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[protege-discussion] protege-discussion Digest, Vol 64, Issue 23

Girish Joglekar gjogleka at purdue.edu
Fri Nov 18 12:14:52 PST 2011


On 11/18/2011 3:03 PM, protege-discussion-request at lists.stanford.edu wrote:
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> Today's Topics:
>
>     1. Re: Protege as core to a software development environment
>        (Csongor Nyulas)
>     2. Re: Protege as core to a software development	environment
>        (Nick Khamis)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 17 Nov 2011 17:41:55 -0800
> From: Csongor Nyulas<csongor.nyulas at stanford.edu>
> To: protege-discussion at lists.stanford.edu
> Subject: Re: [protege-discussion] Protege as core to a software
> 	development environment
> Message-ID:<4EC5B7E3.9020001 at stanford.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Ron, and all,
>
> I would suggest you to look at the papers that came out from the NCBO
> BioPortal project:
> http://bmir.stanford.edu/publications/project.php/ncbo
>
> As well as other (more recent) paper's from the authors:
> http://bmir.stanford.edu/publications/by_author.php/csongor_i_nyulas
> http://bmir.stanford.edu/publications/by_author.php/natasha_f_noy
> http://bmir.stanford.edu/publications/by_author.php/michael_v_dorf
>
> Here are just a couple of the papers that could be of more interest:
> http://bmir.stanford.edu/publications/view.php/semantic_infrastructure_to_enable_collaboration_in_ontology_development
> http://bmir.stanford.edu/publications/view.php/bioportal_enhanced_functionality_via_new_web_services_from_the_national_center_for_biomedical_ontology_to_access_and_use_ontologies_in_software_applications
>
> The statement in the abstract that you have cited has definitely kept
> its validity. After more than 2 years, the metadata infrastructure of
> the BioPortal is still maintained as an ontology, which described in the
> paper (and which, in the meantime, has evolved of course), and this had
> provided us with great flexibility and opportunities in extending the
> functionality and the services provided by the platform. We are using
> ontologies also to define the structure of the *notes and mappings in
> BioPortal*, which offered us the same great flexibility and
> opportunities to evolve.
>
> I hope this helps,
> Csongor
>
> On 11/16/2011 6:53 AM, Ron Schultz wrote:
>    
>> A while ago I read the Protege Team article Ontology-Driven
>> Software:What We Learned From Using Ontologies As Infrastructure For
>> Software. I was wondering if there were any follow-on articles,
>> presentations, or conference proceedings further detailing this approach.
>>
>> I am particularly intrigued in the assertion in the abstract that "we
>> show that it is feasible to describe the structure of the data that
>> drives an application using anthologies rather than database schemas,
>> which are used traditionally to store the infrastructure data. We also
>> show that such an approach provides critical advantages in terms of
>> flexibility and adaptability of the tool itself. We demonstrate the
>> extensibility of the approach by enabling representation of views on
>> ontology's and their corresponding metadata in the same framework."
>>
>>
>> -- 
>> Ron
>>
>>
>> _______________________________________________
>> protege-discussion mailing list
>> protege-discussion at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
>> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>>      
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>
> ------------------------------
>
> Message: 2
> Date: Thu, 17 Nov 2011 20:46:22 -0500
> From: Nick Khamis<symack at gmail.com>
> To: User support for Core Protege and the Protege-Frames editor
> 	<protege-discussion at lists.stanford.edu>
> Subject: Re: [protege-discussion] Protege as core to a software
> 	development	environment
> Message-ID:
> 	<CAGWRaZYLg5Ffn6uOGLyDPZc0zJ0T=NRPrk3KzNWJRgdXShXDtA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> And you could visit our research lab website at:
>
> www.semanticsoftware.info
> www.aseg.cs.concordia.ca
>
> Ninus.
>
> On Thu, Nov 17, 2011 at 8:41 PM, Csongor Nyulas
> <csongor.nyulas at stanford.edu>  wrote:
>    
>> Hi Ron, and all,
>>
>> I would suggest you to look at the papers that came out from the NCBO
>> BioPortal project:
>> http://bmir.stanford.edu/publications/project.php/ncbo
>>
>> As well as other (more recent) paper's from the authors:
>> http://bmir.stanford.edu/publications/by_author.php/csongor_i_nyulas
>> http://bmir.stanford.edu/publications/by_author.php/natasha_f_noy
>> http://bmir.stanford.edu/publications/by_author.php/michael_v_dorf
>>
>> Here are just a couple of the papers that could be of more interest:
>> http://bmir.stanford.edu/publications/view.php/semantic_infrastructure_to_enable_collaboration_in_ontology_development
>> http://bmir.stanford.edu/publications/view.php/bioportal_enhanced_functionality_via_new_web_services_from_the_national_center_for_biomedical_ontology_to_access_and_use_ontologies_in_software_applications
>>
>> The statement in the abstract that you have cited has definitely kept its
>> validity. After more than 2 years, the metadata infrastructure of the
>> BioPortal is still maintained as an ontology, which described in the paper
>> (and which, in the meantime, has evolved of course), and this had provided
>> us with great flexibility and opportunities in extending the functionality
>> and the services provided by the platform. We are using ontologies also to
>> define the structure of the notes and mappings in BioPortal, which offered
>> us the same great flexibility and opportunities to evolve.
>>
>> I hope this helps,
>> Csongor
>>
>> On 11/16/2011 6:53 AM, Ron Schultz wrote:
>>
>> A while ago I read the Protege Team article?Ontology-Driven Software:What We
>> Learned From Using Ontologies As Infrastructure For Software. I was
>> wondering if there were any follow-on articles, presentations, or conference
>> proceedings further detailing this approach.
>> I am particularly intrigued in the assertion in the abstract that "we show
>> that it is feasible to describe the structure of the data that drives an
>> application using anthologies rather than database schemas, which are used
>> traditionally to store the infrastructure data. We also show that such an
>> approach provides critical advantages in terms of flexibility and
>> adaptability of the tool itself. We demonstrate the extensibility of the
>> approach by enabling representation of views on ontology's and their
>> corresponding metadata in the same framework."
>>
>> --
>> Ron
>>
>>
>> _______________________________________________
>> protege-discussion mailing list
>> protege-discussion at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
>> Instructions for unsubscribing:
>> http://protege.stanford.edu/doc/faq.html#01a.03
>>
>>
>> _______________________________________________
>> protege-discussion mailing list
>> protege-discussion at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
>> Instructions for unsubscribing:
>> http://protege.stanford.edu/doc/faq.html#01a.03
>>
>>
>>      
>
> ------------------------------
>
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>
> End of protege-discussion Digest, Vol 64, Issue 23
> **************************************************
>    
For the understanding of the overall concepts behind Semantic Web and 
modeling in RDF, RDFS and OWL I strongly recommend the following book:

Semantic Web for the Working Ontologists, Dean Allemang and James 
Handler, Elsevier 2008.

Girish


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