subject:"Jena \+ pellet Reasoner"

Re: Jena + Pellet Reasoner

2015-12-02 Thread Nicolas Paris

Hi,

I recently succeeded in making it working
Take a look at
https://groups.google.com/forum/#!topic/pellet-users/VpKDI0gFmjo

Hope this helps

2015-12-02 22:10 GMT+01:00 Chris Snyder :

> I’m trying out some different reasoners in my test application. I wanted
> to try Pellet so I updated my Maven to grab:
> 
> com.github.ansell.pellet
> pellet-jena
> 2.3.6-ansell
> 
>
> When I try to access the reasoner factory it is apparent from the error
> that the Pellet jar is using its own Jena version.
> java.lang.ClassCastException:
> org.mindswap.pellet.jena.PelletReasonerFactory cannot be cast to
> org.apache.jena.reasoner.ReasonerFactory
>
> And upon further inspection I see:
> package org.mindswap.pellet.jena;
>
> import com.hp.hpl.jena.ontology.OntModelSpec;
> import com.hp.hpl.jena.rdf.model.Model;
> import com.hp.hpl.jena.rdf.model.ModelFactory;
> import com.hp.hpl.jena.rdf.model.Resource;
> import com.hp.hpl.jena.reasoner.Reasoner;
> import com.hp.hpl.jena.reasoner.ReasonerFactory;
> import com.hp.hpl.jena.reasoner.ReasonerRegistry;
> import com.hp.hpl.jena.vocabulary.RDFS;
> import com.hp.hpl.jena.vocabulary.ReasonerVocabulary;
>
> /**
>  * @author Evren Sirin
>  *
>  */
> public class PelletReasonerFactory implements ReasonerFactory {
>
> and I can understand why there is a class cast error. Is there a version
> of the Pellet reasoner that I can plug in to an application already using
> the org.apache.jena.* ?
>
> Thanks,
> Chris
>
>

Jena + Pellet Reasoner

2015-12-02 Thread Chris Snyder

I’m trying out some different reasoners in my test application. I wanted to try 
Pellet so I updated my Maven to grab:

com.github.ansell.pellet
pellet-jena
2.3.6-ansell


When I try to access the reasoner factory it is apparent from the error that 
the Pellet jar is using its own Jena version. 
java.lang.ClassCastException: org.mindswap.pellet.jena.PelletReasonerFactory 
cannot be cast to org.apache.jena.reasoner.ReasonerFactory

And upon further inspection I see:
package org.mindswap.pellet.jena;

import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.reasoner.Reasoner;
import com.hp.hpl.jena.reasoner.ReasonerFactory;
import com.hp.hpl.jena.reasoner.ReasonerRegistry;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.ReasonerVocabulary;

/**
 * @author Evren Sirin
 *
 */
public class PelletReasonerFactory implements ReasonerFactory {

and I can understand why there is a class cast error. Is there a version of the 
Pellet reasoner that I can plug in to an application already using the 
org.apache.jena.* ?

Thanks,
Chris

Re: Jena + pellet Reasoner

2014-03-19 Thread Dave Reynolds


On 19/03/14 17:26, Adeeb Noor wrote:

Hi Dave:

Thanks for your answer.

  owl:onProperty ddids:x-kegg.pathway;
 owl:hasValue http://identifiers.org/kegg.pathway/hsa04110 ] .

What data type should I give to hasValue object property to accept the URI.


No data type, http://identifiers.org/kegg.pathway/hsa04110 is a 
resource not a literal.


Dave


thanks


On Mon, Mar 17, 2014 at 4:28 AM, Dave Reynolds dave.e.reyno...@gmail.comwrote:


On 14/03/14 08:08, Adeeb Noor wrote:


Hello everyone:

I have been struggling a lot with a problem that I did not find a solution
for, so hopefully guys can guide me or help me with it.

I have my data (rdfs) store in jena tdb as model and my owl (schema) using
protoge.

Here is the code to merge data and schema:

System.out.println(creting infeer dataset );
  Dataset dataset = TDBFactory.createDataset(data.infereedTDB);

  System.out.println(creting OntModel );
  OntModel Infmodel =
ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
dataset.getNamedModel(this.URL));

  System.out.println(adding schema (OWL) to OntModel);
  Infmodel.add(this.owl);

  System.out.println(adding data (RDF) to OntModel );
  Infmodel.add(data.tdb);

  System.out.println(creting ModelExtractor );
  ModelExtractor ext = new ModelExtractor(Infmodel);

  dataset.replaceNamedModel(this.URL, ext.extractModel());

  System.out.println(saving infead model);
  Infmodel.close();
  System.out.println(closing infeed dataset);
  dataset.close();



Unless something has changed then Pellet is an in-memory reasoner so
reasoning directly over the TDB data doesn't necessarily enable you to
scale beyond memory sized data and may be a performance hit.


  So I have the ability to store my inferred data into new tdb and to reason

or build any rule based on Literal values . For example: this is one
triple
that has UMLS_type as a property and I can group all subjects with two or
more UMLS_types for instance.



