Don't know how to create axioms and rules in Protégé 4.3

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Don't know how to create axioms and rules in Protégé 4.3

Tob Mang
Morning,

I am developing an ontology for my research using protégé 4.3, but i have some struggles related to how to write axioms and rules.
 
Please Help!

M. Manga Tobie Armand
Master en Informatique
tel: (237) 694329689
Keep Moving forward



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Re: Don't know how to create axioms and rules in Protégé 4.3

Michael DeBellis-2
That's a pretty open ended question, usually people come to the list with specific questions or problems. But here are some suggestions:  

First, you should be using the latest version not an older version, especially one as old as 4.3. Go to the Protege site and download the latest version which I think if 5.2 but whatever the latest one on the Protege site is that is what I would recommend. There is a beta version but I recommend that since you are not an experienced user you stick with the latest tested version. If you use the old version it will be almost impossible to help you debug any problems because so few people are using it anymore. Also, things like Java change and you may run into problems caused by using the latest version of Java with such an old version of Protege. 

Second: do some tutorials. At a bare minimum do the Pizza tutorial. I would also recommend doing the Manchester FHKB tutorial, it helps understand some of the power of DL and of relations (object properties). If you are interested in rules I wrote a very basic SWRL tutorial which can be found here: https://symbolicshacker.blogspot.com/2017/06/swrl-process-modeling-tutorial.html  I think there is also a more recent and probably better SWRL tutorial on the Protege web site. Note: some of these tutorials, especially the Pizza tutorial are a bit dated and so the UI has changed in fairly minor ways from what is in the tutorial and what the UI currently looks like. It's been a long time since I did the tutorials but one thing I remember is that in the tutorial it says something like "Add class Foo in the Superclass assertions" where as in the UI it now says "SubclassOf" rather than "Superclass".  Depending on how familiar you are with concepts from set theory and OOP (even though there are very significant differences between Protege objects and traditional OOP many of the basic terms and concept are the same) you should be able to figure out what to do even though the language or UI in the tutorial may be a bit different but if you get stuck those are the kind of specific questions people here can answer easily and quickly. 

Finally, if you aren't familiar with set theory and logic I recommend reading a basic intro. So much of the power of Protege comes from the way it implements Decision Logic (which is a subset of First Order Logic). If you look at the link I gave above to my SWRL tutorial on that page there is also a PDF that is a good overview of set theory and logic basics. Also, Elements of the Theory of Computation by Papadimitriou and Lewis is a book often used in computer science theory classes and the first chapter of that book also has an excellent overview of set theory and logic. 

Hope that helps.

Michael

On Fri, Jan 25, 2019 at 1:52 AM Tob Mang <[hidden email]> wrote:
Morning,

I am developing an ontology for my research using protégé 4.3, but i have some struggles related to how to write axioms and rules.
 
Please Help!

M. Manga Tobie Armand
Master en Informatique
tel: (237) 694329689
Keep Moving forward


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Re: Don't know how to create axioms and rules in Protégé 4.3

Luis Enrique Ramos García
In reply to this post by Tob Mang
Dear Tob, 

about your question, I recommend you to begin working with protegé 3.x version where an axiom and rule editor is available, facilitating the job, and understanding, I guess. About the logic, behind OWL it is Description Logic, which actually it is a family of logics that begin with AL (attributive logics) and currently works with sroiq (http://www.cs.ox.ac.uk/people/ian.horrocks/Publications/download/2006/HoKS06a.pdf). Please, take in account that working with those versions of protégé means you are working with different versions of owl. 

About DL, I recommend you to read the book of baader, the description logic hand book;


Best regards


Luis Ramos




El vie., 25 ene. 2019 a las 5:52, Tob Mang (<[hidden email]>) escribió:
Morning,

I am developing an ontology for my research using protégé 4.3, but i have some struggles related to how to write axioms and rules.
 
Please Help!

