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

Nathan Baker nathanandrewbaker at gmail.com
Fri May 14 04:34:23 PDT 2010


Hi Trish –

 

That’s great news; thanks a lot!



-- Nathan

 

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Friday, May 14, 2010 2:49 AM
To: Dennis Thomas
Cc: Nathan Baker; support
Subject: Re: NPO v. 2010-04-30 for release

 

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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