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[bioontology-support] Problems with root concepts in a SKOS ontology

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Mar 3 15:57:34 PST 2020


Hello Manuel,


On Mar 3, 2020, at 8:25 AM, Manuel Fiorelli <manuel.fiorelli at gmail.com<mailto:manuel.fiorelli at gmail.com>> wrote:

Hi Jennifer

thank you very much for the time that you spent on my request for support. I was aware of the limitation regarding the assignment of SKOS concepts to schemes; consequently, I added the "inverse" statements, which unfortunately were written at the end of the submission in a separate rdf:Description.

<rdf:Description rdf:about="http://example.org/conceptScheme_07199b34">
   <skos:hasTopConcept rdf:resource="http://example.org/c_48989b6a"/>
   <skos:hasTopConcept rdf:resource="http://example.org/c_e17f8367"/>
   <skos:hasTopConcept rdf:resource="http://example.org/c_4b2068df"/>
   <skos:hasTopConcept rdf:resource="http://example.org/c_4e52523a"/>
  <skos:hasTopConcept rdf:resource="http://example.org/c_968694e7"/>
</rdf:Description>

The motivation of this "strange" serialization is that it was generated automatically without enabling the pretty print routines. Do you think that this might explain why root classes aren't found.


When I investigated your problem report, I downloaded the file that was associated with your latest submission (the 6th file that you uploaded that is marked as version “1000” in the user interface). That source file doesn’t contain any of the hasTopConcept properties that you list above.

After reading this follow-up message from you, I downloaded one of your previous submissions (the 5th file that you uploaded). In that source file, I do see these hasTopConcept properties. It shouldn’t matter that they are listed at the end of your file in a separate rdf:Description. I went ahead and uploaded this source file to our staging environment (this is a private instance that we use internally for testing), and I can confirm that BioPortal properly detected the root classes and the 404 error no longer appears in the user interface:



[cid:572FD2E1-25A6-407C-BDB8-49D409755157 at stanford.edu]


Here is the REST call to retrieve the roots that no longer returns an empty set:


[cid:F5BD56DA-E0CD-4CD1-9FE2-DE3840FCDF25 at stanford.edu]


If you would like to upload a new version of your source file with these hasTopConcept properties, you should be able to successfully see the class tree in the user interface. One thing to note is that BioPortal has several caches in place for performance reasons. When you upload a new submission, the new data may not appear immediately.

Kind regards,
Jennifer


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