Export inferred view of SNOMED CT

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Export inferred view of SNOMED CT

Campbell, James R
At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?
Jim Campbell



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Re: Export inferred view of SNOMED CT

Matthew Horridge-2
Administrator
Hi Jim,

Which axiom types do you have checked on the first page of the export wizard?  (I’m unable to read the text in the screenshot btw).  Would you be able to try with just “Subclasses” and let me know what happens?

Cheers,

Matthew


On Jun 1, 2019, at 05:30, Campbell, James R <[hidden email]> wrote:

At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?
Jim Campbell

<image.png>

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
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Re: Export inferred view of SNOMED CT

samsontu
Hi,

I suspect that the problem is memory requirement of saving the large inferred ontology. Yesterday I tried to save the inferred SNOMED CT and saw the same behavior that Jim observed. This morning I tried various combination of axiom types and found that saving subclass, equivalent classes, annotations, and asserted ontology resulted in a saved ontology within a few minutes, with Protege taking up the 5+ GB memory that I’ve allocated for it. Added sub-object properties axioms resulted in hung behavior, with the Protege process struggling at 5.9 GB memory level.

With best regards,
Samson


On Jun 1, 2019, at 7:39 AM, Matthew Horridge <[hidden email]> wrote:

Hi Jim,

Which axiom types do you have checked on the first page of the export wizard?  (I’m unable to read the text in the screenshot btw).  Would you be able to try with just “Subclasses” and let me know what happens?

Cheers,

Matthew


On Jun 1, 2019, at 05:30, Campbell, James R <[hidden email]> wrote:

At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?
Jim Campbell

<image.png>

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Export inferred view of SNOMED CT

Campbell, James R
Thanks Samson.

I stopped the process at 48 hours run time with no progress to show.  I revised run.bat as follows
Xmx=8GB
Xms=4GB
Xss=320M
Using these memory parameters, I rebooted windows then Protege and reloaded SNOMED CT.  I was able to get a successful export selecting axioms of Subclasses and Equivalent classes but I got no progress when I added Equivalent object properties.  As Samson suggested, I included annotations but ignored asserted logical axioms.  I used the default of RDF/XML as the export format.

The inferred ontology looked OK on reloading but the DL query function did not work, I presume because I did not include Equivalent object properties.  When examining the classes in Entities tab, Annotations and subclass axioms appeared but no Equivalent object properties (not surprizingly).  

I must have the full object definitions for my work and so I will try another export adding Equivalent object properties and let it run longer to see if I get any results.  Is one output format better than another for my purpose or for Protege efficiency?
Jim

From: protege-user <[hidden email]> on behalf of Samson Tu <[hidden email]>
Sent: Saturday, June 1, 2019 10:38 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Export inferred view of SNOMED CT
 
Non-UNMC email
Hi,

I suspect that the problem is memory requirement of saving the large inferred ontology. Yesterday I tried to save the inferred SNOMED CT and saw the same behavior that Jim observed. This morning I tried various combination of axiom types and found that saving subclass, equivalent classes, annotations, and asserted ontology resulted in a saved ontology within a few minutes, with Protege taking up the 5+ GB memory that I’ve allocated for it. Added sub-object properties axioms resulted in hung behavior, with the Protege process struggling at 5.9 GB memory level.

With best regards,
Samson


On Jun 1, 2019, at 7:39 AM, Matthew Horridge <[hidden email]> wrote:

Hi Jim,

Which axiom types do you have checked on the first page of the export wizard?  (I’m unable to read the text in the screenshot btw).  Would you be able to try with just “Subclasses” and let me know what happens?

Cheers,

Matthew


On Jun 1, 2019, at 05:30, Campbell, James R <[hidden email]> wrote:

At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?
Jim Campbell

<image.png>

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.
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Re: Export inferred view of SNOMED CT

Matthew Horridge-2
Administrator
Hi Jim,

You need to include the asserted logical axioms for what you want to do.  However, if you do this, and you’re using a reasoner with the DL query tab (which is the only way that it works), then you are far better off just using the vanilla version of SNOMED CT.

