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[bioontology-support] [BioPortal] Feedback from mkalas

Matus Kalas Matus.Kalas at uib.no
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 http://edamohntology.org/topic_0077 instead of 
http://edamontology.org/topic_0077. Searching for "RNA" in the GUI and 
selecting the one with "RNA" in capitals, without any other words (or 
alternatively just going to 
conceptid=http%3A%2F%2Fedamontology.org%2Ftopic_0099), will show up as 
hanging underneath a non-labelled class topic_0077.

The second version of EDAM_1.21.owl fixes this, and "RNA" 
(conceptid=http%3A%2F%2Fedamontology.org%2Ftopic_0099) appears correctly 
underneath "Nucleic acids".

A million thanks again for your prompt help!
Matus


On 2018-07-31 05:02, Jennifer Leigh Vendetti wrote:
> Hi Matus,
> 
>> On Jul 30, 2018, at 7:30 PM, support at bioontology.org 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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