Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Manuel Fiorelli manuel.fiorelli at gmail.com
Wed Mar 4 15:49:46 PST 2020


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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200305/2c4045c0/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-03-03 15.46.09.png
Type: image/png
Size: 111616 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200305/2c4045c0/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-03-03 15.53.59.png
Type: image/png
Size: 130557 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200305/2c4045c0/attachment-0003.png>


More information about the bioontology-support mailing list