Cheers,

Matthew


On Jun 2, 2019, at 06:51, Campbell, James R <[hidden email]> wrote:

Thanks Samson.

I stopped the process at 48 hours run time with no progress to show.  I revised run.bat as follows
Xmx=8GB
Xms=4GB
Xss=320M
Using these memory parameters, I rebooted windows then Protege and reloaded SNOMED CT.  I was able to get a successful export selecting axioms of Subclasses and Equivalent classes but I got no progress when I added Equivalent object properties.  As Samson suggested, I included annotations but ignored asserted logical axioms.  I used the default of RDF/XML as the export format.

The inferred ontology looked OK on reloading but the DL query function did not work, I presume because I did not include Equivalent object properties.  When examining the classes in Entities tab, Annotations and subclass axioms appeared but no Equivalent object properties (not surprizingly).  

I must have the full object definitions for my work and so I will try another export adding Equivalent object properties and let it run longer to see if I get any results.  Is one output format better than another for my purpose or for Protege efficiency?
Jim

From: protege-user <[hidden email]> on behalf of Samson Tu <[hidden email]>
Sent: Saturday, June 1, 2019 10:38 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Export inferred view of SNOMED CT
 
Non-UNMC email 
Hi,

I suspect that the problem is memory requirement of saving the large inferred ontology. Yesterday I tried to save the inferred SNOMED CT and saw the same behavior that Jim observed. This morning I tried various combination of axiom types and found that saving subclass, equivalent classes, annotations, and asserted ontology resulted in a saved ontology within a few minutes, with Protege taking up the 5+ GB memory that I’ve allocated for it. Added sub-object properties axioms resulted in hung behavior, with the Protege process struggling at 5.9 GB memory level.

With best regards,
Samson


On Jun 1, 2019, at 7:39 AM, Matthew Horridge <[hidden email]> wrote:

Hi Jim,

Which axiom types do you have checked on the first page of the export wizard?  (I’m unable to read the text in the screenshot btw).  Would you be able to try with just “Subclasses” and let me know what happens?

Cheers,

Matthew


On Jun 1, 2019, at 05:30, Campbell, James R <[hidden email]> wrote:

At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?
Jim Campbell

<image.png>

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender._______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Export inferred view of SNOMED CT

samsontu
In reply to this post by Campbell, James R
Jim,

Export the inferred axioms WITH asserted logical axioms, annotations, and subclass/equivalence class axioms. The resulting ontology still works with DL query, although, as Matthew says, you gain nothing over doing the same query in the original ontology. Exporting inferred axioms as an ontology is useful only when the applications that use the exported ontology have no access to a reasoner.

In any case, I don’t think SNOMED CT has any inferred subproperty or equivalent property axioms. The Elk reasoner doesn’t implement getEquivalentObjectProperties(…) method and the “Unsupported inference Types” warning panel says to turn off Displayed Object/Data Property Inferences. In fact, maybe the export is hanging when the sub/equivalent properties are checked not because of memory limitation, but because the Elk reasoner doesn’t support those inferences. In that case there may be a bug or missing feature in Protege or in the Elk reasoner.Trying to export unsupported inferred axiom types should have more graceful behavior. 

With best regards,
Samson


On Jun 2, 2019, at 6:51 AM, Campbell, James R <[hidden email]> wrote:

Thanks Samson.

I stopped the process at 48 hours run time with no progress to show.  I revised run.bat as follows
Xmx=8GB
Xms=4GB
Xss=320M
Using these memory parameters, I rebooted windows then Protege and reloaded SNOMED CT.  I was able to get a successful export selecting axioms of Subclasses and Equivalent classes but I got no progress when I added Equivalent object properties.  As Samson suggested, I included annotations but ignored asserted logical axioms.  I used the default of RDF/XML as the export format.

The inferred ontology looked OK on reloading but the DL query function did not work, I presume because I did not include Equivalent object properties.  When examining the classes in Entities tab, Annotations and subclass axioms appeared but no Equivalent object properties (not surprizingly).  

