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[protege-discussion] Working with large ontologies in Web Protege 2

Timothy Redmond tredmond at
Thu Sep 6 08:27:26 PDT 2012

I am not the best person to answer this but I can give some answers and 
forward it to people who will give more information.

On 09/05/2012 04:09 PM, Rajeev Singh wrote:
> Hi,
> I aplogize for re-sending. Going with the assumption that my earlier 
> mail (08/31) fell through the cracks.
> The features in WebProtege 2 are very promising and will definitely 
> help in increasing adoption of semantic technologies in the area of 
> knowledge
> management. Thanks for this valuable effort.
> Have a couple of questions regarding working with large ontologies in 
> WebProtege. Let us assume that we are working with ontology with about
> 50000 TBox & 100000 ABox nodes. Also assume that each TBox class has 
> 10 properties(5 data and 5 object)

50,000 classes is not really very large.  Protege 4 loads ontologies 
with about 90,000 classes in less than 15 seconds.  In the Protege 3 
Web-Protege, putting this information into a database will take some 
time but it should still be very workable.

I have less experience with large numbers of individuals.

> - How does WebProtege store ontologies. As RDF files or in RDF triple 
> store (DB based)

Protege 3 based WebProtege stores the ontology in a Protege 3 database.  
It also can be configured to load the ontology in memory which would run 
a lot faster but which requires a server with more memory.

The OWL api based Web Protege stores the ontology on disk and in 
memory.  It uses a file format that allows it to load large ontologies 
very quickly (SNOMED in under 2 seconds) so it can be somewhat 
aggressive about removing an in-memory ontology.

> - Given a massive ontology does the back end server load the entire 
> ontology in memory when a web Client opens it

Protege 3 based web protege can store the ontology in a Protege 3 database.

> - When a web client opens a large ontology is the entire ontology sent 
> to the client

Web Protege never sends the entire ontology to the client.


> Thanks, -Rajeev
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