How can I use related terms in Protege ontology

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

How can I use related terms in Protege ontology

Leila Kiani
Hi everyone,
Could you please let me know how can I define that a term is related to another term in the hierarchy? 
When it is not belong to Broader or Narrower, can I add "owl:disjointWith" or "see also"? Could you please tell me what is the best option for that? 
THANKS A LOT. Best, Leila.

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: How can I use related terms in Protege ontology

Michael DeBellis-2
Leila, there isn't a simple answer to your question because there are many ways that "terms" can be related in OWL. Some of what I'm going to say may be stuff you already know but I always think it's better to say too much rather than to risk not giving enough info. 

So first, you need to clarify if by term you mean a class (e.g., Dog, Animal, Cat) or an Individual (Fido, Whiskers). For background I recommend you read up on or refresh your memory on basic set theory because set theory is what OWL is really all about. If you look at my blog page here: https://symbolicshacker.blogspot.com/2017/06/swrl-process-modeling-tutorial.html  there is a link to a chapter called Basic Concepts of Set Theory from a book on Linguistics that gives a very good overview toward the bottom of that page. 

Classes can be related by subclass relations. So Dog and Cat are subclasses of Animal. This has the identical meaning as saying the sets Dog and Cat are subsets of the set Animal. E.g., all Dogs are Animals but not all Animals are Dogs. Individuals are instances of classes. So Fido could be an instance (also can be described as having the type) of the class Dog. 

Classes can also be related to other classes by Properties. So for example the property hasPet could be a relation between the Person Class and the Pet Class (where Pet would be a subclass of Animal). The definition of properties is in terms of classes (their domain and range, although note that both of those are completely optional in OWL, you can have properties with no specified domain or range). The instantiation of properties is between individuals. So at the individual level you might have Joe (instance of Person) hasPet Fido (instance of Dog and instance of Pet). 

I'm not sure what you mean by broader and narrower. What disjoint means is the same as saying two sets are disjoint, i.e., the union of those two sets is the empty set, i.e., the two sets have no elements in common. So the sets Car and Animal for example would be disjoint, nothing can be both a Car and an Animal. Similarly Dog and Cat would be disjoint. Pet and Dog would not be disjoint since some dogs are pets. But note Pet probably wouldn't be a superclass of Dog either since some wild dogs are not pets. 

If you haven't done the Pizza tutorial I recommend you do that, it explains a lot of this stuff and more. I also recommend the Manchester FHKB tutorial. One of the biggest differences between OWL and standard object-oriented design is the way properties are modeled in OWL and the FHKB tutorial does a good job of showing the capabilities and power of properties in OWL that are different from standard OO modeling. Hope that helps. 

Michael

On Thu, Sep 5, 2019 at 8:23 AM Leila Kiani <[hidden email]> wrote:
Hi everyone,
Could you please let me know how can I define that a term is related to another term in the hierarchy? 
When it is not belong to Broader or Narrower, can I add "owl:disjointWith" or "see also"? Could you please tell me what is the best option for that? 
THANKS A LOT. Best, Leila.
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: How can I use related terms in Protege ontology

Michael DeBellis-2
In reply to this post by Leila Kiani
Sorry, minor correction: in my previous message I said two sets are disjoint if their union is the empty set. Of course I should have said if their intersection is the empty set.

On Thu, Sep 5, 2019 at 8:23 AM Leila Kiani <[hidden email]> wrote:
Hi everyone,
Could you please let me know how can I define that a term is related to another term in the hierarchy? 
When it is not belong to Broader or Narrower, can I add "owl:disjointWith" or "see also"? Could you please tell me what is the best option for that? 
THANKS A LOT. Best, Leila.
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: How can I use related terms in Protege ontology

Leila Kiani
Dear Michael, 
I do really appreciate your answer. It was a great point that I have to study more. My ontology is  for animal use alternatives and they can be related to biomedical, laws, animal science, human and biological science and pharmacology and anything in these subjects.
I'll go ahead and study more and I'll get back to you soon. 
Thank you so much again for all your supports.
Best, Leila.

On Thu, Sep 5, 2019 at 12:51 PM Michael DeBellis <[hidden email]> wrote:
Sorry, minor correction: in my previous message I said two sets are disjoint if their union is the empty set. Of course I should have said if their intersection is the empty set.