M. Manga Tobie Armand
Master en Informatique
tel: (237) 694329689
Keep Moving forward


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Re: Don't know how to create axioms and rules in Protégé 4.3

Robert Rynasiewicz
Do you have a complete citation for the Horrocks et.al. piece you sent the link for below?


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Re: Don't know how to create axioms and rules in Protégé 4.3

Luis Enrique Ramos García

El dom., 27 ene. 2019 a las 9:51, Robert Rynasiewicz (<[hidden email]>) escribió:
Do you have a complete citation for the Horrocks et.al. piece you sent the link for below?

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Re: Don't know how to create axioms and rules in Protégé 4.3

Michael DeBellis-2
In reply to this post by Luis Enrique Ramos García
I disagree about using the 3.x version. It's no longer supported so it will be very hard for you to get support. If you have further questions once you say you are using 3.x most of us won't be able to help at all. Also, most if not all of the plugins will probably no longer work and it is very possible there will be problems between your version of Java (which is much newer than the version the 3.x Protege worked with) and using that old a version. I assumed when you meant "writing axioms" what you meant was just things like creating classes, properties, individuals, giving values for properties to individuals, and writing SWRL rules. Protege will do all that for you and generate the appropriate axioms.  If you actually want to write the OWL axioms yourself than don't bother with Protege and use a text editor or some other tool. Just my opinion. 

Michael

On Sun, Jan 27, 2019 at 3:20 AM Luis Enrique Ramos García <[hidden email]> wrote:
Dear Tob, 

about your question, I recommend you to begin working with protegé 3.x version where an axiom and rule editor is available, facilitating the job, and understanding, I guess. About the logic, behind OWL it is Description Logic, which actually it is a family of logics that begin with AL (attributive logics) and currently works with sroiq (http://www.cs.ox.ac.uk/people/ian.horrocks/Publications/download/2006/HoKS06a.pdf). Please, take in account that working with those versions of protégé means you are working with different versions of owl. 

About DL, I recommend you to read the book of baader, the description logic hand book;


Best regards


Luis Ramos




El vie., 25 ene. 2019 a las 5:52, Tob Mang (<[hidden email]>) escribió:
Morning,

I am developing an ontology for my research using protégé 4.3, but i have some struggles related to how to write axioms and rules.
 
Please Help!

M. Manga Tobie Armand
Master en Informatique
tel: (237) 694329689
Keep Moving forward


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Re: Don't know how to create axioms and rules in Protégé 4.3

Luis Enrique Ramos García
Dear Michael, 

When I recommended the use of version 3.x was with the idea of facilitating the familiarization of the user with symbols used in logic. I must clarify that writing axioms is not only creating classes, properties or individuals, in protégé we have two kind of classes i protégé primitive and define classes, the difference among them is the use of axiom to define them. Moreover, to get individuals classified into a class you need defined classes. 

Anyway the discussion is interesting, 


Luis  

El dom., 27 ene. 2019 a las 11:27, Michael DeBellis (<[hidden email]>) escribió:
I disagree about using the 3.x version. It's no longer supported so it will be very hard for you to get support. If you have further questions once you say you are using 3.x most of us won't be able to help at all. Also, most if not all of the plugins will probably no longer work and it is very possible there will be problems between your version of Java (which is much newer than the version the 3.x Protege worked with) and using that old a version. I assumed when you meant "writing axioms" what you meant was just things like creating classes, properties, individuals, giving values for properties to individuals, and writing SWRL rules. Protege will do all that for you and generate the appropriate axioms.  If you actually want to write the OWL axioms yourself than don't bother with Protege and use a text editor or some other tool. Just my opinion. 

Michael

On Sun, Jan 27, 2019 at 3:20 AM Luis Enrique Ramos García <[hidden email]> wrote:
Dear Tob, 

about your question, I recommend you to begin working with protegé 3.x version where an axiom and rule editor is available, facilitating the job, and understanding, I guess. About the logic, behind OWL it is Description Logic, which actually it is a family of logics that begin with AL (attributive logics) and currently works with sroiq (http://www.cs.ox.ac.uk/people/ian.horrocks/Publications/download/2006/HoKS06a.pdf). Please, take in account that working with those versions of protégé means you are working with different versions of owl. 

