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

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:

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
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

@@ Line 1: / Line 1: @@
 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.
-It will include details of the software to install and their configuration along with test ontologies to download.  Please check back closer to the session for details.
 == Program ==
@@ Line 12: / Line 9: @@
 == Slides ==
-Coming soon
+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)
-== Test ontologies ==
+[http://caro2.googlecode.com/svn/trunk/scratch/tutorial_slides3.pdf draft slides PDF version] (may change slightly)
+== Test ontology ==
+[http://caro2.googlecode.com/svn/trunk/scratch/tutorial.obo tutorial.obo]
+Right click and choose 'save link as'
 == Software to install ==
@@ Line 25: / Line 29: @@
 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 ===
-Download the latest version of the Obo Ontology Release Tool GUI from here:
+Download the latest version (0.3) of the Obo Ontology Release Tool GUI from here:
 * http://code.google.com/p/owltools/downloads/list
@@ Line 47: / Line 53: @@
 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]