Cy3: problem importing gene ontologies

[Corinna Vehlow]

Hi there,

I tried to import Gene Ontology files as described here:
http://wiki.cytoscape.org/Cytoscape_3/UserManual
Select File → Import → Ontology and Annotation... to open the "Import Ontology and Annotation" window. 

Unfortunately, the window doesn't open and I get the following output on the command line:

Cytoscape 3.1.0-beta1> CurrentNetworkViewChangedListener: number of network views = 1
handleEvent(SessionLoadedEvent evt): Session loaded: galFiltered in /Applications/Cytoscape_v3.1.0-beta1/sampleData/
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
    at java.util.Vector.removeElementAt(Vector.java:511)
    at javax.swing.table.DefaultTableModel.removeRow(DefaultTableModel.java:446)
    at org.cytoscape.tableimport.internal.ui.ImportTablePanel.useFirstRow(ImportTablePanel.java:1435)
    at org.cytoscape.tableimport.internal.ui.ImportTablePanel.setPreviewPanel(ImportTablePanel.java:1578)
    at org.cytoscape.tableimport.internal.ui.ImportTablePanel.<init>(ImportTablePanel.java:348)
    at org.cytoscape.tableimport.internal.task.ImportOntologyAndAnnotationAction.actionPerformed(ImportOntologyAndAnnotationAction.java:89)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
    ...


Does anyone have any ideas about this problem?
Are there any requirements for the networks in order to be able to import the gene ontology information?

Corinna

[Scooter Morris]

Hi Corinna,
Nope, it's definitely a bug -- I ran into the same thing and logged
a bug.

-- scooter

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[Corinna Vehlow]

I figured that it's working on the Cytoscape 3.0.1 version.

I'm a bit confused though about the edge rows in the table. Usually the column 'shared name' contains the information which nodes are connected, so I was expecting entries like "GO:id1 (is_a) GO:id2" if the interaction type is 'is_a'. Bizarrely, the entries are empty for that column after I imported the gene ontology (only the interaction-, selected- and SUID-columns contain entries), although the edges are visible in the network view.
How do I get the parent information for nodes (GO-terms)?

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