Not sure what you mean by grouping here. This is not one triple but one
resource which is the subject of a number of triples.



ddidd:C0007586 | ddids:label
 | Cell Cycle
ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
ddids:Pathway
ddidd:C0007586 | ddids:UMLS_type
 | T043
ddidd:C0007586 |
ddids:x-kegg.pathway | 
http://identifiers.org/kegg.pathway/hsa04110




  However, as you can see from the triple above I have x-kegg.pathway  as an

external uri. By default protoge takes it to be object property. What I
cannot do is to write a rule for example to group all subject under same
x-kegg.pathway number since it is external URI.



What you do you mean by group?

What do you mean by rule here?  Swrl rules?  If so then you need to ask
the Pellet folks for support on that.

Why is the URI being external of any relevance here?  Normally that
wouldn't matter at all.


   For example, I want to

create a class called sameKEGG that its members has 
http://identifiers.org/kegg.pathway/hsa04110  value for example.



That you could do directly in OWL, no need for rules, something like:

eg:sameKEGG a owl:Class;
 owl:equivalentClass  [
 a owl:Restriction;
 owl:onProperty ddids:x-kegg.pathway;
 owl:hasValue http://identifiers.org/kegg.pathway/hsa04110 ] .

Dave

Re: Jena + pellet Reasoner

2014-03-19 Thread Adeeb Noor

Thanks Dave

I am using protoge 4.2.0. I created the class sameKEGG and the
object property ddids:x-kegg.pathway; but I am not able to find the
hasValue restriction. any idea ?

Thanks




On Wed, Mar 19, 2014 at 11:33 AM, Dave Reynolds
dave.e.reyno...@gmail.comwrote:

 On 19/03/14 17:26, Adeeb Noor wrote:

 Hi Dave:

 Thanks for your answer.

   owl:onProperty ddids:x-kegg.pathway;
  owl:hasValue http://identifiers.org/kegg.pathway/hsa04110 ] .

 What data type should I give to hasValue object property to accept the
 URI.


 No data type, http://identifiers.org/kegg.pathway/hsa04110 is a
 resource not a literal.

 Dave


  thanks


 On Mon, Mar 17, 2014 at 4:28 AM, Dave Reynolds dave.e.reyno...@gmail.com
 wrote:

  On 14/03/14 08:08, Adeeb Noor wrote:

  Hello everyone:

 I have been struggling a lot with a problem that I did not find a
 solution
 for, so hopefully guys can guide me or help me with it.

 I have my data (rdfs) store in jena tdb as model and my owl (schema)
 using
 protoge.

 Here is the code to merge data and schema:

 System.out.println(creting infeer dataset );
   Dataset dataset = TDBFactory.createDataset(data.infereedTDB);

   System.out.println(creting OntModel );
   OntModel Infmodel =
 ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
 dataset.getNamedModel(this.URL));

   System.out.println(adding schema (OWL) to OntModel);
   Infmodel.add(this.owl);

   System.out.println(adding data (RDF) to OntModel );
   Infmodel.add(data.tdb);

   System.out.println(creting ModelExtractor );
   ModelExtractor ext = new ModelExtractor(Infmodel);

   dataset.replaceNamedModel(this.URL, ext.extractModel());

   System.out.println(saving infead model);
   Infmodel.close();
   System.out.println(closing infeed dataset);
   dataset.close();


 Unless something has changed then Pellet is an in-memory reasoner so
 reasoning directly over the TDB data doesn't necessarily enable you to
 scale beyond memory sized data and may be a performance hit.


   So I have the ability to store my inferred data into new tdb and to
 reason

 or build any rule based on Literal values . For example: this is one
 triple
 that has UMLS_type as a property and I can group all subjects with two
 or
 more UMLS_types for instance.


 Not sure what you mean by grouping here. This is not one triple but one
 resource which is the subject of a number of triples.


  ddidd:C0007586 | ddids:label
  | Cell Cycle
 ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
 ddids:Pathway
 ddidd:C0007586 | ddids:UMLS_type
  | T043
 ddidd:C0007586 |
 ddids:x-kegg.pathway | 
 http://identifiers.org/kegg.pathway/hsa04110



   However, as you can see from the triple above I have x-kegg.pathway
  as an

 external uri. By default protoge takes it to be object property. What I
 cannot do is to write a rule for example to group all subject under same
 x-kegg.pathway number since it is external URI.


 What you do you mean by group?

 What do you mean by rule here?  Swrl rules?  If so then you need to ask
 the Pellet folks for support on that.

 Why is the URI being external of any relevance here?  Normally that
 wouldn't matter at all.


For example, I want to

 create a class called sameKEGG that its members has 
 http://identifiers.org/kegg.pathway/hsa04110  value for example.


 That you could do directly in OWL, no need for rules, something like:

 eg:sameKEGG a owl:Class;
  owl:equivalentClass  [
  a owl:Restriction;
  owl:onProperty ddids:x-kegg.pathway;
  owl:hasValue http://identifiers.org/kegg.pathway/hsa04110 ] .

