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[bioontology-support] virtual appliance population workflow problem

Nikolina Koleva nikolina.koleva19 at yahoo.de
Tue Jun 18 06:27:34 PDT 2013


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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