I must have the full object definitions for my work and so I will try another export adding Equivalent object properties and let it run longer to see if I get any results.  Is one output format better than another for my purpose or for Protege efficiency?
Jim

From: protege-user <[hidden email]> on behalf of Samson Tu <[hidden email]>
Sent: Saturday, June 1, 2019 10:38 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Export inferred view of SNOMED CT
 
Non-UNMC email 
Hi,

I suspect that the problem is memory requirement of saving the large inferred ontology. Yesterday I tried to save the inferred SNOMED CT and saw the same behavior that Jim observed. This morning I tried various combination of axiom types and found that saving subclass, equivalent classes, annotations, and asserted ontology resulted in a saved ontology within a few minutes, with Protege taking up the 5+ GB memory that I’ve allocated for it. Added sub-object properties axioms resulted in hung behavior, with the Protege process struggling at 5.9 GB memory level.

With best regards,
Samson


On Jun 1, 2019, at 7:39 AM, Matthew Horridge <[hidden email]> wrote:

Hi Jim,

Which axiom types do you have checked on the first page of the export wizard?  (I’m unable to read the text in the screenshot btw).  Would you be able to try with just “Subclasses” and let me know what happens?

Cheers,

Matthew


On Jun 1, 2019, at 05:30, Campbell, James R <[hidden email]> wrote:

At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?
Jim Campbell

<image.png>

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.


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Re: Export inferred view of SNOMED CT

samsontu
Hi,

I verified that Protege doesn’t behave well when exporting inferred Elk reasoner axioms, with the subproperty/equivalent property axiom types checked, even when the ontology involved is tiny. In this case Protege doesn’t create the inferred ontology file and show no error panel, but is still responsive. I’ve logged an issue on the desktop Protege GitHub repository.

With best regards,
Samson


On Jun 2, 2019, at 9:26 AM, Samson Tu <[hidden email]> wrote:

Jim,

Export the inferred axioms WITH asserted logical axioms, annotations, and subclass/equivalence class axioms. The resulting ontology still works with DL query, although, as Matthew says, you gain nothing over doing the same query in the original ontology. Exporting inferred axioms as an ontology is useful only when the applications that use the exported ontology have no access to a reasoner.

In any case, I don’t think SNOMED CT has any inferred subproperty or equivalent property axioms. The Elk reasoner doesn’t implement getEquivalentObjectProperties(…) method and the “Unsupported inference Types” warning panel says to turn off Displayed Object/Data Property Inferences. In fact, maybe the export is hanging when the sub/equivalent properties are checked not because of memory limitation, but because the Elk reasoner doesn’t support those inferences. In that case there may be a bug or missing feature in Protege or in the Elk reasoner.Trying to export unsupported inferred axiom types should have more graceful behavior. 

With best regards,
Samson


On Jun 2, 2019, at 6:51 AM, Campbell, James R <[hidden email]> wrote:

Thanks Samson.

I stopped the process at 48 hours run time with no progress to show.  I revised run.bat as follows
Xmx=8GB
Xms=4GB
Xss=320M
Using these memory parameters, I rebooted windows then Protege and reloaded SNOMED CT.  I was able to get a successful export selecting axioms of Subclasses and Equivalent classes but I got no progress when I added Equivalent object properties.  As Samson suggested, I included annotations but ignored asserted logical axioms.  I used the default of RDF/XML as the export format.

The inferred ontology looked OK on reloading but the DL query function did not work, I presume because I did not include Equivalent object properties.  When examining the classes in Entities tab, Annotations and subclass axioms appeared but no Equivalent object properties (not surprizingly).  

I must have the full object definitions for my work and so I will try another export adding Equivalent object properties and let it run longer to see if I get any results.  Is one output format better than another for my purpose or for Protege efficiency?
Jim

From: protege-user <[hidden email]> on behalf of Samson Tu <[hidden email]>
Sent: Saturday, June 1, 2019 10:38 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Export inferred view of SNOMED CT
 
Non-UNMC email 
Hi,

I suspect that the problem is memory requirement of saving the large inferred ontology. Yesterday I tried to save the inferred SNOMED CT and saw the same behavior that Jim observed. This morning I tried various combination of axiom types and found that saving subclass, equivalent classes, annotations, and asserted ontology resulted in a saved ontology within a few minutes, with Protege taking up the 5+ GB memory that I’ve allocated for it. Added sub-object properties axioms resulted in hung behavior, with the Protege process struggling at 5.9 GB memory level.

