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

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Nov 29 16:13:19 PST 2016


Hi Vincent,


On Nov 28, 2016, at 9:54 PM, vincentguo <gjw_0418 at sina.com<mailto:gjw_0418 at sina.com>> wrote:

I uploaded NCBITAXON.ttl on my Virtual Appliance directly and got "Rdf
Error”.


When you attempted to upload the NCBITAXON.ttl file, did you specify the ontology format as “UMLS”?  Here’s a screen shot from the BioPortal UI to indicate the section I’m referring to in the Add New Submission form:


[cid:6FEF8246-8BBF-45F5-82E4-D8C02391321B at stanford.edu]


I’m assuming you got the TTL file from us?


Then I converted the ttl file into owl using Protege 5.0.0 and its
status is always "uploaded". In its parsing.log, I found "ERROR -- :
NoMethodError: undefined method `get_code_from_id' for nil:NilClass".


Would it be possible for you to send us the entire parsing.log file for this ontology from your environment?

Kind regards,
Jennifer


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