 Dave








-- 
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303
Email: adeeb.n...@colorado.edu

Re: Jena + pellet Reasoner

2014-03-19 Thread Adeeb Noor

will do, thanks



On Wed, Mar 19, 2014 at 12:30 PM, Dave Reynolds
dave.e.reyno...@gmail.comwrote:

 On 19/03/14 18:04, Adeeb Noor wrote:

 Thanks Dave

 I am using protoge 4.2.0. I created the class sameKEGG and the
 object property ddids:x-kegg.pathway; but I am not able to find the
 hasValue restriction. any idea ?


 Sorry no. Last time I used protege was a long time ago and then it was
 pretty obvious (create restriction, select hasValue and fill in the
 form). If it's no longer obvious then you'll need to ask on a protege list.

 Dave



 On Wed, Mar 19, 2014 at 11:33 AM, Dave Reynolds
 dave.e.reyno...@gmail.comwrote:

  On 19/03/14 17:26, Adeeb Noor wrote:

  Hi Dave:

 Thanks for your answer.

owl:onProperty ddids:x-kegg.pathway;
   owl:hasValue http://identifiers.org/kegg.pathway/hsa04110
 ] .

 What data type should I give to hasValue object property to accept the
 URI.


 No data type, http://identifiers.org/kegg.pathway/hsa04110 is a
 resource not a literal.

 Dave


   thanks



 On Mon, Mar 17, 2014 at 4:28 AM, Dave Reynolds 
 dave.e.reyno...@gmail.com

 wrote:


   On 14/03/14 08:08, Adeeb Noor wrote:


   Hello everyone:


 I have been struggling a lot with a problem that I did not find a
 solution
 for, so hopefully guys can guide me or help me with it.

 I have my data (rdfs) store in jena tdb as model and my owl (schema)
 using
 protoge.

 Here is the code to merge data and schema:

 System.out.println(creting infeer dataset );
Dataset dataset = TDBFactory.createDataset(data.
 infereedTDB);

System.out.println(creting OntModel );
OntModel Infmodel =
 ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
 dataset.getNamedModel(this.URL));

System.out.println(adding schema (OWL) to OntModel);
Infmodel.add(this.owl);

System.out.println(adding data (RDF) to OntModel );
Infmodel.add(data.tdb);

System.out.println(creting ModelExtractor );
ModelExtractor ext = new ModelExtractor(Infmodel);

dataset.replaceNamedModel(this.URL, ext.extractModel());

System.out.println(saving infead model);
Infmodel.close();
System.out.println(closing infeed dataset);
dataset.close();


  Unless something has changed then Pellet is an in-memory reasoner so
 reasoning directly over the TDB data doesn't necessarily enable you to
 scale beyond memory sized data and may be a performance hit.


So I have the ability to store my inferred data into new tdb and to
 reason

  or build any rule based on Literal values . For example: this is one
 triple
 that has UMLS_type as a property and I can group all subjects with two
 or
 more UMLS_types for instance.


  Not sure what you mean by grouping here. This is not one triple
 but one
 resource which is the subject of a number of triples.


   ddidd:C0007586 | ddids:label

   | Cell Cycle
 ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
 ddids:Pathway
 ddidd:C0007586 | ddids:UMLS_type
   | T043
 ddidd:C0007586 |
 ddids:x-kegg.pathway
 | 
 http://identifiers.org/kegg.pathway/hsa04110



However, as you can see from the triple above I have x-kegg.pathway
   as an

  external uri. By default protoge takes it to be object property. What
 I
 cannot do is to write a rule for example to group all subject under
 same
 x-kegg.pathway number since it is external URI.


  What you do you mean by group?

 What do you mean by rule here?  Swrl rules?  If so then you need to ask
 the Pellet folks for support on that.

 Why is the URI being external of any relevance here?  Normally that
 wouldn't matter at all.


 For example, I want to

  create a class called sameKEGG that its members has 
 http://identifiers.org/kegg.pathway/hsa04110  value for example.


  That you could do directly in OWL, no need for rules, something like:

 eg:sameKEGG a owl:Class;
   owl:equivalentClass  [
   a owl:Restriction;
   owl:onProperty ddids:x-kegg.pathway;
   owl:hasValue http://identifiers.org/kegg.pathway/hsa04110
 ] .

 Dave












-- 
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303
Email: adeeb.n...@colorado.edu

Re: Jena + pellet Reasoner

2014-03-19 Thread Dave Reynolds


On 19/03/14 18:04, Adeeb Noor wrote:

Thanks Dave

I am using protoge 4.2.0. I created the class sameKEGG and the
object property ddids:x-kegg.pathway; but I am not able to find the
hasValue restriction. any idea ?


Sorry no. Last time I used protege was a long time ago and then it was 
pretty obvious (create restriction, select hasValue and fill in the 
form). If it's no longer obvious then you'll need to ask on a protege list.


Dave



On Wed, Mar 19, 2014 at 11:33 AM, Dave Reynolds
dave.e.reyno...@gmail.comwrote:


On 19/03/14 17:26, Adeeb Noor wrote:


Hi Dave:

Thanks for your answer.

   owl:onProperty ddids:x-kegg.pathway;
  owl:hasValue http://identifiers.org/kegg.pathway/hsa04110 ] .

