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[bioontology-support] Feedback

Trish Whetzel whetzel at stanford.edu
Wed Mar 16 21:15:43 PDT 2011


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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