With best regards,
Samson


On Jun 1, 2019, at 7:39 AM, Matthew Horridge <[hidden email]> wrote:

Hi Jim,

Which axiom types do you have checked on the first page of the export wizard?  (I’m unable to read the text in the screenshot btw).  Would you be able to try with just “Subclasses” and let me know what happens?

Cheers,

Matthew


On Jun 1, 2019, at 05:30, Campbell, James R <[hidden email]> wrote:

At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?
Jim Campbell

<image.png>

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.



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Re: Export inferred view of SNOMED CT

Alan Ruttenberg-2
Have you looked at https://github.com/IHTSDO/snomed-owl-toolkit - I haven't tried it yet, but plan to.

Alan

On Sun, Jun 2, 2019 at 1:32 PM Samson Tu <[hidden email]> wrote:
Hi,

I verified that Protege doesn’t behave well when exporting inferred Elk reasoner axioms, with the subproperty/equivalent property axiom types checked, even when the ontology involved is tiny. In this case Protege doesn’t create the inferred ontology file and show no error panel, but is still responsive. I’ve logged an issue on the desktop Protege GitHub repository.

With best regards,
Samson


On Jun 2, 2019, at 9:26 AM, Samson Tu <[hidden email]> wrote:

Jim,

Export the inferred axioms WITH asserted logical axioms, annotations, and subclass/equivalence class axioms. The resulting ontology still works with DL query, although, as Matthew says, you gain nothing over doing the same query in the original ontology. Exporting inferred axioms as an ontology is useful only when the applications that use the exported ontology have no access to a reasoner.

In any case, I don’t think SNOMED CT has any inferred subproperty or equivalent property axioms. The Elk reasoner doesn’t implement getEquivalentObjectProperties(…) method and the “Unsupported inference Types” warning panel says to turn off Displayed Object/Data Property Inferences. In fact, maybe the export is hanging when the sub/equivalent properties are checked not because of memory limitation, but because the Elk reasoner doesn’t support those inferences. In that case there may be a bug or missing feature in Protege or in the Elk reasoner.Trying to export unsupported inferred axiom types should have more graceful behavior. 

With best regards,
Samson


On Jun 2, 2019, at 6:51 AM, Campbell, James R <[hidden email]> wrote:

Thanks Samson.

I stopped the process at 48 hours run time with no progress to show.  I revised run.bat as follows
Xmx=8GB
Xms=4GB
Xss=320M
Using these memory parameters, I rebooted windows then Protege and reloaded SNOMED CT.  I was able to get a successful export selecting axioms of Subclasses and Equivalent classes but I got no progress when I added Equivalent object properties.  As Samson suggested, I included annotations but ignored asserted logical axioms.  I used the default of RDF/XML as the export format.

The inferred ontology looked OK on reloading but the DL query function did not work, I presume because I did not include Equivalent object properties.  When examining the classes in Entities tab, Annotations and subclass axioms appeared but no Equivalent object properties (not surprizingly).  

I must have the full object definitions for my work and so I will try another export adding Equivalent object properties and let it run longer to see if I get any results.  Is one output format better than another for my purpose or for Protege efficiency?
Jim

From: protege-user <[hidden email]> on behalf of Samson Tu <[hidden email]>
Sent: Saturday, June 1, 2019 10:38 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Export inferred view of SNOMED CT
 
Non-UNMC email 
Hi,

I suspect that the problem is memory requirement of saving the large inferred ontology. Yesterday I tried to save the inferred SNOMED CT and saw the same behavior that Jim observed. This morning I tried various combination of axiom types and found that saving subclass, equivalent classes, annotations, and asserted ontology resulted in a saved ontology within a few minutes, with Protege taking up the 5+ GB memory that I’ve allocated for it. Added sub-object properties axioms resulted in hung behavior, with the Protege process struggling at 5.9 GB memory level.

