Index

_

__call__() (kazu.language.string_similarity_scorers.BooleanStringSimilarityScorer method) (kazu.language.string_similarity_scorers.EntityNounModifierStringSimilarityScorer method) (kazu.language.string_similarity_scorers.EntitySubtypeStringSimilarityScorer class method) (kazu.language.string_similarity_scorers.NumberMatchStringSimilarityScorer class method) (kazu.language.string_similarity_scorers.RapidFuzzStringSimilarityScorer static method) (kazu.language.string_similarity_scorers.SapbertStringSimilarityScorer method) (kazu.language.string_similarity_scorers.StringSimilarityScorer method) (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) (kazu.ontology_preprocessing.autocuration.AutoCurationAction method) (kazu.ontology_preprocessing.autocuration.AutoCurator method) (kazu.ontology_preprocessing.autocuration.IsCommmonWord method) (kazu.ontology_preprocessing.autocuration.LikelyAcronym method) (kazu.ontology_preprocessing.autocuration.MaxLength method) (kazu.ontology_preprocessing.autocuration.MinLength method) (kazu.ontology_preprocessing.autocuration.SymbolicToCaseSensitiveAction method) (kazu.ontology_preprocessing.synonym_generation.CombinatorialSynonymGenerator method) (kazu.ontology_preprocessing.synonym_generation.SynonymGenerator method) (kazu.pipeline.FailedDocsFileHandler method) (kazu.pipeline.FailedDocsHandler method) (kazu.pipeline.FailedDocsLogHandler method) (kazu.pipeline.Pipeline method) (kazu.steps.document_post_processing.abbreviation_finder.AbbreviationFinderStep method) (kazu.steps.joint_ner_and_linking.explosion.ExplosionStringMatchingStep method) (kazu.steps.joint_ner_and_linking.memory_efficient_string_matching.MemoryEfficientStringMatchingStep method) (kazu.steps.linking.dictionary.DictionaryEntityLinkingStep method) (kazu.steps.linking.entity_class_disambiguation.EntityClassDisambiguationStep method) (kazu.steps.linking.post_processing.disambiguation.context_scoring.GildaTfIdfScorer method) (kazu.steps.linking.post_processing.disambiguation.context_scoring.TfIdfScorer method) (kazu.steps.linking.post_processing.disambiguation.strategies.DisambiguationStrategy method) (kazu.steps.linking.post_processing.mapping_step.MappingStep method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.MappingStrategy method) (kazu.steps.linking.post_processing.strategy_runner.ConfidenceLevelStrategyExecution method) (kazu.steps.linking.post_processing.strategy_runner.StrategyRunner method) (kazu.steps.linking.rules_based_disambiguation.RulesBasedEntityClassDisambiguationFilterStep method) (kazu.steps.ner.entity_post_processing.NonContiguousEntitySplitter method) (kazu.steps.ner.entity_post_processing.SplitOnConjunctionPattern method) (kazu.steps.ner.entity_post_processing.SplitOnNumericalListPatternWithPrefix method) (kazu.steps.ner.gliner.GLiNERStep method) (kazu.steps.ner.hf_token_classification.TransformersModelForTokenClassificationNerStep method) (kazu.steps.ner.llm_ner.LLMModel method) (kazu.steps.ner.llm_ner.LLMNERStep method) (kazu.steps.ner.opsin.OpsinStep method) (kazu.steps.ner.seth.SethStep method) (kazu.steps.ner.spacy_ner.SpacyNerStep method) (kazu.steps.ner.tokenized_word_processor.MultilabelSpanFinder method) (kazu.steps.ner.tokenized_word_processor.SimpleSpanFinder method) (kazu.steps.ner.tokenized_word_processor.SpanFinder method) (kazu.steps.ner.tokenized_word_processor.TokenizedWordProcessor method) (kazu.steps.other.cleanup.CleanupStep method) (kazu.steps.other.cleanup.DropMappingsByConfidenceMappingFilter method) (kazu.steps.other.cleanup.DropUnmappedEntityFilter method) (kazu.steps.other.merge_overlapping_ents.MergeOverlappingEntsStep method) (kazu.steps.other.stanza.StanzaStep method) (kazu.steps.step.Step method) (kazu.utils.abbreviation_detector.KazuAbbreviationDetector method) (kazu.utils.caching.Memoization method) (kazu.utils.spacy_object_mapper.KazuToSpacyObjectMapper method) (kazu.utils.utils.EntityClassFilter method) (kazu.utils.utils.Singleton method) __init__() (kazu.annotation.acceptance_test.AggregatedAccuracyResult method) (kazu.annotation.acceptance_test.SectionScorer method) (kazu.annotation.label_studio.LabelStudioAnnotationView method) (kazu.annotation.label_studio.LabelStudioManager method) (kazu.annotation.label_studio.LSToKazuConversion method) (kazu.data.CharSpan method) (kazu.data.Document method) (kazu.data.Entity method) (kazu.data.EquivalentIdSet method) (kazu.data.GlobalParserActions method) (kazu.data.LinkingCandidate method) (kazu.data.LinkingMetrics method) (kazu.data.Mapping method) (kazu.data.OntologyStringResource method) (kazu.data.ParserAction method) (kazu.data.Section method) (kazu.data.Synonym method) (kazu.database.in_memory_db.MetadataDatabase method) (kazu.database.in_memory_db.SynonymDatabase method) (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) (kazu.krt.resource_discrepancy_editor.components.ResourceDiscrepancyResolutionForm method) (kazu.krt.resource_discrepancy_editor.utils.ResourceDiscrepancyManger method) (kazu.krt.resource_discrepancy_editor.utils.SynonymDiscrepancy method) (kazu.krt.resource_manager.ResourceManager method) (kazu.krt.string_editor.utils.ResourceConflict method) (kazu.krt.string_editor.utils.ResourceConflictManager method) (kazu.language.string_similarity_scorers.EntityNounModifierStringSimilarityScorer method) (kazu.language.string_similarity_scorers.SapbertStringSimilarityScorer method) (kazu.language.string_similarity_scorers.StringSimilarityScorer method) (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) (kazu.ontology_matching.ontology_matcher.OntologyMatcherConfig method) (kazu.ontology_preprocessing.autocuration.AutoCurationAction method) (kazu.ontology_preprocessing.autocuration.AutoCurator method) (kazu.ontology_preprocessing.autocuration.IsCommmonWord method) (kazu.ontology_preprocessing.autocuration.LikelyAcronym method) (kazu.ontology_preprocessing.autocuration.MaxLength method) (kazu.ontology_preprocessing.autocuration.MinLength method) (kazu.ontology_preprocessing.autocuration.SymbolicToCaseSensitiveAction method) (kazu.ontology_preprocessing.base.OntologyParser method) (kazu.ontology_preprocessing.curation_utils.OntologyResourceProcessor method) (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetCompleteReport method) (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetConflictReport method) (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetMergeReport method) (kazu.ontology_preprocessing.curation_utils.OntologyStringConflictAnalyser method) (kazu.ontology_preprocessing.downloads.ChemblParquetOntologyDownloader method) (kazu.ontology_preprocessing.downloads.OpenTargetsOntologyDownloader method) (kazu.ontology_preprocessing.downloads.SimpleOntologyDownloader method) (kazu.ontology_preprocessing.ontology_upgrade_report.OntologyUpgradeReport method) (kazu.ontology_preprocessing.parsers.ATCDrugClassificationParser