Difference between revisions of "A practical introduction to OBO-Edit2"
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| − | == | + | === Tutorial by David Osumi-Sutherland (FlyBase) === |
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'''Date: ???''' | '''Date: ???''' | ||
| − | [http://oboedit.org/ OBO-Edit2], the new version of the popular ontology editing | + | [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 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''' | + | ''''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 | ||
| Line 25: | Line 23: | ||
:: 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. | ||
| Line 31: | Line 29: | ||
'''Faculty''' | '''Faculty''' | ||
| − | David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for | + | 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. |
'''References''' | '''References''' | ||
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[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. | ||
| − | [2] Smith B, et al., 2005 [http://genomebiology.com/2005/6/5/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, wt 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 | + | [3] Smith B, wt 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. |
Latest revision as of 04:03, 10 November 2008
Tutorial by David Osumi-Sutherland (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 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.
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.