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[bioontology-support] NPO v. 2010-04-30 for release

Trish Whetzel whetzel at stanford.edu
Fri May 14 00:49:15 PDT 2010


Hi Dennis,

I re-saved the only from Protege 4 as RDF/XML and was able to load the  
file into BioPortal. The ontology can now be visualized in BioPortal  
and results for the Resource Index can now be browsed in addition to  
being accessible directly from the Resource Index Web services. Note,  
the version of the ontology used to annotate the resources is  
2010-01-29 (inferred).

Trish


On May 3, 2010, at 7:57 AM, Dennis Thomas wrote:

> Hi Trish,
>
> I created the inferred version in Protege 4.0.  But, I am getting  
> errors when I try to load the inferred version in Protege 3.2.1, and  
> ends up not opening in 3.2.1.
>
> There are several terms that have part_of or has_part.  For  
> example,  the class "nanoparticle characterization" (NPO_1413) has  
> "has_part" relations to its sibling classes, but these are not  
> showing up in the asserted version at BioPortal.
>
> Thanks,
>
> Dennis
>
> On Mon, May 3, 2010 at 9:46 AM, Trish Whetzel <whetzel at stanford.edu>  
> wrote:
> Hi Dennis and Nathan,
>
> Are you able to open the inferred version in Protege 3.4.4? What  
> terms in the asserted version have the relationships part_of or  
> has_part?
>
> Trish
>
>
>
> On May 3, 2010, at 7:30 AM, Nathan Baker wrote:
>
> Hi Dennis --
>
> I'm not sure but will Cc Trish for her suggestions.
>
> Thanks,
>
> Nathan
>
> On Mon, May 3, 2010 at 9:23 AM, Dennis Thomas <dgthomas78 at gmail.com>  
> wrote:
> Hi Nathan,
>
> I was just looking at the NPO on BioPortal.  It seems that the  
> inferred NPO
> is not showing up on the page.
> However, I am able to view the asserted NPO.  But, in the asserted  
> NPO, I am
> not able to see term-to-term relationships (e.g., part_of, has_part,  
> etc.)
> which actually are present in the OWL file.
>
> I am thinking this could be a parsing problem and could be because  
> we have
> new OWL annotation properties added to support the use of NCI Protege
> editor.
>
> Dennis
>
>
>
> On Sat, May 1, 2010 at 12:25 PM, Nathan Baker  
> <baker at biochem.wustl.edu>
> wrote:
>
> Uploaded -- thanks!
>
> On Apr 30, 2010, at 10:25 PM, Dennis Thomas wrote:
>
> Hi Nathan,
>
> I've attached the OWL files of the new NPO version (v. 2010-04-30) for
> uploading into BioPortal.  The release notes are available at the  
> project
> website:  http://www.nano-ontology.org/documentation/version-release-notes 
>  .
>
> Thank you,
> Dennis
>
> --
> Dennis G. Thomas, D. Sc.
> Washington University in St. Louis
> Phone (Office): 314-362-1938
> <npo-04-30-2010_asserted.owl><npo-04-30-2010_inferred.owl>
>
> --
> Nathan Baker (http://www.nabgroup.org)
> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
> Director, Computational and Molecular Biophysics Graduate Program
> Center for Computational Biology, Washington University in St. Louis
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
> Dennis G. Thomas, D. Sc.
> Washington University in St. Louis
> Phone (Office): 314-362-1938
>
>
>
>
> -- 
> Nathan Baker (http://www.nabgroup.org)
> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
> Director, Computational and Molecular Biophysics Graduate Program
> Center for Computational Biology, Washington University in St. Louis
>
>
>
>
> -- 
> Dennis G. Thomas, D. Sc.
> Washington University in St. Louis
> Phone (Office): 314-362-1938

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