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

Trish Whetzel whetzel at stanford.edu
Mon May 3 09:41:51 PDT 2010


I was able to open the file in Protege 4 and see that there are some  
extra XML tags that we may want to parse out before loading. Natasha  
runs a pre-processing step on the NCIt before uploading and can  
provide comments on this.

I saved the file as RDF/XML from Protege 4 and was able to load this  
file to the Stage server, however I do not see the "has_part"  
relationships and will need to review further.

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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