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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:
On Aug 11, 2020, at 6:31 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:
Thanks! Can you confirm the last link where you refer to a script but that link is the same as the previous link?
On Tue, Aug 11, 2020 at 6:18 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
On Aug 10, 2020, at 5:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:
Email: rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>
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:
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:
It’s also possible to upload ontologies programmatically. An appliance user submitted the following script to our code sample repository:
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.
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