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[bioontology-support] How to upload NCBITAXON.ttl on VA?

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Nov 30 12:41:32 PST 2016


Hi Vincent,


On Nov 30, 2016, at 12:30 AM, vincentguo <gjw_0418 at sina.com<mailto:gjw_0418 at sina.com>> wrote:

Hi Jennifer,

   Thank you for your prompt reply.

   I specified the format as "UMLS", but got the same error. This is my
parsing log:  parsing.log
<http://ncbo-support.2288202.n4.nabble.com/file/n4655184/parsing.log>


Thank you for sending us the log file.  According to the contents, it looks like for this attempt you submitted an OWL file (ncbitaxon.owl).  Apologies if this wasn’t clear from my response yesterday, but if you submit an OWL ontology, you should also specify the format as OWL.  I had asked what format you used on your initial attempt, because I thought you might have submitted a TTL file, and specified the format as OWL instead of UMLS, which could have caused issues.

Irregardless, according to the contents of the log file, the ontology parsing portion finished successfully:

I, [2016-11-28T18:12:46.934366 #28801]  INFO -- : OWLAPI java parse finished OK.

The issue happens later on when the BioPortal software attempts to assign a status to the ontology submission object.  An “undefined method” exception at this point in the code seems odd, and we’re wondering if there could be a corrupt entry in the BioPortal cache.

Would you be willing to restart the system (which would clear the application caches)?  You can can use the command “bprestart”, as documented in the system administration section on our wiki:

https://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance#Basic_System_Administration

After doing so, could you let us know if the ontology summary page for NCBITAXON still displays the “Error Rdf” status that you mentioned previously?

Thanks,
Jennifer

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