├── .gitignore ├── .travis.yml ├── Dockerfile ├── README.md ├── configuration-samples └── configuration-all.yaml ├── docs ├── owlsim_logo.ai ├── owlsim_logo.png ├── owlsim_logo_dark_background.ai └── owlsim_logo_dark_background.png ├── owlsim-core ├── Makefile ├── bin │ └── pom.xml ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── monarchinitiative │ │ └── owlsim │ │ ├── compute │ │ ├── classmatch │ │ │ ├── ClassMatcher.java │ │ │ ├── SimpleClassMatch.java │ │ │ └── package-info.java │ │ ├── cpt │ │ │ ├── ConditionalProbabilityIndex.java │ │ │ ├── IncoherentStateException.java │ │ │ ├── SimplePairwiseConditionalProbabilityIndex.java │ │ │ ├── impl │ │ │ │ ├── AbstractConditionalProbabilityIndex.java │ │ │ │ ├── DefaultSimplePairwiseConditionalProbabilityIndex.java │ │ │ │ ├── NodeProbabilities.java │ │ │ │ ├── ThreeStateConditionalProbabilityIndex.java │ │ │ │ ├── TwoStateConditionalProbabilityIndex.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ ├── enrich │ │ │ ├── EnrichmentConfig.java │ │ │ ├── EnrichmentEngine.java │ │ │ ├── EnrichmentQuery.java │ │ │ ├── EnrichmentResult.java │ │ │ ├── EnrichmentResultSet.java │ │ │ ├── impl │ │ │ │ ├── EnrichmentAllByAll.java │ │ │ │ ├── EnrichmentQueryImpl.java │ │ │ │ ├── EnrichmentResultImpl.java │ │ │ │ ├── EnrichmentResultSetImpl.java │ │ │ │ ├── HypergeometricEnrichmentEngine.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ ├── matcher │ │ │ ├── IncrementalProfileMatcher.java │ │ │ ├── NegationAwareProfileMatcher.java │ │ │ ├── ProfileMatcher.java │ │ │ ├── impl │ │ │ │ ├── AbstractProfileMatcher.java │ │ │ │ ├── AbstractSemanticSimilarityProfileMatcher.java │ │ │ │ ├── BayesianNetworkProfileMatcher.java │ │ │ │ ├── GridNegatedProfileMatcher.java │ │ │ │ ├── GridProfileMatcher.java │ │ │ │ ├── JaccardSimilarityProfileMatcher.java │ │ │ │ ├── MaximumInformationContentSimilarityProfileMatcher.java │ │ │ │ ├── NaiveBayesFixedWeightThreeStateProfileMatcher.java │ │ │ │ ├── NaiveBayesFixedWeightTwoStateNoBlanketProfileMatcher.java │ │ │ │ ├── NaiveBayesFixedWeightTwoStateProfileMatcher.java │ │ │ │ ├── NaiveBayesVariableWeightProfileMatcher.java │ │ │ │ ├── PhenodigmICProfileMatcher.java │ │ │ │ ├── ThreeStateBayesianNetworkProfileMatcher.java │ │ │ │ ├── cosine │ │ │ │ │ ├── CosineNegativeSimilarityProfileMatcher.java │ │ │ │ │ ├── CosineSimilarityProfileMatcher.java │ │ │ │ │ ├── CosineWeightedSimilarityProfileMatcher.java │ │ │ │ │ └── package-info.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ ├── mica │ │ │ ├── MICAStore.java │ │ │ ├── MostInformativeCommonAncestorCalculator.java │ │ │ ├── impl │ │ │ │ ├── MICAStoreImpl.java │ │ │ │ ├── MostInformativeCommonAncestorCalculatorImpl.java │ │ │ │ ├── NoRootException.