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Re: [OWLAPI-developer] How get SuperClass without Reasoner?
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From: Celso F. <ce...@gm...> - 2011-02-21 23:18:20
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Thanks for the answers !!! Im my tool has a button with "reasoning" (true or false) ! But... I just wanted know the full potential that I could get with OWLAPI without the reasoner (pellet in my case) Very Thanks, Celso. 2011/2/20 <owl...@li...> > Send Owlapi-developer mailing list submissions to > owl...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/owlapi-developer > or, via email, send a message with subject or body 'help' to > owl...@li... > > You can reach the person managing the list at > owl...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Owlapi-developer digest..." > > > Today's Topics: > > 1. How get SuperClass without Reasoner? (Celso Fontes) > 2. Re: How get SuperClass without Reasoner? (Lorenz B?hmann) > 3. Re: How get SuperClass without Reasoner? (Ignazio Palmisano) > 4. document IRI and ontology IRI conflict! (sridevi polavaram) > 5. Re: document IRI and ontology IRI conflict! (Ignazio Palmisano) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 19 Feb 2011 16:46:45 -0300 > From: Celso Fontes <ce...@gm...> > Subject: [OWLAPI-developer] How get SuperClass without Reasoner? > To: owl...@li... > Message-ID: > <AANLkTim4KWKR9G6H9GLwKnuF0HHiHUceaa02qN_=O3...@ma...> > Content-Type: text/plain; charset="iso-8859-1" > > Hi ! > How get SuperClass of an OWLClass without reasoner? > Is possible a reverse way of subclasses? > > Thanks, > Celso. > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 2 > Date: Sat, 19 Feb 2011 21:29:33 +0100 > From: Lorenz B?hmann <spo...@st...> > Subject: Re: [OWLAPI-developer] How get SuperClass without Reasoner? > To: owl...@li... > Message-ID: <4D6...@st...> > Content-Type: text/plain; charset="iso-8859-1" > > On 19.02.2011 20:46, Celso Fontes wrote: > > Hi ! > > How get SuperClass of an OWLClass without reasoner? > > Is possible a reverse way of subclasses? > > > > Thanks, > > Celso. > > > > > > > ------------------------------------------------------------------------------ > > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: > > Pinpoint memory and threading errors before they happen. > > Find and fix more than 250 security defects in the development cycle. > > Locate bottlenecks in serial and parallel code that limit performance. > > http://p.sf.net/sfu/intel-dev2devfeb > > > > > > _______________________________________________ > > Owlapi-developer mailing list > > Owl...@li... > > https://lists.sourceforge.net/lists/listinfo/owlapi-developer > Hello, > > > OWLClass has a method to get superclasses, called getSuperClasses(). But > this will only return the superClasses, or to be more exactly complex > class expressions, which are asserted in the ontology. So for inferred > superclasses you will have to implement it for your own, or maybe you > can use the StructuralReasoner class, which also only analyses the > asserted axioms. But i don't know if it really returns completely all > superclasses. Matthew or Ignazio should be able to answer this question > better than me. > > Regards, > Lorenz > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 3 > Date: Sat, 19 Feb 2011 20:45:48 +0000 > From: Ignazio Palmisano <ipa...@gm...> > Subject: Re: [OWLAPI-developer] How get SuperClass without Reasoner? > To: owl...@li... > Message-ID: > <AAN...@ma...> > Content-Type: text/plain; charset=ISO-8859-1 > > 2011/2/19 Lorenz B?hmann <spo...@st...>: > > On 19.02.2011 20:46, Celso Fontes wrote: > > > > Hi ! > > How get SuperClass of an OWLClass without reasoner? > > Is possible a reverse way of subclasses? > > > > Thanks, > > Celso. > > > > > ------------------------------------------------------------------------------ > > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: > > Pinpoint memory and threading errors before they happen. > > Find and fix more than 250 security defects in the development cycle. > > Locate bottlenecks in serial and parallel code that limit performance. > > http://p.sf.net/sfu/intel-dev2devfeb > > > > _______________________________________________ > > Owlapi-developer mailing list > > Owl...