Protege-5.5 and owl file load

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Protege-5.5 and owl file load

Surya Dhullipalla
Hi
I am unable to load the dron.owl file or any of the individual files below from protege5.5.

Please advise me on which are the better tools to view these files.

<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/dron.owl">
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-ingredient.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-hand.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-ndc.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-chebi.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-pro.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-upper.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-rxnorm.owl"/>







Thanks
Surya Dhullipalla Ph.D
Health Care Data Architect
IBM Watson Health


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Re: Protege-5.5 and owl file load

sanju tiwari
Can you send the dron.owl in text file?

On Tue, 5 May 2020, 18:51 Surya Dhullipalla, <[hidden email]> wrote:
Hi
I am unable to load the dron.owl file or any of the individual files below from protege5.5.

Please advise me on which are the better tools to view these files.

<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/dron.owl">
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-ingredient.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-hand.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-ndc.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-chebi.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-pro.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-upper.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-rxnorm.owl"/>







Thanks
Surya Dhullipalla Ph.D
Health Care Data Architect
IBM Watson Health

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Re: Protege-5.5 and owl file load

Surya Dhullipalla
Thanks Dr.Tiwari for a quick reponse.

Here is the attached file.



Thanks
Surya Dhullipalla Ph.D
Health Care Data Architect
IBM Watson Health


-----"protege-user" <[hidden email]> wrote: -----
To: User support for WebProtege and Protege Desktop <[hidden email]>
From: "Dr. Sanju Tiwari"
Sent by: "protege-user"
Date: 05/05/2020 10:51AM
Subject: [EXTERNAL] Re: [protege-user] Protege-5.5 and owl file load

Can you send the dron.owl in text file?

On Tue, 5 May 2020, 18:51 Surya Dhullipalla, <[hidden email]> wrote:
Hi
I am unable to load the dron.owl file or any of the individual files below from protege5.5.

Please advise me on which are the better tools to view these files.

<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/dron.owl">
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-ingredient.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-hand.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-ndc.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-chebi.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-pro.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-upper.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-rxnorm.owl"/>







Thanks
Surya Dhullipalla Ph.D
Health Care Data Architect
IBM Watson Health

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dron-full.owl (3K) Download Attachment
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Re: Protege-5.5 and owl file load

Michael DeBellis-2
In reply to this post by Surya Dhullipalla
I was able to load the main ontology dron.owl from the URL and as it loaded it also went and loaded a bunch of other ontologies from other URLs. It took a while to load, like around 3-5 minutes. I wasn't able to run the Pellet reasoner though. The reasoner ran for about a minute and then I got an out of Java memory error message (see below). I'll try with Hermit, in the past I've seen some ontologies work with Hermit that don't work with Pellet even though I prefer Pellet because it has support for SWRL. 

My guess is the reason you weren't even able to load it has to do with how your iri file is configured. I changed mine recently because I was dealing with really large ontologies so I set the Java memory requirements to be much higher than the defaults. But even with that I ran out of memory doing the classification. 

In your Protege5 directory you should have a file called Protege.l4j.ini  in that file there should be 3 parameters with default values: 

-Xms200M
-Xmx500M
-Xss16M

Xmx is the maximum memory allocation pool for a Java virtual machine (JVM), while Xms is the initial memory allocation pool. You might try increasing the Xmx number and see if that at least lets you load the files. I'm going to try using Hermit right now and see if I can get the ontology to classify. 

Michael


 ERROR  07:56:46  An error occurred during reasoning: GC overhead limit exceeded.
java.lang.OutOfMemoryError: GC overhead limit exceeded
at org.mindswap.pellet.utils.iterator.MultiIterator.<init>(MultiIterator.java:26) ~[na:na]
at org.mindswap.pellet.tbox.impl.TBoxExpImpl.unfold(TBoxExpImpl.java:518) ~[na:na]
at org.mindswap.pellet.taxonomy.AbstractDefinitionOrder.processDefinitions(AbstractDefinitionOrder.java:62) ~[na:na]
at org.mindswap.pellet.taxonomy.AbstractDefinitionOrder.<init>(AbstractDefinitionOrder.java:45) ~[na:na]
at org.mindswap.pellet.taxonomy.JGraphBasedDefinitionOrder.<init>(JGraphBasedDefinitionOrder.java:44) ~[na:na]
at org.mindswap.pellet.taxonomy.DefinitionOrderFactory.createDefinitionOrder(DefinitionOrderFactory.java:29) ~[na:na]
at org.mindswap.pellet.taxonomy.CDOptimizedTaxonomyBuilder.createDefinitionOrder(CDOptimizedTaxonomyBuilder.java:374) ~[na:na]
at org.mindswap.pellet.taxonomy.CDOptimizedTaxonomyBuilder.prepare(CDOptimizedTaxonomyBuilder.java:291) ~[na:na]
at org.mindswap.pellet.taxonomy.CDOptimizedTaxonomyBuilder.classify(CDOptimizedTaxonomyBuilder.java:174) ~[na:na]
at org.mindswap.pellet.KnowledgeBase.classify(KnowledgeBase.java:2095) ~[na:na]
at com.clarkparsia.pellet.owlapiv3.PelletReasoner.precomputeInferences(PelletReasoner.java:1067) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.precompute(OWLReasonerManagerImpl.java:447) ~[na:na]
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:388) ~[na:na]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_121]