method) (kazu.ontology_preprocessing.parsers.BiologicalProcessGeneOntologyParser method) (kazu.ontology_preprocessing.parsers.CellularComponentGeneOntologyParser method) (kazu.ontology_preprocessing.parsers.CLOntologyParser method) (kazu.ontology_preprocessing.parsers.CLOOntologyParser method) (kazu.ontology_preprocessing.parsers.GeneOntologyParser method) (kazu.ontology_preprocessing.parsers.HGNCGeneOntologyParser method) (kazu.ontology_preprocessing.parsers.MeddraOntologyParser method) (kazu.ontology_preprocessing.parsers.MolecularFunctionGeneOntologyParser method) (kazu.ontology_preprocessing.parsers.OpenTargetsDiseaseOntologyParser method) (kazu.ontology_preprocessing.parsers.OpenTargetsTargetOntologyParser method) (kazu.ontology_preprocessing.parsers.RDFGraphParser method) (kazu.ontology_preprocessing.parsers.SKOSXLGraphParser method) (kazu.ontology_preprocessing.parsers.StatoParser method) (kazu.ontology_preprocessing.parsers.TabularOntologyParser method) (kazu.ontology_preprocessing.parsers.UberonOntologyParser method) (kazu.ontology_preprocessing.synonym_generation.CombinatorialSynonymGenerator method) (kazu.ontology_preprocessing.synonym_generation.NgramHyphenation method) (kazu.ontology_preprocessing.synonym_generation.SeparatorExpansion method) (kazu.ontology_preprocessing.synonym_generation.SpellingVariationReplacement method) (kazu.ontology_preprocessing.synonym_generation.StringReplacement method) (kazu.ontology_preprocessing.synonym_generation.SuffixReplacement method) (kazu.ontology_preprocessing.synonym_generation.TokenListReplacementGenerator method) (kazu.ontology_preprocessing.synonym_generation.VerbPhraseVariantGenerator method) (kazu.pipeline.FailedDocsFileHandler method) (kazu.pipeline.FailedDocsHandler method) (kazu.pipeline.Pipeline method) (kazu.steps.document_post_processing.abbreviation_finder.AbbreviationFinderStep method) (kazu.steps.joint_ner_and_linking.explosion.ExplosionStringMatchingStep method) (kazu.steps.joint_ner_and_linking.memory_efficient_string_matching.MemoryEfficientStringMatchingStep method) (kazu.steps.linking.dictionary.DictionaryEntityLinkingStep method) (kazu.steps.linking.entity_class_disambiguation.EntityClassDisambiguationStep method) (kazu.steps.linking.entity_class_disambiguation.EntityClassTfIdfScorer method) (kazu.steps.linking.post_processing.disambiguation.context_scoring.GildaTfIdfScorer method) (kazu.steps.linking.post_processing.disambiguation.context_scoring.TfIdfScorer method) (kazu.steps.linking.post_processing.disambiguation.strategies.DefinedElsewhereInDocumentDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.DisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.GildaTfIdfDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.PreferDefaultLabelMatchDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.PreferNearestEmbeddingToDefaultLabelDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.TfIdfDisambiguationStrategy method) (kazu.steps.linking.post_processing.mapping_step.MappingStep method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.MappingStrategy method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.StrongMatchMappingStrategy method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.StrongMatchWithEmbeddingConfirmationStringMatchingStrategy method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.SynNormIsSubStringMappingStrategy method) (kazu.steps.linking.post_processing.strategy_runner.ConfidenceLevelStrategyExecution method) (kazu.steps.linking.post_processing.strategy_runner.StrategyRunner method) (kazu.steps.linking.post_processing.xref_manager.CrossReferenceManager method) (kazu.steps.linking.post_processing.xref_manager.OxoCrossReferenceManager method) (kazu.steps.linking.rules_based_disambiguation.RulesBasedEntityClassDisambiguationFilterStep method) (kazu.steps.ner.entity_post_processing.NonContiguousEntitySplitter method) (kazu.steps.ner.entity_post_processing.SplitOnConjunctionPattern method) (kazu.steps.ner.entity_post_processing.SplitOnNumericalListPatternWithPrefix method) (kazu.steps.ner.gliner.ConflictScorer method) (kazu.steps.ner.gliner.GliNERBatchItem method) (kazu.steps.ner.gliner.GLiNERStep method) (kazu.steps.ner.gliner.MajorityVoteScorer method) (kazu.steps.ner.gliner.MaxScoreScorer method) (kazu.steps.ner.hf_token_classification.HFDataset method) (kazu.steps.ner.hf_token_classification.TransformersModelForTokenClassificationNerStep method) (kazu.steps.ner.llm_ner.AzureOpenAILLMModel method) (kazu.steps.ner.llm_ner.LLMNERStep method) (kazu.steps.ner.llm_ner.VertexLLMModel method) (kazu.steps.ner.opsin.OpsinStep method) (kazu.steps.ner.seth.SethStep method) (kazu.steps.ner.spacy_ner.SpacyNerStep method) (kazu.steps.ner.tokenized_word_processor.MultilabelSpanFinder method) (kazu.steps.ner.tokenized_word_processor.SimpleSpanFinder method) (kazu.steps.ner.tokenized_word_processor.SpanFinder method) (kazu.steps.ner.tokenized_word_processor.TokenizedWord method) (kazu.steps.ner.tokenized_word_processor.TokenizedWordProcessor method) (kazu.steps.ner.tokenized_word_processor.TokWordSpan method) (kazu.steps.other.cleanup.CleanupAction method) (kazu.steps.other.cleanup.CleanupStep method) (kazu.steps.other.cleanup.DropMappingsByConfidenceMappingFilter method) (kazu.steps.other.cleanup.DropMappingsByParserNameRankAction method) (kazu.steps.other.cleanup.DropUnmappedEntityFilter method) (kazu.steps.other.cleanup.EntityFilterCleanupAction method) (kazu.steps.other.cleanup.LinkingCandidateRemovalCleanupAction method) (kazu.steps.other.cleanup.MappingFilterCleanupAction method) (kazu.steps.other.cleanup.StripMappingURIsAction method) (kazu.steps.other.merge_overlapping_ents.MergeOverlappingEntsStep method) (kazu.steps.other.stanza.StanzaStep method) (kazu.steps.step.ParserDependentStep method) (kazu.steps.step.Step method) (kazu.utils.abbreviation_detector.KazuAbbreviationDetector method) (kazu.utils.build_and_test_model_packs.BuildConfiguration method) (kazu.utils.build_and_test_model_packs.ModelPackBuilder method) (kazu.utils.caching.CacheProtocol method) (kazu.utils.caching.EntityLinkingLookupCache method) (kazu.utils.caching.Memoization method) (kazu.utils.download_gilda_contexts.WikipediaEnsemblMapping method) (kazu.utils.link_index.DictionaryIndex method) (kazu.utils.sapbert.HFSapbertInferenceDataset method) (kazu.utils.sapbert.SapBertHelper method) (kazu.utils.spacy_object_mapper.KazuToSpacyObjectMapper method) (kazu.utils.spacy_pipeline.SpacyPipelines method) (kazu.utils.string_normalizer.EntityClassNormalizer method) (kazu.utils.utils.EntityClassFilter method) (kazu.web.jwtauth.JWTAuthenticationBackend method) (kazu.web.jwtauth.JWTUser method) (kazu.web.ls_web_utils.LSWebUtils method) (kazu.web.req_id_header.AddRequestIdMiddleware method) (kazu.web.server.SingleEntityDocumentConverter method)

