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[bioontology-support] virtual appliance population workflow problem

Trish Whetzel whetzel at stanford.edu
Tue Jun 18 09:46:08 PDT 2013


The wiki contains information on loading ontologies from the NCBO instance of BioPortal into your own instance: 
http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_migrate_ontologies_from_BioPortal_or_previous_NCBO_Virtual_Appliance_versions_into_a_new_Appliance.3F

Cheers,
Trish 


On Jun 18, 2013, at 6:27 AM, Nikolina Koleva <nikolina.koleva19 at yahoo.de> wrote:

> Dear Ray,
> 
> thank you very much for the reply!
> I still have questions
> On Jun 17, 2013, at 9:13 PM, Ray Fergerson <ray.fergerson at stanford.edu> wrote:
> 
>> I’m unclear about what exactly you have done. Have you added the ontology to the appliance version of BioPortal? If not then you need to do this first.
> Should this be done manually? 
> Actually would like to have all ontologies that are contained in BioPoral and potentially also update the resources each six months. 
> 
>> Then you need to (re)run the annotation hierarchy and the resource index update processes for this ontology to be available for annotation and resource search.
> Is it what you refer to described here:
> http://www.bioontology.org/wiki/index.php/Annotator_Dataset_Workflow_Howto
> 
>> Note that I believe that the resource index population relies on the annotation hierarchy population process already having been run.
> 
> Best,
> Nikolina
> 
>>  
>> From: bioontology-support-bounces at lists.stanford.edu [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Nikolina Koleva
>> Sent: Monday, June 17, 2013 6:19 AM
>> To: bioontology-support at lists.stanford.edu
>> Subject: [bioontology-support] virtual appliance population workflow problem
>>  
>>  
>> 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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