OBO-Edit

2010-07-22T05:00:17Z

Alice.thomas222:

'''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 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 [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'''

[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 Relations in Biomedical Ontologies], Genome Biology, 2005, 6:R46.

[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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