What data type should I give to hasValue object property to accept the
URI.



No data type, http://identifiers.org/kegg.pathway/hsa04110 is a
resource not a literal.

Dave


  thanks



On Mon, Mar 17, 2014 at 4:28 AM, Dave Reynolds dave.e.reyno...@gmail.com

wrote:


  On 14/03/14 08:08, Adeeb Noor wrote:


  Hello everyone:


I have been struggling a lot with a problem that I did not find a
solution
for, so hopefully guys can guide me or help me with it.

I have my data (rdfs) store in jena tdb as model and my owl (schema)
using
protoge.

Here is the code to merge data and schema:

System.out.println(creting infeer dataset );
   Dataset dataset = TDBFactory.createDataset(data.infereedTDB);

   System.out.println(creting OntModel );
   OntModel Infmodel =
ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
dataset.getNamedModel(this.URL));

   System.out.println(adding schema (OWL) to OntModel);
   Infmodel.add(this.owl);

   System.out.println(adding data (RDF) to OntModel );
   Infmodel.add(data.tdb);

   System.out.println(creting ModelExtractor );
   ModelExtractor ext = new ModelExtractor(Infmodel);

   dataset.replaceNamedModel(this.URL, ext.extractModel());

   System.out.println(saving infead model);
   Infmodel.close();
   System.out.println(closing infeed dataset);
   dataset.close();



Unless something has changed then Pellet is an in-memory reasoner so
reasoning directly over the TDB data doesn't necessarily enable you to
scale beyond memory sized data and may be a performance hit.


   So I have the ability to store my inferred data into new tdb and to
reason


or build any rule based on Literal values . For example: this is one
triple
that has UMLS_type as a property and I can group all subjects with two
or
more UMLS_types for instance.



Not sure what you mean by grouping here. This is not one triple but one
resource which is the subject of a number of triples.


  ddidd:C0007586 | ddids:label

  | Cell Cycle
ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
ddids:Pathway
ddidd:C0007586 | ddids:UMLS_type
  | T043
ddidd:C0007586 |
ddids:x-kegg.pathway | 
http://identifiers.org/kegg.pathway/hsa04110




   However, as you can see from the triple above I have x-kegg.pathway
  as an


external uri. By default protoge takes it to be object property. What I
cannot do is to write a rule for example to group all subject under same
x-kegg.pathway number since it is external URI.



What you do you mean by group?

What do you mean by rule here?  Swrl rules?  If so then you need to ask
the Pellet folks for support on that.

Why is the URI being external of any relevance here?  Normally that
wouldn't matter at all.


For example, I want to


create a class called sameKEGG that its members has 
http://identifiers.org/kegg.pathway/hsa04110  value for example.



That you could do directly in OWL, no need for rules, something like:

eg:sameKEGG a owl:Class;
  owl:equivalentClass  [
  a owl:Restriction;
  owl:onProperty ddids:x-kegg.pathway;
  owl:hasValue http://identifiers.org/kegg.pathway/hsa04110 ] .

Dave

Re: Jena + pellet Reasoner

2014-03-17 Thread Dave Reynolds


On 14/03/14 08:08, Adeeb Noor wrote:

Hello everyone:

I have been struggling a lot with a problem that I did not find a solution
for, so hopefully guys can guide me or help me with it.

I have my data (rdfs) store in jena tdb as model and my owl (schema) using
protoge.

Here is the code to merge data and schema:

System.out.println(creting infeer dataset );
 Dataset dataset = TDBFactory.createDataset(data.infereedTDB);

 System.out.println(creting OntModel );
 OntModel Infmodel =
ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
dataset.getNamedModel(this.URL));

 System.out.println(adding schema (OWL) to OntModel);
 Infmodel.add(this.owl);

 System.out.println(adding data (RDF) to OntModel );
 Infmodel.add(data.tdb);

 System.out.println(creting ModelExtractor );
 ModelExtractor ext = new ModelExtractor(Infmodel);

 dataset.replaceNamedModel(this.URL, ext.extractModel());

 System.out.println(saving infead model);
 Infmodel.close();
 System.out.println(closing infeed dataset);
 dataset.close();


Unless something has changed then Pellet is an in-memory reasoner so 
reasoning directly over the TDB data doesn't necessarily enable you to 
scale beyond memory sized data and may be a performance hit.



So I have the ability to store my inferred data into new tdb and to reason
or build any rule based on Literal values . For example: this is one triple
that has UMLS_type as a property and I can group all subjects with two or
more UMLS_types for instance.


Not sure what you mean by grouping here. This is not one triple but 
one resource which is the subject of a number of triples.


ddidd:C0007586 | ddids:label
| Cell Cycle
ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
ddids:Pathway
ddidd:C0007586 | ddids:UMLS_type
| T043
ddidd:C0007586 |
ddids:x-kegg.pathway | 
http://identifiers.org/kegg.pathway/hsa04110




However, as you can see from the triple above I have x-kegg.pathway  as an
external uri. By default protoge takes it to be object property. What I
cannot do is to write a rule for example to group all subject under same
x-kegg.pathway number since it is external URI.


