PSI-MI in OWL

One of the goals of the crowd who would like to see more use of OWL in BioPAX is the import of external vocabularies into a format that OWL understands. To this end this page records an attempt do this for the psi-mi openControlledVocabulary.

Steps:

Download DAG-Edit from https://sourceforge.net/project/showfiles.php?group_id=36855

I'm using OS X. I uncompressed to the Desktop and then

cd ~/Desktop/dagedit_1_419-rev-3 ./dagedit

Ignore some errors printed to the shell.

Download http://psidev.sourceforge.net/mi/controlledVocab/psi-mi2.dag

From the menu, choose File, Load Terms. Below the File Paths sections, click the Add button. Click the Browse button beside the lower of two newly created text fields in that section. Browse to the downloaded psi-mi2.dag. Click open and then ok in the Load Terms dialog.

You should now see the psi-mi hierarchy.

Choose File, Save As...

From the Choose Data Adaptor popup, choose Owl Adaptor.

In file path type "/Users/ /Desktop/psimi.owl"

Click commit. File should be created.

You want to do some edits now.

The header reads:



I think we want it to read something like:

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns="http://www.biopax.org/external/psimi#" xml:base="http://www.biopax.org/external/psimi#" xmlns:psimi="http://www.biopax.org/external/psimi#"

Change all instances of the string '<rdfs:subClassOf rdf:resource="' to '<rdfs:subClassOf rdf:resource="#'

Done. You can get this file here attachment:PSI-MI_in_OWL/psimi.owl

(Alan Ruttenberg 2005-07-11)