Use Jena 2.12.1 implementation of the rulesys reasoner #36
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Make OntologyTermSimple serializable.
Add LanguageLevel so that one can configure the level of OWL supported. Remove unused getSpec() in AbstractOntologyService.
The implementation supplied by Jena 2.7 is very inefficient because it has a O(n^2) complexity for inferring axioms. This is achieved by shading Jena under ubic.basecode.ontology.jena.impl package namespace. It also implicates that baseCode does not depend on Jena anymore. Jena 2.13.0 has breaking implementation changes and cannot be integrated this way.
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With f31c6c7 workaround, this might not be necessary unless we opt for using an OWL reasoner in Gemma for some of our ontologies. |
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The implementation supplied by Jena 2.7 is very inefficient because it has a O(n^2) complexity for inferring axioms.
This is achieved by shading Jena under ubic.basecode.ontology.jena.impl package namespace. It also implicates that baseCode does not depend on Jena anymore.
Jena 2.13.0 has breaking implementation changes and cannot be integrated this way.