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

Joachim Baran joachim.baran at gmail.com
Mon Jun 23 18:04:06 PDT 2014


Is BioPortal updated once a day or at certain times only? I uploaded a
version of GFVO without imports and equivalences, but it still shows ~3900
classes (should be: 90).

Kim


On 23 June 2014 16:30, Paul R Alexander <palexander at stanford.edu> wrote:

> 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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