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[protege-discussion] Protege as core to a software development environment

Csongor Nyulas csongor.nyulas at
Thu Nov 17 17:41:55 PST 2011

Hi Ron, and all,

I would suggest you to look at the papers that came out from the NCBO 
BioPortal project:

As well as other (more recent) paper's from the authors:

Here are just a couple of the papers that could be of more interest:

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,

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
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