__new__() (kazu.data.DisambiguationConfidence method) (kazu.data.EquivalentIdAggregationStrategy method) (kazu.data.MentionConfidence method) (kazu.data.OntologyStringBehaviour method) (kazu.data.ParserBehaviour method) (kazu.data.StringMatchConfidence method) (kazu.ontology_preprocessing.curation_utils.AutofixStrategy method) (kazu.ontology_preprocessing.curation_utils.LinkingCandidateModificationResult method) (kazu.steps.linking.entity_class_disambiguation.ScoredContext static method) (kazu.steps.linking.entity_class_disambiguation.TfIdfDisambiguationEntry static method) (kazu.steps.linking.rules_based_disambiguation.MatcherResult method)

A

AbbreviationFinderStep (class in kazu.steps.document_post_processing.abbreviation_finder) acceptance_criteria() (in module kazu.annotation.acceptance_test) acceptance_test_json_path (kazu.utils.build_and_test_model_packs.BuildConfiguration attribute) AcceptanceTestFailure actions (kazu.data.GlobalParserActions attribute) active_ner_synonyms() (kazu.data.OntologyStringResource method) add_fn() (kazu.annotation.acceptance_test.AggregatedAccuracyResult method) ADD_FOR_LINKING_ONLY (kazu.data.OntologyStringBehaviour attribute) ADD_FOR_NER_AND_LINKING (kazu.data.OntologyStringBehaviour attribute) add_fp() (kazu.annotation.acceptance_test.AggregatedAccuracyResult method) add_from_func() (kazu.utils.spacy_pipeline.SpacyPipelines static method) add_from_path() (kazu.utils.spacy_pipeline.SpacyPipelines static method) add_mapping() (kazu.data.Entity method) add_or_update_linking_candidate() (kazu.data.Entity method) add_or_update_linking_candidates() (kazu.data.Entity method) add_parser() (kazu.database.in_memory_db.MetadataDatabase method) (kazu.database.in_memory_db.SynonymDatabase method) add_reload_callback_func() (kazu.utils.spacy_pipeline.SpacyPipelines static method) additional_to_source (kazu.data.OntologyStringResource property) AddRequestIdMiddleware (class in kazu.web.req_id_header) aggregate_linking_results() (in module kazu.annotation.acceptance_test) aggregate_ner_results() (in module kazu.annotation.acceptance_test) aggregated_by (kazu.data.LinkingCandidate attribute) AggregatedAccuracyResult (class in kazu.annotation.acceptance_test) all_stopwords (kazu.ontology_preprocessing.synonym_generation.StopWordRemover attribute) all_strings() (kazu.data.OntologyStringResource method) ALL_SUBS (kazu.ontology_preprocessing.synonym_generation.GreekSymbolSubstitution attribute) all_synonym_column_names (kazu.ontology_preprocessing.base.OntologyParser attribute) all_synonyms() (kazu.data.OntologyStringResource method) allowed_additional_chars (kazu.utils.string_normalizer.DefaultStringNormalizer attribute)

alternative_synonyms (kazu.data.OntologyStringResource attribute) AMBIGUOUS (kazu.data.DisambiguationConfidence attribute) analyse_annotation_consistency() (in module kazu.annotation.acceptance_test) analyse_full_pipeline() (in module kazu.annotation.acceptance_test) AnatomyStringNormalizer (class in kazu.utils.string_normalizer) ANNOTATION_FIELDS (kazu.ontology_preprocessing.parsers.OpenTargetsTargetOntologyParser attribute) AnnotationLevelDisambiguationStrategy (class in kazu.steps.linking.post_processing.disambiguation.strategies) apply_autofix_to_all() (kazu.krt.resource_discrepancy_editor.utils.ResourceDiscrepancyManger method) apply_boolean_scorers() (kazu.utils.link_index.DictionaryIndex method) apply_merge_configurations() (kazu.utils.build_and_test_model_packs.ModelPackBuilder method) as_brat() (kazu.data.Entity method) as_path() (in module kazu.utils.utils) ASSOCIATE_ID_SET_DF (kazu.krt.components.ResourceEditor attribute) ASSOCIATE_ID_SET_EDITOR (kazu.krt.components.ResourceEditor attribute) associated_id_sets (kazu.data.LinkingCandidate attribute) (kazu.data.OntologyStringResource attribute) AssociatedIdSets (in module kazu.data) ATCDrugClassificationParser (class in kazu.ontology_preprocessing.parsers) ATTEMPT_AUTOFIX (kazu.krt.resource_discrepancy_editor.components.ResourceDiscrepancyResolutionForm attribute) ATTEMPT_DOWNLOAD (kazu.krt.ontology_update_editor.components.OntologyUpdateForm attribute) attempt_strip_suffixes() (kazu.steps.ner.tokenized_word_processor.TokenizedWordProcessor method) authenticate() (kazu.web.jwtauth.JWTAuthenticationBackend method) auto_resolve() (kazu.krt.resource_discrepancy_editor.utils.SynonymDiscrepancy method) autocuration_results (kazu.data.OntologyStringResource attribute) AutoCurationAction (class in kazu.ontology_preprocessing.autocuration) AutoCurator (class in kazu.ontology_preprocessing.autocuration) autofix_resources() (kazu.ontology_preprocessing.curation_utils.OntologyStringConflictAnalyser method) AutofixStrategy (class in kazu.ontology_preprocessing.curation_utils) AutoNameEnum (class in kazu.data) AzureOpenAILLMModel (class in kazu.steps.ner.llm_ner)

B

basic_spacy_pipeline() (in module kazu.utils.spacy_pipeline) batch() (in module kazu.ontology_preprocessing.curation_utils) batch_metrics() (in module kazu.pipeline) batch_resolve() (kazu.krt.string_editor.utils.ResourceConflict method) behaviour (kazu.data.OntologyStringResource attribute) (kazu.data.ParserAction attribute) BEHAVIOUR_APPLICATION_ORDER (kazu.ontology_preprocessing.curation_utils.OntologyResourceProcessor attribute) BEHAVIOUR_SELECTOR (kazu.krt.components.ResourceEditor attribute) BiologicalProcessGeneOntologyParser (class in kazu.ontology_preprocessing.parsers) bool_score (kazu.data.LinkingMetrics attribute) BooleanStringSimilarityScorer (class in kazu.language.string_similarity_scorers) build_all_model_packs() (in module kazu.utils.build_and_test_model_packs)

build_caches_and_run_sanity_checks() (kazu.utils.build_and_test_model_packs.ModelPackBuilder method) build_id_set_representation() (kazu.steps.linking.post_processing.disambiguation.strategies.TfIdfDisambiguationStrategy method) build_index_cache() (kazu.utils.link_index.DictionaryIndex method) build_labels() (kazu.annotation.label_studio.LabelStudioAnnotationView method) build_model_pack() (kazu.utils.build_and_test_model_packs.ModelPackBuilder method) build_synonym_defaultdict() (kazu.ontology_preprocessing.curation_utils.OntologyStringConflictAnalyser static method) build_taxonomy() (kazu.annotation.label_studio.LabelStudioAnnotationView static method) build_tfidf_documents() (kazu.steps.linking.entity_class_disambiguation.EntityClassTfIdfScorer static method) build_vectorizers() (kazu.steps.linking.post_processing.disambiguation.context_scoring.TfIdfScorer method) build_xref_cache() (kazu.steps.linking.post_processing.xref_manager.CrossReferenceManager method) (kazu.steps.linking.post_processing.xref_manager.OxoCrossReferenceManager method) BuildConfiguration (class in kazu.utils.build_and_test_model_packs)

