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

John Graybeal jgraybeal at stanford.edu
Wed Mar 4 17:37:03 PST 2020


Manuel, I'm seeing 5 countries as the classes and 5 properties, and several class mappings for each class.

If you use the Developer view on your browser (CMD-OPTION-I for MacOS Chrome) you can hold down the reload button to clear your local cache, that may do the trick.

john

On Mar 4, 2020, at 3:49 PM, Manuel Fiorelli <manuel.fiorelli at gmail.com<mailto:manuel.fiorelli at gmail.com>> wrote:

Hi Jennifer

I made a new submission this afternoon, which should contain the triples with the predicate hasTopConcept.

I can fetch roots with the REST API:

https://data.bioontology.org/ontologies/TESTTES/classes/roots

but still the user interfaces produces an error. I hope that this is an issue with caching. I will try again in the next few days.

Regards
Manuel

Il giorno mer 4 mar 2020 alle ore 00:57 Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> ha scritto:
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:



<Screenshot 2020-03-03 15.46.09.png>


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


<Screenshot 2020-03-03 15.53.59.png>


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




--
Manuel Fiorelli
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
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





Begin forwarded message:


From: Manuel Fiorelli <manuel.fiorelli at gmail.com<mailto:manuel.fiorelli at gmail.com>>

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

Date: March 4, 2020 at 3:49:46 PM PST

To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>

Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>


Hi Jennifer

I made a new submission this afternoon, which should contain the triples with the predicate hasTopConcept.

I can fetch roots with the REST API:

https://data.bioontology.org/ontologies/TESTTES/classes/roots

but still the user interfaces produces an error. I hope that this is an issue with caching. I will try again in the next few days.

Regards
Manuel

Il giorno mer 4 mar 2020 alle ore 00:57 Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> ha scritto:
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:170a7f174ba1d916d701]


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


[cid:170a7f174bb82ba90ef2]


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




--
Manuel Fiorelli
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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