running the reasoner with different ontologies of different formats

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running the reasoner with different ontologies of different formats

Karen Moll
I was wondering if anyone has had the problem of running the reasoner with different ontologies that are formatted differently. I tried running HermiT1.3.8.4.13. The ontology that I'm working currently contains 7 ontologies that were directly imported in the desktop version. However, some use quotes instead of camel case. Others have different types of camel case, e.g. camelCase v. CamelCase v. 'camel case' . Does anyone know if this can cause a problem? If so, what is the easiest way to convert each owl file to a consistent format?

Thank you so much,
Karen

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Re: running the reasoner with different ontologies of different formats

Michael DeBellis-2
Karen, can you tell us the kind of error you are getting? I've never had a problem with the reasoner and different styles of names except I think there was one time when SWRL didn't like names that had quotes and spaces from a List ontology that I imported. Someone helped me fix that but I can't remember what the fix was, if you describe the error you are getting it may jog my memory if it was the same problem. 

If you are using SWRL I would recommend using Pellet anyway, it has the best support for the SWRL built-ins. If you aren't using SWRL my guess (which could be wrong) is that it's not due to the different names but some other inconsistency between the various ontologies.  If you haven't already tried this one thing I would recommend is that when you build your big ontology that incorporates the 7 others you try importing the ontologies one at a time and you run the reasoner every time after you import a new ontology. That may give you a better idea what is causing the problem. Good luck.

Michael

On Fri, Jul 6, 2018 at 7:59 AM, Karen Moll <[hidden email]> wrote:
I was wondering if anyone has had the problem of running the reasoner with different ontologies that are formatted differently. I tried running HermiT1.3.8.4.13. The ontology that I'm working currently contains 7 ontologies that were directly imported in the desktop version. However, some use quotes instead of camel case. Others have different types of camel case, e.g. camelCase v. CamelCase v. 'camel case' . Does anyone know if this can cause a problem? If so, what is the easiest way to convert each owl file to a consistent format?

Thank you so much,
Karen

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Re: running the reasoner with different ontologies of different formats

Karen Moll
In reply to this post by Karen Moll

Hi Michael,
Thank you so much for your reply. Ive tried a number of different reasoners. When I ran HermiT last, the reasoner seems to run correctly, but Protege gets hung up and eventually stops responding. I've tried this on my ontology combined with several different single ontologies to determine whether one specific ontology I'm importing is the source of the problem. When I run my ontology by itself, everything runs smoothly and quickly. 

I'm also playing around with running HermiT on the command line as a work around to Protege to see if that helps...

Do you have any other ideas as to why Protege might be getting hung up?

Thank you so much for your help.
Karen

Karen, can you tell us the kind of error you are getting? I've never had a
problem with the reasoner and different styles of names except I think
there was one time when SWRL didn't like names that had quotes and spaces
from a List ontology that I imported. Someone helped me fix that but I
can't remember what the fix was, if you describe the error you are getting
it may jog my memory if it was the same problem.

If you are using SWRL I would recommend using Pellet anyway, it has the
best support for the SWRL built-ins. If you aren't using SWRL my guess
(which could be wrong) is that it's not due to the different names but some
other inconsistency between the various ontologies.  If you haven't already
tried this one thing I would recommend is that when you build your big
ontology that incorporates the 7 others you try importing the ontologies
one at a time and you run the reasoner every time after you import a new
ontology. That may give you a better idea what is causing the problem. Good
luck.

Michael

On Fri, Jul 6, 2018 at 7:59 AM, Karen Moll <[hidden email]> wrote:

> I was wondering if anyone has had the problem of running the reasoner with
> different ontologies that are formatted differently. I tried running
> HermiT1.3.8.4.13. The ontology that I'm working currently contains 7
> ontologies that were directly imported in the desktop version. However,
> some use quotes instead of camel case. Others have different types of camel
> case, e.g. camelCase v. CamelCase v. 'camel case' . Does anyone know if
> this can cause a problem? If so, what is the easiest way to convert each
> owl file to a consistent format?
>
> Thank you so much,
> Karen

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Re: running the reasoner with different ontologies of different formats

Michael DeBellis-2
Karen, Sorry, without seeing any error messages it's hard to say what the problem might be. But here are some more ideas on how to debug it.

