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[protege-discussion] Protege as data access layer for"serious"multi-userapplication

protege at protege at
Tue Jan 22 11:03:07 PST 2008

Hello Sergey, 

I think in theory Protege can be used as a simple database application since it has all three tiers required for that. However, I see no benefit in using Protege back end as database tier for any "serios" application, except knowledge base. I do see a pottential benefit in enhancing Protege back end to provide better support for ontology sharing. But that is quite different from EPR application. What makes sense in your situation - is to use Protege as robust middle tier with available support for reach application meta-data, inference and Semantic Web interoperability. That does not exclude using your application back end for storing some Protege data. 

You may be interested in the work I have done along these lines.

>-----Original Message-----
>From: Sergey V. Gerasimov [mailto:gerasimov at]
>Sent: Wednesday, January 16, 2008 09:57 AM
>To: 'User support for Core Protege and the Protege-Frames editor'
>Subject: Re: [protege-discussion] Protege as data access layer for	"serious"multi-user application
>I like very Protege's ontology evulation and form editor features.
>And schedule to write Hibernate-like back-end to use both technologies 
>(Protege, Hibernate)
>What do you think reg. my idea?
>----- Original Message ----- 
>From: "Samson Tu" <swt at>
>To: <protege-discussion at>
>Sent: Wednesday, January 16, 2008 3:49 AM
>Subject: Re: [protege-discussion] Protege as data access layer for 
>"serious"multi-user application
>> It depends on what you mean by 'serious multi-user application.'
>> It is difficult to write a new Protege backend. I don't expect you'll
>> want to use Protege's default database backend as the data
>> representation for your EPR data. You want other applications to query
>> data without going through Protege.
>> We've developed and deployed multi-user multi-clinic decision support
>> applications using Protege. We used Protege to encode the knowledge base
>> (the decision-support business logic). At runtime, we query a relational
>> database to get the needed data for decision-support purpose. We applied
>> the "business logic" to patient-specific data in Java (using Protege
>> API), as multiple queries to database turned out to be too inefficient.
>> Yes, eventually there will be a database backend in Protege 4.
>> Samson
>> Sergey V. Gerasimov wrote:
>>> Hello,
>>> I'm from Moscow State University.
>>> We are working on project connected to developement of
>>> customizable elctronical patient record system (EPR) with decision
>>> support fetures.
>>> Can you please advise if Protege can be used in our project.
>>> Open questions are as follows:
>>> 1. Can Protege API be used as data access layer for "serious" multi-user
>>> application?
>>> Can business logic of the application efficiently use Protege quering 
>>> API?
>>> Or Protege is additional framework for knowledge management tasks?
>>> I found simple one-table relational default back-end plug-in and
>>> article reg. motivation of this solution.
>>> Slot values are stored as strings and if I understand correctly queries 
>>> with
>>> conditions x > 5 can't use database indexes (Am I right?)
>>> But if I understood correctly custom backend plug-in can be implemented.
>>> For example something like class->table and slot/property->column 
>>> strategy.
>>> I also found Protege server feature..
>>> But question is open.
>>> 2. I didn't find form editor and database backend feature in Protege 4.0
>>> Alpha.
>>> Will this features implemented later or not?
>>> Will 3.x versions of Protege supported in the next 2-3 years?
>>> Thanks a lot!
>>> Sergey Gerasimov,
>>> MSU
>>> ------------------------------------------------------------------------
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>> -- 
>> Samson Tu                                   email: swt at
>> Senior Research Scientist                   web:
>> Center for Biomedical Informatics Research  phone: 1-650-725-3391
>> Stanford University                         fax: 1-650-725-7944
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