What you do you mean by group?

What do you mean by rule here?  Swrl rules?  If so then you need to ask 
the Pellet folks for support on that.


Why is the URI being external of any relevance here?  Normally that 
wouldn't matter at all.



 For example, I want to
create a class called sameKEGG that its members has 
http://identifiers.org/kegg.pathway/hsa04110  value for example.


That you could do directly in OWL, no need for rules, something like:

eg:sameKEGG a owl:Class;
owl:equivalentClass  [
a owl:Restriction;
owl:onProperty ddids:x-kegg.pathway;
owl:hasValue http://identifiers.org/kegg.pathway/hsa04110 ] .

Dave

Re: Jena + pellet Reasoner

2014-03-16 Thread Adeeb Noor

Thanks a lot Miguel.

My TDB is around 17G and Jena rule engine will take for ever to do the
inferring.

Thanks


On Sat, Mar 15, 2014 at 5:53 AM, Miguel Bento Alves
mbentoal...@gmail.comwrote:

 In the best of my knowledge, you can¹t do it with OWL or OWL2(pellet
 reasoner). You need something like rules or spin-rules.

 Miguel

 On 15/03/14 03:14, Adeeb Noor adeeb.n...@colorado.edu wrote:

 Would someone please help me with the question
 
 Thanks in advance
 
 
 On Fri, Mar 14, 2014 at 3:04 PM, Adeeb Noor adeeb.n...@colorado.edu
 wrote:
 
 
  Need your advice below please when you have a chance .
 
  Miguel though I need to do it with RuleEngine but in fact I want to do
 the
  work with pellet reasoner.
 
  thanks and sorry for bothering.
 
 
  -- Forwarded message --
  From: Adeeb Noor adeeb.n...@colorado.edu
  Date: Fri, Mar 14, 2014 at 2:08 AM
  Subject: Jena + pellet Reasoner
  To: users@jena.apache.org users@jena.apache.org
 
 
  Hello everyone:
 
  I have been struggling a lot with a problem that I did not find a
 solution
  for, so hopefully guys can guide me or help me with it.
 
  I have my data (rdfs) store in jena tdb as model and my owl (schema)
 using
  protoge.
 
  Here is the code to merge data and schema:
 
  System.out.println(creting infeer dataset );
  Dataset dataset = TDBFactory.createDataset(data.infereedTDB);
 
  System.out.println(creting OntModel );
  OntModel Infmodel =
  ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
  dataset.getNamedModel(this.URL));
 
  System.out.println(adding schema (OWL) to OntModel);
  Infmodel.add(this.owl);
 
  System.out.println(adding data (RDF) to OntModel );
  Infmodel.add(data.tdb);
 
  System.out.println(creting ModelExtractor );
  ModelExtractor ext = new ModelExtractor(Infmodel);
 
  dataset.replaceNamedModel(this.URL, ext.extractModel());
 
  System.out.println(saving infead model);
  Infmodel.close();
  System.out.println(closing infeed dataset);
  dataset.close();
 
  So I have the ability to store my inferred data into new tdb and to
 reason
  or build any rule based on Literal values . For example: this is one
 triple
  that has UMLS_type as a property and I can group all subjects with two
 or
  more UMLS_types for instance.
 
  ddidd:C0007586 | ddids:label
 | Cell Cycle
  ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
  ddids:Pathway
  ddidd:C0007586 | ddids:UMLS_type
   | T043
  ddidd:C0007586 |
  ddids:x-kegg.pathway | 
  http://identifiers.org/kegg.pathway/hsa04110
 
  However, as you can see from the triple above I have x-kegg.pathway  as
 an
  external uri. By default protoge takes it to be object property. What I
  cannot do is to write a rule for example to group all subject under same
  x-kegg.pathway number since it is external URI.   For example, I want to
  create a class called sameKEGG that its members has 
  http://identifiers.org/kegg.pathway/hsa04110  value for example. BTW,
 I
  can do such a thing easily by SPARQL but I would love to use the
 reasoner
  to make complex rules.
 
  I have been struggling with this for awhile and I frankly appreciate any
  comments or feedback.
 
  --
  Adeeb Noor
  Ph.D. Candidate
  Dept of Computer Science
  University of Colorado at Boulder
  Cell: 571-484-3303
  Email: adeeb.n...@colorado.edu
 
 
 
  --
  Adeeb Noor
  Ph.D. Candidate
  Dept of Computer Science
  University of Colorado at Boulder
  Cell: 571-484-3303
  Email: adeeb.n...@colorado.edu
 
 
 
 
 --
 Adeeb Noor
 Ph.D. Candidate
 Dept of Computer Science
 University of Colorado at Boulder
 Cell: 571-484-3303
 Email: adeeb.n...@colorado.edu





-- 
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303
Email: adeeb.n...@colorado.edu

Re: Jena + pellet Reasoner

2014-03-15 Thread Miguel Bento Alves

In the best of my knowledge, you can¹t do it with OWL or OWL2(pellet
reasoner). You need something like rules or spin-rules.

