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[protege-owl] config for handling big ontologies

Timothy Redmond tredmond at
Thu Sep 10 07:53:52 PDT 2009

Hi Ronald,

This is an interesting set of challenges.  I have been thinking about  
them for a few days.  Much of what you are describing sounds like web  
protege.  It is currently actively being developed and an early  
version exists here [1].  It uses a thin client. It gets information  
about an ontology as it is needed.  One might think that retrieving  
parts of the ontology on an as-needed basis would lead to performance  
problems.  If the connection to the server is slow then the client  
will have to wait. But the underlying technology is highly  
asynchronous.  This means that the user experience will not hang  
because of a single rpc call.  Tania tells me that the user experience  
is good even with high latency.  This has been much harder to achieve  
with the Protege 3 client-server where a single rpc can stall the  

We are also looking at creating servers that provide something like  
dynamic svn-like access to ontologies.  I have also been thinking that  
this could be integrated with web-protege and incremental inference.   
The incremental inference work has already been done by Clark-Parsia  
and is being used (with the NCI Protege client-server) by NCI.  If we  
combine these technologies we might get something like what you are  

But this is all still just vision.  I have been picking off some of  
the pieces of this but there is a lot more work to go.



On Sep 8, 2009, at 3:45 AM, Ronald Cornet wrote:

> What I would like is:
> * a server that preloads and classifies an ontology.
> * a client that connects to the server and asynchronously builds a  
> tree-representation of (part of) the ontology.
> Or more general, a thin client that retrieves only what's needed  
> from the server (which may include / require preloading of classes).
> Regards,
> Ronald
> ###############################################################
> Ronald Cornet, PhD                    email: R.Cornet at
> dept. of Medical Informatics          phone: +31 (0)20 566 5188
> Academic Medical Center, Room J1B-115 fax:   +31 (0)20 691 9840
> P.O.Box 22700                         www:
> 1100 DE  Amsterdam
> The Netherlands                       'The truth is out there'
>> -----Original Message-----
>> From: protege-owl-bounces at
>> [mailto:protege-owl-bounces at] On Behalf
>> Of Timothy Redmond
>> Sent: Tuesday, September 08, 2009 04:57
>> To: User support for the Protege-OWL editor
>> Subject: Re: [protege-owl] config for handling big ontologies
>> The first  thing that occurred to me was the ability to tell
>> the client to preload certain classes [2].  If a user knows
>> what parts of the tree they usually look at, this can make
>> navigation work much quicker after the client starts up.
>> Another thing that is very important is the network latency.
>> We have tried as much as possible to make the protege client
>> work well with latencies ranging from 1ms to 100ms.  But a
>> latency of 100ms is very hard to work wtih and users will notice.
>> We have done a lot of work on the client-server tutorial [1]
>> so there are probably many things that can be found there.
>> -Timothy
>> [1]
>> r_Tutorial
>> [2]
>> r_Tutorial_Advanced#Client_Side_Settings
>> On Sep 4, 2009, at 10:42 AM, Olivier Dameron wrote:
>>> Dear protégéans,
>>>  Our team is in the process of defining the specs for a new server.
>>> This one should be able to run protégé and some classifier on
>>> potentially big ontologies (ncit, maybe fma,...)
>>>  I would like to invite you to share with me any experience and
>>> advice about what works and what does not work, with which
>>> configuration.
>>> Thank you
>>> olivier
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