration], Nature Biotechnology 25, 1251 - 1255. |
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| + | [http://www.seoprofessionalsonline.com professional seo] | ||
| + | [http://www.seoprofessionalsonline.com/website-optimizer.asp website optimizer] | ||
| + | [http://www.designerevaluation.com/logo-design/ logo design] | ||
| + | [http://www.realsofttech.com/ realsoft tech] | ||
Latest revision as of 21:00, 21 July 2010
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