Miguel

On 15/03/14 03:14, Adeeb Noor adeeb.n...@colorado.edu wrote:

Would someone please help me with the question

Thanks in advance


On Fri, Mar 14, 2014 at 3:04 PM, Adeeb Noor adeeb.n...@colorado.edu
wrote:


 Need your advice below please when you have a chance .

 Miguel though I need to do it with RuleEngine but in fact I want to do
the
 work with pellet reasoner.

 thanks and sorry for bothering.


 -- Forwarded message --
 From: Adeeb Noor adeeb.n...@colorado.edu
 Date: Fri, Mar 14, 2014 at 2:08 AM
 Subject: Jena + pellet Reasoner
 To: users@jena.apache.org users@jena.apache.org


 Hello everyone:

 I have been struggling a lot with a problem that I did not find a
solution
 for, so hopefully guys can guide me or help me with it.

 I have my data (rdfs) store in jena tdb as model and my owl (schema)
using
 protoge.

 Here is the code to merge data and schema:

 System.out.println(creting infeer dataset );
 Dataset dataset = TDBFactory.createDataset(data.infereedTDB);

 System.out.println(creting OntModel );
 OntModel Infmodel =
 ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
 dataset.getNamedModel(this.URL));

 System.out.println(adding schema (OWL) to OntModel);
 Infmodel.add(this.owl);

 System.out.println(adding data (RDF) to OntModel );
 Infmodel.add(data.tdb);

 System.out.println(creting ModelExtractor );
 ModelExtractor ext = new ModelExtractor(Infmodel);

 dataset.replaceNamedModel(this.URL, ext.extractModel());

 System.out.println(saving infead model);
 Infmodel.close();
 System.out.println(closing infeed dataset);
 dataset.close();

 So I have the ability to store my inferred data into new tdb and to
reason
 or build any rule based on Literal values . For example: this is one
triple
 that has UMLS_type as a property and I can group all subjects with two
or
 more UMLS_types for instance.

 ddidd:C0007586 | ddids:label
| Cell Cycle
 ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
 ddids:Pathway
 ddidd:C0007586 | ddids:UMLS_type
  | T043
 ddidd:C0007586 |
 ddids:x-kegg.pathway | 
 http://identifiers.org/kegg.pathway/hsa04110

 However, as you can see from the triple above I have x-kegg.pathway  as
an
 external uri. By default protoge takes it to be object property. What I
 cannot do is to write a rule for example to group all subject under same
 x-kegg.pathway number since it is external URI.   For example, I want to
 create a class called sameKEGG that its members has 
 http://identifiers.org/kegg.pathway/hsa04110  value for example. BTW, I
 can do such a thing easily by SPARQL but I would love to use the
reasoner
 to make complex rules.

 I have been struggling with this for awhile and I frankly appreciate any
 comments or feedback.

 --
 Adeeb Noor
 Ph.D. Candidate
 Dept of Computer Science
 University of Colorado at Boulder
 Cell: 571-484-3303
 Email: adeeb.n...@colorado.edu



 --
 Adeeb Noor
 Ph.D. Candidate
 Dept of Computer Science
 University of Colorado at Boulder
 Cell: 571-484-3303
 Email: adeeb.n...@colorado.edu




-- 
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303
Email: adeeb.n...@colorado.edu

Jena + pellet Reasoner

2014-03-14 Thread Adeeb Noor

Hello everyone:

I have been struggling a lot with a problem that I did not find a solution
for, so hopefully guys can guide me or help me with it.

I have my data (rdfs) store in jena tdb as model and my owl (schema) using
protoge.

Here is the code to merge data and schema:

System.out.println(creting infeer dataset );
Dataset dataset = TDBFactory.createDataset(data.infereedTDB);

System.out.println(creting OntModel );
OntModel Infmodel =
ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
dataset.getNamedModel(this.URL));

System.out.println(adding schema (OWL) to OntModel);
Infmodel.add(this.owl);

System.out.println(adding data (RDF) to OntModel );
Infmodel.add(data.tdb);

System.out.println(creting ModelExtractor );
ModelExtractor ext = new ModelExtractor(Infmodel);

dataset.replaceNamedModel(this.URL, ext.extractModel());

System.out.println(saving infead model);
Infmodel.close();
System.out.println(closing infeed dataset);
dataset.close();

So I have the ability to store my inferred data into new tdb and to reason
or build any rule based on Literal values . For example: this is one triple
that has UMLS_type as a property and I can group all subjects with two or
more UMLS_types for instance.

ddidd:C0007586 | ddids:label
   | Cell Cycle
ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
ddids:Pathway
ddidd:C0007586 | ddids:UMLS_type
   | T043
ddidd:C0007586 |
ddids:x-kegg.pathway | 
http://identifiers.org/kegg.pathway/hsa04110

However, as you can see from the triple above I have x-kegg.pathway  as an
external uri. By default protoge takes it to be object property. What I
cannot do is to write a rule for example to group all subject under same
x-kegg.pathway number since it is external URI.   For example, I want to
create a class called sameKEGG that its members has 
http://identifiers.org/kegg.pathway/hsa04110  value for example. BTW, I
can do such a thing easily by SPARQL but I would love to use the reasoner
to make complex rules.

