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	COBrA Curation Tool README 
      	Mon Jan 22 10:47:28 GMT 2007
     	Stuart Aitken and Yin Chen {stuart,ychen3}@inf.ed.ac.uk
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This README covers the COBrA-CT OBO Explorer
The OBO Explorer is a Protege Plug-in.

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COBrA-CT OBO Explorer

The OBO Explorer allows Protege users to view and edit the 
definitions and other annotations for OBO and Gene Ontology
terms.

Distribution
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On all platforms, the plug-in is installed  by expanding the archive 
at the top level of the Protege installation directory, e.g. in
/Protege_3.2. The archive will create a new directory in 
the ./plugins directory. Expand the archive using WinZip,
or at the commandline: tar -xvf obo-explorer.tar.
The archive should create this README plus:
 ./plugins/uk.ac.ed.aiai.cobract	:the plugin
./explorer.html				:the help file
./LICENSE-COBrA-CT-OE.txt           :license agreement

Installation
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The OBO Explorer requires no further installation, however, it requires 
Protege 3.2  to be installed, see http://protege.stanford.edu/download/download.html
Java 1.5 is also required, see: http://java.sun.com/j2se/1.5.0/
OS X users should refer to: http://docs.info.apple.com/article.html?artnum=301073
Typing java -version at the commandline should return:
java version "1.5.0_06" on OS X or
java version "1.5.0_04" on Linux

Licensing
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The OBO Explorer is distributed under the University of Edinburgh
open source licence.

Use
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1. Protege must be started first, double-click on the icon.
2. Load an OBO OWL ontology into Protege (use the Open option
    under File), or Create a new OWL project (use the New Project 
    option under File).
3. Configure the project to show the OBO Explorer Tab: under Project,
    select Configure, then in the list of tools select the OboClassesTab and OboOntologyTab
4.  Two tabs titled "OBO Explorer" and "OBO Ontology Metadata" should appear. They can be used to edit OBO Ontologies.
5. More detailed help can be found in explorer.html
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