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ ├── runner │ │ │ ├── Job.java │ │ │ ├── PairwiseJob.java │ │ │ ├── RunConfiguration.java │ │ │ ├── RunEngine.java │ │ │ ├── RunnerUtil.java │ │ │ ├── SearchJob.java │ │ │ └── package-info.java │ │ ├── stats │ │ │ ├── CoAnnotationElement.java │ │ │ ├── CoAnnotationStats.java │ │ │ ├── ICDistribution.java │ │ │ ├── ICDistributionValue.java │ │ │ ├── ICStatsCalculator.java │ │ │ ├── KBMatcherCalculator.java │ │ │ ├── KBStatsCalculator.java │ │ │ ├── SetDescriptiveStatistics.java │ │ │ ├── SumMatrixChangingVisitor.java │ │ │ └── package-info.java │ │ └── weights │ │ │ ├── SpreadingActivationNetworkUtil.java │ │ │ └── package-info.java │ │ ├── eval │ │ ├── CompareAllByAll.java │ │ ├── ProfileMatchEvaluator.java │ │ ├── ProfileMutator.java │ │ ├── RandomOntologyMaker.java │ │ ├── TestQuery.java │ │ ├── data │ │ │ ├── AbstractSimulatedData.java │ │ │ ├── BackgroundData.java │ │ │ ├── LiftAllSimulatedData.java │ │ │ ├── LiftOneSimulatedData.java │ │ │ ├── RandomChooseNSimulatedData.java │ │ │ ├── RemoveByCategorySimulatedData.java │ │ │ ├── RemoveByICThresholdSimulatedData.java │ │ │ └── SimulatedData.java │ │ └── package-info.java │ │ ├── io │ │ ├── AbstractWriter.java │ │ ├── JSONWriter.java │ │ ├── OWLLoader.java │ │ ├── Ontology.java │ │ ├── OntologyLoadException.java │ │ ├── OntologySourceData.java │ │ ├── OwlKnowledgeBase.java │ │ ├── ReadMappingsUtil.java │ │ ├── WeightedSimpleGraphWriter.java │ │ └── package-info.java │ │ ├── kb │ │ ├── BMKnowledgeBase.java │ │ ├── CURIEMapper.java │ │ ├── GraphUtils.java │ │ ├── LabelMapper.java │ │ ├── NonUniqueLabelException.java │ │ ├── UnindexedClassException.java │ │ ├── ewah │ │ │ ├── EWAHKnowledgeBaseStore.java │ │ │ ├── EWAHUtils.java │ │ │ └── package-info.java │ │ ├── filter │ │ │ ├── AnonIndividualFilter.java │ │ │ ├── Filter.java │ │ │ ├── FilterEngine.java │ │ │ ├── FilterSet.java │ │ │ ├── IdFilter.java │ │ │ ├── IdPrefixFilter.java │ │ │ ├── PropertyValueFilter.java │ │ │ ├── TypeFilter.java │ │ │ ├── UnknownFilterException.java │ │ │ └── package-info.java │ │ ├── impl │ │ │ ├── BMKnowledgeBaseOWLAPIImpl.java │ │ │ ├── CURIEMapperImpl.java │ │ │ ├── ClassFrequencyStoreImpl.java │ │ │ ├── LabelMapperImpl.java │ │ │ └── package-info.java │ │ └── package-info.java │ │ ├── model │ │ ├── kb │ │ │ ├── Association.java │ │ │ ├── Attribute.java │ │ │ ├── Entity.java │ │ │ ├── KBMetadata.java │ │ │ ├── SimpleObject.java │ │ │ └── package-info.java │ │ └── match │ │ │ ├── ClassMatch.java │ │ │ ├── ExecutionMetadata.java │ │ │ ├── Match.java │ │ │ ├── MatchSet.java │ │ │ ├── MethodMetadata.java │ │ │ ├── ProfileQuery.java │ │ │ ├── ProfileQueryFactory.java │ │ │ ├── QueryWithNegation.java │ │ │ ├── WeightedQuery.java │ │ │ ├── impl │ │ │ ├── ClassMatchImpl.java │ │ │ ├── ExecutionMetadataImpl.java │ │ │ ├── GridMatchImpl.java │ │ │ ├── MatchImpl.java │ │ │ ├── MatchSetImpl.java │ │ │ ├── ProfileQueryImpl.java │ │ │ ├── QueryWithNegationImpl.java │ │ │ ├── WeightedQueryImpl.java │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ └── package-info.java │ └── test │ ├── java │ └── org │ │ └── monarchinitiative │ │ └── owlsim │ │ ├── compute │ │ ├── classmatch │ │ │ └── ClassMatcherTest.java │ │ ├── cpt │ │ │ ├── AbstractThreeStateConditionalProbabilityIndexTest.java │ │ │ ├── AbstractTwoStateConditionalProbabilityIndexTest.java │ │ │ ├── ConditionalProbabilityIndexTest.java │ │ │ ├── DefaultSimplePairwiseConditionalProbabilityIndexTest.java │ │ │ ├── FlatThreeStateConditionalProbabilityIndexTest.java │ │ │ ├── SimpleConditionalProbabilityIndexTest.java │ │ │ ├── SimpleThreeStateConditionalProbabilityIndexTest.java │ │ │ └── perf │ │ │ │ ├── ThreeStateConditionalProbabilityIndexHPPerfIT.java │ │ │ │ └── package-info.java │ │ ├── enrich │ │ │ └── impl │ │ │ │ ├── AbstractEnrichmentTest.java │ │ │ │ ├── EnrichmentAllByAllTest.java │ │ │ │ └── HypergeometricEnrichmentEngineTest.java │ │ ├── eval │ │ │ └── data │ │ │ │ ├── MakeBackgroundDataTest.java │ │ │ │ └── SimulatedDataTest.java │ │ ├── kb │ │ │ └── impl │ │ │ │ ├── AbstractOwlTest.java │ │ │ │ ├── BMKnowledgeBaseOWLAPIImplTest.java │ │ │ │ ├── CurieMapperImplTest.java │ │ │ │ ├── DisjointClassesTest.java │ │ │ │ └── EquivalentClassesOwlTest.java │ │ ├── matcher │ │ │ ├── AbstractProfileMatcherTest.java │ │ │ ├── BayesianNetworkProfileMatcherTest.java │ │ │ ├── CosineNegatedSimilarityProfileMatcherTest.java │ │ │ ├── FlatThreeStateBayesianNetworkProfileMatcherTest.java │ │ │ ├── NaiveBayesFixedWeightThreeStateProfileMatcherTest.java │ │ │ ├── NaiveBayesFixedWeightTwoStateProfileMatcherTest.java │ │ │ ├── PhenodigmICProfileMatcherTest.java │ │ │ ├── ProfileMatcherComparisonTest.java │ │ │ ├── ThreeStateBayesianNetworkProfileMatcherTest.java │ │ │ ├── mp │ │ │ │ ├── AbstractProfileMatcherMPTest.java │ │ │ │ ├── BasicProbabilisticProfileMatcherMPTest.java │ │ │ │ ├── BayesianNetworkProfileMatcherMPTest.java │ │ │ │ ├── CosineSimilarityProfileMatcherMPTest.java │ │ │ │ ├── GridProfileMatcherMPTest.java │ │ │ │ ├── JaccardSimilarityProfileMatcherMPTest.java │ │ │ │ ├── MaximumInformationContentSimilarityProfileMatcherMPTest.java │ │ │ │ ├── PhenodigmICProfileMatcherMPTest.java │ │ │ │ ├── ProfileMatcherComparisonMPTest.java │ │ │ │ ├── ProfileMatcherWithNegationMPTest.java │ │ │ │ └── package-info.java │ │ │ ├── perf │ │ │ │ ├── AbstractProfileMatcherPerfIT.java │ │ │ │ ├── BasicProbabilisticProfileMatcherHPPerfIT.java │ │ │ │ ├── BayesianNetworkProfileMatcherPerfIT.java │ │ │ │ ├── CompareMatchersPerfIT.java │ │ │ │ ├── GridProfileMatcherPerfIT.java │ │ │ │ ├── HomologyPhenoPerfIT.java │ │ │ │ ├── MaximumInformationContentSimilarityProfileMatcherPerfIT.java │ │ │ │ ├── NaiveBayesianFixedWeightThreeStateMatcherPerfIT.java │ │ │ │ ├── NaiveBayesianFixedWeightTwoStateMatcherPerfIT.java │ │ │ │ ├── PhenodigmMatcherAllByAllPerfIT.java │ │ │ │ ├── PhenodigmMatcherPerfIT.java │ │ │ │ ├── RunMatchersOnGoPerfIT.java │ │ │ │ └── ThreeStateBayesianNetworkProfileMatcherPerfIT.java │ │ │ └── sp │ │ │ │ ├── MultiMatcherSpeciesTest.java │ │ │ │ ├── ProfileMatcherSpeciesTest.java │ │ │ │ ├── ProfileMatcherWithNegationSpeciesTest.java │ │ │ │ └── package-info.java │ │ ├── mica │ │ │ ├── AbstractMICAStoreTest.java │ │ │ ├── MICAStoreBench.java │ │ │ ├── MICAStoreMPTest.java │ │ │ ├── MICAStoreTest.java │ │ │ └── perf │ │ │ │ ├── MICAStoreHPPerfIT.java │ │ │ │ ├── MICAStorePerfIT.java │ │ │ │ └── package-info.java │ │ ├── runner │ │ │ └── RunEngineTest.java │ │ ├── stats │ │ │ ├── CoAnnotationStatsTest.java │ │ │ ├── ICDistributionTest.java │ │ │ └── ICStorePerfTest.java │ │ └── weights │ │ │ └── SpreadingActivationNetworkUtilTest.java │ │ ├── io │ │ ├── OntologySourceDataTest.java │ │ ├── OntologyTest.java │ │ └── OwlKnowledgeBaseTest.java │ │ └── kb │ │ └── filter │ │ ├── AbstractFilterEngineTest.java │ │ └── FilterEngineTest.java │ └── resources │ ├── .gitignore │ ├── SimpleDAG.owl │ ├── ab-ontology.owl │ ├── abc-linear-neg.owl │ ├── abc-linear.owl │ ├── abc-ontology.owl │ ├── data │ ├── gene2taxon.tsv.gz │ ├── human-pheno.assocs.gz │ ├── mouse-pheno.assocs.gz │ └── species-individuals.tsv │ ├── equivalentClassesTest.owl │ ├── filter-test-ontology.owl │ ├── go-pheno-test.owl │ ├── log4j-travis.properties │ ├── log4j.properties │ ├── mica-test.owl │ ├── mp-subset.ttl │ ├── no-hierarchy-negation-test.owl │ ├── ontologies │ └── mammal.obo.gz │ ├── runner │ └── run.json │ ├── simple-pheno-with-freqs.owl │ ├── simple-pheno-with-negation-with-annprops.owl │ ├── simple-pheno-with-negation.owl │ ├── species-no-individuals.owl │ ├── species.owl │ └── speciesWithNegation.owl ├── owlsim-services ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── monarchinitiative │ │ │ └── owlsim │ │ │ └── services │ │ │ ├── OwlSimServiceApplication.java │ │ │ ├── configuration │ │ │ └── ApplicationConfiguration.java │ │ │ ├── exceptions │ │ │ ├── NonNegatedMatcherException.java │ │ │ └── UnknownMatcherException.java │ │ │ ├── modules │ │ │ ├── EnrichmentMapModule.java │ │ │ ├── KnowledgeBaseModule.java │ │ │ ├── MatcherMapModule.java │ │ │ ├── MatcherModule.java │ │ │ └── bindings │ │ │ │ ├── IndicatesDataTsvs.java │ │ │ │ ├── IndicatesOwlDataOntologies.java │ │ │ │ └── IndicatesOwlOntologies.java │ │ │ └── resources │ │ │ ├── AncestorResource.java │ │ │ ├── EnrichmentResource.java │ │ │ ├── MatchResource.java │ │ │ └── OntologyMatchResource.java │ └── resources │ │ ├── banner.txt │ │ └── swagger │ │ ├── css │ │ ├── print.css │ │ ├── reset.css │ │ ├── screen.css │ │ ├── style.css │ │ └── typography.css │ │ ├── fonts │ │ ├── DroidSans-Bold.ttf │ │ └── DroidSans.ttf │ │ ├── images │ │ ├── collapse.gif │ │ ├── expand.gif │ │ ├── explorer_icons.png │ │ ├── favicon-16x16.png │ │ ├── favicon-32x32.png │ │ ├── favicon.ico │ │ ├── logo_small.png │ │ ├── pet_store_api.png │ │ ├── throbber.gif │ │ └── wordnik_api.png │ │ ├── index.html │ │ ├── lang │ │ ├── ca.js │ │ ├── el.js │ │ ├── en.js │ │ ├── es.js │ │ ├── fr.js │ │ ├── geo.js │ │ ├── it.js │ │ ├── ja.js │ │ ├── ko-kr.js │ │ ├── pl.js │ │ ├── pt.js │ │ ├── ru.js │ │ ├── tr.js │ │ 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