I have been struggling with this for awhile and I frankly appreciate any
comments or feedback.

-- 
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303
Email: adeeb.n...@colorado.edu

Re: Jena + pellet Reasoner

2014-03-14 Thread Miguel Bento Alves

Hi Adeed, 

I see sameKEGG as an objectProperty and not as a class. The rule should be
something like:

(?x ex:sameKEGG_p ?y) -
(?x ddids:x-kegg.pathway ?z),
(?y ddids:x-kegg.pathway ?z),
notEqual(?x, ?y). 

But you can get all the subjects that have others with a same value under
a class with: 

(?x rdf:type ex:sameKEGG_c) -
(?x ex:sameKEGG_p ?y).

Miguel


On 14/03/14 08:08, Adeeb Noor adeeb.n...@colorado.edu wrote:

Hello everyone:

I have been struggling a lot with a problem that I did not find a solution
for, so hopefully guys can guide me or help me with it.

I have my data (rdfs) store in jena tdb as model and my owl (schema) using
protoge.

Here is the code to merge data and schema:

System.out.println(creting infeer dataset );
Dataset dataset = TDBFactory.createDataset(data.infereedTDB);

System.out.println(creting OntModel );
OntModel Infmodel =
ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
dataset.getNamedModel(this.URL));

System.out.println(adding schema (OWL) to OntModel);
Infmodel.add(this.owl);

System.out.println(adding data (RDF) to OntModel );
Infmodel.add(data.tdb);

System.out.println(creting ModelExtractor );
ModelExtractor ext = new ModelExtractor(Infmodel);

dataset.replaceNamedModel(this.URL, ext.extractModel());

System.out.println(saving infead model);
Infmodel.close();
System.out.println(closing infeed dataset);
dataset.close();

So I have the ability to store my inferred data into new tdb and to reason
or build any rule based on Literal values . For example: this is one
triple
that has UMLS_type as a property and I can group all subjects with two or
more UMLS_types for instance.

ddidd:C0007586 | ddids:label
   | Cell Cycle
ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
ddids:Pathway
ddidd:C0007586 | ddids:UMLS_type
   | T043
ddidd:C0007586 |
ddids:x-kegg.pathway | 
http://identifiers.org/kegg.pathway/hsa04110

However, as you can see from the triple above I have x-kegg.pathway  as an
external uri. By default protoge takes it to be object property. What I
cannot do is to write a rule for example to group all subject under same
x-kegg.pathway number since it is external URI.   For example, I want to
create a class called sameKEGG that its members has 
http://identifiers.org/kegg.pathway/hsa04110  value for example. BTW, I
can do such a thing easily by SPARQL but I would love to use the reasoner
to make complex rules.

I have been struggling with this for awhile and I frankly appreciate any
comments or feedback.

-- 
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303
Email: adeeb.n...@colorado.edu

Re: Jena + pellet Reasoner

2014-03-14 Thread Adeeb Noor

Thanks Alves,

May be I was not clear enough. I do not want to use the rule engine.
Instead I would like to use protege to add the rule.

Thanks

On Friday, March 14, 2014, Miguel Bento Alves mbentoal...@gmail.com wrote:

 Hi Adeed,

 I see sameKEGG as an objectProperty and not as a class. The rule should be
 something like:

 (?x ex:sameKEGG_p ?y) -
 (?x ddids:x-kegg.pathway ?z),
 (?y ddids:x-kegg.pathway ?z),
 notEqual(?x, ?y).

 But you can get all the subjects that have others with a same value under
 a class with:

 (?x rdf:type ex:sameKEGG_c) -
 (?x ex:sameKEGG_p ?y).

 Miguel


 On 14/03/14 08:08, Adeeb Noor adeeb.n...@colorado.edu javascript:;
 wrote:

 Hello everyone:
 
 I have been struggling a lot with a problem that I did not find a solution
 for, so hopefully guys can guide me or help me with it.
 
 I have my data (rdfs) store in jena tdb as model and my owl (schema) using
 protoge.
 
 Here is the code to merge data and schema:
 
 System.out.println(creting infeer dataset );
 Dataset dataset = TDBFactory.createDataset(data.infereedTDB);
 
 System.out.println(creting OntModel );
 OntModel Infmodel =
 ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
 dataset.getNamedModel(this.URL));
 
 System.out.println(adding schema (OWL) to OntModel);
 Infmodel.add(this.owl);
 
 System.out.println(adding data (RDF) to OntModel );
 Infmodel.add(data.tdb);
 
 System.out.println(creting ModelExtractor );
 ModelExtractor ext = new ModelExtractor(Infmodel);
 
 dataset.replaceNamedModel(this.URL, ext.extractModel());
 
 System.out.println(saving infead model);
 Infmodel.close();
 System.out.println(closing infeed dataset);
 dataset.close();
 
