├── AnnotationUtils ├── pom.xml └── src │ └── main │ ├── java │ └── edu │ │ └── mayo │ │ └── bsi │ │ └── nlp2fhir │ │ ├── anafora │ │ ├── AnaforaFHIRSchemaGenerator.java │ │ ├── deserialization │ │ │ └── Anafora2CASAnalysisEngine.java │ │ ├── model │ │ │ ├── annotation │ │ │ │ ├── AnaforaAnnotation.java │ │ │ │ ├── AnnotationCollection.java │ │ │ │ ├── AnnotationMeta.java │ │ │ │ ├── Annotations.java │ │ │ │ ├── Property.java │ │ │ │ ├── SchemaInfo.java │ │ │ │ └── serialization │ │ │ │ │ ├── AnnotationDeserializer.java │ │ │ │ │ ├── AnnotationSerializer.java │ │ │ │ │ ├── PropertyDeserializer.java │ │ │ │ │ └── PropertySerializer.java │ │ │ └── schema │ │ │ │ ├── Entity.java │ │ │ │ ├── EntityCollection.java │ │ │ │ ├── Property.java │ │ │ │ ├── Relation.java │ │ │ │ ├── RelationCollection.java │ │ │ │ └── Schema.java │ │ └── serialization │ │ │ └── CAS2AnaforaAnalysisEngine.java │ │ ├── common │ │ ├── FHIRJSONSchemaReader.java │ │ └── model │ │ │ ├── UIMA.java │ │ │ ├── annotation │ │ │ └── ResourceAnnotation.java │ │ │ └── schema │ │ │ ├── ArrayPropertyDefinition.java │ │ │ ├── FHIRSchema.java │ │ │ ├── InstancePropertyDefinition.java │ │ │ ├── PropertyDefinition.java │ │ │ ├── SchemaResource.java │ │ │ └── ValuePropertyDefinition.java │ │ ├── jackson │ │ └── DuplicateElementUntypedObjectDeserializer.java │ │ └── knowtator │ │ ├── KnowtatorFHIROntologyClassdefGenerator.java │ │ ├── KnowtatorPINSCompiler.java │ │ └── model │ │ ├── KnowtatorAnnotationDef.java │ │ ├── KnowtatorClassDef.java │ │ └── KnowtatorSlotDef.java │ └── resources │ └── edu │ └── mayo │ └── bsi │ └── nlp2fhir │ └── fhir │ └── schema │ └── dstu3.zip ├── FHIR-Typesystem-UIMA ├── pom.xml └── src │ └── main │ └── resources │ ├── META-INF │ └── org.apache.uima.fit │ │ └── types.txt │ └── typesystems │ └── FHIRTypeSystem.xml ├── NLP2FHIR-GUI ├── pom.xml └── src │ └── main │ ├── java │ └── edu │ │ └── mayo │ │ └── bsi │ │ └── nlp2fhir │ │ └── gui │ │ ├── CLI.java │ │ ├── GUI.java │ │ ├── layout │ │ ├── OptionPane.java │ │ └── RelativeLayout.java │ │ └── model │ │ └── pipelinebuilder │ │ ├── BuildablePipeline.java │ │ ├── PipelineTask.java │ │ ├── options │ │ └── Option.java │ │ └── tasks │ │ ├── DeserializationTask.java │ │ ├── ResourceTask.java │ │ └── SerializationTask.java │ └── resources │ └── resources │ ├── META-INF │ └── org.apache.uima.fit │ │ └── types.txt │ ├── org │ └── apache │ │ └── ctakes │ │ └── relationextractor │ │ └── models │ │ ├── degree_of │ │ └── model_fhir.jar │ │ ├── location_of │ │ └── model_fhir.jar │ │ └── modifier_extractor │ │ └── model_fhir.jar │ ├── sections.tsv │ └── typesystems │ ├── CustomNLPTypeSystem.xml │ ├── FHIRTypeSystem.xml │ ├── KnowtatorTypeSystem.xml │ ├── MedTaggerTypeSystem.xml │ ├── MedTimeTypeSystem.xml │ ├── MedXNTypeSystem.xml │ └── OHNLPTypeSystem.xml ├── NLP2FHIR-STREAM ├── pom.xml └── src │ └── main │ ├── java │ ├── edu │ │ └── mayo │ │ │ └── bsi │ │ │ └── nlp2fhir │ │ │ └── stream │ │ │ ├── CompositionCasInitializer.java │ │ │ ├── NLP2FHIRPlugin.java │ │ │ └── NLP2FHIRResourceBundleSerializer.java │ └── org │ │ └── apache │ │ └── ctakes │ │ └── lvg │ │ └── resource │ │ └── LvgCmdApiResourceImpl.java │ └── resources │ └── plugin-class.info ├── NLP2FHIR-WEB ├── pom.xml └── src │ └── main │ ├── java │ └── edu │ │ └── mayo │ │ └── bsi │ │ └── nlp2fhir │ │ └── web │ │ ├── WebApplication.java │ │ ├── controllers │ │ └── PipelineController.java │ │ └── pipeline │ │ └── ProcessingRequest.java │ ├── resources │ ├── META-INF │ │ └── resources │ │ │ └── js │ │ │ └── nlp2fhir.js │ └── application.properties │ └── webapp │ └── WEB-INF │ └── jsp │ ├── error.jsp │ └── index.jsp ├── NLP2FHIRAnnotators ├── pom.xml └── src │ └── main │ ├── java │ ├── edu │ │ └── mayo │ │ │ └── bsi │ │ │ └── nlp2fhir │ │ │ ├── Pipeline.java │ │ │ ├── RegexpStatements.java │ │ │ ├── Util.java │ │ │ ├── deconstructors │ │ │ └── FHIRToCTAKESFamilyMemberHistory.java │ │ │ ├── evaluation │ │ │ ├── EvaluationXMIReader.java │ │ │ ├── GoldStandardEvaluationAnalysisEngine.java │ │ │ ├── SHARPKnowtatorXMLReaderWrapper.java │ │ │ ├── SHARPNGoldStandardAnalysisEngine.java │ │ │ ├── api │ │ │ │ ├── EvaluationTask.java │ │ │ │ └── ResourceEvaluationTask.java │ │ │ ├── evaluators │ │ │ │ └── DeepSearchResourceEvaluator.java │ │ │ └── types │ │ │ │ ├── DosageAdditionalInstructionsEvaluator.java │ │ │ │ ├── DosageAsNeededBooleanEvaluator.java │ │ │ │ ├── DosageAsNeededCodeableConceptEvaluator.java │ │ │ │ ├── DosageMethodEvaluator.java │ │ │ │ ├── DosageQuantityEvaluator.java │ │ │ │ ├── DosageQuantityUnitEvaluator.java │ │ │ │ ├── DosageReasonCodeEvaluator.java │ │ │ │ ├── DosageRouteEvaluator.java │ │ │ │ ├── DosageSiteEvaluator.java │ │ │ │ ├── DosageTimingCodeEvaluator.java │ │ │ │ ├── DosageWhenEvaluator.java │ │ │ │ ├── IngredientDenominatorUnitEvaluator.java │ │ │ │ ├── IngredientDenominatorValueEvaluator.java │ │ │ │ ├── IngredientNumeratorUnitEvaluator.java │ │ │ │ ├── IngredientNumeratorValueEvaluator.java │ │ │ │ ├── MedicationCodeableConceptEvaluator.java │ │ │ │ ├── MedicationFormEvaluator.java │ │ │ │ ├── TimingDurationUnitEvaluator.java │ │ │ │ ├── TimingDurationValueEvaluator.java │ │ │ │ ├── TimingFrequencyEvaluator.java │ │ │ │ ├── TimingFrequencyMaxEvaluator.java │ │ │ │ ├── TimingPeriodMaxEvaluator.java │ │ │ │ ├── TimingPeriodUnitEvaluator.java │ │ │ │ └── TimingPeriodValueEvaluator.java │ │ │ ├── extractors │ │ │ ├── ConTexTAssertionAnnotator.java │ │ │ ├── GenericFHIRElementRelationExtractor.java │ │ │ ├── SectionExtractor.java │ │ │ ├── SnomedCTDictionaryLookupExtractor.java │ │ │ ├── context │ │ │ │ └── ConTexTSettings.java │ │ │ ├── features │ │ │ │ ├── CTakesNamedEntityFeatureExtractor.java │ │ │ │ ├── DependencyPathFeatureExtractor.java │ │ │ │ ├── DependencyTreeFeatureExtractor.java │ │ │ │ ├── FeatureExtractor.java │ │ │ │ ├── PartOfSpeechFeatureExtractor.java │ │ │ │ ├── PhraseChunkingFeatureExtractor.java │ │ │ │ ├── TokenFeatureExtractor.