C

cacheable_build_document_representation() (kazu.steps.linking.post_processing.disambiguation.strategies.GildaTfIdfDisambiguationStrategy static method) (kazu.steps.linking.post_processing.disambiguation.strategies.TfIdfDisambiguationStrategy static method) CacheProtocol (class in kazu.utils.caching) calc_doc_size() (in module kazu.pipeline) calc_starts_and_ends() (kazu.data.Entity method) calculate_linking_matches() (kazu.annotation.acceptance_test.SectionScorer method) calculate_ner_matches() (kazu.annotation.acceptance_test.SectionScorer method) calculate_span_offsets() (kazu.steps.ner.tokenized_word_processor.TokenizedWordProcessor method) call() (kazu.ontology_preprocessing.synonym_generation.NgramHyphenation method) (kazu.ontology_preprocessing.synonym_generation.SeparatorExpansion method) (kazu.ontology_preprocessing.synonym_generation.SpellingVariationReplacement method) (kazu.ontology_preprocessing.synonym_generation.StopWordRemover class method) (kazu.ontology_preprocessing.synonym_generation.StringReplacement method) (kazu.ontology_preprocessing.synonym_generation.SuffixReplacement method) (kazu.ontology_preprocessing.synonym_generation.SynonymGenerator method) (kazu.ontology_preprocessing.synonym_generation.TokenListReplacementGenerator method) (kazu.ontology_preprocessing.synonym_generation.VerbPhraseVariantGenerator method) call_llm() (kazu.steps.ner.llm_ner.AzureOpenAILLMModel method) (kazu.steps.ner.llm_ner.LLMModel method) (kazu.steps.ner.llm_ner.VertexLLMModel method) CandidatesToMetrics (in module kazu.data) case_conflicts (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetConflictReport attribute) CASE_SELECTOR (kazu.krt.components.ResourceEditor attribute) case_sensitive (kazu.data.Synonym attribute) CaseConflictResolutionRequest (class in kazu.krt.string_editor.utils) cell_line_re (kazu.ontology_preprocessing.parsers.CellosaurusOntologyParser attribute) CellosaurusOntologyParser (class in kazu.ontology_preprocessing.parsers) CellularComponentGeneOntologyParser (class in kazu.ontology_preprocessing.parsers) CharSpan (class in kazu.data) check_annotation_consistency() (in module kazu.annotation.acceptance_test) check_ent_class_consistency() (in module kazu.annotation.acceptance_test) check_ent_mapping_consistency() (in module kazu.annotation.acceptance_test) check_ent_match_abnormalities() (in module kazu.annotation.acceptance_test) check_for_case_conflicts_across_resources() (kazu.ontology_preprocessing.curation_utils.OntologyStringConflictAnalyser static method) check_for_normalised_behaviour_conflicts_and_merge_if_possible() (kazu.ontology_preprocessing.curation_utils.OntologyStringConflictAnalyser method) check_lookup_cache() (kazu.utils.caching.EntityLinkingLookupCache method) check_results_meet_threshold() (in module kazu.annotation.acceptance_test) CHEMBL_FILENAME_TEMPLATE (kazu.ontology_preprocessing.downloads.ChemblParquetOntologyDownloader attribute) CHEMBL_QUERY (kazu.ontology_preprocessing.downloads.ChemblParquetOntologyDownloader attribute) CHEMBL_TEMPLATE (kazu.ontology_preprocessing.downloads.ChemblParquetOntologyDownloader attribute) ChemblOntologyParser (class in kazu.ontology_preprocessing.parsers) ChemblParquetOntologyDownloader (class in kazu.ontology_preprocessing.downloads) ChemblParquetOntologyParser (class in kazu.ontology_preprocessing.parsers) classify_symbolic() (kazu.utils.string_normalizer.StringNormalizer static method) clazz (kazu.steps.ner.tokenized_word_processor.TokWordSpan attribute) clean_resources (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetConflictReport attribute) cleanup() (kazu.steps.other.cleanup.CleanupAction method) (kazu.steps.other.cleanup.DropMappingsByParserNameRankAction method) (kazu.steps.other.cleanup.EntityFilterCleanupAction method) (kazu.steps.other.cleanup.LinkingCandidateRemovalCleanupAction method) (kazu.steps.other.cleanup.MappingFilterCleanupAction method) (kazu.steps.other.cleanup.StripMappingURIsAction method)

CleanupAction (class in kazu.steps.other.cleanup) CleanupStep (class in kazu.steps.other.cleanup) clear() (kazu.utils.caching.CacheProtocol method) clear_all() (kazu.utils.utils.Singleton static method) clear_cache() (kazu.ontology_preprocessing.base.OntologyParser method) clear_cached_resources_from_model_pack_dir() (kazu.utils.build_and_test_model_packs.ModelPackBuilder method) clear_invalid_caches() (kazu.krt.resource_manager.ResourceManager method) CLOntologyParser (class in kazu.ontology_preprocessing.parsers) CLOOntologyParser (class in kazu.ontology_preprocessing.parsers) close_spans() (kazu.steps.ner.tokenized_word_processor.MultilabelSpanFinder method) (kazu.steps.ner.tokenized_word_processor.SimpleSpanFinder method) CombinatorialSynonymGenerator (class in kazu.ontology_preprocessing.synonym_generation) comment (kazu.data.OntologyStringResource attribute) commit() (kazu.krt.resource_discrepancy_editor.utils.ResourceDiscrepancyManger method) CompanyStringNormalizer (class in kazu.utils.string_normalizer) CONFIDENCE_SELECTOR (kazu.krt.components.ResourceEditor attribute) ConfidenceLevelStrategyExecution (class in kazu.steps.linking.post_processing.strategy_runner) ConflictScorer (class in kazu.steps.ner.gliner) convert_docs_to_tasks() (kazu.annotation.label_studio.KazuToLabelStudioConverter class method) convert_multiple_docs_to_tasks() (kazu.annotation.label_studio.KazuToLabelStudioConverter class method) convert_single_doc_to_tasks() (kazu.annotation.label_studio.KazuToLabelStudioConverter class method) convert_tasks_to_docs() (kazu.annotation.label_studio.LSToKazuConversion class method) convert_to_kazu_documents() (kazu.web.server.DocumentCollection method) (kazu.web.server.SingleEntityDocumentConverter method) convert_to_rdflib_ref() (kazu.ontology_preprocessing.parsers.RDFGraphParser static method) copy_resources_to_target() (kazu.utils.build_and_test_model_packs.ModelPackBuilder method) create_char_ngrams() (in module kazu.utils.utils) create_ents() (kazu.annotation.label_studio.LSToKazuConversion method) create_linking_project() (kazu.annotation.label_studio.LabelStudioManager method) create_main_view() (kazu.annotation.label_studio.LabelStudioAnnotationView method) create_mapping() (kazu.steps.linking.post_processing.mapping_strategies.strategies.MappingFactory static method) create_mapping_from_id_set() (kazu.steps.linking.post_processing.mapping_strategies.strategies.MappingFactory static method) create_mapping_from_id_sets() (kazu.steps.linking.post_processing.mapping_strategies.strategies.MappingFactory static method) create_mappings() (kazu.annotation.label_studio.LSToKazuConversion method) create_new_resource_with_updated_synonyms() (in module kazu.krt.utils) create_oxo_dump() (kazu.steps.linking.post_processing.xref_manager.OxoCrossReferenceManager method) create_phrasematchers() (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) create_placeholder_resource() (kazu.krt.components.PlaceholderResource static method) create_section() (kazu.annotation.label_studio.LSToKazuConversion method) create_simple_document() (kazu.data.Document class method) create_wiki_mappings() (in module kazu.utils.download_gilda_contexts) create_word_and_char_ngrams() (in module kazu.steps.linking.post_processing.disambiguation.context_scoring) create_word_ngrams() (in module kazu.utils.utils) create_xref_mappings() (kazu.steps.linking.post_processing.xref_manager.CrossReferenceManager method) CrossReferenceManager (class in kazu.steps.linking.post_processing.xref_manager) CurationError CUSTOM (kazu.data.EquivalentIdAggregationStrategy attribute) (kazu.krt.string_editor.utils.CaseConflictResolutionRequest attribute)

D

DASHES_OR_SPACE_PATTERN (kazu.utils.string_normalizer.GildaUtils attribute) DATA_ORIGIN (in module kazu.ontology_preprocessing.constants) DATAFRAME (kazu.krt.string_editor.components.StringConflictForm attribute) dataframe() (kazu.krt.resource_discrepancy_editor.utils.SynonymDiscrepancy method) DATAFRAME_SELECTION (kazu.krt.string_editor.components.StringConflictForm attribute) default() (kazu.web.ls_web_utils.LSWebUtils static method) default_config (kazu.utils.spacy_pipeline.KazuCustomEnglish attribute) DEFAULT_LABEL (in module kazu.ontology_preprocessing.constants) default_label (kazu.data.Mapping attribute) DEFAULT_RAY_TIMEOUT (in module kazu.utils.build_and_test_model_packs) Defaults (kazu.utils.spacy_pipeline.KazuCustomEnglish attribute) DefaultStringNormalizer (class in kazu.utils.string_normalizer) DefinedElsewhereInDocumentDisambiguationStrategy (class in kazu.steps.linking.post_processing.disambiguation.strategies) delete() (kazu.utils.caching.CacheProtocol method) delete_placeholder() (kazu.krt.components.PlaceholderResource static method) delete_previous() (kazu.ontology_preprocessing.downloads.OntologyDownloader method) (kazu.ontology_preprocessing.downloads.OpenTargetsOntologyDownloader method) delete_project_if_exists() (kazu.annotation.label_studio.LabelStudioManager method) delete_resource() (kazu.krt.resource_manager.ResourceManager method) depluralize() (kazu.utils.string_normalizer.DefaultStringNormalizer static method) (kazu.utils.string_normalizer.GildaUtils static method) DF_XREF_FIELD_NAME (kazu.ontology_preprocessing.parsers.OpenTargetsDiseaseOntologyParser attribute) DictionaryEntityLinkingStep (class in kazu.steps.linking.dictionary) DictionaryIndex (class in kazu.utils.link_index) disambiguate() (kazu.steps.linking.post_processing.disambiguation.strategies.AnnotationLevelDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.DefinedElsewhereInDocumentDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.DisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.GildaTfIdfDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.PreferDefaultLabelMatchDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.PreferNearestEmbeddingToDefaultLabelDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.TfIdfDisambiguationStrategy method) disambiguate_if_required() (kazu.steps.linking.post_processing.mapping_strategies.strategies.MappingStrategy method) disambiguation_confidence (kazu.data.Mapping attribute) disambiguation_entry_to_tfidf_entry() (kazu.steps.linking.entity_class_disambiguation.EntityClassTfIdfScorer static method) DISAMBIGUATION_NOT_REQUIRED (kazu.steps.linking.post_processing.mapping_strategies.strategies.MappingStrategy attribute) disambiguation_strategy (kazu.data.Mapping attribute)

