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[bioontology-support] [BioPortal] Feedback from mkalas

Matus Kalas Matus.Kalas at
Tue Jul 31 09:09:05 PDT 2018

Thank you so much, Jennifer!

The problem is now fixed after your adjustments.

You understood the problem exactly right.

The first version of the EDAM_1.21.owl had a typo in 2 super-class URIs 
stating instead of Searching for "RNA" in the GUI and 
selecting the one with "RNA" in capitals, without any other words (or 
alternatively just going to, will show up as 
hanging underneath a non-labelled class topic_0077.

The second version of EDAM_1.21.owl fixes this, and "RNA" 
( appears correctly 
underneath "Nucleic acids".

A million thanks again for your prompt help!

On 2018-07-31 05:02, Jennifer Leigh Vendetti wrote:
> Hi Matus,
>> On Jul 30, 2018, at 7:30 PM, support at wrote:
>> We're releasing a new version of the EDAM ontology now (during today
>> and tomorrow).
>> I must say that I'm impressed that most of the previous problems
>> with updating have been solved. Awesome!
>> There is still a problem, though:
>> After I updated the new version with a new uploaded OWL file (fixing
>> an error), I get some leftovers of the previous troublesome
>> behavior:
>  I didn’t quite follow what you did. Are you saying that you created
> a new submission (version 1.21) with one OWL file, then edited the
> submission to upload a second version of the OWL file because the
> first one had an error?
>> - Clicking "1.21" returns "We're sorry but something has gone wrong.
>> We have been notified of this error." in a usual web browser.
>> - Clicking "Classes" returns "Problem retrieving classes"
> I looked at the parsing log files for your ontology and I didn’t see
> any errors, although I did notice that the system was reporting no
> metrics for this latest version. I ran a script to reprocess the
> metrics data and reset the application caches so that they’re now
> visible in the UI. So far I’m not able to reproduce either the 500
> error, or the error about retrieving classes.
> Are these still occurring for you after that adjustment I made? If so,
> could you let me know what browser you’re using?
>> - In a new web browser, those return a view of the FIRST UPLOADED
>> "version" of this particular, that is NOT THE FIXED ONE
>> - CSV download also returns the FIRST UPLOADED "version" of this
>> particular, that is NOT THE FIXED ONE
> I can test this on my end and look at the files on our production
> server, but I’ll need you to give me some kind of indication of how
> I would know if we’re seeing your “fixed” OWL file, e.g., is
> there some specific text I can search for?
> Kind regards,
> Jennifer

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