On Tue, May 5, 2020 at 6:21 AM Surya Dhullipalla <[hidden email]> wrote:
Hi
I am unable to load the dron.owl file or any of the individual files below from protege5.5.

Please advise me on which are the better tools to view these files.

<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/dron.owl">
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-ingredient.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-hand.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-ndc.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-chebi.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-pro.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-upper.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/dron/dron-rxnorm.owl"/>







Thanks
Surya Dhullipalla Ph.D
Health Care Data Architect
IBM Watson Health

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Re: Protege-5.5 and owl file load

samsontu


On May 5, 2020, at 8:06 AM, Michael DeBellis <[hidden email]> wrote:

In your Protege5 directory you should have a file called Protege.l4j.ini  in that file there should be 3 parameters with default values: 

-Xms200M
-Xmx500M
-Xss16M

Xmx is the maximum memory allocation pool for a Java virtual machine (JVM), while Xms is the initial memory allocation pool. You might try increasing the Xmx number and see if that at least lets you load the files. I'm going to try using Hermit right now and see if I can get the ontology to classify. 


A Windows installation of Protege has the Protege.l4j.ini configuration file. On a Mac, edit the memory allocation specified in /Applications/Protege-5.5.0/Protégé.app/Contents/Info.plist.

With best regards,
Samson


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Re: Protege-5.5 and owl file load

Michael DeBellis-2
Samson, thanks for that, yes, I do all my development on Windows now so what I said was for the Windows installation. 

I wasn't able to get it to classify with Hermit either. I also tried unchecking a lot of the boxes in the Reasoner>Configure  preference (things like equivalent class/property, satisfiability, domain, and range) but even with that I still got an out of memory error. You might want to try contacting the people at OBO and see how they configure Protege's memory to get this to work or if it is even meant to work within Protege. Or perhaps Samson or others have additional ideas about how to deal with large ontologies.   

BTW, the odd thing is there just seem to be around 20-40 instances. Although, perhaps there are many more in some of the other ontologies that get loaded. And of course it isn't just instances that cause memory problems, it can also happen due to complex axioms that end up requiring a lot of reasoning. I notice in the Metrics for the ontology there are 53,364 axioms which I think is a lot. 

On Tue, May 5, 2020 at 8:18 AM Samson Tu <[hidden email]> wrote:


On May 5, 2020, at 8:06 AM, Michael DeBellis <[hidden email]> wrote:

In your Protege5 directory you should have a file called Protege.l4j.ini  in that file there should be 3 parameters with default values: 

-Xms200M
-Xmx500M
-Xss16M

Xmx is the maximum memory allocation pool for a Java virtual machine (JVM), while Xms is the initial memory allocation pool. You might try increasing the Xmx number and see if that at least lets you load the files. I'm going to try using Hermit right now and see if I can get the ontology to classify. 


A Windows installation of Protege has the Protege.l4j.ini configuration file. On a Mac, edit the memory allocation specified in /Applications/Protege-5.5.0/Protégé.app/Contents/Info.plist.

With best regards,
Samson

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Re: Protege-5.5 and owl file load

samsontu
Hi,

On May 5, 2020, at 8:33 AM, Michael DeBellis <[hidden email]> wrote:

BTW, the odd thing is there just seem to be around 20-40 instances. Although, perhaps there are many more in some of the other ontologies that get loaded. And of course it isn't just instances that cause memory problems, it can also happen due to complex axioms that end up requiring a lot of reasoning. I notice in the Metrics for the ontology there are 53,364 axioms which I think is a lot.

I loaded the drone.owl ontology, and the Metric panel shows that the ontology has 555,040 classes and 2,404,625 axioms. The ontology has low complexity though. (NDC and RxNorm, both drug ontologies that drone.owl imports, each has tens of thousands of classes, but no deep modeling.) The ELK reasoner [1], which supports OWL 2 EL profile, classified it in no time. (I allocate 5G of memory to Protege.)