About DL, I recommend you to read the book of baader, the description logic hand book;


Best regards


Luis Ramos




El vie., 25 ene. 2019 a las 5:52, Tob Mang (<[hidden email]>) escribió:
Morning,

I am developing an ontology for my research using protégé 4.3, but i have some struggles related to how to write axioms and rules.
 
Please Help!

M. Manga Tobie Armand
Master en Informatique
tel: (237) 694329689
Keep Moving forward


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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: Don't know how to create axioms and rules in Protégé 4.3

Michael DeBellis-2
Thanks Luis. I understand what defined classes are,  but you can create defined classes in Protege 5.2 as well. Also, regarding terminology when you say "  the difference among them is the use of axiom to define them" I don't think that is actually true. My understanding is that every definition in OWL is an axiom. So if I say Animal is a class and Mammal is a subclass of Animal those are all axioms in OWL even though they are primitive classes. I think there are better ways to understand logic than using an outdated version of Protege. That's why I point people to various PDFs or books with introductions to logic. 

We can agree to disagree but personally I think it's a very bad idea for a new user to try learning Protege with an out-dated version.  Any benefits in learning logic from the different UI are IMO going to be vastly outweighed by the fact that the user won't be able to get support, will be learning a version that she will eventually need to transition away from anyway, won't be able to use many plugins, and will quite possibly encounter unknown bugs as a result of using a version of Protege with versions of the operating system and Java that 3.x was never rigorously tested with. 

Michael

On Sun, Jan 27, 2019 at 7:50 AM Luis Enrique Ramos García <[hidden email]> wrote:
Dear Michael, 

When I recommended the use of version 3.x was with the idea of facilitating the familiarization of the user with symbols used in logic. I must clarify that writing axioms is not only creating classes, properties or individuals, in protégé we have two kind of classes i protégé primitive and define classes, the difference among them is the use of axiom to define them. Moreover, to get individuals classified into a class you need defined classes. 

Anyway the discussion is interesting, 


Luis  

El dom., 27 ene. 2019 a las 11:27, Michael DeBellis (<[hidden email]>) escribió:
I disagree about using the 3.x version. It's no longer supported so it will be very hard for you to get support. If you have further questions once you say you are using 3.x most of us won't be able to help at all. Also, most if not all of the plugins will probably no longer work and it is very possible there will be problems between your version of Java (which is much newer than the version the 3.x Protege worked with) and using that old a version. I assumed when you meant "writing axioms" what you meant was just things like creating classes, properties, individuals, giving values for properties to individuals, and writing SWRL rules. Protege will do all that for you and generate the appropriate axioms.  If you actually want to write the OWL axioms yourself than don't bother with Protege and use a text editor or some other tool. Just my opinion. 

Michael

On Sun, Jan 27, 2019 at 3:20 AM Luis Enrique Ramos García <[hidden email]> wrote:
Dear Tob, 

about your question, I recommend you to begin working with protegé 3.x version where an axiom and rule editor is available, facilitating the job, and understanding, I guess. About the logic, behind OWL it is Description Logic, which actually it is a family of logics that begin with AL (attributive logics) and currently works with sroiq (http://www.cs.ox.ac.uk/people/ian.horrocks/Publications/download/2006/HoKS06a.pdf). Please, take in account that working with those versions of protégé means you are working with different versions of owl. 

About DL, I recommend you to read the book of baader, the description logic hand book;


Best regards


Luis Ramos




El vie., 25 ene. 2019 a las 5:52, Tob Mang (<[hidden email]>) escribió:
Morning,

I am developing an ontology for my research using protégé 4.3, but i have some struggles related to how to write axioms and rules.
 
Please Help!

M. Manga Tobie Armand
Master en Informatique
tel: (237) 694329689
Keep Moving forward


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: Don't know how to create axioms and rules in Protégé 4.3

Luis Enrique Ramos García
Okay Michael, I only made reference to the older editor, which I think is easier to understand, that´s all. 

