A practical introduction to OBO-Edit2 - Revision history

Djs93 at 12:03, 10 November 2008

2008-11-10T12:03:55Z

2008-11-10T12:03:24Z

2008-11-10T12:03:02Z

2008-11-10T12:02:13Z

Tutorial by David Osumi-Sustherland (FlyBase)

2008-11-10T12:01:19Z

The following topics will be covered

2008-11-10T11:59:58Z

Tutorial by David Osumi-Sustherland (FlyBase)

2008-11-10T11:58:38Z

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2008-11-10T11:55:15Z

An introduction to OBO-Edit2

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@@ Line 29: / Line 29: @@
 '''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 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'''

@@ Line 29: / Line 29: @@
 '''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'''

@@ Line 35: / Line 35: @@
 [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.
+[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"], Nature Biotechnology 25, 1251 - 1255.
+[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.

@@ Line 1: / Line 1: @@
-=== Tutorial by David Osumi-Sustherland (FlyBase) ===
+=== Tutorial by David Osumi-Sutherland (FlyBase) ===
 '''Date: ???'''
@@ Line 5: / Line 5: @@
 [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''
@@ Line 27: / Line 27: @@
 ::	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 [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'''
 [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.

@@ Line 7: / Line 7: @@
 ==== The following topics will be covered ====
-:OBO basics
+:''OBO basics''
 ::	The type/instance distinction [2]
 ::	Theory of OBO relations [2]
 ::	Necessary and sufficient definitions
 ::	Avoiding tangled hierarchies [1]
-:OBO-Edit2 basics
+:''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:
+:''OBO-Edit2 advanced use''
 ::	Advanced searching and rendering
 ::	Using renders to track editing progress
@@ Line 23: / Line 23: @@
 ::	Tracking redundancy
 ::	Graphing with OBO-Edit
-:Preparing OBO files for release:
+:''Preparing OBO files for release''
 ::	Verification
 ::	Making implied links hard and stripping redundancy.

@@ Line 1: / Line 1: @@
 == An introduction to OBO-Edit2 ==
-'''Tutorial by David Osumi-Sutherland (FlyBase)'''
+'''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 logically defined terms.
+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:
 '''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'''
 '''Links'''