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[bioontology-support] Fwd: [BioPortal] Feedback from shaker

Samson Tu swt at stanford.edu
Tue May 16 12:00:09 PDT 2017


Dr. El-Sappagh,

Please make comments on the Bioportal support (or Protege) mailing list and refrain from emailing individuals at Stanford.

My point was that the ontology on Bioportal is not the same ontology you used to produce the “correct” figure. Unless you provide us with the right ontology, there is nothing we can do.

With best regards,
Samson



> Begin forwarded message:
> 
> From: Shaker El-Sappagh <shaker_elsapagh at yahoo.com>
> Subject: Re: [bioontology-support] [BioPortal] Feedback from shaker
> Date: May 16, 2017 at 11:27:24 AM PDT
> To: Samson Tu <swt at stanford.edu>
> Reply-To: Shaker El-Sappagh <shaker_elsapagh at yahoo.com>
> 
> Thanks Mr./Mrs. Samson.
> Exactly what you said. I have imported Time and other ontologies under BFO. This is the main problem now. When we upload the ontology on BioPortal. Time classes do not appear in its correct place under BFO universals.
> 
> Regards.
>  
> Shaker El-Sappagh, Ph.D. 
> ------------------------------------------------
> Information Systems Dept. 
> Faculty of Computers and Information.
> Mansura University.
> Email: Shaker_elsapagh at yahoo.com <http://us.mc1126.mail.yahoo.com/mc/compose?to=Shaker_elsapagh@yahoo.com>, sh.elsappagh at gmail.com <applewebdata://F6641675-34D8-4AA4-8553-E90B43F284F4>. 
> 
> 
> On Tuesday, May 16, 2017 8:43 PM, Samson Tu <swt at stanford.edu> wrote:
> 
> 
> Dr. Shaker asked about his ontology on the Protege mailing list. I looked at the figures he posted and commented that the ontology shown in the “correct” figure cannot be the same ontology in Bioportal because the entity class in the “correct” figures has no siblings whereas the ontology in Bioportal shows siblings derived from the 2006 W3C Time Ontology. I happen to know that the 2006 W3C Time Ontology has a number of top-level classes. Unless Dr. Shaker had mapped these classes to be subclasses of the BFO ontology class, the ontology in the “correct” figure doesn’t include the Time ontology.
> 
> Dr. Shaker needs to produce the ontology he used to generated the “correct” figure.
> 
> With best regards,
> Samson
> 
>> On May 16, 2017, at 10:17 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu <mailto:vendetti at stanford.edu>> wrote:
>> 
> 
> Hello Dr. El-Sappagh,
> 
> Protege 4.2 is a very old version of Protege (4 years old), that is no longer supported.
> 
> Your ontology file looks identical in BioPortal and Protege 5.2.0, which is the most recent version of Protege.  If you can send me a screen shot of your ontology in Protege 5.2.0 that looks different than what BioPortal displays, we could perhaps offer further assistance.
> 
> Protege 5.2.0 is freely available for download from the Protege website:
> 
> http://protege.stanford.edu/products.php#desktop-protege <http://protege.stanford.edu/products.php#desktop-protege>
> 
> Jennifer
> 
> 
>> On May 16, 2017, at 7:58 AM, Shaker <shaker_elsapagh at yahoo.com <mailto:shaker_elsapagh at yahoo.com>> wrote:
>> 
>> Hi,
>> DMTO has to appear like that:
>> <http://ncbo-support.2288202.n4.nabble.com/file/n4655584/1.jpg <http://ncbo-support.2288202.n4.nabble.com/file/n4655584/1.jpg>> 
>> 
>> This is what I receive when I work with it in protege 4.2.
>> 
>> However, on Bioportal, the ontology appears in a different way.
>> 
>> 
>> 
>> --
>> View this message in context: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-shaker-tp4655582p4655584.html <http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-shaker-tp4655582p4655584.html>
>> Sent from the NCBO Support mailing list archive at Nabble.com <http://nabble.com/>.
>> _______________________________________________
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>> bioontology-support at lists.stanford.edu <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support <https://mailman.stanford.edu/mailman/listinfo/bioontology-support>
> 
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> 
> -- 
> Samson Tu                                                      email: swt at stanford.edu <mailto:swt at stanford.edu>
> Senior Research Engineer                              web: www.stanford.edu/~swt/ <http://www.stanford.edu/~swt/>
> Center for Biomedical Informatics Research 	phone: 1-650-725-3391
> Stanford University                                          fax: 1-650-725-7944
> 
> 
> 
> 
> 

-- 
Samson Tu                                                      email: swt at stanford.edu
Senior Research Engineer                              web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research 	phone: 1-650-725-3391
Stanford University                                          fax: 1-650-725-7944



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