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

Dennis Thomas dgthomas78 at gmail.com
Fri May 14 17:01:21 PDT 2010


Thanks Trish. I will check this out and let you know if I have any questions
or comments.

Dennis

On Fri, May 14, 2010 at 12:49 AM, Trish Whetzel <whetzel at stanford.edu>wrote:

> 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
>
>
>


-- 
Dennis G. Thomas, D. Sc.
Washington University in St. Louis
Phone (Office): 314-362-1938
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