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

bio-ontology at imagemagick.org bio-ontology at imagemagick.org
Tue Apr 21 15:52:57 PDT 2015


> 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


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