 So I have the ability to store my inferred data into new tdb and to reason
 or build any rule based on Literal values . For example: this is one
 triple
 that has UMLS_type as a property and I can group all subjects with two or
 more UMLS_types for instance.
 
 ddidd:C0007586 | ddids:label
| Cell Cycle
 ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
 ddids:Pathway
 ddidd:C0007586 | ddids:UMLS_type
| T043
 ddidd:C0007586 |
 ddids:x-kegg.pathway | 
 http://identifiers.org/kegg.pathway/hsa04110
 
 However, as you can see from the triple above I have x-kegg.pathway  as an
 external uri. By default protoge takes it to be object property. What I
 cannot do is to write a rule for example to group all subject under same
 x-kegg.pathway number since it is external URI.   For example, I want to
 create a class called sameKEGG that its members has 
 http://identifiers.org/kegg.pathway/hsa04110  value for example. BTW, I
 can do such a thing easily by SPARQL but I would love to use the reasoner
 to make complex rules.
 
 I have been struggling with this for awhile and I frankly appreciate any
 comments or feedback.
 
 --
 Adeeb Noor
 Ph.D. Candidate
 Dept of Computer Science
 University of Colorado at Boulder
 Cell: 571-484-3303
 Email: adeeb.n...@colorado.edu javascript:;




-- 
Sent from Gmail Mobile

Re: Jena + pellet Reasoner

2014-03-14 Thread Adeeb Noor

Would someone please help me with the question

Thanks in advance


On Fri, Mar 14, 2014 at 3:04 PM, Adeeb Noor adeeb.n...@colorado.edu wrote:


 Need your advice below please when you have a chance .

 Miguel though I need to do it with RuleEngine but in fact I want to do the
 work with pellet reasoner.

 thanks and sorry for bothering.


 -- Forwarded message --
 From: Adeeb Noor adeeb.n...@colorado.edu
 Date: Fri, Mar 14, 2014 at 2:08 AM
 Subject: Jena + pellet Reasoner
 To: users@jena.apache.org users@jena.apache.org


 Hello everyone:

 I have been struggling a lot with a problem that I did not find a solution
 for, so hopefully guys can guide me or help me with it.

 I have my data (rdfs) store in jena tdb as model and my owl (schema) using
 protoge.

 Here is the code to merge data and schema:

 System.out.println(creting infeer dataset );
 Dataset dataset = TDBFactory.createDataset(data.infereedTDB);

 System.out.println(creting OntModel );
 OntModel Infmodel =
 ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC,
 dataset.getNamedModel(this.URL));

 System.out.println(adding schema (OWL) to OntModel);
 Infmodel.add(this.owl);

 System.out.println(adding data (RDF) to OntModel );
 Infmodel.add(data.tdb);

 System.out.println(creting ModelExtractor );
 ModelExtractor ext = new ModelExtractor(Infmodel);

 dataset.replaceNamedModel(this.URL, ext.extractModel());

 System.out.println(saving infead model);
 Infmodel.close();
 System.out.println(closing infeed dataset);
 dataset.close();

 So I have the ability to store my inferred data into new tdb and to reason
 or build any rule based on Literal values . For example: this is one triple
 that has UMLS_type as a property and I can group all subjects with two or
 more UMLS_types for instance.

 ddidd:C0007586 | ddids:label
| Cell Cycle
 ddidd:C0007586 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |
 ddids:Pathway
 ddidd:C0007586 | ddids:UMLS_type
  | T043
 ddidd:C0007586 |
 ddids:x-kegg.pathway | 
 http://identifiers.org/kegg.pathway/hsa04110

 However, as you can see from the triple above I have x-kegg.pathway  as an
 external uri. By default protoge takes it to be object property. What I
 cannot do is to write a rule for example to group all subject under same
 x-kegg.pathway number since it is external URI.   For example, I want to
 create a class called sameKEGG that its members has 
 http://identifiers.org/kegg.pathway/hsa04110  value for example. BTW, I
 can do such a thing easily by SPARQL but I would love to use the reasoner
 to make complex rules.

 I have been struggling with this for awhile and I frankly appreciate any
 comments or feedback.

 --
 Adeeb Noor
 Ph.D. Candidate
 Dept of Computer Science
 University of Colorado at Boulder
 Cell: 571-484-3303
 Email: adeeb.n...@colorado.edu



 --
 Adeeb Noor
 Ph.D. Candidate
 Dept of Computer Science
 University of Colorado at Boulder
 Cell: 571-484-3303
 Email: adeeb.n...@colorado.edu




-- 
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303
Email: adeeb.n...@colorado.edu

Re: Jena + Pellet Reasoner

Jena + Pellet Reasoner

Re: Jena + pellet Reasoner

Re: Jena + pellet Reasoner

Re: Jena + pellet Reasoner

Re: Jena + pellet Reasoner

Re: Jena + pellet Reasoner

Re: Jena + pellet Reasoner

Re: Jena + pellet Reasoner

Jena + pellet Reasoner

Re: Jena + pellet Reasoner

Re: Jena + pellet Reasoner

Re: Jena + pellet Reasoner

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