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[bioontology-support] [BioPortal] Feedback from mikayla-grace

Paul R Alexander palexander at stanford.edu
Tue Apr 21 16:28:08 PDT 2015


In the UI of your appliance, you can go to the ontology and look for the link titled "Edit submission information". On that form, under the "Format" section, you should enter the following URIs in their corresponding property:
Preferred Name: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P108 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P108>
Synonym: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90>
Definition: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P97 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P97>

And then click the "Save submission" button. This should queue the ontology for reprocessing or you can follow the steps you indicated to process it right away.

NCIT uses URIs to identify these property types that our system won't recognize by default, hence the need to add them.

Paul


> On Apr 21, 2015, at 3:52 PM, bio-ontology at imagemagick.org wrote:
> 
>> First troubleshooting step would be to restart the appliance.
>> 
>> You can do so by running bprestart command form the OS command line or you 
>> can simply reboot the VM.
> 
> Thank you for your suggestions.  We ran bprestart and restarted the
> appliance and even reimported the appliance.  None of these steps
> helped-- that is annotations for NCIT were still not available.  We did
> finally get annotations working by manually parsing the ontology as suggested @
> http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F.
> Now we can annotate with the REST API against NCIT except synonyms and
> definitions are missing (e.g. only matchType of PREF is returned).  We have
> over 1 million abstracts to annotate but we cannot proceed until synonyms
> are available (i.e. we need annotations of matchType SYN).  Do you have any
> suggestions to get synonyms included with NCIT on the appliance?  We need the
> appliance to return the same results as bioportal.bioontology.org.
> 
> Thanks,
> 
> Mikayla Grace
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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