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ │ ├── performance │ │ │ └── structs │ │ │ │ └── AnnotationCache.java │ │ │ ├── pipelines │ │ │ ├── EvaluationPipeline.java │ │ │ ├── PipelineDependency.java │ │ │ ├── PlainTextAllResourcesPipeline.java │ │ │ ├── ProduceCompositionJSONPipeline.java │ │ │ ├── ProduceCompositionResourcesPipeline.java │ │ │ ├── SourceNLPSystem.java │ │ │ ├── TrainingPipeline.java │ │ │ ├── evaluation │ │ │ │ └── EvaluationPipelineBuilder.java │ │ │ ├── package-info.java │ │ │ ├── resources │ │ │ │ └── ResourcePipelineBuilder.java │ │ │ └── serialization │ │ │ │ └── SerializationPipelineBuilder.java │ │ │ ├── postprocessors │ │ │ ├── CAS2FHIRJSONPostProcessor.java │ │ │ ├── Document2KnowtatorPostProcessor.java │ │ │ ├── DocumentTextContentPostProcessor.java │ │ │ ├── FHIR2KnowtatorPostProcessor.java │ │ │ ├── XMIWriterPostProcessor.java │ │ │ ├── cas2fhir │ │ │ │ ├── Cas2FHIRUtils.java │ │ │ │ ├── ResourceProducer.java │ │ │ │ ├── ResourceProducers.java │ │ │ │ └── impl │ │ │ │ │ ├── CompositionResourceProducer.java │ │ │ │ │ ├── ConditionResourceProducer.java │ │ │ │ │ ├── FamilyMemberHistoryResourceProducer.java │ │ │ │ │ ├── MedicationResourceProducer.java │ │ │ │ │ ├── MedicationStatementResourceProducer.java │ │ │ │ │ ├── ObservationResourceProducer.java │ │ │ │ │ └── ProcedureResourceProducer.java │ │ │ ├── mayo │ │ │ │ ├── Sections2KnowtatorPostProcessor.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ │ ├── preprocessors │ │ │ ├── FHIRFileSystemReader.java │ │ │ ├── FHIRJSONBundleResourceReader.java │ │ │ ├── FHIRJSONCompositionResourceReader.java │ │ │ └── FHIRXMIFileSystemReader.java │ │ │ ├── specialized │ │ │ ├── SectionReader.java │ │ │ └── package-info.java │ │ │ ├── transformers │ │ │ ├── CTAKESGenericToFHIRObservation.java │ │ │ ├── CTAKESToFHIRFamilyMemberHistory.java │ │ │ ├── CTAKESToFHIRMedications.java │ │ │ ├── CTAKESToFHIRProblemList.java │ │ │ ├── MedExtractorsToFHIRMedications.java │ │ │ ├── MedTimeToFHIRMedications.java │ │ │ └── package-info.java │ │ │ └── valuesets │ │ │ ├── TimingAbbreviation.java │ │ │ └── package-info.java │ └── org │ │ ├── apache │ │ └── ctakes │ │ │ ├── core │ │ │ └── sentence │ │ │ │ └── SentenceSpan.java │ │ │ └── lvg │ │ │ └── resource │ │ │ └── LvgCmdApiResourceImpl.java │ │ └── ohnlp │ │ ├── medtagger │ │ └── ae │ │ │ └── LineSentenceDetector.java │ │ └── medtime │ │ └── ae │ │ ├── MedTimeAnnotator.java │ │ └── MedTimeAnnotatorRuntimeInterceptor.java │ └── resources │ ├── META-INF │ └── org.apache.uima.fit │ │ └── types.txt │ ├── edu │ └── mayo │ │ └── advance │ │ └── context │ │ └── context_rules.txt │ └── typesystems │ ├── CustomNLPTypeSystem.xml │ ├── FHIRTypeSystem.xml │ ├── KnowtatorTypeSystem.xml │ ├── MedTaggerTypeSystem.xml │ ├── MedTimeTypeSystem.xml │ ├── MedXNTypeSystem.xml │ └── OHNLPTypeSystem.xml ├── README.md ├── nlp2fhir-system-architecture.png └── pom.xml /AnnotationUtils/pom.xml: 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