Ontology extensions

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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

  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


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>