[topbraid-users] detecting inconsistencies in an ontology
I have what I believe is a simple question that has, unfortunately, got me stymied. How are inconsistencies in an ontology detected in TBC-ME? In particular, if I declare two classes to be disjoint and then create a subClass of each of the classes, I would have thought that the reasoner would tell me that the ontology was now inconsistent. The documentation says: *Semantic checking* The built-in OWL DL inferencer OWLIM (or any other inferencer of your choice integrated with Composer) can be used to check the semantic validity of your model. Consistency is a check to see whether a particular class can have members if the class can have members, then it is consistent. After you run http://127.0.0.1:52987/help/topic/org.topbraidcomposer.help/html/Inferences.htm an OWL DL-aware inference engines, inconsistent classes will be made subclasses of owl:Nothing and also listed in the Inferences View http://127.0.0.1:52987/help/topic/org.topbraidcomposer.help/html/Inferences_Panel.htm . I configured the reasoner to run OWLIM. The note that comes up says that it doesn't provide all OWL-DL inferences, but I'm assuming it should provide consistency checking as noted in the documentation. However, running the reasoner does not produce the described result. I even tried creating instances of my inconsistent subclasses but still got no notice of inconsistency. I have run my simple ontology through the Fact++ reasoner in Protégé and indeed the inconsistencies are detected (although I realize that the Protégé reasoner is most likely not an OWL-RL-compliant reasoner.) Any ideas? Thanks in advance -- charlie -- -- You received this message because you are subscribed to the Google Group TopBraid Suite Users, the topics of which include Enterprise Vocabulary Network (EVN), TopBraid Composer, TopBraid Live, TopBraid Insight, SPARQLMotion, SPARQL Web Pages and SPIN. To post to this group, send email to topbraid-users@googlegroups.com To unsubscribe from this group, send email to topbraid-users+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/topbraid-users?hl=en --- You received this message because you are subscribed to the Google Groups TopBraid Suite Users group. To unsubscribe from this group and stop receiving emails from it, send an email to topbraid-users+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [topbraid-users] Periodic Workspace Save Error
Hi Mark, Possible related to eclipse functionality. But do you have an extended version of the error message - often a 'caused by' entry is entered into the error logs. Thanks, Mark Thanks, Mark Mark Graham TopQuadrant Support On Fri, Jul 25, 2014 at 11:08 AM, Mark van Berkel m...@hunchmanifest.com wrote: Hi, I'd like to setup periodic saves but I get an error. What would you say is the cause of this periodic workspace save error message? java.lang.IllegalArgumentException: Cannot set lower sequence number for root (previous: 117, new: 110). Location: /home/hunch/TBCMEWorkspace/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources at org.eclipse.core.runtime.Assert.isLegal(Assert.java:63) at org.eclipse.core.internal.resources.SaveManager.validateMasterTableBeforeSave(SaveManager.java:1564) at org.eclipse.core.internal.resources.SaveManager.saveMasterTable(SaveManager.java:1228) at org.eclipse.core.internal.resources.SaveManager.saveMasterTable(SaveManager.java:1220) at org.eclipse.core.internal.resources.SaveManager.save(SaveManager.java:1197) at org.eclipse.core.internal.resources.SaveManager.save(SaveManager.java:1109) at org.eclipse.core.internal.resources.DelayedSnapshotJob.run(DelayedSnapshotJob.java:51) at org.eclipse.core.internal.jobs.Worker.run(Worker.java:53) -- -- You received this message because you are subscribed to the Google Group TopBraid Suite Users, the topics of which include Enterprise Vocabulary Network (EVN), TopBraid Composer, TopBraid Live, TopBraid Insight, SPARQLMotion, SPARQL Web Pages and SPIN. To post to this group, send email to topbraid-users@googlegroups.com To unsubscribe from this group, send email to topbraid-users+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/topbraid-users?hl=en --- You received this message because you are subscribed to the Google Groups TopBraid Suite Users group. To unsubscribe from this group and stop receiving emails from it, send an email to topbraid-users+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. -- -- You received this message because you are subscribed to the Google Group TopBraid Suite Users, the topics of which include Enterprise Vocabulary Network (EVN), TopBraid Composer, TopBraid Live, TopBraid Insight, SPARQLMotion, SPARQL Web Pages and SPIN. To post to this group, send email to topbraid-users@googlegroups.com To unsubscribe from this group, send email to topbraid-users+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/topbraid-users?hl=en --- You received this message because you are subscribed to the Google Groups TopBraid Suite Users group. To unsubscribe from this group and stop receiving emails from it, send an email to topbraid-users+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [topbraid-users] faceted search on classes rather than instances?