When you say the reasoner seems to run correctly does that mean that it completes and in the lower right hand corner of the Protege window you see the message "Reasoner active"? That is the message that tells you the reasoner has completed on the current version of your ontology. One suggestion I have, is to keep checking the Log window. You can see that by the menu option Window>Show log...  I would check that after you run the reasoner, sometimes the reasoner may not find an error that causes a logical inconsistency (which you can't miss because big parts of your ontology will be displayed in red) but there is some other problem that while not making the ontology inconsistent may be making it very slow for Protege to do basic things like displaying windows and/or resulting in Protege crashing eventually. 

Another thing you might want to do is to check the Preferences for the reasoner. You can see these by doing Protege>Preferences and then click on the Reasoner tab on the window that pops up, or you can just go to Reasoner>Configure...  both options take you to the same window.   My default is to check all the boxes but for some large or complex ontologies (especially if you have things like Transitive properties) the reasoning can get so complex that it causes problems, this can help you focus in on what is causing the problem. Just select a minimum number of boxes and see if that makes a difference and then gradually re-check the boxes.  I know that's a long shot but it helped me find a problem one time. 

I assume you've also tried loading each individual ontology by itself and running the reasoner? It doesn't happen often but sometimes even ontologies that are published and used by others end up with issues such as using features that were changed in newer versions of OWL. 

You also asked in a previous message about changing the names of objects. I wouldn't start doing this until you had better evidence that it was the problem but I assume you know that it is very easy to change the name of anything in Protege. Just click the class/property/etc. and select Refactor>Rename entity.  That will change the name everywhere in the ontology.  Also, if you have names with quotes or unusual symbols sometimes the name may show up in a different way than you expect when you go to edit it.  If this happens click on the box that says "Show full IRI".  This box shows up in any window where you are using the name of some object, such as the Rename refactoring command. When you see the full IRI you should see a long name that looks like a URL (which is more or less what an IRI is) and after the last "/" it should say something like "/NameOfOntology123.owl#ClassName". So for example class Animal in EvolutionOntology would look like: ".../EvolutionOntology.owl#Animal"  If you go to rename it you want to start after the # sign. Usually you never have to worry about that but as I said some non-standard names require you to know this if you want to change them. 

Michael

On Wed, Jul 11, 2018 at 8:19 AM, Karen Moll <[hidden email]> wrote:

Hi Michael,
Thank you so much for your reply. Ive tried a number of different reasoners. When I ran HermiT last, the reasoner seems to run correctly, but Protege gets hung up and eventually stops responding. I've tried this on my ontology combined with several different single ontologies to determine whether one specific ontology I'm importing is the source of the problem. When I run my ontology by itself, everything runs smoothly and quickly. 

I'm also playing around with running HermiT on the command line as a work around to Protege to see if that helps...

Do you have any other ideas as to why Protege might be getting hung up?

Thank you so much for your help.
Karen


Karen, can you tell us the kind of error you are getting? I've never had a
problem with the reasoner and different styles of names except I think
there was one time when SWRL didn't like names that had quotes and spaces
from a List ontology that I imported. Someone helped me fix that but I
can't remember what the fix was, if you describe the error you are getting
it may jog my memory if it was the same problem.

If you are using SWRL I would recommend using Pellet anyway, it has the
best support for the SWRL built-ins. If you aren't using SWRL my guess
(which could be wrong) is that it's not due to the different names but some
other inconsistency between the various ontologies.  If you haven't already
tried this one thing I would recommend is that when you build your big
ontology that incorporates the 7 others you try importing the ontologies
one at a time and you run the reasoner every time after you import a new
ontology. That may give you a better idea what is causing the problem. Good
luck.

Michael

On Fri, Jul 6, 2018 at 7:59 AM, Karen Moll <[hidden email]> wrote:

> I was wondering if anyone has had the problem of running the reasoner with
> different ontologies that are formatted differently. I tried running
> HermiT1.3.8.4.13. The ontology that I'm working currently contains 7
> ontologies that were directly imported in the desktop version. However,
> some use quotes instead of camel case. Others have different types of camel
> case, e.g. camelCase v. CamelCase v. 'camel case' . Does anyone know if
> this can cause a problem? If so, what is the easiest way to convert each
> owl file to a consistent format?
>
> Thank you so much,
> Karen

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



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Re: running the reasoner with different ontologies of different formats

Lorenz Buehmann

In addition, there must be only a single axiom from an imported axiom such that the reasoning goes from instant to taking ages. That's the nature of Description Logics and tableau reasoning even with all the implemented performance optimization - the complexity class remains 2NexpTime


On 12.07.2018 20:16, Michael DeBellis wrote:
Karen, Sorry, without seeing any error messages it's hard to say what the problem might be. But here are some more ideas on how to debug it.

