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[protege-owl] Newbie question about loading a big ontology file

Timothy Redmond tredmond at stanford.edu
Mon Nov 1 16:00:48 PDT 2010


> But the bottom line is that OpenCyc.owl is a beast - everything has 
> monstrously cryptic names, and searches for their non-cryptic labels 
> are very slow. 

There is another thing that you may know already.  In order to see the 
opencyc in an understandable manner, you need to set the rendering 
preferences.  Click File->Preferences and select the Renderer tab.  In 
there select "Render entities using annotation values". Then the names 
of the classes in OpenCyc should be more as you expect.  You can search 
for things with these names using the text field with the binoculars in 
the upper right corner.

-Timothy




On 10/29/2010 09:11 AM, Eric Scott wrote:
> I was using the same version and build as the one you referenced in 
> your response.
>
> I was able to correct the problem when I went into the run.bat file 
> and set the java -Xms and -Xmx parameters appropriately, then invoked 
> run.bat.
>
> The problem persists if I run Protege from the Start menu 
> (->protege.exe), but I can work with that.
>
> Thanks for your help!
>
> But the bottom line is that OpenCyc.owl is a beast - everything has 
> monstrously cryptic names, and searches for their non-cryptic labels 
> are very slow.
>
>
>
>
>
>
> On 10/28/2010 10:05 AM, Timothy Redmond wrote:
>> On 10/27/2010 04:20 PM, Eric Scott wrote:
>>> Hi all -
>>>
>>> I'm trying to load the OpenCyc ontology file into Protege, which I 
>>> just installed yesterday, so I'm probably just making a newbie error.
>>
>> It doesn't sound like you are making a newbie error.  My guess is 
>> that you are using Protege 3.  When I tried it over here with Protege 
>> 3 I was seeing a huge number of class cast exceptions.  I didn't let 
>> it continue but I suspect this goes on until Protege 3 dies.
>>
>> I tried Protege 4 and it loaded in 50 seconds.
>>
>> Let me know if this is not the issue.   You can check that your 
>> attempts to change the max memory are working by looking at the 
>> console.  Near the top of the console logs there is a message that 
>> goes something like this:
>>
>>     Starting Protege 4 OWL Editor (Version 4.1.0, Build = 209)
>>     Platform:
>>          Java: JVM 1.6.0_22-b04 Memory: 2330M
>>          Language: en, Country: US
>>          Framework: Apache Software Foundation (1.5)
>>          OS: linux (2.6.35-22-generic)
>>          Processor: x86-64
>>
>>
>> In the run above I gave it 2.5G of memory but it worked with 2G in 
>> the previous run.  The 12G that you are currently trying is too much 
>> for your machine because java doesn't swap well.
>>
>> I don't why Protege 3 is failing.  There are several possibilities.  
>> It could be that the file uses OWL 2 constructs (which means that 
>> Protege 3 will fail) or that there is an issue with the Protege 3 parser.
>>
>> -Timothy
>>
>>
>>
>>>
>>> The OpenCyc owl file is 153MB, and is said to contain 1.6 million 
>>> triples.
>>>
>>> After selecting the file and waiting somewhere between 5 and 10 
>>> minutes, I get this message and a stack trace:
>>>
>>> 'Out of memory error: java heap space'
>>>
>>> I've tried this several times, each time bumping up the following 
>>> parameter in my .lax file, the latest being:
>>>
>>> lax.nl.java.option.java.heap.size.max=12000000000
>>>
>>> ...which seems pretty big.
>>>
>>> previous values were 6G, and 3G.
>>>
>>> I'm running on Vista, 64 bit with 4G ram.  This happens when I have 
>>> no other apps running besides Protege, and the memory monitor says 
>>> I'm using 50-60% of memory capacity.
>>>
>>> Any help would be appreciated.
>>>
>>> Thanks,
>>>
>>> Eric in San Diego
>>>
>>>
>>>
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>>
>>
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>
>
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