With best regards,
Samson


On Jun 1, 2019, at 7:39 AM, Matthew Horridge <[hidden email]> wrote:

Hi Jim,

Which axiom types do you have checked on the first page of the export wizard?  (I’m unable to read the text in the screenshot btw).  Would you be able to try with just “Subclasses” and let me know what happens?

Cheers,

Matthew


On Jun 1, 2019, at 05:30, Campbell, James R <[hidden email]> wrote:

At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?
Jim Campbell

<image.png>

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Export inferred view of SNOMED CT

Campbell, James R
That is what we used to build our
First OWL instance of SNOMED 
core + US extension + Nebraska
 Lexicon!

Jim Campbell


On Jun 2, 2019, at 1:15 PM, Alan Ruttenberg <[hidden email]> wrote:

Non-UNMC email
Have you looked at https://github.com/IHTSDO/snomed-owl-toolkit - I haven't tried it yet, but plan to.

Alan

On Sun, Jun 2, 2019 at 1:32 PM Samson Tu <[hidden email]> wrote:
Hi,

I verified that Protege doesn’t behave well when exporting inferred Elk reasoner axioms, with the subproperty/equivalent property axiom types checked, even when the ontology involved is tiny. In this case Protege doesn’t create the inferred ontology file and show no error panel, but is still responsive. I’ve logged an issue on the desktop Protege GitHub repository.

With best regards,
Samson


On Jun 2, 2019, at 9:26 AM, Samson Tu <[hidden email]> wrote:

Jim,

Export the inferred axioms WITH asserted logical axioms, annotations, and subclass/equivalence class axioms. The resulting ontology still works with DL query, although, as Matthew says, you gain nothing over doing the same query in the original ontology. Exporting inferred axioms as an ontology is useful only when the applications that use the exported ontology have no access to a reasoner.

In any case, I don’t think SNOMED CT has any inferred subproperty or equivalent property axioms. The Elk reasoner doesn’t implement getEquivalentObjectProperties(…) method and the “Unsupported inference Types” warning panel says to turn off Displayed Object/Data Property Inferences. In fact, maybe the export is hanging when the sub/equivalent properties are checked not because of memory limitation, but because the Elk reasoner doesn’t support those inferences. In that case there may be a bug or missing feature in Protege or in the Elk reasoner.Trying to export unsupported inferred axiom types should have more graceful behavior. 

With best regards,
Samson


On Jun 2, 2019, at 6:51 AM, Campbell, James R <[hidden email]> wrote:

Thanks Samson.

I stopped the process at 48 hours run time with no progress to show.  I revised run.bat as follows
Xmx=8GB
Xms=4GB
Xss=320M
Using these memory parameters, I rebooted windows then Protege and reloaded SNOMED CT.  I was able to get a successful export selecting axioms of Subclasses and Equivalent classes but I got no progress when I added Equivalent object properties.  As Samson suggested, I included annotations but ignored asserted logical axioms.  I used the default of RDF/XML as the export format.

The inferred ontology looked OK on reloading but the DL query function did not work, I presume because I did not include Equivalent object properties.  When examining the classes in Entities tab, Annotations and subclass axioms appeared but no Equivalent object properties (not surprizingly).  

I must have the full object definitions for my work and so I will try another export adding Equivalent object properties and let it run longer to see if I get any results.  Is one output format better than another for my purpose or for Protege efficiency?
Jim

From: protege-user <[hidden email]> on behalf of Samson Tu <[hidden email]>
Sent: Saturday, June 1, 2019 10:38 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Export inferred view of SNOMED CT
 
Non-UNMC email 
Hi,

I suspect that the problem is memory requirement of saving the large inferred ontology. Yesterday I tried to save the inferred SNOMED CT and saw the same behavior that Jim observed. This morning I tried various combination of axiom types and found that saving subclass, equivalent classes, annotations, and asserted ontology resulted in a saved ontology within a few minutes, with Protege taking up the 5+ GB memory that I’ve allocated for it. Added sub-object properties axioms resulted in hung behavior, with the Protege process struggling at 5.9 GB memory level.

