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

Joachim Baran joachim.baran at gmail.com
Tue Jun 24 11:40:45 PDT 2014


Okay, it works now (removed imports and equivalences).

It is just a bit weird that at some point the summary statistics (no. of
classes, etc.) were updated, but the class browser still showed the old
ontology. After a while the browser also updated.

Perhaps have a pop-up notifying users that it takes 24h for *everything* to
update?

Kim



On 23 June 2014 18:04, Paul R Alexander <palexander at stanford.edu> wrote:

> It updates once a day, yes. It will show a new entry in the Submissions
> table on the Summary page for the ontology one we have found the new
> version.
>
> Paul
>
>
> On Jun 23, 2014, at 6:04 PM, Joachim Baran <joachim.baran at gmail.com>
> wrote:
>
> 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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