DisambiguationConfidence (class in kazu.data) DisambiguationEntry (class in kazu.steps.linking.entity_class_disambiguation) DisambiguationStrategy (class in kazu.steps.linking.post_processing.disambiguation.strategies) DiseaseStringNormalizer (class in kazu.utils.string_normalizer) dispatch() (kazu.web.req_id_header.AddRequestIdMiddleware method) display_case_sensitivity_and_confidence_selector() (kazu.krt.components.ResourceEditor static method) display_download_config_modifier_form() (kazu.krt.ontology_update_editor.components.OntologyUpdateForm static method) display_download_form() (kazu.krt.ontology_update_editor.components.OntologyUpdateForm static method) display_main_form() (kazu.krt.ontology_update_editor.components.OntologyUpdateForm static method) (kazu.krt.resource_discrepancy_editor.components.ResourceDiscrepancyResolutionForm method) display_name (kazu.web.jwtauth.JWTUser property) display_new_downloader_config_as_yaml() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) display_new_parser_config_as_yaml() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) display_parser_selector() (kazu.krt.components.ParserSelector static method) display_resource_editor() (kazu.krt.components.ResourceEditor static method) divide_chunks() (in module kazu.utils.download_gilda_contexts) doc (kazu.steps.ner.gliner.GliNERBatchItem attribute) Document (class in kazu.data) document_batch_step() (in module kazu.steps.step) document_iterating_step() (in module kazu.steps.step) DocumentCollection (class in kazu.web.server) DocumentCollection.Config (class in kazu.web.server) documents_to_document_section_batch_encodings_map() (in module kazu.utils.utils) documents_to_id_section_map() (in module kazu.utils.utils) download() (kazu.ontology_preprocessing.downloads.ChemblParquetOntologyDownloader method) (kazu.ontology_preprocessing.downloads.OntologyDownloader method) (kazu.ontology_preprocessing.downloads.OpenTargetsOntologyDownloader method) (kazu.ontology_preprocessing.downloads.SimpleOntologyDownloader method) DOWNLOAD_COMPLETED_OR_SKIPPED (kazu.krt.ontology_update_editor.components.OntologyUpdateForm attribute) download_ontology() (kazu.ontology_preprocessing.base.OntologyParser method) download_ontology_with_new_config() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) DROP_FOR_LINKING (kazu.data.OntologyStringBehaviour attribute) DROP_IDS_FROM_PARSER (kazu.data.ParserBehaviour attribute) DropMappingsByConfidenceMappingFilter (class in kazu.steps.other.cleanup) DropMappingsByParserNameRankAction (class in kazu.steps.other.cleanup) DropUnmappedEntityFilter (class in kazu.steps.other.cleanup) dump_ontology_string_resources() (in module kazu.ontology_preprocessing.curation_utils)

E

effective_resources (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetMergeReport attribute) embed_score (kazu.data.LinkingMetrics attribute) end (kazu.data.CharSpan attribute) (kazu.data.Entity attribute) end_span (kazu.steps.ner.gliner.GliNERBatchItem attribute) ensembl_gene_id (kazu.utils.download_gilda_contexts.WikipediaEnsemblMapping attribute) ensembl_protein_ids (kazu.utils.download_gilda_contexts.WikipediaEnsemblMapping attribute) entities (kazu.data.Section attribute) Entity (class in kazu.data) entity_class (kazu.data.Entity attribute) (kazu.steps.linking.entity_class_disambiguation.DisambiguationEntry attribute) (kazu.steps.linking.entity_class_disambiguation.ScoredContext attribute) (kazu.steps.linking.entity_class_disambiguation.TfIdfDisambiguationEntry attribute) entity_classes (kazu.utils.spacy_object_mapper.KazuToSpacyObjectMapper attribute) entity_to_entity_key() (in module kazu.steps.linking.post_processing.strategy_runner) EntityClassDisambiguationStep (class in kazu.steps.linking.entity_class_disambiguation) EntityClassFilter (class in kazu.utils.utils) EntityClassNormalizer (class in kazu.utils.string_normalizer)

EntityClassTfIdfScorer (class in kazu.steps.linking.entity_class_disambiguation) EntityFilterCleanupAction (class in kazu.steps.other.cleanup) EntityLinkingLookupCache (class in kazu.utils.caching) EntityNounModifierStringSimilarityScorer (class in kazu.language.string_similarity_scorers) EntitySubtypeStringSimilarityScorer (class in kazu.language.string_similarity_scorers) EquivalentIdAggregationStrategy (class in kazu.data) EquivalentIdSet (class in kazu.data) exact_match (kazu.data.LinkingMetrics attribute) ExactMatchMappingStrategy (class in kazu.steps.linking.post_processing.mapping_strategies.strategies) example_string() (kazu.krt.resource_discrepancy_editor.utils.SynonymDiscrepancy method) execute_full_pipeline_acceptance_test() (in module kazu.annotation.acceptance_test) execute_hit_post_processing_strategies() (kazu.steps.linking.post_processing.strategy_runner.StrategyRunner method) ExplosionStringMatchingStep (class in kazu.steps.joint_ner_and_linking.explosion) export_from_ls() (kazu.annotation.label_studio.LabelStudioManager method) export_resources_and_final_candidates() (kazu.ontology_preprocessing.curation_utils.OntologyResourceProcessor method) extendString() (kazu.steps.ner.opsin.OpsinStep static method) extract_entity_data_from_spans() (kazu.steps.joint_ner_and_linking.explosion.ExplosionStringMatchingStep method) extract_form_data_from_state() (kazu.krt.components.ResourceEditor static method) extract_open_targets() (in module kazu.utils.download_gilda_contexts)

F

FailedDocsFileHandler (class in kazu.pipeline) FailedDocsHandler (class in kazu.pipeline) FailedDocsLogHandler (class in kazu.pipeline) filter_by_contexts() (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) filter_candidates() (kazu.steps.linking.post_processing.mapping_strategies.strategies.ExactMatchMappingStrategy static method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.MappingStrategy method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.StrongMatchMappingStrategy method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.StrongMatchWithEmbeddingConfirmationStringMatchingStrategy method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.SymbolMatchMappingStrategy class method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.SynNormIsSubStringMappingStrategy method) filter_ents_across_class() (kazu.steps.other.merge_overlapping_ents.MergeOverlappingEntsStep method) filter_matches() (in module kazu.utils.abbreviation_detector) final_conflict_report (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetCompleteReport attribute) finalise() (kazu.steps.ner.gliner.ConflictScorer method) find_abbreviation() (in module kazu.utils.abbreviation_detector) find_case_conflicts() (kazu.ontology_preprocessing.curation_utils.OntologyStringConflictAnalyser static method) find_document_from_entity() (in module kazu.utils.utils) find_kb() (kazu.ontology_preprocessing.base.OntologyParser method) (kazu.ontology_preprocessing.parsers.CellosaurusOntologyParser method) (kazu.ontology_preprocessing.parsers.ChemblOntologyParser method) (kazu.ontology_preprocessing.parsers.ChemblParquetOntologyParser method) (kazu.ontology_preprocessing.parsers.CLOntologyParser method) (kazu.ontology_preprocessing.parsers.CLOOntologyParser method) (kazu.ontology_preprocessing.parsers.HGNCGeneFamilyParser method) (kazu.ontology_preprocessing.parsers.HGNCGeneOntologyParser method) (kazu.ontology_preprocessing.parsers.HPOntologyParser method) (kazu.ontology_preprocessing.parsers.MeddraOntologyParser method) (kazu.ontology_preprocessing.parsers.MondoOntologyParser method) (kazu.ontology_preprocessing.parsers.OpenTargetsDiseaseOntologyParser method) (kazu.ontology_preprocessing.parsers.OpenTargetsMoleculeOntologyParser method) (kazu.ontology_preprocessing.parsers.OpenTargetsTargetOntologyParser method) (kazu.ontology_preprocessing.parsers.RDFGraphParser method) (kazu.ontology_preprocessing.parsers.StatoParser method) (kazu.ontology_preprocessing.parsers.TabularOntologyParser method) (kazu.ontology_preprocessing.parsers.UberonOntologyParser method)

