Difference between revisions of "From OBO to OWL and back"
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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. | 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 == | ||
| + | Slides from the whole ICBO anatomy workshop, including the obo to owl portion, are located here: | ||
| + | [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) | ||
| + | [http://caro2.googlecode.com/svn/trunk/scratch/tutorial_slides3.pdf draft slides PDF version] (may change slightly) | ||
| − | == Test | + | == Test ontology == |
| + | [http://caro2.googlecode.com/svn/trunk/scratch/tutorial.obo tutorial.obo] | ||
| + | Right click and choose 'save link as' | ||
== Software to install == | == Software to install == | ||
| Line 17: | Line 28: | ||
=== OBO-Edit 2.1 === | === OBO-Edit 2.1 === | ||
| + | Please use [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/oboedit-2.1beta16/ 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 === | === OBO to OWL conversion tool === | ||
| + | Download the latest version (0.3) of the Obo Ontology Release Tool GUI from here: | ||
| + | |||
| + | * http://code.google.com/p/owltools/downloads/list | ||
| + | |||
| + | Installers are available for mac, windows and unix. After installation, you will have two applications: | ||
| + | * The obo2owl converter | ||
| + | * [http://code.google.com/p/owltools/wiki/OBOReleaseManagerGUIDocumentation The Obo Ontology Release Tool] | ||
=== Protege 4.1 === | === Protege 4.1 === | ||
| + | Please install [http://protege.stanford.edu/download/protege/4.1/installanywhere/Web_Installers/ 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: | |
| + | [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
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:
- The obo2owl converter
- The Obo Ontology Release Tool
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