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

Manuel Fiorelli manuel.fiorelli at gmail.com
Thu Mar 5 14:25:35 PST 2020


Hi John

I logged in BioPortal and now I can see my thesaurus. However, I don't know
whether it was a server-side or client-side cache.

I would like to thank you and Jennifer for the support.

Regards
Manuel


Il giorno gio 5 mar 2020 alle ore 02:37 John Graybeal <
jgraybeal at stanford.edu> ha scritto:

> 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>
> 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> ha scritto:
>
>> Hello Manuel,
>>
>>
>> On Mar 3, 2020, at 8:25 AM, Manuel Fiorelli <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
> 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>
>
> 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>
>
> Cc: "support at bioontology.org" <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> ha scritto:
>
>> Hello Manuel,
>>
>>
>> On Mar 3, 2020, at 8:25 AM, Manuel Fiorelli <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:
>>
>>
>>
>>
>>
>>
>> Here is the REST call to retrieve the roots that no longer returns an
>> empty set:
>>
>>
>>
>>
>> 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
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>

-- 
Manuel Fiorelli
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