Difference between revisions of "A practical introduction to OBO-Edit2"
(New page: == An introduction to OBO-Edit2 == '''Tutorial by David Osumi-Sutherland (FlyBase)''' '''Date: ???''' This tutorial will provide an introduction to the use of OBO-Edit2 to build and mai...) |
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== An introduction to OBO-Edit2 == | == An introduction to OBO-Edit2 == | ||
| − | '''Tutorial by David Osumi- | + | '''Tutorial by David Osumi-Sustherland (FlyBase)''' |
'''Date: ???''' | '''Date: ???''' | ||
| − | This tutorial will provide an introduction to the use of OBO-Edit2 to build and maintain ontologies with special emphasis on working with | + | This tutorial will provide an introduction to the use of [http://*** OBO-Edit2] to build and maintain ontologies with special emphasis on working with necessary and sufficient definitions |
| + | Topics to be addressed will include: | ||
| − | + | OBO basics: | |
| + | The type/instance distinction | ||
| + | Theory of OBO relations | ||
| + | Necessary and sufficient definitions | ||
| + | Avoiding tangled hierarchies | ||
| + | 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 | ||
| + | Useful renders for tracking 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''' | '''Faculty''' | ||
| − | David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for editing the Drosophila anatomy and development ontologies. He is a member of the OBO-Edit working group | + | David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for editing the Drosophila [link anatomy] and [link development ontologies]. He is a member of the OBO-Edit working group and the OBO foundry relations ontology working group. |
| − | |||
'''References''' | '''References''' | ||
| + | Smith B, et al., 2005 [http://genomebiology.com/2005/6/5/R46 "Relations in Biomedical Ontologies"], Genome Biology, 2005, 6:R46. | ||
| + | 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. | ||
| + | Rector paper on disentangling | ||
| − | |||
'''Links''' | '''Links''' | ||
| + | |||
| + | [http:// *** download OBO-Edit2] (currently in beta - full release expected well before the data of this tutorial) | ||
| + | [http://*** OBO-edit manual] | ||
| + | [http:// ] | ||
Revision as of 04:35, 10 November 2008
An introduction to OBO-Edit2
Tutorial by David Osumi-Sustherland (FlyBase)
Date: ???
This tutorial will provide an introduction to the use of OBO-Edit2 to build and maintain ontologies with special emphasis on working with necessary and sufficient definitions
Topics to be addressed will include:
OBO basics: The type/instance distinction Theory of OBO relations Necessary and sufficient definitions Avoiding tangled hierarchies 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 Useful renders for tracking 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 [link anatomy] and [link development ontologies]. He is a member of the OBO-Edit working group and the OBO foundry relations ontology working group.
References
Smith B, et al., 2005 "Relations in Biomedical Ontologies", Genome Biology, 2005, 6:R46. Smith B, wt al., 2007 "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration", Nature Biotechnology 25, 1251 - 1255. Rector paper on disentangling
Links
[http:// *** download OBO-Edit2] (currently in beta - full release expected well before the data of this tutorial) OBO-edit manual [http:// ]