With best regards,
Samson

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Re: Protege-5.5 and owl file load

Surya Dhullipalla
This is what i originally have in Protege:

-Xms200M
-Xmx800M
-Xss16M

Please advise on what I should be stetting in the Protege.l4j file to increase the memory.

Thanks
Surya Dhullipalla Ph.D
Health Care Data Architect
IBM Watson Health


-----"protege-user" <[hidden email]> wrote: -----
To: User support for WebProtege and Protege Desktop <[hidden email]>
From: Samson Tu
Sent by: "protege-user"
Date: 05/05/2020 11:56AM
Subject: [EXTERNAL] Re: [protege-user] Protege-5.5 and owl file load

Hi,

On May 5, 2020, at 8:33 AM, Michael DeBellis <[hidden email]> wrote:

BTW, the odd thing is there just seem to be around 20-40 instances. Although, perhaps there are many more in some of the other ontologies that get loaded. And of course it isn't just instances that cause memory problems, it can also happen due to complex axioms that end up requiring a lot of reasoning. I notice in the Metrics for the ontology there are 53,364 axioms which I think is a lot.

I loaded the drone.owl ontology, and the Metric panel shows that the ontology has 555,040 classes and 2,404,625 axioms. The ontology has low complexity though. (NDC and RxNorm, both drug ontologies that drone.owl imports, each has tens of thousands of classes, but no deep modeling.) The ELK reasoner [1], which supports OWL 2 EL profile, classified it in no time. (I allocate 5G of memory to Protege.)

With best regards,
Samson
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Re: Protege-5.5 and owl file load

samsontu
Hi,

On May 5, 2020, at 9:24 AM, Surya Dhullipalla <[hidden email]> wrote:

This is what i originally have in Protege:

-Xms200M
-Xmx800M
-Xss16M

Please advise on what I should be stetting in the Protege.l4j file to increase the memory.


The activity monitor on my Mac shows that the Protege app, with the drone.owl loaded, is taking up 4.22G of memory. Set -Xmx to 5G if your machine has enough memory to spare.

With best regards,
Samson



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Re: Protege-5.5 and owl file load

Surya Dhullipalla
Although I increased to
-Xms200M
-Xmx20000M
-Xss16M

- my Protege5.5 does not allow me to open the file



I am not sure where i am going wrong...

-----"protege-user" <[hidden email]> wrote: -----
To: User support for WebProtege and Protege Desktop <[hidden email]>
From: Samson Tu
Sent by: "protege-user"
Date: 05/05/2020 01:04PM
Subject: [EXTERNAL] Re: [protege-user] Protege-5.5 and owl file load

Hi,

On May 5, 2020, at 9:24 AM, Surya Dhullipalla <[hidden email]> wrote:

This is what i originally have in Protege:

-Xms200M
-Xmx800M
-Xss16M

Please advise on what I should be stetting in the Protege.l4j file to increase the memory.


The activity monitor on my Mac shows that the Protege app, with the drone.owl loaded, is taking up 4.22G of memory. Set -Xmx to 5G if your machine has enough memory to spare.

With best regards,
Samson


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Re: Protege-5.5 and owl file load

Michael DeBellis-2
A couple things to consider: 1) Remember you need to quit Protege and restart it to get the new ini file to take effect. 2) I think you have it set for 20G which seems to me to be a lot. 

Remember that the number has to be less than the total Ram you have for your computer (check in the System>About in Windows if you aren't sure how much RAM you have) and you don't want to be right up against the limit either because you are going to need Ram for the OS and you probably want at least a browser and most likely some other tools open at the same time as Protege. Try bringing it down to 5G as Samson suggested. 

On Tue, May 5, 2020 at 11:02 AM Surya Dhullipalla <[hidden email]> wrote:
Although I increased to
-Xms200M
-Xmx20000M
-Xss16M

- my Protege5.5 does not allow me to open the file



I am not sure where i am going wrong...

-----"protege-user" <[hidden email]> wrote: -----
To: User support for WebProtege and Protege Desktop <[hidden email]>
From: Samson Tu
Sent by: "protege-user"
Date: 05/05/2020 01:04PM
Subject: [EXTERNAL] Re: [protege-user] Protege-5.5 and owl file load

Hi,

On May 5, 2020, at 9:24 AM, Surya Dhullipalla <[hidden email]> wrote:

This is what i originally have in Protege:

-Xms200M
-Xmx800M
-Xss16M

Please advise on what I should be stetting in the Protege.l4j file to increase the memory.


The activity monitor on my Mac shows that the Protege app, with the drone.owl loaded, is taking up 4.22G of memory. Set -Xmx to 5G if your machine has enough memory to spare.

With best regards,
Samson


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protege-user mailing list
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