Difference between revisions of "From OBO to OWL and back"

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== Slides ==
 
== Slides ==
  
Coming soon
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Slides from the whole ICBO anatomy workshop, including the obo to owl portion, are located here:
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[http://icbo.buffalo.edu/2011/slides/Anatomy%20Workshop/ anatomy workshop slides]
 +
 
 +
[http://caro2.googlecode.com/svn/trunk/scratch/tutorial_slides3.ppt draft slides ppt version] (may change slightly)
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[http://caro2.googlecode.com/svn/trunk/scratch/tutorial_slides3.pdf draft slides PDF version] (may change slightly)
  
 
== Test ontology ==
 
== Test ontology ==
  
Coming soon
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[http://caro2.googlecode.com/svn/trunk/scratch/tutorial.obo tutorial.obo]
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Right click and choose 'save link as'
  
 
== Software to install ==
 
== Software to install ==
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Please use [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/oboedit-2.1beta16/ OBO-Edit 2.1beta16].
 
Please use [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/oboedit-2.1beta16/ OBO-Edit 2.1beta16].
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 +
Note - for (recent versions of?) Windows, the Java Virtual Machine is limited to 1G.  If OBO-Edit fails to load in windows with the default memory settings, please re-install with memory set to 1024M.
  
 
=== OBO to OWL conversion tool ===
 
=== OBO to OWL conversion tool ===
  
Download the latest version of the Obo Ontology Release Tool GUI from here:
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Download the latest version (0.3) of the Obo Ontology Release Tool GUI from here:
  
 
* http://code.google.com/p/owltools/downloads/list
 
* http://code.google.com/p/owltools/downloads/list
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http://code.google.com/p/caro2/wiki/Getting_started
 
http://code.google.com/p/caro2/wiki/Getting_started
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=== Optional ===
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Kent's test ontology from the anatomy workshop:
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[http://caro2.googlecode.com/svn/trunk/scratch/icbo-snomed-partonomy-test.owl icbo-snomed-partonomy-test.owl]

Latest revision as of 12:42, 10 August 2011

This page is the location for downloads and instructions for the ICBO 2011 tutorial "From OBO to OWL and back again" to be held on July 27th.

Program

The program, including suggestions for preparatory reading, can be found here:

http://icbo.buffalo.edu/2011/TutorialF.pdf

Slides

Slides from the whole ICBO anatomy workshop, including the obo to owl portion, are located here: anatomy workshop slides

draft slides ppt version (may change slightly)

draft slides PDF version (may change slightly)

Test ontology

tutorial.obo

Right click and choose 'save link as'

Software to install

OBO-Edit 2.1

Please use OBO-Edit 2.1beta16.

Note - for (recent versions of?) Windows, the Java Virtual Machine is limited to 1G. If OBO-Edit fails to load in windows with the default memory settings, please re-install with memory set to 1024M.

OBO to OWL conversion tool

Download the latest version (0.3) of the Obo Ontology Release Tool GUI from here:

Installers are available for mac, windows and unix. After installation, you will have two applications:

Protege 4.1

Please install Protege 4.1 release candidate 5 (build 235).

This version of Protege should not need any configuring.

Previous version required configuring to ensure labels (OBO names) are displayed in all components instead of IDs. Try loading an OBO file to test this (it should load straight in, even though the dialog box asks you to choose and OWL file). If you can only see IDs in the class hierarchy, then you should configure following the instructions here:

http://code.google.com/p/caro2/wiki/Getting_started

Optional

Kent's test ontology from the anatomy workshop: icbo-snomed-partonomy-test.owl