fn (kazu.annotation.acceptance_test.AggregatedAccuracyResult attribute) fn_counter (kazu.annotation.acceptance_test.AggregatedAccuracyResult attribute) fn_info (kazu.annotation.acceptance_test.AggregatedAccuracyResult property) fn_items_to_tasks (kazu.annotation.acceptance_test.AggregatedAccuracyResult attribute) FORM_PICKER (kazu.krt.string_editor.components.StringConflictForm attribute) fp (kazu.annotation.acceptance_test.AggregatedAccuracyResult attribute) fp_counter (kazu.annotation.acceptance_test.AggregatedAccuracyResult attribute) fp_info (kazu.annotation.acceptance_test.AggregatedAccuracyResult property) fp_items_to_tasks (kazu.annotation.acceptance_test.AggregatedAccuracyResult attribute) frame_to_tok_word() (kazu.steps.ner.hf_token_classification.TransformersModelForTokenClassificationNerStep method) from_dict() (kazu.data.Document static method) (kazu.data.Entity static method) (kazu.data.GlobalParserActions class method) (kazu.data.LinkingCandidate static method) (kazu.data.LinkingMetrics static method) (kazu.data.Mapping static method) (kazu.data.OntologyStringResource class method) (kazu.data.ParserAction class method) (kazu.data.Section static method) from_disk() (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) from_json() (kazu.data.Document static method) (kazu.data.OntologyStringResource static method) from_named_section_texts() (kazu.data.Document class method) from_spans() (kazu.data.Entity class method) from_spans_to_sentence_disambiguator() (kazu.steps.linking.entity_class_disambiguation.EntityClassTfIdfScorer static method)

G

gene_name_suffixes (kazu.utils.string_normalizer.GeneStringNormalizer attribute) gene_token_classifier() (kazu.utils.string_normalizer.GeneStringNormalizer static method) GeneOntologyParser (class in kazu.ontology_preprocessing.parsers) GeneStringNormalizer (class in kazu.utils.string_normalizer) get() (kazu.database.in_memory_db.SynonymDatabase method) (kazu.utils.caching.CacheProtocol method) get_all() (kazu.database.in_memory_db.MetadataDatabase method) (kazu.database.in_memory_db.SynonymDatabase method) get_all_tasks() (kazu.annotation.label_studio.LabelStudioManager method) get_attempt_autofix_key() (kazu.krt.resource_discrepancy_editor.components.ResourceDiscrepancyResolutionForm static method) get_attempt_download_key() (kazu.krt.ontology_update_editor.components.OntologyUpdateForm static method) get_bio_and_class_labels() (kazu.steps.ner.tokenized_word_processor.SimpleSpanFinder method) get_biomart_gene_to_protein() (in module kazu.utils.download_gilda_contexts) get_by_idx() (kazu.database.in_memory_db.MetadataDatabase method) get_class_labels() (kazu.steps.ner.tokenized_word_processor.MultilabelSpanFinder method) get_context() (kazu.utils.download_gilda_contexts.WikipediaEnsemblMapping method) get_dataloader() (kazu.steps.ner.hf_token_classification.TransformersModelForTokenClassificationNerStep method) get_download_completed_or_skipped() (kazu.krt.ontology_update_editor.components.OntologyUpdateForm static method) get_downloader_args_and_types() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) get_downloader_args_and_vals() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) get_embedding_dataloader_from_strings() (kazu.utils.sapbert.SapBertHelper method) get_embeddings() (kazu.utils.sapbert.SapBertHelper static method) get_embeddings_for_strings() (kazu.utils.sapbert.SapBertHelper method) get_embeddings_from_dataloader() (kazu.utils.sapbert.SapBertHelper method) get_entities() (kazu.data.Document method) get_id_log_prefix_if_available() (in module kazu.web.server) get_list_of_batch_encoding_frames_for_section() (kazu.steps.ner.hf_token_classification.TransformersModelForTokenClassificationNerStep static method) get_manager() (in module kazu.krt.string_editor.components) get_match_entity_class_hash() (in module kazu.utils.utils) get_model() (kazu.utils.spacy_pipeline.SpacyPipelines static method) get_multilabel_activations() (kazu.steps.ner.hf_token_classification.TransformersModelForTokenClassificationNerStep method) get_or_build_upgrade_report() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) get_placeholder_resource() (kazu.krt.components.PlaceholderResource static method)

get_prediction_from_batch() (kazu.utils.sapbert.SapBertHelper static method) get_request_id() (in module kazu.web.server) get_resource_manager() (in module kazu.krt.utils) get_resource_merge_manager() (in module kazu.krt.resource_discrepancy_editor.components) get_resource_merge_manager_for_parser() (in module kazu.krt.resource_discrepancy_editor.components) get_retry() (in module kazu.utils.download_gilda_contexts) get_selected_parser_name() (kazu.krt.components.ParserSelector static method) get_single_label_activations() (kazu.steps.ner.hf_token_classification.TransformersModelForTokenClassificationNerStep method) get_sparql_df() (in module kazu.utils.download_gilda_contexts) get_strategies_for_entity_class() (kazu.steps.linking.post_processing.strategy_runner.ConfidenceLevelStrategyExecution method) get_syns_for_id() (kazu.database.in_memory_db.SynonymDatabase method) get_tasks() (kazu.annotation.label_studio.LabelStudioManager method) get_token_from_header() (kazu.web.jwtauth.JWTAuthenticationBackend class method) get_updates_saved() (kazu.krt.ontology_update_editor.components.OntologyUpdateForm static method) get_updates_saved_key() (kazu.krt.ontology_update_editor.components.OntologyUpdateForm static method) get_upgrade_manager() (in module kazu.krt.ontology_update_editor.components) get_wikipedia_contents_from_urls() (in module kazu.utils.download_gilda_contexts) get_wikipedia_url_from_wikidata_id() (in module kazu.utils.download_gilda_contexts) getDOM() (kazu.annotation.label_studio.LabelStudioAnnotationView static method) GildaTfIdfDisambiguationStrategy (class in kazu.steps.linking.post_processing.disambiguation.strategies) GildaTfIdfScorer (class in kazu.steps.linking.post_processing.disambiguation.context_scoring) GildaUtils (class in kazu.utils.string_normalizer) GliNERBatchItem (class in kazu.steps.ner.gliner) GLiNERStep (class in kazu.steps.ner.gliner) GlobalParserActions (class in kazu.data) greek_letter (kazu.ontology_preprocessing.synonym_generation.GreekSymbolSubstitution attribute) greek_subs (kazu.utils.string_normalizer.DefaultStringNormalizer attribute) greek_subs_upper (kazu.utils.string_normalizer.DefaultStringNormalizer attribute) GREEK_VARIANT_PREFIX_SUFFIX (kazu.ontology_preprocessing.synonym_generation.StringReplacement attribute) GreekSymbolSubstitution (class in kazu.ontology_preprocessing.synonym_generation) group_entities_by_location() (kazu.steps.other.merge_overlapping_ents.MergeOverlappingEntsStep method) group_entities_by_symbolism() (kazu.steps.linking.post_processing.strategy_runner.StrategyRunner static method) group_mappings_by_source() (kazu.annotation.acceptance_test.SectionScorer static method)