@li... > > https://lists.sourceforge.net/lists/listinfo/owlapi-developer > > > > Hello, > > > > > > OWLClass has a method to get superclasses, called getSuperClasses(). But > > this will only return the superClasses, or to be more exactly complex > class > > expressions, which are asserted in the ontology. So for inferred > > superclasses you will have to implement it for your own, or maybe you can > > use the StructuralReasoner class, which also only analyses the asserted > > axioms. But i don't know if it really returns completely all > superclasses. > > Matthew or Ignazio should be able to answer this question better than me. > > > > Regards, > > Lorenz > > I believe Lorenz's answer is correct and complete :-) I don't know > what StructuralReasoner does in detail, but it's not a complete OWL > reasoner for sure. > > I have another question: why don't you want to use a reasoner? Without > it, you are either restricted to what's asserted or you need to > implement your own code to build the inferences. The only case in > which I would do this is if I needed only a small set of inferences, > or if the ontology I'm forced to use is hard to reason about or is > inconsistent. > HTH, > I. > > > > > > ------------------------------------------------------------------------------ > > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: > > Pinpoint memory and threading errors before they happen. > > Find and fix more than 250 security defects in the development cycle. > > Locate bottlenecks in serial and parallel code that limit performance. > > http://p.sf.net/sfu/intel-dev2devfeb > > _______________________________________________ > > Owlapi-developer mailing list > > Owl...@li... > > https://lists.sourceforge.net/lists/listinfo/owlapi-developer > > > > > > > > ------------------------------ > > Message: 4 > Date: Sun, 20 Feb 2011 02:16:09 -0500 > From: sridevi polavaram <spo...@gm...> > Subject: [OWLAPI-developer] document IRI and ontology IRI conflict! > To: owl...@li... > Cc: Chris Mungall <CJM...@lb...> > Message-ID: > <AAN...@ma...> > Content-Type: text/plain; charset="iso-8859-1" > > Dear All: > > I am trying to make a sub ontology from a given ontology. > I am able to extract the content as I wanted. > I tried using two methods for this: > 1. Using the module extraction as shown in Example16 in the docs. > SyntacticLocalityModuleExtractor sme = new > SyntacticLocalityModuleExtractor(man, origOnt, ModuleType.STAR); > OWLOntology mod = sme.extractAsOntology(seedSig, moduleIRI); > 2. I have also tried using the reasoner and recursively calling the > subclasses and super classes > > But the problem that I am having in both the cases is when I want to save > the new ontology using manager.saveontology(ontology) > I am getting a conflict between the document base IRI and the URI of the > class entities as the later is derived directly from the original ontology. > It seems like I can't have the same IRI also as the OWLOntologyManager > throws OntologyAlreadyExits error. > > This problem is mainly because, after extracting the sub ontology, I have > to > add new instances/individuals with the same prefixmanager URI of the > original ontology. > > for(String clsiri : nmoMappedClses.keySet() ){ > System.out.println("keys:"+clsiri); > // Get the reference to the class entity (e.g., the full > IRI will be <http://mouse.brain-map.org/atlas/index.html#CTX>) > OWLClass mapregion = dataFactory.getOWLClass(":"+clsiri, > origpm); > // Get the reference to the individual entity (the full IRI > will be <http://mouse.brain-map.org/atlas/index.html#NMODB12>) > OWLNamedIndividual mapinstance = > dataFactory.getOWLNamedIndividual(":"+nmoMappedClses.get(clsiri), origpm); > // Now create a ClassAssertion to specify that :NMODB12 is > an instance of :CTX > OWLClassAssertionAxiom classAssertion = > dataFactory.getOWLClassAssertionAxiom(mapregion, mapinstance); > // Add the class assertion > manager.addAxiom(ont, classAssertion); > System.out.println("Get > individuals:"+classAssertion.getIndividual()); > } > > Although, I managed to get the new OWL ontology without getting > programmatic > errors, I get the following error when I try to open this in Protege. > > [line=3884:column=89] URI ' > http://mouse.brain-map.org/atlas/index.html#dorsal pallidum' cannot be > resolved against current base URI > file:/home/spolavar/projects/ontology/data/brainregions/NMOABA_v1.0.owl > > Please let me know how can I resolve this. In fact, I don't want to change > the document IRI for my new ontology, but since this is stored locally, the > physical file location automatically becomes its ontology base URI! > > Thanks much! > Sridevi Polavaram > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 5 > Date: Sun, 20 Feb 2011 13:10:45 +0000 > From: Ignazio Palmisano <ipa...@gm...> > Subject: Re: [OWLAPI-developer] document IRI and ontology IRI > conflict! > To: owl...@li... > Message-ID: > <AAN...@ma...> > Content-Type: text/plain; charset=ISO-8859-1 > > 2011/2/20 sridevi polavaram <spo...@gm...