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[protege-discussion] NullPointerException:null

jayadianti herlina herlinajayadianti at gmail.com
Fri Feb 3 03:02:47 PST 2012


Dear Mathew and Timothy

is there any difference when I save the file of source ontology into target
ontology with rdf / xml format, manchester owl syntax or owl functional
syntax? is there any relation between the "null window" that occurs with an
error when saving a file?
Thank you very much

Sincerely
Jayadianti



On Fri, Feb 3, 2012 at 10:50 AM, jayadianti herlina <
herlinajayadianti at gmail.com> wrote:

> Dear Timothy
>
> Thank you very much for your explanation Mr Timothy
> About inconsistent ontology, based on my small experience, if there is an
> inconsistency in my ontology then the protege will display a window *"
> explain Inconsistent ontology"* and some or all of the classes, instances
> and properties that are inconsistent will be *colored** red*.
> But this situation doesn't happen on ontologies that I created, initially the
> query can be done well, and there are no signs of inconsistency until then I
> save the file, and when it re-opened, I wasn't able to perform queries as
> before, and the "null" warning appears although the source ontologies still
> remains in the same position as before. Thank you very much.
>
>
> Sincerely
> Jayadianti
>
>
>
>
> On Thu, Feb 2, 2012 at 6:38 PM, Timothy Redmond <tredmond at stanford.edu>wrote:
>
>>
>> There is a missing null pointer check and I will try to fix this.  It is
>> happening because the reasoner factory is refusing to create a reasoner.
>> The reasoner factory doesn't throw an execption it just returns null.  I
>> have seen this before but not for some time.
>>
>> I believe that it means that the ontology is inconsistent.  If you
>> restart Protege and try a different reasoner you may get the reasoner to
>> tell you this.
>>
>> To me it looks like the cause of the inconsistency is that the ontology
>> has some problems.  So for instance, the ontology contains a statement that
>> the Family class is equivalent to the person class.  A simple
>> straightforward interpretation of this claim fails.  For example I would
>> guess that the Kennedy family would be an instance of the Family class.
>> But that would mean that the Kennedy family is a person which I would not
>> expect.
>>
>> I wasn't able to replicate your situation and provide more certain
>> information because I was unsure of your notation.  I was not sure if the
>> "C1 Subclass C2" meant that C1 is a subclass of C2 or if you really mean
>> the more traditional subClassOf.
>>
>> -Timothy
>>
>>
>>
>>
>>
>> On 2/2/12 7:15 AM, jayadianti herlina wrote:
>>
>> Dear Mathew
>>
>> Here is a part of my ontologies:
>>
>> *ONTOLOGY 1*
>> Class:
>> Family
>>  Subclass - HeadOfFamily (instance gitopawiro, agussusilo )
>>  Subclass - MemberOfFamily
>> TypeOfFood
>> (Instance chicken, meat, egg..etc)
>> ObjectProperty :
>> hasRarelyEaten
>>  *ONTOLOGY 2*
>> Class:
>> person
>>  Subclass - MemberOfHouseHolder (instance GitoPawiro, AgusSusilo)
>>  Subclass - HeadOfHouseHolder
>> ConsumeFood
>> (instance Chicken, Meat, Egg..etc)
>> ObjectProperty :
>> hasFrequentlyEatenFood
>>  *ONTOLOGY 3*
>> Class:
>> People
>>  Subclass - Familymember
>>  Subclass - HouseHolder
>> DataProperty:
>> hasConsumeFood
>>  *COMONTOLOGY*
>> Class:
>> people ≡ Family ≡ person ≡ People
>> Food ≡ ConsumeFood ≡ TypeOfFood
>> ObjectProperty:
>> hasConsumeFood
>>  *DLQUERY example :*
>> people and hasRarelyEaten value meat or hasFrequentlyEatenFood value egg
>> or hasConsumeFood value "egg"^^string
>>
>> *RESULT*
>> Agus Susilo
>>
>>
>>  *Everything goes well, I save my ontologies and then appear the dialog
>> box nullexpresiaon:null (I attached the image)*
>> *I need you help. Thank you*
>>  Warm regards
>> Lina jayadianti
>>
>>
>> *RDF/XML COMONTOLOGY*
>>  <?xml version="1.0"?>
>>
>> <!DOCTYPE rdf:RDF [
>> <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
>> <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
>> <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
>> <!ENTITY ontology3 "http://www.semanticweb.org/ontology3.owl#" >
>> <!ENTITY ontology2 "http://www.semanticweb.org/ontology2.owl#" >
>> <!ENTITY ontology1 "http://www.semanticweb.org/ontology1.owl#" >