H

handle_lower_case_prefixes() (kazu.utils.string_normalizer.DefaultStringNormalizer static method) has_own_config (kazu.utils.build_and_test_model_packs.BuildConfiguration attribute) headers (kazu.steps.linking.post_processing.xref_manager.OxoCrossReferenceManager attribute) HFDataset (class in kazu.steps.ner.hf_token_classification) HFSapbertInferenceDataset (class in kazu.utils.sapbert) HGNCGeneFamilyParser (class in kazu.ontology_preprocessing.parsers)

HGNCGeneOntologyParser (class in kazu.ontology_preprocessing.parsers) HIGHLY_LIKELY (kazu.data.DisambiguationConfidence attribute) (kazu.data.MentionConfidence attribute) (kazu.data.StringMatchConfidence attribute) HIT (kazu.steps.linking.rules_based_disambiguation.MatcherResult attribute) HPOntologyParser (class in kazu.ontology_preprocessing.parsers) human_conflict_report (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetCompleteReport attribute)

I

id2labels_from_label_list() (kazu.steps.ner.tokenized_word_processor.TokenizedWordProcessor static method) ID_SET_MODIFIED (kazu.ontology_preprocessing.curation_utils.LinkingCandidateModificationResult attribute) ids (kazu.data.EquivalentIdSet property) ids_and_source (kazu.data.EquivalentIdSet attribute) IDX (in module kazu.ontology_preprocessing.constants) idx (kazu.data.Document attribute) (kazu.data.Mapping attribute) IGNORE (kazu.data.MentionConfidence attribute) infixes (kazu.utils.spacy_pipeline.KazuCustomEnglishDefaults attribute) initial_lowercase_then_upper_to_case_sensitive() (in module kazu.ontology_preprocessing.autocuration) instances (kazu.ontology_preprocessing.parsers.GeneOntologyParser attribute) instances_in_dbs (kazu.ontology_preprocessing.parsers.GeneOntologyParser attribute) instantiate_parser_with_new_config() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) intermediate_linking_candidates (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetCompleteReport attribute) is_ambiguous (kazu.data.LinkingCandidate property) is_authenticated (kazu.web.jwtauth.JWTUser property)

is_completely_overlapped() (kazu.data.CharSpan method) (kazu.data.Entity method) is_partially_overlapped() (kazu.data.CharSpan method) (kazu.data.Entity method) is_symbol_like() (kazu.utils.string_normalizer.AnatomyStringNormalizer static method) (kazu.utils.string_normalizer.CompanyStringNormalizer static method) (kazu.utils.string_normalizer.DefaultStringNormalizer static method) (kazu.utils.string_normalizer.DiseaseStringNormalizer static method) (kazu.utils.string_normalizer.EntityClassNormalizer static method) (kazu.utils.string_normalizer.GeneStringNormalizer static method) is_symbolic (kazu.data.LinkingCandidate attribute) is_upper_case_word_to_case_insensitive() (in module kazu.ontology_preprocessing.autocuration) is_valid_iri() (kazu.ontology_preprocessing.parsers.MondoOntologyParser method) (kazu.ontology_preprocessing.parsers.RDFGraphParser method) IsCommmonWord (class in kazu.ontology_preprocessing.autocuration) Item (class in kazu.utils.grouping)

J

json_dict_to_parser_records() (kazu.ontology_preprocessing.parsers.JsonLinesOntologyParser method) (kazu.ontology_preprocessing.parsers.OpenTargetsDiseaseOntologyParser method) (kazu.ontology_preprocessing.parsers.OpenTargetsMoleculeOntologyParser method) (kazu.ontology_preprocessing.parsers.OpenTargetsTargetOntologyParser method)

JsonEncodable (in module kazu.data) JsonLinesOntologyParser (class in kazu.ontology_preprocessing.parsers) JWTAuthenticationBackend (class in kazu.web.jwtauth) JWTUser (class in kazu.web.jwtauth)

K

kazu module kazu.annotation module kazu.annotation.acceptance_test module kazu.annotation.label_studio module kazu.data module kazu.database module kazu.database.in_memory_db module kazu.krt module kazu.krt.components module kazu.krt.ontology_update_editor module kazu.krt.ontology_update_editor.components module kazu.krt.ontology_update_editor.utils module kazu.krt.resource_discrepancy_editor module kazu.krt.resource_discrepancy_editor.components module kazu.krt.resource_discrepancy_editor.utils module kazu.krt.resource_manager module kazu.krt.string_editor module kazu.krt.string_editor.components module kazu.krt.string_editor.utils module kazu.krt.utils module kazu.language module kazu.language.language_phenomena module kazu.language.string_similarity_scorers module kazu.ontology_matching module kazu.ontology_matching.assemble_pipeline module kazu.ontology_matching.ontology_matcher module kazu.ontology_preprocessing module kazu.ontology_preprocessing.autocuration module kazu.ontology_preprocessing.base module kazu.ontology_preprocessing.constants module kazu.ontology_preprocessing.curation_utils module kazu.ontology_preprocessing.downloads module kazu.ontology_preprocessing.ontology_upgrade_report module kazu.ontology_preprocessing.parsers module kazu.ontology_preprocessing.synonym_generation module kazu.pipeline module kazu.steps module kazu.steps.document_post_processing module kazu.steps.document_post_processing.abbreviation_finder module kazu.steps.joint_ner_and_linking module kazu.steps.joint_ner_and_linking.explosion module kazu.steps.joint_ner_and_linking.memory_efficient_string_matching module kazu.steps.linking module kazu.steps.linking.dictionary module kazu.steps.linking.entity_class_disambiguation module kazu.steps.linking.post_processing module kazu.steps.linking.post_processing.disambiguation module kazu.steps.linking.post_processing.disambiguation.context_scoring module

kazu.steps.linking.post_processing.disambiguation.strategies module kazu.steps.linking.post_processing.mapping_step module kazu.steps.linking.post_processing.mapping_strategies module kazu.steps.linking.post_processing.mapping_strategies.strategies module kazu.steps.linking.post_processing.strategy_runner module kazu.steps.linking.post_processing.xref_manager module kazu.steps.linking.rules_based_disambiguation module kazu.steps.ner module kazu.steps.ner.entity_post_processing module kazu.steps.ner.gliner module kazu.steps.ner.hf_token_classification module kazu.steps.ner.llm_ner module kazu.steps.ner.opsin module kazu.steps.ner.seth module kazu.steps.ner.spacy_ner module kazu.steps.ner.tokenized_word_processor module kazu.steps.other module kazu.steps.other.cleanup module kazu.steps.other.merge_overlapping_ents module kazu.steps.other.stanza module kazu.steps.step module kazu.utils module kazu.utils.abbreviation_detector module kazu.utils.build_and_test_model_packs module kazu.utils.caching module kazu.utils.constants module kazu.utils.download_gilda_contexts module kazu.utils.grouping module kazu.utils.link_index module kazu.utils.sapbert module kazu.utils.spacy_object_mapper module kazu.utils.spacy_pipeline module kazu.utils.stanza_pipeline module kazu.utils.string_normalizer module kazu.utils.utils module kazu.web module kazu.web.jwtauth module kazu.web.ls_web_utils module kazu.web.req_id_header module kazu.web.routes module kazu.web.server module kazu_disk_cache (in module kazu.utils.caching) kazu_doc_to_ls() (kazu.web.ls_web_utils.LSWebUtils method) kazu_json_converter (in module kazu.data) KAZU_WEBSERVER_SPINUP_TIMEOUT (in module kazu.web.server) KazuAbbreviationDetector (class in kazu.utils.abbreviation_detector) KazuConfigurationError KazuCustomEnglish (class in kazu.utils.spacy_pipeline) KazuCustomEnglishDefaults (class in kazu.utils.spacy_pipeline) KazuToLabelStudioConverter (class in kazu.annotation.label_studio) KazuToSpacyObjectMapper (class in kazu.utils.spacy_object_mapper) Key (class in kazu.utils.grouping) known_disease_short_nouns (kazu.utils.string_normalizer.DiseaseStringNormalizer attribute)

