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[bioontology-support] Error - Cannot add custom ontology set

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed May 2 11:19:15 PDT 2018


Hi Xindi,


On May 1, 2018, at 12:21 PM, Xindi Guo <xindi.guo at sagebase.org<mailto:xindi.guo at sagebase.org>> wrote:

I was trying to add the NCIT<https://bioportal.bioontology.org/ontologies/NCIT> ontology to my custom ontology set. However, it went to the error page (image attached) when I clicked on "Save Custom Ontologies". Also, my colleague has tried to add it as well in her account.


As of yet, I haven’t been able to reproduce this error where clicking the “Save Custom Ontologies” button results in a 404 error.


She saw the same error page when trying to access the NCIT link (https://bioportal.bioontology.org/ontologies/NCIT) and she was not even able to find NCIT in the list of the custom ontology set.


I modified my personal account to use a custom ontology set of NCIT, and I was able to reproduce this secondary error where trying to view the NCIT ontology results in a 500 error. There appears to be a bug in the BioPortal software that prevents users with custom ontology sets from accessing certain ontologies. I’ve entered an issue in our tracker with more detail:

https://github.com/ncbo/ontologies_api/issues/47

You can follow our progress there in terms of when we’re able to release a fix.

Apologies that I’m not aware of any workaround at the moment other than removing your custom ontology set. If you navigate to the Account Settings page for your account, you should be able to click “clear selection” link in the Custom Ontology Set section and click the “Save Custom Ontologies” button to clear the set of custom ontologies. This restores your account to the previous state in BioPortal where all public ontologies are visible / accessible.

Kind regards,
Jennifer

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