Do you have a project upload mechanism that I can use. The workspace, compressed, is 223 MB. I have sent a project description to your email address. Jack On Thursday, July 24, 2014 7:47:52 PM UTC-7, Holger Knublauch wrote: Hi Jack, sorry but I believe we will need to get hands on your example file to help you further. Off-list is fine. Holger On 7/25/2014 5:20, Jack Hodges wrote: Hello Irene, I checked all of the classes and they are all rdf:type owl:Class (they subclass owl:Thing). I checked all of the properties I am using as facets and the items in all of their domains and ranges are rdf:type owl:Class. But no faceted search (I closed and opened the model and refreshed the caches and the swp graphs). Jack On Thursday, July 24, 2014 11:26:37 AM UTC-7, Jack Hodges wrote: Thanks! On Thursday, July 24, 2014 8:28:41 AM UTC-7, Irene Polikoff wrote: Jack, I don’t believe sub-classing is either an issue or a requirement here. Faceted search works over instances of a class. Classes are instances of either rdfs:Class or owl:Class. So, you need to be faceting over either rdfs:Class or owl:Class. And properties to select from as facets would need to be associated with these e.g., have owl:Class in their domain. Irene *From:* topbrai...@googlegroups.com [mailto:topbrai...@googlegroups.com] *On Behalf Of *Jack Hodges *Sent:* Thursday, July 24, 2014 11:17 AM *To:* topbrai...@googlegroups.com *Subject:* Re: [topbraid-users] faceted search on classes rather than instances? I am trying to build faceted search across standard models/repositories. In this case the classes are terminals for the repository and contain all the information an instance would carry. For example, in the obolibrary DOID, disease obo:DOID_9352 is fully populated with content, and the disease is unlikely to be subclassed or instantiated. My understanding is that these classes can participate in faceted search under certain circumstances. First, they have to subclassed under one of my classes. Also, for classes to be facetable they need to carry properties and look like resources. I created namespaces such as the following for Symptoms: http://siemens.com/1.0/vocab/biomed-symp and a prefix for it: biomed-symp. I created a class called Symptom and then subclassed several (for the purposes of a demo) of the classes in the obolibrary (e.g., obo:SYMP_455) to biomed-symp:Symptom. I did the same for diseases (etc.). I created facets to bridge the repositories, such as biomed-symp:involvesDisease, that I hung off biomed-symp:Symptom in the defaultFacets property. In the vocabulary, I added these properties (e.g,. obo:SYMP_455 biomed-symp:involvesDisease obo:DOID_9352). Unfortunately this approach isn't working, so I haven't gone far enough in one way or another, and figure that you guys might know how to do it. Any help would be appreciated as faceted search is very important to this project. My faceted search in other parts of the project, created the same way but on class instances, are working fine. Jack On Sunday, July 13, 2014 8:22:44 AM UTC-7, Irene Polikoff wrote: What would you use as facets? On Jul 13, 2014, at 11:11 AM, Jack Hodges jhodg...@gmail.com wrote: Can I build a faceted search on classes rather than on class instances? If I have a repository that is basically a taxonomy and has all of the content at the class level, then faceted search on the classes would provide the same benefit as faceted search on instances. Jack -- -- You received this message because you are subscribed to the Google Group TopBraid Suite Users, the topics of which include Enterprise Vocabulary Network (EVN), TopBraid Composer, TopBraid Live, TopBraid Insight, SPARQLMotion, SPARQL Web Pages and SPIN. To post to this group, send email to topbrai...@googlegroups.com To unsubscribe from this group, send email to topbraid-user...@googlegroups.com For more options, visit this group at http://groups.google.com/group/topbraid-users?hl=en --- You received this message because you are subscribed to the Google Groups TopBraid Suite Users group. To unsubscribe from this group and stop receiving emails from it, send an email to topbraid-user...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. -- -- You received this message because you are subscribed to the Google Group TopBraid Suite Users, the topics of which include Enterprise Vocabulary Network (EVN), TopBraid Composer, TopBraid Live, TopBraid Insight, SPARQLMotion, SPARQL Web Pages and SPIN. To post to this group, send email to topbrai...@googlegroups.com To unsubscribe from this group, send email to topbraid-user...@googlegroups.com For more options, visit this group at http://groups.google.com/group/topbraid-users?hl=en --- You received this message because you are
