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[bioontology-support] VO visualization in BioPortal

Trish Whetzel whetzel at stanford.edu
Thu Jun 25 15:43:10 PDT 2009


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>  
> wrote:
> Hi Trish,
> I have updated VO again. See:
> 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> 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>  
> wrote:
> Hi Trish,
> I uploaded Vaccine Ontology (VO) in BioPortal yesterday:
> 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
> Tel: 734-615-8231 (O); 734-615-2455 (L)
> Fax: 734-936-3235
> http://www.ulam.umich.edu/academic/he.htm
> http://www.med.umich.edu/microbio/bio/he.htm
> http://www.hegroup.org/
>
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