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[bioontology-support] Feedback

Stephan Schurer PhD stephan.schurer at gmail.com
Thu Mar 17 08:39:11 PDT 2011


Sam, thank you. That's what I thought. It's still not clear to me why
specifically "percent viability" is shown incorrectly, we have other
concepts that have these constructs.
Let's see what Trish and the engineering folks suggest. We do not want
to downgrade BAO to OWL 1.0, but we need to find a way to visualize it
correctly in NCBO.
Need the experts' help for this.
Trish, should I contact somebody specifically or is this already in progress?

Thanks,

Stephan



On Thu, Mar 17, 2011 at 2:56 AM, Saminda Abeyruwan <samindaa at gmail.com> wrote:
> Protege 3.X is based on OWL 1.0 spec and Protege 4.X is based on OWL 2.0
> spec and suppors 1.0 spec as well. We can express some of BAO concepts
> according to OWL 1.0. In places where we use nominals in expression (e.g.,
> definition of IC50, 50 percent inhibition) we will get into problems. We use
> special constructs in OWL 2.0 to express theses concepts (OWL 2.0 include
> those constructs specifically to support those kind of modeling
> requirements).
> Sam
> On Thu, Mar 17, 2011 at 12:54 AM, Stephan Schurer PhD
> <stephan.schurer at gmail.com> wrote:
>>
>> Trish, Thank you. I guess the Protege 3 vs 4 may have to do with
>> OWL2.0 like Sam suggested.
>> Is there anything we can do about this? Can we trim down the version
>> to be displayed somehow.
>>
>> Uma, can you send Trish a few examples of imported GO and NCBO terms
>> (and IDs) please.
>>
>> Thanks,
>>
>> Stephan
>>
>> On Thu, Mar 17, 2011 at 12:50 AM, Trish Whetzel <whetzel at stanford.edu>
>> wrote:
>> > Updates:
>> > - I removed the Explore link from BioPortal production, leaving the BAO
>> > file available for download
>> > - BioPortal uses Protege 3.4.5 in the backend, and in comparing BAO in
>> > Protege 3.4.5 versus Protege 4.1 the hierarchy errors appear to be due to
>> > differences between these versions of Protege. I have submitted a bug on
>> > this for the developers to investigate further
>> > - Can you send a few examples of imported / linked external classes from
>> > GO and NCBO that are shown by ID, and not the label?
>> >
>> > Thanks,
>> > Trish
>> >
>> >
>> > On Mar 16, 2011, at 9:26 PM, Stephan Schurer PhD wrote:
>> >
>> >> This is a question for Trish. I also checked the consistency with the
>> >> reasoners. I guess Trish is already looking into this.
>> >> Trish, let us know if we can check anything on our side or if there
>> >> are debugging tools at NCBO. Also, is there some testing site to
>> >> upload. With this we can just try a few things / versions w/o having
>> >> to show it publicly. It is strange that just this class was messed up.
>> >> It would be relevant to check if this behavior is reproducible or not.
>> >>
>> >> Thanks,
>> >>
>> >> Stephan
>> >>
>> >> On Thu, Mar 17, 2011 at 12:16 AM, Saminda Abeyruwan
>> >> <samindaa at gmail.com> wrote:
>> >>> BAO ontology reasoned with all consistencies checked through Pellet /
>> >>> Pellet
>> >>> (incremental) and Hermit 1.3.x. This implies that the DL is consistent
>> >>> with
>> >>> the models.
>> >>> Is there a way to get debug/loading etc information from NCBO folks.
>> >>> Sam
>> >>>
>> >>>
>> >>> 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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