>: > > Dear All: > > > > I am trying to make a sub ontology from a given ontology. > > I am able to extract the content as I wanted. > > I tried using two methods for this: > > 1. Using the module extraction as shown in Example16 in the docs. > > ??? SyntacticLocalityModuleExtractor sme = new > > SyntacticLocalityModuleExtractor(man, origOnt, ModuleType.STAR); > > ??? OWLOntology mod = sme.extractAsOntology(seedSig, moduleIRI); > > 2. I have also tried using the reasoner and recursively calling the > > subclasses and super classes > > > > But the problem that I am having in both the cases is when I want to save > > the new ontology using manager.saveontology(ontology) > > I am getting a conflict between the document base IRI and the URI of the > > class entities as the later is derived directly from the original > ontology. > > This is not necessary: URIs of classes defined in one ontology do not > need to be in the same namespace as the ontology. > > > It seems like I can't have the same IRI also as the OWLOntologyManager > > throws OntologyAlreadyExits error. > > > > This problem is mainly because, after extracting the sub ontology, I have > to > > add new instances/individuals with the same prefixmanager URI of the > > original ontology. > > > > ? for(String clsiri : nmoMappedClses.keySet() ){ > > ??????????? ??? System.out.println("keys:"+clsiri); > > ??????????? ??? ?// Get the reference to the class entity (e.g., the full > > IRI will be <http://mouse.brain-map.org/atlas/index.html#CTX>) > > ??????????? ??? OWLClass mapregion = dataFactory.getOWLClass(":"+clsiri, > > origpm); > > ??????????? ??? ?// Get the reference to the individual entity (the full > IRI > > will be <http://mouse.brain-map.org/atlas/index.html#NMODB12>) > > ??????????????? OWLNamedIndividual mapinstance = > > dataFactory.getOWLNamedIndividual(":"+nmoMappedClses.get(clsiri), > origpm); > > Try using IRI.create("http://mouse.brain-map.org/atlas/index.html#NMODB12 > ") > instead; there might be issues with the prefix handler, which might be > misbehaving with bas namespaces and related stuff. > > > ??????????????? // Now create a ClassAssertion to specify that :NMODB12 > is > > an instance of :CTX > > ??????????????? OWLClassAssertionAxiom classAssertion = > > dataFactory.getOWLClassAssertionAxiom(mapregion, mapinstance); > > ??????????????? // Add the class assertion > > ??????????????? manager.addAxiom(ont, classAssertion); > > ??????????????? System.out.println("Get > > individuals:"+classAssertion.getIndividual()); > > ??????????? } > > > > Although, I managed to get the new OWL ontology without getting > programmatic > > errors, I get the following error when I try to open this in Protege. > > > > [line=3884:column=89] URI > > 'http://mouse.brain-map.org/atlas/index.html#dorsal pallidum' cannot be > > resolved against current base URI > > file:/home/spolavar/projects/ontology/data/brainregions/NMOABA_v1.0.owl > > That sounds strange, it's an absolute URI so it doesn't need to be > resolved at all. > The space between dorsal and pallidum is illegal: such a URI is not a > valid one. That space should be escaped or removed. > HTH, > I. > > > > > Please let me know how can I resolve this. In fact, I don't want to > change > > the document IRI for my new ontology, but since this is stored locally, > the > > physical file location automatically becomes its ontology base URI! > > > > Thanks much! > > Sridevi Polavaram > > > > > ------------------------------------------------------------------------------ > > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: > > Pinpoint memory and threading errors before they happen. > > Find and fix more than 250 security defects in the development cycle. > > Locate bottlenecks in serial and parallel code that limit performance. > > http://p.sf.net/sfu/intel-dev2devfeb > > _______________________________________________ > > Owlapi-developer mailing list > > Owl...@li... > > https://lists.sourceforge.net/lists/listinfo/owlapi-developer > > > > > > > > ------------------------------ > > > ------------------------------------------------------------------------------ > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: > Pinpoint memory and threading errors before they happen. > Find and fix more than 250 security defects in the development cycle. > Locate bottlenecks in serial and parallel code that limit performance. > http://p.sf.net/sfu/intel-dev2devfeb > > ------------------------------ > > _______________________________________________ > Owlapi-developer mailing list > Owl...@li... > https://lists.sourceforge.net/lists/listinfo/owlapi-developer > > > End of Owlapi-developer Digest, Vol 48, Issue 14 > ************************************************ > |