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: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 - it just imports other ontologies
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
Protege tips
Protege 4 makes use of a file called catalog-v001.xml
You can use this to control where ontologies are downloaded from. If you have the GO-SVN tree checked out, you will have a directory called ontology/externals/. This uses a mechanism called "svn externals" to pull in ontologies from other repositories.
You can use a setup like this:
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog"> <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/extensions/x-cell.owl" uri="x-cell.owl"/> <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/extensions/x-metazoan-anatomy.owl" uri="x-metazoan-anatomy.owl"/> <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/extensions/x-plant-anatomy.owl" uri="x-plant-anatomy.owl"/> <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go.owl" uri="../go.owl"/> <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl-basic.owl" uri="../external/cell-ontology/cl-basic.owl"/> </catalog>