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[bioontology-support] virtual appliance population workflow problem

Nikolina Koleva nikolina.koleva19 at yahoo.de
Mon Jun 17 06:19:28 PDT 2013


Dear Trish Whetzel and all,

I tried to execute the workflow for populating for the ncbo appliance as it is described on:

http://www.bioontology.org/wiki/index.php/Resource_Index_Dataset_Workflow_Howto

after fixing some pointers in the build.properties file, the listed commands are working without getting errors.

I tried to add one ontology (GEO) or all of them (GEO,AE,CT,GM,OMIM,CDD,PGDI,PGDR,PGGE,REAC,RXRD,UPKB,WP,BSM,DBK,SMD,CANANO,PC,PCM,GAP,MICAD,PM,AERS,GRANTS)
but in either cases the problem is that no ontology has been found among those.
The message that I am getting is: 

2013-06-17 05:56:13,423 - Populating obs slave tables starts 
2013-06-17 05:56:14,007 - Population of slave data from master obs database started. 
2013-06-17 05:56:14,211 - Number of ontologies added :0 
2013-06-17 05:56:14,212 - Number of ontologies added :0 
2013-06-17 05:56:14,212 - Number of ontology entries added in slave ontology table : 0 
2013-06-17 05:56:14,212 - No new ontology found in master table. 
2013-06-17 05:56:14,212 - Population of slave data from master obs database completed. 
2013-06-17 05:56:14,212 - Population of slave data processed in : 00 hours, 00 minutes, 00 seconds. 
org.ncbo.stanford.obr.exception.NoOntologyFoundException: No new ontology found
	at org.ncbo.stanford.obr.service.obs.impl.ObsDataPopulationServiceImpl.populateObsSlaveData(ObsDataPopulationServiceImpl.java:85)
	at org.ncbo.stanford.obr.service.workflow.impl.ResourceIndexWorkflowImpl.populateObsSlaveTables(ResourceIndexWorkflowImpl.java:81)
	at org.ncbo.stanford.obr.populate.main.PopulateResourceIndex.main(PopulateResourceIndex.java:33)

I would appreciate any ideas on what the problem might be.

Once this works a further question is if there is an automatic way to include other ontologies that are contained in BioPortal.

Best regards,
Nikolina Koleva





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