Re: [protege-user] Protege - crashes when editing ontologies

Subhashree, it could be a memory issue. I wrote a blog article a while back about how to increase memory for Protege and I think what I said still works (traveling so don’t have access to Protege Desktop to try it):  https://www.michaeldebellis.com/post/memory-management-with-prot%C3%A9g%C3%A9

Also, I think since I wrote that article, the new version of Protege supports giving Protege more memory using File>Preferences  

I think a lakh is apx. 100,000 If I’m correct, then I’ve used Protege on ontologies with that many triples. But it depends on how many and especially how complex the axioms are. On any ontology with that many triples I try to keep the axioms to a minimum and fairly simple… or I just stop using Protege. It’s not a database it’s a modeling tool so its impressive that it handles ontologies that large.

It shouldn’t require you to reinstall Protege though. Not sure why that is happening. 

Some other things to try: Use the Elk reasoner. That’s what people in OBO often use because their ontologies are fairly large (although I think in general not 100K triples because they usually don’t include data) But they make up for lack of data with lots of complex axioms. Elk doesn’t do as much reasoning as the other reasoners and for that reason it can handle larger and more complex ontologies. 

Another option is to try the free versions  of GraphDB, Stardog, or AllegroGraph. All have excellent free tools. AllegroGraph supports up to 5M triples for the free version and it (as does Stardog and GraphDB) has lots of great additional tools like implementations of SPARQL that implement the full spec and graphing tools that IMO are much better than those in Protege, especially for large models. IMO the Stardog visualization tool looks much cooler (because it is a lot more recent) but the AllegroGraph graphical browser (Gruff) while not as pretty, has many more features. Have’t had enough  experience with GraphDB to give an opinion.

I don’t know the limit Stardog’s free version puts on graphs but I think it is roughly the same as AllegroGraph, I think a bit lower but you can still use it for real work and I think it could easily handle hundreds of thousands of triples. GraphDB has the best free version in terms of size, there is NO limit on size, just on concurrent users. Also, with all 3 vendors, there are no issues of the free tool expiring after a certain period of time the way many commercial tools do.

Hope that helps.  Good luck,
Michael
https://www.michaeldebellis.com/blog

> On Oct 21, 2025, at 1:11 AM, Subhashree Balachandran <[email protected]> wrote:
> 
> 
> Hi all
> 
> I was using Protege 5.6.5 to edit 3 large corporate ontologies (around 1 lakh triples in each). Suddenly, Protege started to crash. Now I am able to use Protege only to view the ontologies, but I cannot edit any of them. I am not able to create a new toy ontology as well. The moment I start editing any(big or small) ontology, the tool freezes. I even tried uninstalling and reinstalling Protege, but the problem persists. Any idea as to what is causing this? Is it something related to java memory utilisation?
> 
> Thanks in advance,
> Subhashree Balachandran
> CARE2DATA, Chennai, India 
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