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[bioontology-support] VO visualization in BioPortal

Trish Whetzel plwhetzel at gmail.com
Thu Jul 9 19:33:01 PDT 2009


Hi Oliver,

The issue was identified as being caused since Definition (and perhaps other
entities as well) exist both as an annotation property and as a class.

Trish


On Thu, Jun 25, 2009 at 3:43 PM, Trish Whetzel <whetzel at stanford.edu> wrote:

> Loading to stage showed some Protege errors, checking in with others
> however they are at the Protege conference so responses are delayed.
>
> Sent from my iPhone
>
> On Jun 25, 2009, at 6:32 PM, "Yongqun He" <yongqunh at med.umich.edu> wrote:
>
> Hi Trish,
> Thanks for the message. Have you got any results?
> Best,
> --Oliver
>
> >>> Trish Whetzel <plwhetzel at gmail.com> 6/24/2009 12:31 PM >>>
> Sure, I've downloaded 1.0.55 and it opened fine in Protege 3.4 and have
> loaded it to the stage database as a test. I'll check back later this
> afternoon.
>
> Trish
>
>
> On Wed, Jun 24, 2009 at 3:55 AM, Yongqun He < <yongqunh at med.umich.edu>
> yongqunh at med.umich.edu> wrote:
>
>>  Hi Trish,
>>  I have updated VO again. See:
>>  <http://bioportal.bioontology.org/ontologies/40188>
>> http://bioportal.bioontology.org/ontologies/40188
>> We usually use Protege 4 for VO development. This updated VO is confirmed
>> to be saved as a RDF/XML file. I can open it using Protégé 3.4 although some
>> Java bugs were displayed.
>>  Can you download this VO version and test it again?
>>  Thanks!
>>  --Oliver
>>
>> >>> Trish Whetzel < <plwhetzel at gmail.com>plwhetzel at gmail.com> 6/23/2009
>> 12:52 PM >>>
>>
>> Hi Oliver,
>>
>> Apologies for the delay - I was out of town. Are you able to open the file
>> in Protege 3.4? Last I tried to open the file in p4 to save as RDF/XML (to
>> open in Protege 3.4) there were errors.
>>
>> Trish
>>
>>
>>   On Wed, Jun 10, 2009 at 5:03 AM, Yongqun He < <yongqunh at med.umich.edu>
>> yongqunh at med.umich.edu> wrote:
>>
>>>  Hi Trish,
>>>  I uploaded Vaccine Ontology (VO) in BioPortal yesterday:
>>>  <http://bioportal.bioontology.org/ontologies/40116>
>>> http://bioportal.bioontology.org/ontologies/40116
>>> However, the current VO cannot now be visualized in BioPortal.
>>>  Could you help to find out the potential reason(s)? One change we made
>>> is in the "Synonym Slot (Owl Only) (e.g. SKOS:altLabel)", we changed
>>> pervious 'synonym' to 'oboInOwl:Synonym'. We made this change in VO because
>>> it is used in OBO.
>>>  Thanks!
>>>  Oliver
>>>  Yongqun "Oliver" He, DVM, PhD
>>> Assistant Professor
>>> Unit for Laboratory Animal Medicine
>>> Department of Microbiology and Immunology
>>> and Center for Computational Medicine and Biology
>>> University of Michigan Medical School
>>> Office: Room 105, Animal Research Facility (ARF)
>>> Mailing: 018 ARF, 1150 W. Medical Center Dr.
>>> Ann Arbor, MI 48109
>>> Email: <yongqunh at med.umich.edu>yongqunh at med.umich.edu
>>> Tel: 734-615-8231 (O); 734-615-2455 (L)
>>> Fax: 734-936-3235
>>> <http://www.ulam.umich.edu/academic/he.htm>
>>> http://www.ulam.umich.edu/academic/he.htm
>>> <http://www.med.umich.edu/microbio/bio/he.htm>
>>> http://www.med.umich.edu/microbio/bio/he.htm
>>>  <http://www.hegroup.org/>http://www.hegroup.org/
>>>
>>> **********************************************************
>>> Electronic Mail is not secure, may not be read every day, and should not
>>> be used for urgent or sensitive issues
>>>
>>
>>
>> **********************************************************
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>>
>
>
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