├── .classpath ├── .github └── workflows │ └── maven-publish.yml ├── .gitignore ├── .project ├── LICENSE.txt ├── README.md ├── lib ├── google-api-translate-java-0.97.jar ├── readme_mvn_install_google_translate.txt └── seals-omt-client.jar ├── parameters.txt ├── pom.xml └── src ├── main ├── java │ ├── org │ │ ├── ictclas4j │ │ │ └── segment │ │ │ │ └── SegTag2.java │ │ └── semanticweb │ │ │ └── elk │ │ │ └── owlapi │ │ │ └── ElkReasonerAdapted.java │ └── uk │ │ └── ac │ │ ├── manchester │ │ └── syntactic_locality │ │ │ ├── ModuleExtractor.java │ │ │ ├── ModuleExtractorManager.java │ │ │ ├── OntologyModuleExtractor.java │ │ │ ├── SyntacticLocalityChecker.java │ │ │ └── utils │ │ │ ├── ExtractorConstants.java │ │ │ └── ReadFile.java │ │ └── ox │ │ └── krr │ │ ├── logmap2 │ │ ├── AddConfidence2Mappings.java │ │ ├── LogMap2Core.java │ │ ├── LogMap2_CommandLine.java │ │ ├── LogMap2_MappingRanking.java │ │ ├── LogMap2_Matcher.java │ │ ├── LogMap2_OAEI.java │ │ ├── LogMap2_OAEI_BioPortal.java │ │ ├── LogMap2_RepairFacility.java │ │ ├── LogMap3_RepairFacility.java │ │ ├── LogMap_Full.java │ │ ├── OntologyLoader.java │ │ ├── Parameters.java │ │ ├── SIAssessment │ │ │ ├── DataPropertyMappingAssessment.java │ │ │ ├── InstanceMatchingAssessment.java │ │ │ ├── ObjectPropertyMappingAssessment.java │ │ │ └── PropertyMappingAssessment.java │ │ ├── background │ │ │ └── CategoryMappingsLoader.java │ │ ├── bioportal │ │ │ ├── BioPortalAccess.java │ │ │ ├── BioPortalMapping.java │ │ │ ├── BioPortalOntologyInfo.java │ │ │ ├── CandidateMediatingOntology.java │ │ │ ├── MediatingOntologyExtractor.java │ │ │ └── RESTBioPortalAccess.java │ │ ├── division │ │ │ ├── AbstractDivision.java │ │ │ ├── BasicDivision.java │ │ │ ├── BasicDivisionPredictor.java │ │ │ ├── ConceptEmbeddingDivision.java │ │ │ ├── MatchingTask.java │ │ │ ├── OntologyAlignmentDivision.java │ │ │ ├── OverlappingEstimation.java │ │ │ ├── QualityMeasures.java │ │ │ └── WordEmbeddingDivision.java │ │ ├── indexing │ │ │ ├── ExtractStringFromAnnotationAssertionAxiom.java │ │ │ ├── IndexManager.java │ │ │ ├── JointIndexManager.java │ │ │ ├── LightTarjan.java │ │ │ ├── OntologyProcessing.java │ │ │ ├── ReasonerBasedIndexManager.java │ │ │ ├── entities │ │ │ │ ├── ClassIndex.java │ │ │ │ ├── DataPropertyIndex.java │ │ │ │ ├── EntityIndex.java │ │ │ │ ├── IndividualIndex.java │ │ │ │ ├── ObjectPropertyIndex.java │ │ │ │ └── PropertyIndex.java │ │ │ └── labelling_schema │ │ │ │ ├── Interval.java │ │ │ │ ├── IntervalLabelledHierarchy.java │ │ │ │ ├── Node.java │ │ │ │ ├── PostIntervalLabelledHierarchy.java │ │ │ │ ├── PostNode.java │ │ │ │ ├── PreIntervalLabelledHierarchy.java │ │ │ │ ├── PreNode.java │ │ │ │ ├── Test.java │ │ │ │ └── TopologicalSorting.java │ │ ├── interactive │ │ │ ├── InteractiveProcess.java │ │ │ ├── InteractiveProcessAmbiguity.java │ │ │ ├── InteractiveProcessOAEI.java │ │ │ ├── InteractiveProcessThreshold.java │ │ │ └── objects │ │ │ │ └── MappingObjectInteractivity.java │ │ ├── io │ │ │ ├── CopyUtils.java │ │ │ ├── ExtendedFlatTSVAlignmentFormat.java │ │ │ ├── FlatAlignmentFormat.java │ │ │ ├── FlatAlignmentFormatURL.java │ │ │ ├── FlatFormat2OAEIRDFAlignment.java │ │ │ ├── FlatTSVAlignmentFormat.java │ │ │ ├── LogOutput.java │ │ │ ├── OAEIAlignmentOutput.java │ │ │ ├── OAEIRDFAlignmentFormat.java │ │ │ ├── OWL2RDFAlignment.java │ │ │ ├── OWLAlignmentFormat.java │ │ │ ├── OutPutFilesManager.java │ │ │ ├── OutPutFilesManagerStatic.java │ │ │ ├── OutputMappingsFormat.java │ │ │ ├── ReadFile.java │ │ │ ├── TurtleAlignmentFormat.java │ │ │ └── WriteFile.java │ │ ├── lexicon │ │ │ ├── Lex_norm_LRNOM.gz │ │ │ ├── Lex_plurals_LRAGR.gz │ │ │ ├── Lex_spelling_LRSPL.gz │ │ │ ├── LexicalUtilities.java │ │ │ ├── LexicalUtilitiesStatic.java │ │ │ ├── NormalizeDate.java │ │ │ ├── NormalizeNumbers.java │ │ │ ├── stemming │ │ │ │ ├── FileStemmer.java │ │ │ │ ├── IteratedLovinsStemmer.java │ │ │ │ ├── LovinsIterStemmerBridge.java │ │ │ │ ├── LovinsStemmer.java │ │ │ │ ├── LovinsStemmerBridge.java │ │ │ │ ├── PaiceStemmer.java │ │ │ │ ├── PaiceStemmerBridge.java │ │ │ │ ├── PorterStemmer.java │ │ │ │ ├── PorterStemmerBridge.java │ │ │ │ ├── Stemmer.java │ │ │ │ ├── StemmerManager.java │ │ │ │ ├── StemmerTester.java │ │ │ │ ├── StemmingLauncher.java │ │ │ │ ├── StemmingMapLoader.java │ │ │ │ └── stemrules.txt │ │ │ └── stopwords.txt │ │ ├── mappings │ │ │ ├── CandidateMappingManager.java │ │ │ ├── I_Sub.java │ │ │ ├── MappingManager.java │ │ │ ├── WeakCandidate.java │ │ │ └── objects │ │ │ │ ├── MappingObject.java │ │ │ │ ├── MappingObjectIdentifiers.java │ │ │ │ └── MappingObjectStr.java │ │ ├── multilingual │ │ │ ├── GoogleBasedTranslator.java │ │ │ ├── MicrosoftBasedTranslator.java │ │ │ ├── Translator.java │ │ │ └── TranslatorManager.java │ │ ├── oaei │ │ │ ├── FromRDFAlign2OWL.java │ │ │ ├── LogMapMatcherBridge.java │ │ │ ├── MatcherBridge.java │ │ │ ├── OAEI2015InstanceProcessing.java │ │ │ ├── oracle │ │ │ │ ├── LocalOracle.java │ │ │ │ ├── OAEIOracle.java │ │ │ │ ├── OracleManager.java │ │ │ │ └── Oraculo.java │ │ │ └── reader │ │ │ │ ├── EmptyReader.java │ │ │ │ ├── FlatAlignmentReader.java │ │ │ │ ├── MappingsReader.java │ │ │ │ ├── MappingsReaderManager.java │ │ │ │ ├── OWLAlignmentReader.java │ │ │ │ ├── OWLMappingAxiomVisitor.java │ │ │ │ └── RDFAlignReader.java │ │ ├── overlapping │ │ │ ├── LexicalOverlappingExtractor.java │ │ │ ├── NoOverlappingExtractor.java │ │ │ ├── OntologyProcessing4Overlapping.java │ │ │ ├── OverlappingExtractor.java │ │ │ └── OverlappingExtractor4Mappings.java │ │ ├── owlapi │ │ │ └── SynchronizedOWLManager.java │ │ ├── reasoning │ │ │ ├── DisjointnessAxiomExtractor.java │ │ │ ├── ELKAccess.java │ │ │ ├── HermiTAccess.java │ │ │ ├── HermiT_adapted.java │ │ │ ├── ReasonerAccess.java │ │ │ ├── ReasonerAccessImpl.java │ │ │ ├── ReasonerManager.java │ │ │ ├── SatisfiabilityIntegration.java │ │ │ ├── StructuralReasonerExtended.java │ │ │ ├── explanation │ │ │ │ ├── BlackBoxExplanationExtractor.java │ │ │ │ ├── ExplanationProgressManager.java │ │ │ │ └── PlanExtractor.java │ │ │ └── profiles │ │ │ │ └── CheckOWL2Profile.java │ │ ├── repair │ │ │ ├── AnchorAssessment.java │ │ │ ├── AnchorsAssessmentFullReasoning.java │ │ │ ├── RepairmentPlan.java │ │ │ ├── RepairmentPlanComparator.java │ │ │ └── hornSAT │ │ │ │ ├── DowlingGallierHornSAT.java │ │ │ │ ├── HornClause.java │ │ │ │ └── Link.java │ │ ├── statistics │ │ │ ├── StatisticsManager.java │ │ │ └── StatisticsTimeMappings.java │ │ └── utilities │ │ │ ├── ELAxiomVisitor.java │ │ │ ├── HashAlignment.java │ │ │ ├── Lib.java │ │ │ ├── Pair.java │ │ │ ├── PrecomputeIndexCombination.java │ │ │ ├── PrecomputeIndexCombinationStatic.java │ │ │ ├── Relation.java │ │ │ ├── StandardMeasures.java │ │ │ ├── Timer.java │ │ │ └── Utilities.java │ │ └── logmap_lite │ │ ├── LogMap_Lite.java │ │ ├── MappingObjectStr.java │ │ ├── OntologyLoader.java │ │ ├── OntologyProcessing.java │ │ ├── PrecomputeIndexCombination.java │ │ ├── PrecomputeIndexCombinationStatic.java │ │ ├── io │ │ ├── OAEIAlignmentOutput.java │ │ ├── OWLAlignmentFormat.java │ │ ├── OutputMappingsFormat.java │ │ ├── RDFAlignmentFormat.java │ │ ├── ReadFile.java │ │ └── WriteFile.java │ │ └── stopwords.txt └── resources │ └── log4j.properties ├── test └── java │ ├── UsingLogMapMatcher.java │ ├── UsingLogMapRepairFacility.java │ └── uk │ └── ac │ └── ox │ └── krr │ └── logmap2 │ └── test │ ├── bioportal │ ├── ReadBioPortalMappingsFromFile.java │ ├── StoreBioPortalMappings.java │ └── testLoader.java │ ├── oaei │ ├── CreateIIMBSEALS.java │ ├── CreateModulesForBioMLTrack.java │ ├── HashAlignment.java │ ├── OAEITask.java │ ├── Relation.java │ ├── StandardMeasures.java │ ├── TestAlignmentModule2025.java │ ├── TestAnatomy.java │ ├── TestBioDiversityTrack.java │ ├── TestBioMLRanking.java │ ├── TestBioML_NCIT_DOID.java │ ├── TestBioML_OMIM_ORDO.java │ ├── TestBioML_SNOMED_FMA_Body.java │ ├── TestBioML_SNOMED_NCIT_Neoplas.java │ ├── TestBioML_SNOMED_NCIT_Pharma.java │ ├── TestFoodOntologies.java │ ├── TestIIMBTrack.java │ ├── TestIoT.java │ ├── TestKERGameTask.java │ ├── TestKnowledgeGraphTrack2018.java │ ├── TestKnowledgeGraphTrack2021.java │ ├── TestLargeBio_FMA_NCI.java │ ├── TestLargeBio_FMA_SNOMED.java │ ├── TestLargeBio_SNOMED_NCI.java │ ├── TestLoadMappings.java │ ├── TestLogMapBio.java │ ├── TestLogMapFull.java │ ├── TestLogMapLt.java │ ├── TestNIVA.java │ ├── TestOAEITrack.java │ ├── TestPhenotypeTrack.java │ ├── TestPistoiaPhase4.java │ ├── TestPizza.java │ ├── TestRDF2TXTMappings.java │ ├── TestSnomedPunning.java │ ├── TestTSVBioML2RDFMappings.java │ └── interactivity │ │ ├── CorrectnessMappingsToAskOracle.java │ │ ├── PerformanceLogMapAutomaticDecisions.java │ │ ├── TestAnatomyWithLocalOracle.java │ │ ├── TestBioML_NCIT_DOID_WithLocalOracle.java │ │ ├── TestBioML_OMIM_ORDO_WithLocalOracle.java │ │ ├── TestBioML_SNOMED_FMA_Body_WithLocalOracle.java │ │ ├── TestBioML_SNOMED_NCIT_Neoplas_WithLocalOracle.java │ │ ├── TestBioML_SNOMED_NCIT_Pharma_WithLocalOracle.java │ │ ├── TestLargeBio_FMA_NCI_WithLocalOracle.java │ │ ├── TestLargeBio_FMA_SNOMED_WithLocalOracle.java │ │ ├── TestLargeBio_SNOMED_NCI_WithLocalOracle.java │ │ └── TestOAEITrackWithOracle.java │ ├── overlapping │ ├── AbstractTestDivisionAlignmentTask.java │ ├── EvaluateMappingsForDivisionsOld.java │ ├── EvaluateSystemMappingsForDivisions.java │ ├── HashAlignment.java │ ├── Relation.java │ ├── StandardMeasures.java │ ├── TestBasicDivisionAlignmentTask.java │ ├── TestConceptEmbeddingDivisionAlignmentTask.java │ ├── TestLoading.java │ ├── TestModularization.java │ ├── TestOverlapping.java │ ├── TestOverlappingOverestimation.java │ ├── TestPredictionDivisionAlignmentTask.java │ └── TestWordEmbeddingDivisionAlignmentTask.java │ └── sem_tab │ ├── CEA_challenge.java │ └── CEA_challenge_score.java └── web └── java └── uk └── ac └── ox └── krr └── logmap2 └── web_service ├── DateManager.java ├── ELK_WebService.java ├── HTMLResultsFileManager.java ├── HermiT_WebService.java ├── InteractiveProcessRequest.java ├── InteractiveProcess_WebService.java ├── LogMapInteractivity_WebService.java ├── LogMapLite_WebService.java ├── LogMapReasoningException.java ├── LogMapRepair_WebService.java ├── LogMapRequest.java ├── LogMap_WebService.java ├── MappingObjectInteractivity_WebService.java ├── OntologyLibraryRequest.java ├── SendMail.java └── UploadFileRequest.java /.classpath: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ernestojimenezruiz/logmap-matcher/HEAD/.classpath -------------------------------------------------------------------------------- /.github/workflows/maven-publish.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ernestojimenezruiz/logmap-matcher/HEAD/.github/workflows/maven-publish.yml 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