Doubt regarding connecting protege with jena/pellet, swrl

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Doubt regarding connecting protege with jena/pellet, swrl

Ria
Hi!
 I'm thinking of developing an Expert System on disease diagnosis based on an ontology developed in protege. So, how do I connect protege with the reasoner, so that it can make inferences and reason consequently.

Any help shall be very much appreciated.

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Re: Doubt regarding connecting protege with jena/pellet, swrl

Matthew Horridge-2
Administrator
Hi,

I recommend that you use the OWL API to do this.  This is the API that Protege uses under the hood.  It has a general purpose interface (OWLReasoner) which is implemented by Pellet, FaCT++, JFact, HermiT, TrOWL, Elk and others.  There’s some documentation here:   https://github.com/owlcs/owlapi/wiki/Documentation

Cheers,

Matthew



On 15 Oct 2014, at 19:44, Ria Singh <[hidden email]> wrote:

> Hi!
>  I'm thinking of developing an Expert System on disease diagnosis based on an ontology developed in protege. So, how do I connect protege with the reasoner, so that it can make inferences and reason consequently.
>
> Any help shall be very much appreciated.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Doubt regarding connecting protege with jena/pellet, swrl

grantpax
Matthew,

Do you know of any similar projects out in the wild?

Grant

> On Oct 15, 2014, at 3:53 PM, Matthew Horridge <[hidden email]> wrote:
>
> Hi,
>
> I recommend that you use the OWL API to do this.  This is the API that Protege uses under the hood.  It has a general purpose interface (OWLReasoner) which is implemented by Pellet, FaCT++, JFact, HermiT, TrOWL, Elk and others.  There’s some documentation here:   https://github.com/owlcs/owlapi/wiki/Documentation
>
> Cheers,
>
> Matthew
>
>
>
> On 15 Oct 2014, at 19:44, Ria Singh <[hidden email]> wrote:
>
>> Hi!
>> I'm thinking of developing an Expert System on disease diagnosis based on an ontology developed in protege. So, how do I connect protege with the reasoner, so that it can make inferences and reason consequently.
>>
>> Any help shall be very much appreciated.
>> _______________________________________________
>> 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

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Re: Doubt regarding connecting protege with jena/pellet, swrl

Matthew Horridge-2
Administrator
Hi Grant,

Are you looking for projects that use reasoning or an example of how to programmatically use reasoning?

Cheers

Matthew


> On 25 Nov 2014, at 06:48, Grant Pax <[hidden email]> wrote:
>
> Matthew,
>
> Do you know of any similar projects out in the wild?
>
> Grant
>
>> On Oct 15, 2014, at 3:53 PM, Matthew Horridge <[hidden email]> wrote:
>>
>> Hi,
>>
>> I recommend that you use the OWL API to do this.  This is the API that Protege uses under the hood.  It has a general purpose interface (OWLReasoner) which is implemented by Pellet, FaCT++, JFact, HermiT, TrOWL, Elk and others.  There’s some documentation here:   https://github.com/owlcs/owlapi/wiki/Documentation
>>
>> Cheers,
>>
>> Matthew
>>
>>
>>
>> On 15 Oct 2014, at 19:44, Ria Singh <[hidden email]> wrote:
>>
>>> Hi!
>>> I'm thinking of developing an Expert System on disease diagnosis based on an ontology developed in protege. So, how do I connect protege with the reasoner, so that it can make inferences and reason consequently.
>>>
>>> Any help shall be very much appreciated.
>>> _______________________________________________
>>> 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


_______________________________________________
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Ontology and disease diagnosis (was Re: Doubt regarding connecting protege with jena/pellet, swrl)

samsontu
In reply to this post by grantpax
Hi Grant,

You may want to look at [1] and other papers by Berated-Gounot (where he added rules to perform diagnosis).

The limitation of using description logic for diagnosis of diseases is that much diagnostic knowledge is not ontological, but contingent and probabilistic. Often Bayesian networks are used as the formalism for encoding such knowledge.

With best regards,
Samson


[1] Bertaud-Gounot V, Duvauferrier R, Burgun A. Ontology and medical diagnosis. Informatics for health & social care. 2012;37:51-61. http://www.ncbi.nlm.nih.gov/pubmed/22462194



On Nov 25, 2014, at 6:48 AM, Grant Pax <[hidden email]> wrote:

Matthew,

Do you know of any similar projects out in the wild?

Grant

On Oct 15, 2014, at 3:53 PM, Matthew Horridge <[hidden email]> wrote:

Hi,

I recommend that you use the OWL API to do this.  This is the API that Protege uses under the hood.  It has a general purpose interface (OWLReasoner) which is implemented by Pellet, FaCT++, JFact, HermiT, TrOWL, Elk and others.  There’s some documentation here:   https://github.com/owlcs/owlapi/wiki/Documentation

Cheers,

Matthew



On 15 Oct 2014, at 19:44, Ria Singh <[hidden email]> wrote:

Hi!
I'm thinking of developing an Expert System on disease diagnosis based on an ontology developed in protege. So, how do I connect protege with the reasoner, so that it can make inferences and reason consequently.