>> <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
>> <!ENTITY comontology "http://www.semanticweb.org/comontology.owl#" >
>> ]>
>>
>> <rdf:RDF xmlns="http://www.semanticweb.org/comontology.owl#"
>> xml:base="http://www.semanticweb.org/comontology.owl"
>> xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>> xmlns:comontology="http://www.semanticweb.org/comontology.owl#"
>> xmlns:owl="http://www.w3.org/2002/07/owl#"
>> xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>> xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>> xmlns:ontology3="http://www.semanticweb.org/ontology3.owl#"
>> xmlns:ontology2="http://www.semanticweb.org/ontology2.owl#"
>> xmlns:ontology1="http://www.semanticweb.org/ontology1.owl#">
>> <owl:Ontology rdf:about="http://www.semanticweb.org/comontology.owl">
>> <owl:imports rdf:resource="http://www.semanticweb.org/ontology1.owl"/>
>> <owl:imports rdf:resource="http://www.semanticweb.org/ontology2.owl"/>
>> <owl:imports rdf:resource="http://www.semanticweb.org/ontology3.owl"/>
>> </owl:Ontology>
>>
>> <!--
>>
>> ///////////////////////////////////////////////////////////////////////////////////////
>> //
>> // Datatypes
>> //
>>
>> ///////////////////////////////////////////////////////////////////////////////////////
>> -->
>>
>> <!--
>>
>> ///////////////////////////////////////////////////////////////////////////////////////
>> //
>> // Object Properties
>> //
>>
>> ///////////////////////////////////////////////////////////////////////////////////////
>> -->
>>
>> <!-- http://www.semanticweb.org/comontology.owl#hasconsumefood -->
>>  <owl:ObjectProperty rdf:about="&comontology;hasconsumefood">
>> <owl:equivalentProperty rdf:resource="&ontology1;hasRarelyEaten"/>
>> <owl:equivalentProperty rdf:resource="&ontology2;hasFrequentlyEatenFood"/>
>> </owl:ObjectProperty>
>>
>> <!-- http://www.semanticweb.org/ontology1.owl#hasRarelyEaten -->
>>  <rdf:Description rdf:about="&ontology1;hasRarelyEaten"/>
>>
>> <!-- http://www.semanticweb.org/ontology2.owl#hasFrequentlyEatenFood -->
>>  <rdf:Description rdf:about="&ontology2;hasFrequentlyEatenFood"/>
>>
>> <!--
>>
>> ///////////////////////////////////////////////////////////////////////////////////////
>> //
>> // Data properties
>> //
>>
>> ///////////////////////////////////////////////////////////////////////////////////////
>> -->
>>
>> <!-- http://www.semanticweb.org/comontology.owl#name -->
>>  <owl:DatatypeProperty rdf:about="&comontology;name"/>
>>
>> <!--
>>
>> ///////////////////////////////////////////////////////////////////////////////////////
>> //
>> // Classes
>> //
>>
>> ///////////////////////////////////////////////////////////////////////////////////////
>> -->
>>
>> <!-- http://www.semanticweb.org/comontology.owl#Food -->
>>  <owl:Class rdf:about="&comontology;Food">
>> <owl:equivalentClass rdf:resource="&ontology1;TypeOfFood"/>
>> <owl:equivalentClass rdf:resource="&ontology2;ConsumeFood"/>
>> </owl:Class>
>>
>> <!-- http://www.semanticweb.org/comontology.owl#HeadOfHouseHolder -->
>>  <owl:Class rdf:about="&comontology;HeadOfHouseHolder">
>> <owl:equivalentClass rdf:resource="&ontology1;HeadOfFamily"/>
>> <owl:equivalentClass rdf:resource="&ontology2;HeadOfHouseHolder"/>
>> <owl:equivalentClass rdf:resource="&ontology3;FamilyMember"/>
>> <rdfs:subClassOf rdf:resource="&comontology;People"/>
>> </owl:Class>
>>
>> <!-- http://www.semanticweb.org/comontology.owl#MemberOfHouseHolder -->
>>  <owl:Class rdf:about="&comontology;MemberOfHouseHolder">
>> <rdfs:subClassOf rdf:resource="&comontology;People"/>
>> </owl:Class>
>>
>> <!-- http://www.semanticweb.org/comontology.owl#People -->
>>  <owl:Class rdf:about="&comontology;People">
>> <owl:equivalentClass rdf:resource="&ontology1;Family"/>
>> <owl:equivalentClass rdf:resource="&ontology2;person"/>
>> <owl:equivalentClass rdf:resource="&ontology3;people"/>
>> </owl:Class>
>>
>> <!-- http://www.semanticweb.org/ontology1.owl#Family -->
>>  <rdf:Description rdf:about="&ontology1;Family">
>> <owl:equivalentClass rdf:resource="&ontology2;person"/>
>> <owl:equivalentClass rdf:resource="&ontology3;people"/>
>> </rdf:Description>
>>
>> <!-- http://www.semanticweb.org/ontology1.owl#HeadOfFamily -->
>>  <rdf:Description rdf:about="&ontology1;HeadOfFamily">
