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[bioontology-support] Equivalent classes showing as duplicates in BioPortal

Paul R Alexander palexander at stanford.edu
Mon Jun 23 16:30:14 PDT 2014


Is it possible for you to remove the imports prior to uploading? I think typically authors want this information included.

Paul


On Jun 23, 2014, at 2:25 PM, Joachim Baran <joachim.baran at gmail.com> wrote:

> Hi!
> 
>   I think I am actually asking for less. My ontology would render better if external ontologies would not be imported and class equivalences were omitted.
> 
> Kim
> 
> 
> On 23 June 2014 12:00, Paul R Alexander <palexander at stanford.edu> wrote:
> We handle class equivalencies appropriately in the context that we operate, which is that we don’t perform (much) reasoning on the submitted ontologies. We basically only reason enough to provide a hierarchy, which is why the equivalent classes show up with the same subClassOf relationships. However, we don’t do any reasoning beyond this so other properties remain distinct between the classes.
> 
> Tracking imports is extremely complex using the toolchain that we have in place. Though we’re always on the lookout for ways to accommodate this, it isn’t something we’ll be supporting any time soon.
> 
> Best,
> Paul
> 
> 
> On Jun 22, 2014, at 9:49 AM, Joachim Baran <joachim.baran at gmail.com> wrote:
> 
>> Hello,
>> 
>>   I have just uploaded GFVO to BioPortal and it looks like class equivalences are not handled properly. Just like in Protege, classes that are equivalent to each other are shown separately. This will look like duplicates to users (seeing "Name", "name", "Label", "label", etc.), where only hovering over the link reveals where these classes are coming from.
>> 
>>   Having said that, it would also be great to highlight which classes are defined in the ontology that was uploaded, in contrast to the classes that were imported.
>> 
>>   http://bioportal.bioontology.org/ontologies/GFVO?p=classes
>> 
>> Thanks,
>> 
>> Kim
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> 

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