Re: [topbraid-users] detecting inconsistencies in an ontology
Charlie; A couple of thinks here. First, the kind of inference you are looking for is possible using the OWL 2 RL profile. The one extra step is to choose 'Inference... Configure Inferencing' and check the "Complete mode" box. If you don't do that, then Composer will take it that the subclass inferences are implied and not find the disjoint problem. Use the Problems View (Window Show View Problems) to see the inconsistencies. If you also turn on "Display constraint violation warnings" (yellow warning triangle in Composer's top icon bar), and navigate to an inconsistent resource, the yellow warning will appear in the form. You can click on that to get an explanation of the constraint violation. The second issue is that the passage in the Help file you cite is not correct. The OWLIM reasoner is not an OWL DL reasoner and will not create subclasses of owl:Nothing. We will correct this before the next release of TopBraid. -- Scott On 7/25/2014, 4:14 AM, Charles Mead wrote: I have what I believe is a simple question that has, unfortunately, got me stymied. How are inconsistencies in an ontology detected in TBC-ME? In particular, if I declare two classes to be disjoint and then create a subClass of each of the classes, I would have thought that the reasoner would tell me that the ontology was now inconsistent. The documentation says: Semantic checking The built-in OWL DL inferencer OWLIM (or any other inferencer of your choice integrated with Composer) can be used to check the semantic validity of your model. Consistency is a check to see whether a particular class can have members if the class can have members, then it is consistent. After you run an OWL DL-aware inference engines, inconsistent classes will be made subclasses of owl:Nothing and also listed in the Inferences View. I configured the reasoner to run OWLIM. The note that comes up says that it doesn't provide all OWL-DL inferences, but I'm assuming it should provide consistency checking as noted in the documentation. However, running the reasoner does not produce the described result. I even tried creating instances of my inconsistent subclasses but still got no notice of inconsistency. I have run my simple ontology through the Fact++ reasoner in Protégé and indeed the inconsistencies are detected (although I realize that the Protégé reasoner is most likely not an OWL-RL-compliant reasoner.) Any ideas? Thanks in advance -- charlie -- -- You received this message because you are subscribed to the Google Group "TopBraid Suite Users", the topics of which include Enterprise Vocabulary Network (EVN), TopBraid Composer, TopBraid Live, TopBraid Insight, SPARQLMotion, SPARQL Web Pages and SPIN. To post to this group, send email to topbraid-users@googlegroups.com To unsubscribe from this group, send email to topbraid-users+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/topbraid-users?hl=en --- You received this message because you are subscribed to the Google Groups "TopBraid Suite Users" group. To unsubscribe from this group and stop receiving emails from it, send an email to topbraid-users+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. -- -- You received this message because you are subscribed to the Google Group TopBraid Suite Users, the topics of which include Enterprise Vocabulary Network (EVN), TopBraid Composer, TopBraid Live, TopBraid Insight, SPARQLMotion, SPARQL Web Pages and SPIN. To post to this group, send email to topbraid-users@googlegroups.com To unsubscribe from this group, send email to topbraid-users+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/topbraid-users?hl=en --- You received this message because you are subscribed to the Google Groups TopBraid Suite Users group. To unsubscribe from this group and stop receiving emails from it, send an email to topbraid-users+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