On Thu, Sep 5, 2019 at 8:23 AM Leila Kiani <[hidden email]> wrote:
Hi everyone,
Could you please let me know how can I define that a term is related to another term in the hierarchy? 
When it is not belong to Broader or Narrower, can I add "owl:disjointWith" or "see also"? Could you please tell me what is the best option for that? 
THANKS A LOT. Best, Leila.
_______________________________________________
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

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: How can I use related terms in Protege ontology

Michael DeBellis-2
Leila, Glad I could help. 

That sounds like an interesting domain. I've audited a few biology classes recently and there are some animal experiments where my first reaction is "how amazing!" but then my second reaction is "how awful!". 

E.g., there is an experiment where they put the gene that grows an eye in mice into the locus that would control growth of legs in flies and the fly ends up with an eye in one of its legs:  https://www.sciencemag.org/news/1997/01/fly-eyes-have-it-second-master-gene  The experiment gives some incredible insight into how genes work.  But even though its only flies it still seems cruel. 

If you get stuck in a tutorial or have other additional questions feel free to send more questions to the list. Your domain sounds particularly interesting to me and I like building and helping to build ontologies so if you need some individual help let me know.

Michael

On Thu, Sep 5, 2019 at 9:56 AM Leila Kiani <[hidden email]> wrote:
Dear Michael, 
I do really appreciate your answer. It was a great point that I have to study more. My ontology is  for animal use alternatives and they can be related to biomedical, laws, animal science, human and biological science and pharmacology and anything in these subjects.
I'll go ahead and study more and I'll get back to you soon. 
Thank you so much again for all your supports.
Best, Leila.

On Thu, Sep 5, 2019 at 12:51 PM Michael DeBellis <[hidden email]> wrote:
Sorry, minor correction: in my previous message I said two sets are disjoint if their union is the empty set. Of course I should have said if their intersection is the empty set.

On Thu, Sep 5, 2019 at 8:23 AM Leila Kiani <[hidden email]> wrote:
Hi everyone,
Could you please let me know how can I define that a term is related to another term in the hierarchy? 
When it is not belong to Broader or Narrower, can I add "owl:disjointWith" or "see also"? Could you please tell me what is the best option for that? 
THANKS A LOT. Best, Leila.
_______________________________________________
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
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: How can I use related terms in Protege ontology

Leila Kiani
Hi Michael,
I just got back to you because I think I did something wrong (following my last email about related terms) I am sending you this screen shot of visualization of terminology that I have made. Do you think I am in right path?
Thanks a lot in advance for your help. 
Best, Leila.

image.png

On Thu, Sep 5, 2019 at 1:31 PM Michael DeBellis <[hidden email]> wrote:
Leila, Glad I could help. 

That sounds like an interesting domain. I've audited a few biology classes recently and there are some animal experiments where my first reaction is "how amazing!" but then my second reaction is "how awful!". 

E.g., there is an experiment where they put the gene that grows an eye in mice into the locus that would control growth of legs in flies and the fly ends up with an eye in one of its legs:  https://www.sciencemag.org/news/1997/01/fly-eyes-have-it-second-master-gene  The experiment gives some incredible insight into how genes work.  But even though its only flies it still seems cruel. 

If you get stuck in a tutorial or have other additional questions feel free to send more questions to the list. Your domain sounds particularly interesting to me and I like building and helping to build ontologies so if you need some individual help let me know.

Michael

On Thu, Sep 5, 2019 at 9:56 AM Leila Kiani <[hidden email]> wrote:
Dear Michael, 
I do really appreciate your answer. It was a great point that I have to study more. My ontology is  for animal use alternatives and they can be related to biomedical, laws, animal science, human and biological science and pharmacology and anything in these subjects.
I'll go ahead and study more and I'll get back to you soon. 
Thank you so much again for all your supports.
Best, Leila.

On Thu, Sep 5, 2019 at 12:51 PM Michael DeBellis <[hidden email]> wrote:
Sorry, minor correction: in my previous message I said two sets are disjoint if their union is the empty set. Of course I should have said if their intersection is the empty set.

On Thu, Sep 5, 2019 at 8:23 AM Leila Kiani <[hidden email]> wrote:
Hi everyone,
Could you please let me know how can I define that a term is related to another term in the hierarchy? 
When it is not belong to Broader or Narrower, can I add "owl:disjointWith" or "see also"? Could you please tell me what is the best option for that? 
THANKS A LOT. Best, Leila.
_______________________________________________
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
_______________________________________________
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

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