will do, thanks
On Wed, Mar 19, 2014 at 12:30 PM, Dave Reynolds
<dave.e.reyno...@gmail.com>wrote:
> 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.com>wrote:
>>
>> 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
