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[bioontology-support] [BioPortal] Feedback from shaker

Samson Tu swt at
Tue May 16 10:43:32 PDT 2017

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,

> On May 16, 2017, at 10:17 AM, Jennifer Leigh Vendetti <vendetti at> 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:
> <>
> Jennifer
>> On May 16, 2017, at 7:58 AM, Shaker <shaker_elsapagh at <mailto:shaker_elsapagh at>> wrote:
>> Hi,
>> DMTO has to appear like that:
>> < <>> 
>> 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: <>
>> Sent from the NCBO Support mailing list archive at <>.
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Samson Tu                                                      email: swt at
Senior Research Engineer                              web:
Center for Biomedical Informatics Research 	phone: 1-650-725-3391
Stanford University                                          fax: 1-650-725-7944

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