Re: [OWLAPI-developer] Snorocket

[Ignazio P. <ipa...@gm...>]

On Fri, 27 Aug 2021, 16:44 Wynne, Robert (NIH/NLM/LHC) [C] via
Owlapi-developer, <owl...@li...> wrote:

> 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.
>
>
>

There's no 4.6 version at all yet - snorocket uses "4.6)" as upper limit,
which excludes any 4.6 version from being used. Possibly overly
prescriptive, but at the moment it has no effect.

Cheers,
I.

          <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...> 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.)
>
>
>
>
>
>
>
>
>
>
>
> *From:* Ignazio Palmisano <ipa...@gm...>
> *Sent:* Tuesday, August 17, 2021 1:20 PM
> *To:* 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...> 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
>
>
>
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