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[bioontology-support] [BioPortal] Feedback from rakesh

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Aug 12 12:47:55 PDT 2020


Sorry about that Rakesh - I meant to send a link to this script in our sample code repository:

https://github.com/ncbo/ncbo_rest_sample_code/blob/master/ruby/bioportal_ontologies_import.rb



On Aug 11, 2020, at 6:31 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:

Jennifer,
     Thanks! Can you confirm the last link where you refer to a script but that link is the same as the previous link?

Thanks,
Rakesh

On Tue, Aug 11, 2020 at 6:18 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Rakesh,


On Aug 10, 2020, at 5:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: rakesh

Email: rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2F

Feedback:

Hello,
I am using v2.5 of the Ontoportal appliance and have successfully loaded NCIT a few times now. I am now attempting to load SNOMED-CT after conversion from the UMLS using umls2rdf as a .ttl file. I have selected UMLS as the format but I have now tried twice to upload via UI and the server threw an error saying 'something went wrong and administrators have been notified. However I dont know what happened. Are there logs on the server to check?

There are some instructions for locating log files here:

https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#is-there-a-log-file-for-parsing


Any other ideas to help troubleshoot? Finally are there commands to load directly on the server I may use?



I’m not certain this is what you’re asking for, but you can manually re-parse an ontology submission using this methodology:

https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console

It’s also possible to upload ontologies programmatically. An appliance user submitted the following script to our code sample repository:

https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console

It’s a script that imports ontologies from on appliance instance to another, which is not what you’re doing. However, I thought that some portions of the code might be of interest to you.

Kind regards,
Jennifer



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Rakesh Nagarajan

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