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[bioontology-support] Feedback

Stephan Schurer PhD stephan.schurer at gmail.com
Wed Mar 16 21:23:06 PDT 2011


Trish, Yes, let's remove the explore link for the moment until we
understand what happened and can fix it.

Thank you,

Stephan

On Thu, Mar 17, 2011 at 12:15 AM, Trish Whetzel <whetzel at stanford.edu> wrote:
> I'm looking into this now; comparing between Protege and BioPortal.
> Would you like me to remove the Explore link on BioPortal in the meantime?
> Trish
>
> On Mar 16, 2011, at 9:11 PM, Saminda Abeyruwan wrote:
>
> Let me do a quick search and see why NCBI having problem displaying SROIQ(D)
> expressive ontologies.
> Sam
>
> On Thu, Mar 17, 2011 at 12:08 AM, Stephan Schurer PhD
> <stephan.schurer at gmail.com> wrote:
>>
>> Was wondering the same, but did not see anything that would explain
>> it. We should not leave this up at NCBO like this - really gives the
>> wrong impression. The file downloaded from NCBO looks fine in Protege.
>>
>> Trish, we have a number of other (not subsumption) relationships. I
>> assume NCBO is just showing the subsumption hierarchies?
>>
>> Thanks,
>>
>> Stephan
>>
>> On Wed, Mar 16, 2011 at 10:57 PM, Vempati, Uma <UVempati at med.miami.edu>
>> wrote:
>> > Stephan,
>> > I see the same problems that you pointed out. Sam can you comment if the
>> > display of BAO at NCBO BioPortal
>> > (http://bioportal.bioontology.org/visualize/45388) has anything to do with
>> > the modeling of BAO? Or is it an error generated during parsing?
>> >
>> > Thanks,
>> > Uma
>> > ________________________________________
>> > From: Stephan Schurer PhD [stephan.schurer at gmail.com]
>> > Sent: Wednesday, March 16, 2011 5:10 PM
>> > To: Trish Whetzel
>> > Cc: support at bioontology.org; Vempati, Uma; Saminda Abeyruwan
>> > Subject: Re: [bioontology-support] Feedback
>> >
>> > Hallo Trish - thank you. But there is an error in the visualization.
>> > If you download the ontology and open it in Protege it is correct.
>> > Specifically the class 'percent viability' must not be at the root,
>> > but under 'bioassay component' > endpoint > response.
>> > And the class bioassay in missing from the root.
>> > Another issue is that the imported / linked external classes from GO
>> > and NCBO are shown by ID, and not the label. Again in Protege I see
>> > the label, which would be much easier to users.
>> >
>> > I can re-upload the file, but not sure if this will change anything.
>> >
>> > I also see a root level class for all disjoint classes and
>> > individuals, but this is not wrong.
>> >
>> > I ask Uma to look for other potential errors.
>> >
>> > Do you know what is going on; can you please help. I include the
>> > uploaded file here, but even if you download the file from NCBO and
>> > open in protege it is shown correct.
>> >
>> > Thanks,
>> >
>> > Stephan
>> >
>> > On Wed, Mar 16, 2011 at 4:42 PM, Trish Whetzel <whetzel at stanford.edu>
>> > wrote:
>> >> Sure, the owl/xml uploaded entry is removed and the new upload of BAO
>> >> has finished parsing and can now be explored.
>> >>
>> >> Trish
>> >>
>> >>
>> >>
>> >> On Mar 16, 2011, at 11:45 AM, Stephan Schurer PhD wrote:
>> >>
>> >>> Hallo Trish,
>> >>>
>> >>> Just uploaded rdf/xml. It is the same ontology version, but there is
>> >>> now a duplicate entry for BAO:
>> >>> http://bioportal.bioontology.org/ontologies/45388
>> >>>
>> >>> Can you remove the one where the explore link gives an error.
>> >>>
>> >>> Thanks,
>> >>>
>> >>> Stephan
>> >>>
>> >>> On Wed, Mar 16, 2011 at 2:10 PM, Trish Whetzel <whetzel at stanford.edu>
>> >>> wrote:
>> >>>> Yes rdf/xml.
>> >>>>
>> >>>> Trish
>> >>>>
>> >>>> On Mar 16, 2011, at 11:01 AM, support at bioontology.org wrote:
>> >>>>
>> >>>>> Name : Stephan Schurer
>> >>>>>
>> >>>>> Email : sschurer at med.miami.edu
>> >>>>>
>> >>>>> Comment:
>> >>>>> BioAssay Ontology Cannot be explored, i.e. gives an error message.
>> >>>>> I uploaded as owl / xml. Should I re-up load as rdf / xml?
>> >>>>>
>> >>>>> Please advise.
>> >>>>>
>> >>>>> Thanks,
>> >>>>>
>> >>>>> Stephan
>> >>>>> _______________________________________________
>> >>>>> bioontology-support mailing list
>> >>>>> bioontology-support at lists.stanford.edu
>> >>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> >>>>
>> >>
>> >>
>> >
>
>
>



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