Any help shall be very much appreciated.
_______________________________________________
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


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Re: Ontology and disease diagnosis (was Re: Doubt regarding connecting protege with jena/pellet, swrl)

grantpax
Thanks, Samson.

Would I be wrong to say that an ontology (consistent yet pathologic) could be profitably examined with a Bayesian network for diagnostic purposes?

On Nov 25, 2014, at 1:15 PM, Samson Tu <[hidden email]> wrote:

Hi Grant,

You may want to look at [1] and other papers by Berated-Gounot (where he added rules to perform diagnosis).

The limitation of using description logic for diagnosis of diseases is that much diagnostic knowledge is not ontological, but contingent and probabilistic. Often Bayesian networks are used as the formalism for encoding such knowledge.

With best regards,
Samson


[1] Bertaud-Gounot V, Duvauferrier R, Burgun A. Ontology and medical diagnosis. Informatics for health & social care. 2012;37:51-61. http://www.ncbi.nlm.nih.gov/pubmed/22462194



On Nov 25, 2014, at 6:48 AM, Grant Pax <[hidden email]> wrote:

Matthew,

Do you know of any similar projects out in the wild?

Grant

On Oct 15, 2014, at 3:53 PM, Matthew Horridge <[hidden email]> wrote:

Hi,

I recommend that you use the OWL API to do this.  This is the API that Protege uses under the hood.  It has a general purpose interface (OWLReasoner) which is implemented by Pellet, FaCT++, JFact, HermiT, TrOWL, Elk and others.  There’s some documentation here:   https://github.com/owlcs/owlapi/wiki/Documentation

Cheers,

Matthew



On 15 Oct 2014, at 19:44, Ria Singh <[hidden email]> wrote:

Hi!
I'm thinking of developing an Expert System on disease diagnosis based on an ontology developed in protege. So, how do I connect protege with the reasoner, so that it can make inferences and reason consequently.

Any help shall be very much appreciated.
_______________________________________________
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


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Re: Doubt regarding connecting protege with jena/pellet, swrl

grantpax
In reply to this post by Matthew Horridge-2
Matthew,

Thank you for asking. In response: the latter (programatic use). Any, as I think about it, Protege is a fine example of doing just that. If there are others you think instructive, I would appreciate the guidance.

Thank you again.

> On Nov 25, 2014, at 12:27 PM, Matthew Horridge <[hidden email]> wrote:
>
> Hi Grant,
> 
> Are you looking for projects that use reasoning or an example of how to programmatically use reasoning?
>
> Cheers
>
> Matthew
>
>
>> On 25 Nov 2014, at 06:48, Grant Pax <[hidden email]> wrote:
>>
>> Matthew,
>>
>> Do you know of any similar projects out in the wild?
>>
>> Grant
>>
>>> On Oct 15, 2014, at 3:53 PM, Matthew Horridge <[hidden email]> wrote:
>>>
>>> Hi,
>>>
>>> I recommend that you use the OWL API to do this.  This is the API that Protege uses under the hood.  It has a general purpose interface (OWLReasoner) which is implemented by Pellet, FaCT++, JFact, HermiT, TrOWL, Elk and others.  There’s some documentation here:   https://github.com/owlcs/owlapi/wiki/Documentation
>>>
>>> Cheers,
>>>
>>> Matthew
>>>
>>>
>>>
>>> On 15 Oct 2014, at 19:44, Ria Singh <[hidden email]> wrote:
>>>
>>>> Hi!
>>>> I'm thinking of developing an Expert System on disease diagnosis based on an ontology developed in protege. So, how do I connect protege with the reasoner, so that it can make inferences and reason consequently.
>>>>
>>>> Any help shall be very much appreciated.
>>>> _______________________________________________
>>>> 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

_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: Ontology and disease diagnosis (was Re: Doubt regarding connecting protege with jena/pellet, swrl)

samsontu
In reply to this post by grantpax
Hi,

I am not sure what you mean by “an ontology could be profitably examined with a Bayesian network.” Technically, I don’t know how to combine ontologies with Bayesian networks. There is a “OWL-PR.org” web site but it seems no longer active. The most related work I know is Daphe Koller’s integration of frames (templates) with Bayesian network [1].

With best regards,
Samson
[1] “Template-Based Representation,” Chapter 6 in Probabilistic Graphical Models, Principles and Techniques. MIT Press 2009.




On Nov 25, 2014, at 10:29 AM, Grant Pax <[hidden email]> wrote:

Thanks, Samson.

Would I be wrong to say that an ontology (consistent yet pathologic) could be profitably examined with a Bayesian network for diagnostic purposes?

On Nov 25, 2014, at 1:15 PM, Samson Tu <[hidden email]> wrote:

Hi Grant,

You may want to look at [1] and other papers by Berated-Gounot (where he added rules to perform diagnosis).

The limitation of using description logic for diagnosis of diseases is that much diagnostic knowledge is not ontological, but contingent and probabilistic. Often Bayesian networks are used as the formalism for encoding such knowledge.

With best regards,
Samson


[1] Bertaud-Gounot V, Duvauferrier R, Burgun A. Ontology and medical diagnosis. Informatics for health & social care. 2012;37:51-61. http://www.ncbi.nlm.nih.gov/pubmed/22462194



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