With best regards,
Samson


On Jun 1, 2019, at 7:39 AM, Matthew Horridge <[hidden email]> wrote:

Hi Jim,

Which axiom types do you have checked on the first page of the export wizard?  (I’m unable to read the text in the screenshot btw).  Would you be able to try with just “Subclasses” and let me know what happens?

Cheers,

Matthew


On Jun 1, 2019, at 05:30, Campbell, James R <[hidden email]> wrote:

At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?
Jim Campbell

<image.png>

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Re: Export inferred view of SNOMED CT

Campbell, James R
Alan
SNOMED CT supports extension development to the core ontology and each participating member nation who is member of the IHTSDO maintains an extension to support their parochial needs for SNOMED CT concepts.  At Nebraska we have been doing significant development of content for problem list and synoptic cancer reporting with biomarkers (cancer genomics).  Some of this content is scheduled to be moved into SNOMED CT core in the near future.  

Much of the dialogue with Samson and user group has been about exporting an inferred ontology of the Obserbales axis of SNOMED CT which is subject of a harmonization effort between SNOMED CT and LOINC.  Much of the cancer synoptic reporting work is part of Observables and LOINC and publishing a version of LOIN-on-OWL for US consumption is what this is all about.

Is that understandable/useful?
Jim

From: Alan Ruttenberg <[hidden email]>
Sent: Sunday, June 2, 2019 4:38 PM
To: Campbell, James R
Subject: Re: [protege-user] Export inferred view of SNOMED CT
 
Non-UNMC email
Doesn't the tool also allow exporting inferred? Curious why you need Protege to do that? I'm not familiar with the lexicon. Is it that you want to classify SNOMED+Lexicon together?

On Sun, Jun 2, 2019 at 4:14 PM Campbell, James R <[hidden email]> wrote:
That is what we used to build our
First OWL instance of SNOMED 
core + US extension + Nebraska
 Lexicon!

Jim Campbell


On Jun 2, 2019, at 1:15 PM, Alan Ruttenberg <[hidden email]> wrote:

Non-UNMC email
Have you looked at https://github.com/IHTSDO/snomed-owl-toolkit - I haven't tried it yet, but plan to.

Alan

On Sun, Jun 2, 2019 at 1:32 PM Samson Tu <[hidden email]> wrote:
Hi,

I verified that Protege doesn’t behave well when exporting inferred Elk reasoner axioms, with the subproperty/equivalent property axiom types checked, even when the ontology involved is tiny. In this case Protege doesn’t create the inferred ontology file and show no error panel, but is still responsive. I’ve logged an issue on the desktop Protege GitHub repository.

With best regards,
Samson


On Jun 2, 2019, at 9:26 AM, Samson Tu <[hidden email]> wrote:

Jim,

Export the inferred axioms WITH asserted logical axioms, annotations, and subclass/equivalence class axioms. The resulting ontology still works with DL query, although, as Matthew says, you gain nothing over doing the same query in the original ontology. Exporting inferred axioms as an ontology is useful only when the applications that use the exported ontology have no access to a reasoner.

In any case, I don’t think SNOMED CT has any inferred subproperty or equivalent property axioms. The Elk reasoner doesn’t implement getEquivalentObjectProperties(…) method and the “Unsupported inference Types” warning panel says to turn off Displayed Object/Data Property Inferences. In fact, maybe the export is hanging when the sub/equivalent properties are checked not because of memory limitation, but because the Elk reasoner doesn’t support those inferences. In that case there may be a bug or missing feature in Protege or in the Elk reasoner.Trying to export unsupported inferred axiom types should have more graceful behavior. 

With best regards,
Samson


On Jun 2, 2019, at 6:51 AM, Campbell, James R <[hidden email]> wrote:

Thanks Samson.

I stopped the process at 48 hours run time with no progress to show.  I revised run.bat as follows
Xmx=8GB
Xms=4GB
Xss=320M
Using these memory parameters, I rebooted windows then Protege and reloaded SNOMED CT.  I was able to get a successful export selecting axioms of Subclasses and Equivalent classes but I got no progress when I added Equivalent object properties.  As Samson suggested, I included annotations but ignored asserted logical axioms.  I used the default of RDF/XML as the export format.