When you say the reasoner seems to run correctly does that mean that it completes and in the lower right hand corner of the Protege window you see the message "Reasoner active"? That is the message that tells you the reasoner has completed on the current version of your ontology. One suggestion I have, is to keep checking the Log window. You can see that by the menu option Window>Show log...  I would check that after you run the reasoner, sometimes the reasoner may not find an error that causes a logical inconsistency (which you can't miss because big parts of your ontology will be displayed in red) but there is some other problem that while not making the ontology inconsistent may be making it very slow for Protege to do basic things like displaying windows and/or resulting in Protege crashing eventually. 

Another thing you might want to do is to check the Preferences for the reasoner. You can see these by doing Protege>Preferences and then click on the Reasoner tab on the window that pops up, or you can just go to Reasoner>Configure...  both options take you to the same window.   My default is to check all the boxes but for some large or complex ontologies (especially if you have things like Transitive properties) the reasoning can get so complex that it causes problems, this can help you focus in on what is causing the problem. Just select a minimum number of boxes and see if that makes a difference and then gradually re-check the boxes.  I know that's a long shot but it helped me find a problem one time. 

I assume you've also tried loading each individual ontology by itself and running the reasoner? It doesn't happen often but sometimes even ontologies that are published and used by others end up with issues such as using features that were changed in newer versions of OWL. 

You also asked in a previous message about changing the names of objects. I wouldn't start doing this until you had better evidence that it was the problem but I assume you know that it is very easy to change the name of anything in Protege. Just click the class/property/etc. and select Refactor>Rename entity.  That will change the name everywhere in the ontology.  Also, if you have names with quotes or unusual symbols sometimes the name may show up in a different way than you expect when you go to edit it.  If this happens click on the box that says "Show full IRI".  This box shows up in any window where you are using the name of some object, such as the Rename refactoring command. When you see the full IRI you should see a long name that looks like a URL (which is more or less what an IRI is) and after the last "/" it should say something like "/NameOfOntology123.owl#ClassName". So for example class Animal in EvolutionOntology would look like: ".../EvolutionOntology.owl#Animal"  If you go to rename it you want to start after the # sign. Usually you never have to worry about that but as I said some non-standard names require you to know this if you want to change them. 

Michael

On Wed, Jul 11, 2018 at 8:19 AM, Karen Moll <[hidden email]> wrote:

Hi Michael,
Thank you so much for your reply. Ive tried a number of different reasoners. When I ran HermiT last, the reasoner seems to run correctly, but Protege gets hung up and eventually stops responding. I've tried this on my ontology combined with several different single ontologies to determine whether one specific ontology I'm importing is the source of the problem. When I run my ontology by itself, everything runs smoothly and quickly. 

I'm also playing around with running HermiT on the command line as a work around to Protege to see if that helps...

Do you have any other ideas as to why Protege might be getting hung up?

Thank you so much for your help.
Karen


Karen, can you tell us the kind of error you are getting? I've never had a
problem with the reasoner and different styles of names except I think
there was one time when SWRL didn't like names that had quotes and spaces
from a List ontology that I imported. Someone helped me fix that but I
can't remember what the fix was, if you describe the error you are getting
it may jog my memory if it was the same problem.

If you are using SWRL I would recommend using Pellet anyway, it has the
best support for the SWRL built-ins. If you aren't using SWRL my guess
(which could be wrong) is that it's not due to the different names but some
other inconsistency between the various ontologies.  If you haven't already
tried this one thing I would recommend is that when you build your big
ontology that incorporates the 7 others you try importing the ontologies
one at a time and you run the reasoner every time after you import a new
ontology. That may give you a better idea what is causing the problem. Good
luck.

Michael

On Fri, Jul 6, 2018 at 7:59 AM, Karen Moll <[hidden email]> wrote:

> I was wondering if anyone has had the problem of running the reasoner with
> different ontologies that are formatted differently. I tried running
> HermiT1.3.8.4.13. The ontology that I'm working currently contains 7
> ontologies that were directly imported in the desktop version. However,
> some use quotes instead of camel case. Others have different types of camel
> case, e.g. camelCase v. CamelCase v. 'camel case' . Does anyone know if
> this can cause a problem? If so, what is the easiest way to convert each
> owl file to a consistent format?
>
> Thank you so much,
> Karen

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




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


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