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[bioontology-support] error with bioportal

John Graybeal jgraybeal at
Fri Jan 7 16:05:12 PST 2022

Thanks Misha.  I'll just add to this that my experience is that if I check the ontology page quickly after submission (but before full processing is complete), I get "Problem retrieving classes." It can then take quite some time before that disappears, and involves refreshing my browser cache for that page *and* that BioPortal's cache has been updated also, which should happen every 2 hours or so I believe.

Sorry we haven't had time to chase that down more precisely, but it may give you an idea how to proceed.


On Jan 5, 2022, at 8:50 AM, Michael Dorf <mdorf at<mailto:mdorf at>> wrote:

Hi Meriam,

Thank you for contacting us.  I’ve checked your ontology, and the classes display correctly on my end. It’s possible that the error you saw was due to our production caches not having been fully refreshed after your ontology had been processed. Error Diff can be ignored for the moment. The error indicates that there is no file in our system to compare the latest version to. This should fix itself with future versions of the ontology.

Let us know if you run into further issues.


On Jan 5, 2022, at 12:37 AM, Meriam Ghardallou <ghardallou.m at<mailto:ghardallou.m at>> wrote:

Dear sir/madam
I ‘m asking about the error message that I obtained when I tried to submit a new version of ontologies;
It is indicated « Error Diff » and « Problem retrieving classes"
Following  screen shots of the error message and the URL of the page

Thank you so much for your help

<Capture d’écran 2022-01-05 à 09.34.37.png><Capture d’écran 2022-01-05 à 09.36.31.png>
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John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360

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