In reference to classes in protégé, I know every definition is an axioms, but protégé differentiates classes as defined and not defined, according to protégé a subsumption relation is not enough to have  defined classes, you have to write an axiom, and I guess that is what our friends is asking. 

An explanation about defined and not define classes are here:


I also wrote some days ago an example for a friend, and I also attached it. 

There are three classes, Hospital, Available Hospital and Non_Available_Hospital, the last ones are defined. 


Luis 



El dom., 27 ene. 2019 a las 12:41, Michael DeBellis (<[hidden email]>) escribió:
Thanks Luis. I understand what defined classes are,  but you can create defined classes in Protege 5.2 as well. Also, regarding terminology when you say "  the difference among them is the use of axiom to define them" I don't think that is actually true. My understanding is that every definition in OWL is an axiom. So if I say Animal is a class and Mammal is a subclass of Animal those are all axioms in OWL even though they are primitive classes. I think there are better ways to understand logic than using an outdated version of Protege. That's why I point people to various PDFs or books with introductions to logic. 

We can agree to disagree but personally I think it's a very bad idea for a new user to try learning Protege with an out-dated version.  Any benefits in learning logic from the different UI are IMO going to be vastly outweighed by the fact that the user won't be able to get support, will be learning a version that she will eventually need to transition away from anyway, won't be able to use many plugins, and will quite possibly encounter unknown bugs as a result of using a version of Protege with versions of the operating system and Java that 3.x was never rigorously tested with. 

Michael

On Sun, Jan 27, 2019 at 7:50 AM Luis Enrique Ramos García <[hidden email]> wrote:
Dear Michael, 

When I recommended the use of version 3.x was with the idea of facilitating the familiarization of the user with symbols used in logic. I must clarify that writing axioms is not only creating classes, properties or individuals, in protégé we have two kind of classes i protégé primitive and define classes, the difference among them is the use of axiom to define them. Moreover, to get individuals classified into a class you need defined classes. 

Anyway the discussion is interesting, 


Luis  

El dom., 27 ene. 2019 a las 11:27, Michael DeBellis (<[hidden email]>) escribió:
I disagree about using the 3.x version. It's no longer supported so it will be very hard for you to get support. If you have further questions once you say you are using 3.x most of us won't be able to help at all. Also, most if not all of the plugins will probably no longer work and it is very possible there will be problems between your version of Java (which is much newer than the version the 3.x Protege worked with) and using that old a version. I assumed when you meant "writing axioms" what you meant was just things like creating classes, properties, individuals, giving values for properties to individuals, and writing SWRL rules. Protege will do all that for you and generate the appropriate axioms.  If you actually want to write the OWL axioms yourself than don't bother with Protege and use a text editor or some other tool. Just my opinion. 

Michael

On Sun, Jan 27, 2019 at 3:20 AM Luis Enrique Ramos García <[hidden email]> wrote:
Dear Tob, 

about your question, I recommend you to begin working with protegé 3.x version where an axiom and rule editor is available, facilitating the job, and understanding, I guess. About the logic, behind OWL it is Description Logic, which actually it is a family of logics that begin with AL (attributive logics) and currently works with sroiq (http://www.cs.ox.ac.uk/people/ian.horrocks/Publications/download/2006/HoKS06a.pdf). Please, take in account that working with those versions of protégé means you are working with different versions of owl. 

About DL, I recommend you to read the book of baader, the description logic hand book;


Best regards


Luis Ramos




El vie., 25 ene. 2019 a las 5:52, Tob Mang (<[hidden email]>) escribió:
Morning,

I am developing an ontology for my research using protégé 4.3, but i have some struggles related to how to write axioms and rules.
 
Please Help!

M. Manga Tobie Armand
Master en Informatique
tel: (237) 694329689
Keep Moving forward


_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: Don't know how to create axioms and rules in Protégé 4.3

Tob Mang
many thanksfull for your support.