The inferred ontology looked OK on reloading but the DL query function did not work, I presume because I did not include Equivalent object properties.  When examining the classes in Entities tab, Annotations and subclass axioms appeared but no Equivalent object properties (not surprizingly).  

I must have the full object definitions for my work and so I will try another export adding Equivalent object properties and let it run longer to see if I get any results.  Is one output format better than another for my purpose or for Protege efficiency?
Jim

From: protege-user <[hidden email]> on behalf of Samson Tu <[hidden email]>
Sent: Saturday, June 1, 2019 10:38 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Export inferred view of SNOMED CT
 
Non-UNMC email 
Hi,

I suspect that the problem is memory requirement of saving the large inferred ontology. Yesterday I tried to save the inferred SNOMED CT and saw the same behavior that Jim observed. This morning I tried various combination of axiom types and found that saving subclass, equivalent classes, annotations, and asserted ontology resulted in a saved ontology within a few minutes, with Protege taking up the 5+ GB memory that I’ve allocated for it. Added sub-object properties axioms resulted in hung behavior, with the Protege process struggling at 5.9 GB memory level.

With best regards,
Samson


On Jun 1, 2019, at 7:39 AM, Matthew Horridge <[hidden email]> wrote:

Hi Jim,

Which axiom types do you have checked on the first page of the export wizard?  (I’m unable to read the text in the screenshot btw).  Would you be able to try with just “Subclasses” and let me know what happens?

Cheers,

Matthew


On Jun 1, 2019, at 05:30, Campbell, James R <[hidden email]> wrote:

At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?
Jim Campbell

<image.png>

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
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The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.


_______________________________________________
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[hidden email]
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The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.
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Re: Export inferred view of SNOMED CT

Wynne, Robert (NIH/NLM/LHC) [C]

At a time (not sure if this is still the case) Protégé 5 would not export NCI Thesaurus inferred.  A custom program[1], using the OWL API and Pellet, was necessary for the publishing pipeline.

 

Rob

 

[1] https://github.com/NCIEVS/ops-owl-applications/tree/master/GenerateOWLAPIInferred

 

From: Campbell, James R <[hidden email]>
Sent: Sunday, June 2, 2019 7:27 PM
To: Alan Ruttenberg <[hidden email]>; User Protege <[hidden email]>
Subject: Re: [protege-user] Export inferred view of SNOMED CT

 

Alan

SNOMED CT supports extension development to the core ontology and each participating member nation who is member of the IHTSDO maintains an extension to support their parochial needs for SNOMED CT concepts.  At Nebraska we have been doing significant development of content for problem list and synoptic cancer reporting with biomarkers (cancer genomics).  Some of this content is scheduled to be moved into SNOMED CT core in the near future.  

 

Much of the dialogue with Samson and user group has been about exporting an inferred ontology of the Obserbales axis of SNOMED CT which is subject of a harmonization effort between SNOMED CT and LOINC.  Much of the cancer synoptic reporting work is part of Observables and LOINC and publishing a version of LOIN-on-OWL for US consumption is what this is all about.

 

Is that understandable/useful?

Jim


From: Alan Ruttenberg <[hidden email]>
Sent: Sunday, June 2, 2019 4:38 PM
To: Campbell, James R
Subject: Re: [protege-user] Export inferred view of SNOMED CT

 

Non-UNMC email

Doesn't the tool also allow exporting inferred? Curious why you need Protege to do that? I'm not familiar with the lexicon. Is it that you want to classify SNOMED+Lexicon together?

 

On Sun, Jun 2, 2019 at 4:14 PM Campbell, James R <[hidden email]> wrote:

That is what we used to build our

First OWL instance of SNOMED 

core + US extension + Nebraska

 Lexicon!

Jim Campbell

 


On Jun 2, 2019, at 1:15 PM, Alan Ruttenberg <[hidden email]> wrote:

Non-UNMC email

Have you looked at https://github.com/IHTSDO/snomed-owl-toolkit - I haven't tried it yet, but plan to.

