paxtools.jar toSif NCI/Nature PID owl throws NullPointerException

[Paul Shannon]

Hi all,

I just made my first attempt to use paxtools. I grabbed an owl file
from NCI/Nature Pathway Interaction Database (the Hedgehog Pathway).
I figured creating a sif file might be the most basic operation.

Pasted in below is what I see. Can anyone help me figure this out? I
am not sure what the 'interface for DATASOURCE' is.

Thanks!

- Paul Shannon

-----------------------------------
java -jar paxtools-4.0.0-20110705.jar toSif hedgehog_2pathway.owl
test.sif
142 [main] ERROR org.biopax.paxtools.model.BioPAXLevel - Could not
find the interface for DATA-SOURCE
143 [main] ERROR org.biopax.paxtools.model.BioPAXLevel -
[Ljava.lang.StackTraceElement;@691e0c13
Exception in thread "main" java.lang.NullPointerException
at
org.biopax.paxtools.impl.BioPAXFactoryAdaptor.mapClassName(BioPAXFactoryAdaptor.java:
20)
at
org.biopax.paxtools.impl.BioPAXFactoryAdaptor.canInstantiate(BioPAXFactoryAdaptor.java:
30)
at
org.biopax.paxtools.io.SimpleIOHandler.createAndBind(SimpleIOHandler.java:
196)
at
org.biopax.paxtools.io.BioPAXIOHandlerAdapter.convertFromOWL(BioPAXIOHandlerAdapter.java:
240)
at org.biopax.paxtools.PaxtoolsMain.getModel(PaxtoolsMain.java:
331)
at org.biopax.paxtools.PaxtoolsMain.toSif(PaxtoolsMain.java:
284)
at org.biopax.paxtools.PaxtoolsMain$Command
$2.run(PaxtoolsMain.java:338)
at org.biopax.paxtools.PaxtoolsMain.main(PaxtoolsMain.java:45)
wombat.hedgehog> dir *jar
-rw-r--r--@ 1 pshannon staff 15119224 Jul 13 17:08
paxtools-4.0.0-20110705.jar

[Emek Demir]

Hi Paul,

This is a level conflict. DATA-SOURCE is BioPAX Level 2. For some reason
Paxtools is expecting Level 3. Can you please post the file you used?

Best,
ED

[Paul Shannon]

Thanks for the response!

Here is the Hedgehog pathway owl file from Nature/NCI.

- Paul

[Paul Shannon]

Thank you, Emek. Removing those 4 lines did indeed fix the problem. Thanks for finding the time to take a look at this.

After running the modified file successfully with 'toSif' (and discovering that not much interaction specificity is reported) I then tried the 'toSifnx' option:

wombat.hedgehog> java -jar paxtools-4.0.0-20110705.jar toSifnx hedgehog_2pathway.owl test.sifnx
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3
at org.biopax.paxtools.PaxtoolsMain.toSifnx(PaxtoolsMain.java:278)
at org.biopax.paxtools.PaxtoolsMain$Command$3.run(PaxtoolsMain.java:341)
at org.biopax.paxtools.PaxtoolsMain.main(PaxtoolsMain.java:45)

Apparently this option needs more arguments on the command line. The help says

toSifnx : file1 outEdges outNodes writePublications prop1,prop2,.. converts model to the extendent simple interaction format

I am not quite sure how to interpret these arguments. A quick web searched did not help.

Can I get a pointer to some documentation, an example, or some advice on how to invoke toSifnx?

My overall goal is to extract all the interaction information I can from the file.

Thanks!

- Paul

On Jul 15, 2011, at 3:12 PM, Emek Demir wrote:

> Hi Paul,
>
> I finally traced it . No it was not a level problem.
>
> This is the text throws Paxtools simple reader off ( hey it is a simple reader). Probably Jena reader would be able to read it all right
>
> <physicalEntity rdf:ID="pid_m" >
> <bp:DATA-SOURCE rdf:resource="#PID_DataSource" />
> <bp:NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></bp:NAME>
> </physicalEntity>
>
> physicalEntity has no namespace - it should be bp:physicalEntity.. Not sure what this 4 lines are or when they were introduced. In any case if you remove them Paxtools reads it normally.
>
> I will report this to NCI. Thanks for catching this.
> Best,
> ED

[Benjamin Gross]

Hi Paul,

Thanks for bringing this to our attention. The paxtools-console program needs its help text updated. An example call of the toSifnx option would be the following:

java -jar paxtools.jar toSifnx ./test.owl ./edges.txt ./nodes.txt "Entity/xef:UnificationXref,Entity/xref:RelationshipXref" "Interaction/dataSource/name,Interaction/xref:PublicationXref"

which would converter the test.owl file and dump SIF interactions and desired edge attributes (in this case data source name and publication xrefs) into edges.txt and node attributes (UnificationXref and RelationshipXref) into nodes.txt.

In this case the test.owl file is BP L3 therefore the attributes requested follow paxtools L2 attribute paths.

Let me know if you have any more problems.

Thanks,
Benjamin

[IgorRodchenkov]

Sadly, there was a typo in the previously posted answer/command: Entity/xef (made my life not easy); use Entity/xref (or even better - use EntityReference/xref there!)

IR.