Ontology extensions

Ontology extensions or bridge modules are sub-ontologies maintained by the GOC that are not merged into the main GO file.

Status

The cross-product files previously had a primary location in the scratch directory in GO CVS. Previously the primary format was obo, and these we hand edited. . These are gradually being moved to the ontology/extensions/ directory in GO SVN.

Browsing

The extension ontologies are in OWL and are best viewed and edited in Protege 4.

The URLs for the GO extensions all start with http://purl.obolibrary.org/obo/go/extensions/

You should load one of the "importer" files into Protege.

E.g.

• http://purl.obolibrary.org/obo/go/extensions/x-cell-importer.owl

Editors Guide

SVN Access

The primary location for the GO extensions are in GO SVN (not supported in the legacy CVS structure) in the ontology/extensions/ directory

For more info see:

• Migration_of_GO_CVS_to_SVN
• Ontology_Release_Files_Proposal

Editing logical definitions in extension ontologies

1. Check out the ontology/ tree from SVN
2. Load the importer ontology into Protege 4
3. In the Protege menu select View/Show all loaded ontologies
4. In the ontology selector bar at the top, select the bridge ontology (not the importer). E.g. x-cell.owl
5. Add, delete and modify logical definitions in extension
6. Save back to extension file (e.g. x-cell.owl)
7. svn commit

Tip for faster access

Protege makes use of a file called catalog-v001.xml

TODO - add tips here