>> <owl:equivalentClass rdf:resource="&ontology2;HeadOfHouseHolder"/>
>> <owl:equivalentClass rdf:resource="&ontology3;FamilyMember"/>
>> </rdf:Description>
>>
>> <!-- http://www.semanticweb.org/ontology1.owl#TypeOfFood -->
>>  <rdf:Description rdf:about="&ontology1;TypeOfFood">
>> <owl:equivalentClass rdf:resource="&ontology2;ConsumeFood"/>
>> </rdf:Description>
>>
>> <!-- http://www.semanticweb.org/ontology2.owl#ConsumeFood -->
>>  <rdf:Description rdf:about="&ontology2;ConsumeFood"/>
>>
>> <!-- http://www.semanticweb.org/ontology2.owl#HeadOfHouseHolder -->
>>  <rdf:Description rdf:about="&ontology2;HeadOfHouseHolder">
>> <owl:equivalentClass rdf:resource="&ontology3;FamilyMember"/>
>> </rdf:Description>
>>
>> <!-- http://www.semanticweb.org/ontology2.owl#person -->
>>  <rdf:Description rdf:about="&ontology2;person">
>> <owl:equivalentClass rdf:resource="&ontology3;people"/>
>> </rdf:Description>
>>
>> <!-- http://www.semanticweb.org/ontology3.owl#FamilyMember -->
>>  <rdf:Description rdf:about="&ontology3;FamilyMember"/>
>>
>> <!-- http://www.semanticweb.org/ontology3.owl#people -->
>>  <rdf:Description rdf:about="&ontology3;people"/>
>>
>> <!--
>>
>> ///////////////////////////////////////////////////////////////////////////////////////
>> //
>> // Individuals
>> //
>>
>> ///////////////////////////////////////////////////////////////////////////////////////
>> -->
>>
>> <!-- http://www.semanticweb.org/comontology.owl#AgusSusilo -->
>>  <owl:NamedIndividual rdf:about="&comontology;AgusSusilo">
>> <rdf:type rdf:resource="&ontology3;FamilyMember"/>
>> <owl:sameAs rdf:resource="&ontology1;agussusilo"/>
>> <owl:sameAs rdf:resource="&ontology3;agus_susilo"/>
>> </owl:NamedIndividual>
>>
>> <!-- http://www.semanticweb.org/comontology.owl#Gitopawiro -->
>>  <owl:NamedIndividual rdf:about="&comontology;Gitopawiro">
>> <rdf:type rdf:resource="&ontology3;FamilyMember"/>
>> <name rdf:datatype="&xsd;string">gito pawiro</name>
>> <owl:sameAs rdf:resource="&ontology1;gitopawiro"/>
>> <owl:sameAs rdf:resource="&ontology2;GitoPawiro"/>
>> <owl:sameAs rdf:resource="&ontology3;gito_pawiro"/>
>> </owl:NamedIndividual>
>>
>> <!-- http://www.semanticweb.org/ontology1.owl#agussusilo -->
>>  <rdf:Description rdf:about="&ontology1;agussusilo">
>> <owl:sameAs rdf:resource="&ontology3;agus_susilo"/>
>> </rdf:Description>
>>
>> <!-- http://www.semanticweb.org/ontology1.owl#gitopawiro -->
>>  <rdf:Description rdf:about="&ontology1;gitopawiro">
>> <owl:sameAs rdf:resource="&ontology2;GitoPawiro"/>
>> <owl:sameAs rdf:resource="&ontology3;gito_pawiro"/>
>> </rdf:Description>
>>
>> <!-- http://www.semanticweb.org/ontology2.owl#GitoPawiro -->
>>  <rdf:Description rdf:about="&ontology2;GitoPawiro">
>> <owl:sameAs rdf:resource="&ontology3;gito_pawiro"/>
>> </rdf:Description>
>>
>> <!-- http://www.semanticweb.org/ontology3.owl#agus_susilo -->
>>  <rdf:Description rdf:about="&ontology3;agus_susilo"/>
>>
>> <!-- http://www.semanticweb.org/ontology3.owl#gito_pawiro -->
>>  <rdf:Description rdf:about="&ontology3;gito_pawiro"/>
>> </rdf:RDF>
>>
>>
>> On Wed, Feb 1, 2012 at 7:37 PM, Matthew Horridge <
>> matthew.horridge at stanford.edu> wrote:
>>
>>> Hi Jayadianti,
>>>
>>> Can you repeat this every time?  Would it be possible to post your
>>> ontologies to the list?
>>>
>>> Cheers,
>>>
>>> Matthew
>>>
>>>
>>> On 30 Jan 2012, at 10:05, jayadianti herlina wrote:
>>>
>>> > Hi all,
>>> > I am using Protege 4.2.0 (build 249), I am working with 3 ontologies
>>> and then importing them into 1 ontology.
>>> > I try to map and match between 3 ontologies. Everything going well.
>>> > I am using DL Query (Version 1.1.0) and select a reasoner (hermit
>>> 1.3.5 and faCT++).
>>> > All as I expected, the query done very well, and mapped out perfectly
>>> :)
>>> >
>>> > Then I save the file as usual, and then I tried to open it again.
>>> > I do a query with DLquery as usual and appeared dialog box:
>>> NullPointerException: null - whereas before all goes well.
>>> > is this a known bug?
>>> > Thank you very much for your help
>>> >
>>> > Warm Regards
>>> > Jayadianti
>>>  > _______________________________________________
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>>
>>
>>
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