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[bioontology-support] [BioPortal] Feedback from k.j.van.der.velde

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Oct 12 12:34:13 PDT 2021


Hello Joeri,


On Oct 11, 2021, at 5:18 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Dear support,

I have uploaded a new ontology last Friday (https://bioportal.bioontology.org/ontologies/DFO) but in the 'Classes' tab there is an error (Problem retrieving classes). Has it not been indexed yet, or did I do something wrong?

I’ve taken a look at our production log files. It appears that your ontology was ingested into the system and processed, i.e., our REST endpoint is currently serving class data for DFO (screenshot attached).

The BioPortal web application is showing an error message when attempting to display the Classes page because our system is unable to calculate the set of root classes for the ontology. The Classes page needs to know the root classes in order to construct the class tree. I looked briefly at your ontology and noticed that it’s an OWL ontology, but the 2 root classes are declared using an obo prefix. It’s not immediately evident to me if this is what’s causing our system difficulties in calculating the roots. I’ve entered an issue in our tracker so that we can investigate further:

https://github.com/ncbo/bioportal-project/issues/220

Kind regards,
Jennifer



[cid:194864A5-479A-4B80-AC80-D86A32331078 at lan]
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