From: Wynne, R. (NIH/NLM/L. [C] <wy...@ma...> - 2021-08-27 13:44:29
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I think after 15 years of working with the owlapi I’ve terminal version-itis. 😊 Found a trivial bug in my class where OWLReasoner was first declared instead of SnorocketOWLReasoner. Reasoners are all invoked differently, and their documentation can be scant. With advice from Dr. Lawley, I was able to get Snorocket working with the deps below. There was mention it should work with owlapi-osgidistribution 4.6, but it’s not on maven central and 4.5.20 seems to work just fine. <dependency> <groupId>net.sourceforge.owlapi</groupId> <artifactId>owlapi-osgidistribution</artifactId> <version>4.5.20</version> </dependency> <dependency> <groupId>au.csiro</groupId> <artifactId>snorocket-owlapi</artifactId> <version>4.0.1</version> </dependency> <dependency> <groupId>au.csiro</groupId> <artifactId>snorocket-core</artifactId> <version>4.0.1</version> </dependency> <dependency> <groupId>au.csiro</groupId> <artifactId>ontology-model</artifactId> <version>4.0.1</version> </dependency> <dependency> <groupId>au.csiro</groupId> <artifactId>ontology-import</artifactId> <version>4.0.1</version> </dependency> From: Ignazio Palmisano <ipa...@gm...> Sent: Thursday, August 19, 2021 1:22 AM To: owl...@li... Subject: Re: [OWLAPI-developer] Snorocket On Tue, 17 Aug 2021, 22:47 Wynne, Robert (NIH/NLM/LHC) [C] via Owlapi-developer, <owl...@li...<mailto:owl...@li...>> wrote: Thanks for your quick reply! My test class is attached. The error occurs with reasoner.getSubClasses(OWLClass, false) From the stack trace, it looks like the error comes from the call to getFlattened(); the reasoner might be returning null on that method. If so, it's a snorocket bug, otherwise there might be an OWLAPI issue involved. The snorocket pom file specifies OWLAPI between 4.3.1 and 4.5.x, so you can try a version in that range and it would be expected to work. Cheers, I. Stacktrace: Aug 17, 2021 2:45:39 PM au.csiro.snorocket.core.NormalisedOntology loadAxioms INFO: Loading 20 axioms Aug 17, 2021 2:45:39 PM au.csiro.snorocket.core.NormalisedOntology loadAxioms INFO: Processing 38 normalised axioms Aug 17, 2021 2:45:39 PM au.csiro.snorocket.core.NormalisedOntology classify INFO: Classifying with 8 threads Aug 17, 2021 2:45:39 PM au.csiro.snorocket.core.NormalisedOntology classify INFO: Running saturation Aug 17, 2021 2:45:39 PM au.csiro.snorocket.core.SnorocketReasoner getClassifiedOntology INFO: Building taxonomy java.lang.NullPointerException at gov.nih.nlm.mor.util.TestSnorocket.run(TestSnorocket.java:40) at gov.nih.nlm.mor.util.TestSnorocket.main(TestSnorocket.java:31) Exception in thread "main" java.lang.NullPointerException at gov.nih.nlm.mor.util.TestSnorocket.run(TestSnorocket.java:44) at gov.nih.nlm.mor.util.TestSnorocket.main(TestSnorocket.java:31) From the documentation on Github, version 3.0.0 is expected to work with OWL API 4. dependencies in pom: <dependency> <groupId>net.sourceforge.owlapi</groupId> <artifactId>owlapi-distribution</artifactId> <version>4.0.0</version> </dependency> <dependency> <groupId>au.csiro</groupId> <artifactId>snorocket-core</artifactId> <version>3.0.0</version> </dependency> <dependency> <groupId>au.csiro</groupId> <artifactId>snorocket-owlapi</artifactId> <version>3.0.0</version> </dependency> From an asserted view, here are screenshots from Protégé. (I can send the ontology off-list if needed.) [cid:image001.png@01D7937C.0F7DF620] [cid:image002.png@01D7937C.79C4D710] [cid:image003.png@01D7937C.79C4D710] From: Ignazio Palmisano <ipa...@gm...<mailto:ipa...@gm...>> Sent: Tuesday, August 17, 2021 1:20 PM To: owl...@li...<mailto:owl...@li...> Subject: Re: [OWLAPI-developer] Snorocket On Tue, 17 Aug 2021, 20:14 Wynne, Robert (NIH/NLM/LHC) [C] via Owlapi-developer, <owl...@li...<mailto:owl...@li...>> wrote: Hi, I’m wondering if Snorocket<https://aehrc.com/snorocket/> is still available for the owlapi, and if so, what Maven dependencies should be used. I’ve tried the latest version but cannot get it to work with very simple EL2 ontologies. Hi, I can't go check snorocket right now, but I'd expect its latest version to work with the latest OWLAPI of the same major version. I think 2.0 was using OWLAPI 4? What errors are you seeing? Cheers, I. My reason for exploring Snorocket is that ELK has an issue returning equivalent classes containing DataHasValue axioms (also with simple EL2 ontologies). Regards, Robert W. Wynne Medical Ontology Research Programmer Contractor, Computational Health Research Branch National Library of Medicine _______________________________________________ Owlapi-developer mailing list Owl...@li...<mailto:Owl...@li...> https://lists.sourceforge.net/lists/listinfo/owlapi-developer _______________________________________________ Owlapi-developer mailing list Owl...@li...<mailto:Owl...@li...> https://lists.sourceforge.net/lists/listinfo/owlapi-developer |