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.
This looks like this:
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/go/extensions/x-cell-importer.owl.owl"> <owl:imports rdf:resource="http://purl.obolibrary.org/obo/cl-basic.owl"/> <owl:imports rdf:resource="http://purl.obolibrary.org/obo/go.owl"/> <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/> <owl:imports rdf:resource="http://purl.obolibrary.org/obo/go/extensions/x-cell.owl"/> </owl:Ontology>
It has no axioms of its own
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:
Editing logical definitions in extension ontologies
- Check out the ontology/ tree from SVN
- Load the importer ontology into Protege 4
- In the Protege menu select View/Show all loaded ontologies
- In the ontology selector bar at the top, select the bridge ontology (not the importer). E.g. x-cell.owl
- Add, delete and modify logical definitions in extension
- Save back to extension file (e.g. x-cell.owl)
- svn commit
Tip for faster access
Protege makes use of a file called catalog-v001.xml
TODO - add tips here