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…ple boolean limit case of other matchers; e.g. jaccard with a floor function. although this is not anticipated to be useful for the general phenotype search use case, it can be useful to leverage owlsim services for doing basic queries of the form: find all genes with phenotypes A and B but not C
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57 loader refactor
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…r creating a BMKnowledgeBaseOWLAPIImpl - @deprecated OWLLoader. Added new supporting classes Ontology and OntologyDataSource, OntologyLoadException to help the OwlKnowledgeBase do its thing. OWLLoader is only partially removed from the tests at present. Removed overly verbose logging from FilterEngine. Added commented-out clean-up of KnowledgeBaseModule - server still fails to start with ot without this.
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…tcher package through java reflection and let the injector construct the objects.
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…oduced from CurieUtil. Removed useless right-hand class types from collection initialisation. e.g. = new ArrayList<String>() -> new ArrayList<>();
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WIP: first pass at frequency-awareness