M. Manga Tobie Armand
Master en Informatique
tel: (237) 694329689
Keep Moving forward




Le dim. 27 janv. 2019 à 18:19, Luis Enrique Ramos García <[hidden email]> a écrit :
Okay Michael, I only made reference to the older editor, which I think is easier to understand, that´s all. 

In reference to classes in protégé, I know every definition is an axioms, but protégé differentiates classes as defined and not defined, according to protégé a subsumption relation is not enough to have  defined classes, you have to write an axiom, and I guess that is what our friends is asking. 

An explanation about defined and not define classes are here:


I also wrote some days ago an example for a friend, and I also attached it. 

There are three classes, Hospital, Available Hospital and Non_Available_Hospital, the last ones are defined. 


Luis 



El dom., 27 ene. 2019 a las 12:41, Michael DeBellis (<[hidden email]>) escribió:
Thanks Luis. I understand what defined classes are,  but you can create defined classes in Protege 5.2 as well. Also, regarding terminology when you say "  the difference among them is the use of axiom to define them" I don't think that is actually true. My understanding is that every definition in OWL is an axiom. So if I say Animal is a class and Mammal is a subclass of Animal those are all axioms in OWL even though they are primitive classes. I think there are better ways to understand logic than using an outdated version of Protege. That's why I point people to various PDFs or books with introductions to logic. 

We can agree to disagree but personally I think it's a very bad idea for a new user to try learning Protege with an out-dated version.  Any benefits in learning logic from the different UI are IMO going to be vastly outweighed by the fact that the user won't be able to get support, will be learning a version that she will eventually need to transition away from anyway, won't be able to use many plugins, and will quite possibly encounter unknown bugs as a result of using a version of Protege with versions of the operating system and Java that 3.x was never rigorously tested with. 

Michael

On Sun, Jan 27, 2019 at 7:50 AM Luis Enrique Ramos García <[hidden email]> wrote:
Dear Michael, 

When I recommended the use of version 3.x was with the idea of facilitating the familiarization of the user with symbols used in logic. I must clarify that writing axioms is not only creating classes, properties or individuals, in protégé we have two kind of classes i protégé primitive and define classes, the difference among them is the use of axiom to define them. Moreover, to get individuals classified into a class you need defined classes. 

Anyway the discussion is interesting, 


Luis  

El dom., 27 ene. 2019 a las 11:27, Michael DeBellis (<[hidden email]>) escribió:
I disagree about using the 3.x version. It's no longer supported so it will be very hard for you to get support. If you have further questions once you say you are using 3.x most of us won't be able to help at all. Also, most if not all of the plugins will probably no longer work and it is very possible there will be problems between your version of Java (which is much newer than the version the 3.x Protege worked with) and using that old a version. I assumed when you meant "writing axioms" what you meant was just things like creating classes, properties, individuals, giving values for properties to individuals, and writing SWRL rules. Protege will do all that for you and generate the appropriate axioms.  If you actually want to write the OWL axioms yourself than don't bother with Protege and use a text editor or some other tool. Just my opinion. 

Michael

On Sun, Jan 27, 2019 at 3:20 AM Luis Enrique Ramos García <[hidden email]> wrote:
Dear Tob, 

about your question, I recommend you to begin working with protegé 3.x version where an axiom and rule editor is available, facilitating the job, and understanding, I guess. About the logic, behind OWL it is Description Logic, which actually it is a family of logics that begin with AL (attributive logics) and currently works with sroiq (http://www.cs.ox.ac.uk/people/ian.horrocks/Publications/download/2006/HoKS06a.pdf). Please, take in account that working with those versions of protégé means you are working with different versions of owl. 

About DL, I recommend you to read the book of baader, the description logic hand book;


Best regards


Luis Ramos




El vie., 25 ene. 2019 a las 5:52, Tob Mang (<[hidden email]>) escribió:
Morning,

I am developing an ontology for my research using protégé 4.3, but i have some struggles related to how to write axioms and rules.
 
Please Help!

M. Manga Tobie Armand
Master en Informatique
tel: (237) 694329689
Keep Moving forward


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