 

Alan

 

On Sun, Jun 2, 2019 at 1:32 PM Samson Tu <[hidden email]> wrote:

Hi,

 

I verified that Protege doesn’t behave well when exporting inferred Elk reasoner axioms, with the subproperty/equivalent property axiom types checked, even when the ontology involved is tiny. In this case Protege doesn’t create the inferred ontology file and show no error panel, but is still responsive. I’ve logged an issue on the desktop Protege GitHub repository.

 

With best regards,

Samson

 



On Jun 2, 2019, at 9:26 AM, Samson Tu <[hidden email]> wrote:

 

Jim,

 

Export the inferred axioms WITH asserted logical axioms, annotations, and subclass/equivalence class axioms. The resulting ontology still works with DL query, although, as Matthew says, you gain nothing over doing the same query in the original ontology. Exporting inferred axioms as an ontology is useful only when the applications that use the exported ontology have no access to a reasoner.

 

In any case, I don’t think SNOMED CT has any inferred subproperty or equivalent property axioms. The Elk reasoner doesn’t implement getEquivalentObjectProperties(…) method and the “Unsupported inference Types” warning panel says to turn off Displayed Object/Data Property Inferences. In fact, maybe the export is hanging when the sub/equivalent properties are checked not because of memory limitation, but because the Elk reasoner doesn’t support those inferences. In that case there may be a bug or missing feature in Protege or in the Elk reasoner.Trying to export unsupported inferred axiom types should have more graceful behavior. 

 

With best regards,

Samson

 



On Jun 2, 2019, at 6:51 AM, Campbell, James R <[hidden email]> wrote:

 

Thanks Samson.

 

I stopped the process at 48 hours run time with no progress to show.  I revised run.bat as follows

Xmx=8GB

Xms=4GB

Xss=320M

Using these memory parameters, I rebooted windows then Protege and reloaded SNOMED CT.  I was able to get a successful export selecting axioms of Subclasses and Equivalent classes but I got no progress when I added Equivalent object properties.  As Samson suggested, I included annotations but ignored asserted logical axioms.  I used the default of RDF/XML as the export format.

 

The inferred ontology looked OK on reloading but the DL query function did not work, I presume because I did not include Equivalent object properties.  When examining the classes in Entities tab, Annotations and subclass axioms appeared but no Equivalent object properties (not surprizingly).  

 

I must have the full object definitions for my work and so I will try another export adding Equivalent object properties and let it run longer to see if I get any results.  Is one output format better than another for my purpose or for Protege efficiency?

Jim


From: protege-user <[hidden email]> on behalf of Samson Tu <[hidden email]>
Sent: Saturday, June 1, 2019 10:38 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Export inferred view of SNOMED CT

 

Non-UNMC email 

Hi,

 

I suspect that the problem is memory requirement of saving the large inferred ontology. Yesterday I tried to save the inferred SNOMED CT and saw the same behavior that Jim observed. This morning I tried various combination of axiom types and found that saving subclass, equivalent classes, annotations, and asserted ontology resulted in a saved ontology within a few minutes, with Protege taking up the 5+ GB memory that I’ve allocated for it. Added sub-object properties axioms resulted in hung behavior, with the Protege process struggling at 5.9 GB memory level.

 

With best regards,

Samson

 



On Jun 1, 2019, at 7:39 AM, Matthew Horridge <[hidden email]> wrote:

 

Hi Jim,

 

Which axiom types do you have checked on the first page of the export wizard?  (I’m unable to read the text in the screenshot btw).  Would you be able to try with just “Subclasses” and let me know what happens?

 

Cheers,

 

Matthew

 



On Jun 1, 2019, at 05:30, Campbell, James R <[hidden email]> wrote:

 

At this point the run time on Protege for exporting inferred axioms using OWL functional view after classifying SNOMED CT is 24 hours.  I am getting reports of unsupported method as shown in the screen shot below.  Can I expect the process to complete? how soon?

Jim Campbell

 

<image.png>


The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

 

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

 


The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

 

 

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.


The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.


_______________________________________________
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