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

Dennis Thomas dgthomas78 at gmail.com
Mon May 3 07:57:52 PDT 2010


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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