L

labels (kazu.ontology_matching.ontology_matcher.OntologyMatcher property) (kazu.ontology_matching.ontology_matcher.OntologyMatcherConfig attribute) LabelStudioAnnotationView (class in kazu.annotation.label_studio) LabelStudioManager (class in kazu.annotation.label_studio) lang (kazu.utils.spacy_pipeline.KazuCustomEnglish attribute) levels_to_ignore (kazu.ontology_preprocessing.parsers.ATCDrugClassificationParser attribute) LikelyAcronym (class in kazu.ontology_preprocessing.autocuration) LINKING_CANDIDATE_ADDED (kazu.ontology_preprocessing.curation_utils.LinkingCandidateModificationResult attribute) LINKING_CANDIDATE_DROPPED (kazu.ontology_preprocessing.curation_utils.LinkingCandidateModificationResult attribute) linking_candidates (kazu.data.Entity attribute) linking_candidates_to_ontology_string_resources() (in module kazu.utils.utils) LinkingCandidate (class in kazu.data) LinkingCandidateModificationResult (class in kazu.ontology_preprocessing.curation_utils) LinkingCandidateRemovalCleanupAction (class in kazu.steps.other.cleanup) LinkingMetrics (class in kazu.data) LLMModel (class in kazu.steps.ner.llm_ner)

LLMNERStep (class in kazu.steps.ner.llm_ner) load_build_configuration() (kazu.utils.build_and_test_model_packs.ModelPackBuilder method) load_cache_state_aware_pipeline() (kazu.krt.resource_manager.ResourceManager method) load_config() (in module kazu.krt) load_contiguous_entity() (kazu.data.Entity class method) load_global_actions() (in module kazu.ontology_preprocessing.curation_utils) load_matcher() (kazu.utils.abbreviation_detector.KazuAbbreviationDetector method) load_ontology_string_resources() (in module kazu.ontology_preprocessing.curation_utils) load_parsers() (in module kazu.krt.utils) load_steps_and_log_memory_usage() (in module kazu.pipeline) loaded_parsers (kazu.database.in_memory_db.MetadataDatabase property) log_request_to_path_with_prefix() (in module kazu.web.server) longest_mapping_strategy_list_size (kazu.steps.linking.post_processing.strategy_runner.ConfidenceLevelStrategyExecution property) lower_greek_letter (kazu.ontology_preprocessing.synonym_generation.GreekSymbolSubstitution attribute) LSToKazuConversion (class in kazu.annotation.label_studio) LSWebUtils (class in kazu.web.ls_web_utils)

M

main() (in module kazu.ontology_matching.assemble_pipeline) MajorityVoteScorer (class in kazu.steps.ner.gliner) make_span_finder() (kazu.steps.ner.tokenized_word_processor.TokenizedWordProcessor method) Mapping (class in kazu.data) MAPPING_TYPE (in module kazu.ontology_preprocessing.constants) mapping_types (kazu.data.LinkingCandidate attribute) MappingFactory (class in kazu.steps.linking.post_processing.mapping_strategies.strategies) MappingFilterCleanupAction (class in kazu.steps.other.cleanup) mappings (kazu.data.Entity attribute) MappingStep (class in kazu.steps.linking.post_processing.mapping_step) MappingStrategy (class in kazu.steps.linking.post_processing.mapping_strategies.strategies) match (kazu.data.Entity attribute) match_id_sep (kazu.ontology_matching.ontology_matcher.OntologyMatcher property) (kazu.ontology_matching.ontology_matcher.OntologyMatcherConfig attribute) match_norm (kazu.data.Entity attribute) match_symbols() (kazu.steps.linking.post_processing.mapping_strategies.strategies.SymbolMatchMappingStrategy static method) MatcherResult (class in kazu.steps.linking.rules_based_disambiguation) MaxLength (class in kazu.ontology_preprocessing.autocuration) MaxScoreScorer (class in kazu.steps.ner.gliner) MeddraOntologyParser (class in kazu.ontology_preprocessing.parsers) Memoization (class in kazu.utils.caching) memoize() (kazu.utils.caching.CacheProtocol method) MemoryEfficientStringMatchingStep (class in kazu.steps.joint_ner_and_linking.memory_efficient_string_matching) mention_confidence (kazu.data.Entity attribute) (kazu.data.Synonym attribute) MentionConfidence (class in kazu.data) merge_human_and_auto_resources() (kazu.ontology_preprocessing.curation_utils.OntologyStringConflictAnalyser method) merge_report (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetCompleteReport attribute) MERGED_AS_NON_SYMBOLIC (kazu.data.EquivalentIdAggregationStrategy attribute) merged_resources (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetConflictReport attribute) MergeOverlappingEntsStep (class in kazu.steps.other.merge_overlapping_ents) metadata (kazu.data.Document attribute) (kazu.data.Entity attribute) (kazu.data.Mapping attribute) (kazu.data.Section attribute) MetadataDatabase (class in kazu.database.in_memory_db) minimum_metadata_column_names (kazu.ontology_preprocessing.base.OntologyParser attribute) MinLength (class in kazu.ontology_preprocessing.autocuration) MISS (kazu.steps.linking.rules_based_disambiguation.MatcherResult attribute) ModelPackBuilder (class in kazu.utils.build_and_test_model_packs) ModelPackBuildError MODIFIED_BY_CURATION (kazu.data.EquivalentIdAggregationStrategy attribute) modify_downloader_cfg_with_new_args() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) modify_parser_cfg_with_new_args() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) module kazu kazu.annotation kazu.annotation.acceptance_test kazu.annotation.label_studio kazu.data kazu.database kazu.database.in_memory_db kazu.krt kazu.krt.components kazu.krt.ontology_update_editor kazu.krt.ontology_update_editor.components kazu.krt.ontology_update_editor.utils kazu.krt.resource_discrepancy_editor kazu.krt.resource_discrepancy_editor.components kazu.krt.resource_discrepancy_editor.utils kazu.krt.resource_manager kazu.krt.string_editor kazu.krt.string_editor.components kazu.krt.string_editor.utils kazu.krt.utils kazu.language kazu.language.language_phenomena kazu.language.string_similarity_scorers kazu.ontology_matching kazu.ontology_matching.assemble_pipeline kazu.ontology_matching.ontology_matcher kazu.ontology_preprocessing kazu.ontology_preprocessing.autocuration kazu.ontology_preprocessing.base kazu.ontology_preprocessing.constants kazu.ontology_preprocessing.curation_utils kazu.ontology_preprocessing.downloads kazu.ontology_preprocessing.ontology_upgrade_report kazu.ontology_preprocessing.parsers kazu.ontology_preprocessing.synonym_generation kazu.pipeline kazu.steps kazu.steps.document_post_processing kazu.steps.document_post_processing.abbreviation_finder kazu.steps.joint_ner_and_linking kazu.steps.joint_ner_and_linking.explosion kazu.steps.joint_ner_and_linking.memory_efficient_string_matching kazu.steps.linking kazu.steps.linking.dictionary kazu.steps.linking.entity_class_disambiguation kazu.steps.linking.post_processing kazu.steps.linking.post_processing.disambiguation kazu.steps.linking.post_processing.disambiguation.context_scoring kazu.steps.linking.post_processing.disambiguation.strategies kazu.steps.linking.post_processing.mapping_step kazu.steps.linking.post_processing.mapping_strategies kazu.steps.linking.post_processing.mapping_strategies.strategies kazu.steps.linking.post_processing.strategy_runner kazu.steps.linking.post_processing.xref_manager kazu.steps.linking.rules_based_disambiguation kazu.steps.ner kazu.steps.ner.entity_post_processing kazu.steps.ner.gliner kazu.steps.ner.hf_token_classification kazu.steps.ner.llm_ner kazu.steps.ner.opsin kazu.steps.ner.seth kazu.steps.ner.spacy_ner kazu.steps.ner.tokenized_word_processor kazu.steps.other kazu.steps.other.cleanup kazu.steps.other.merge_overlapping_ents kazu.steps.other.stanza kazu.steps.step kazu.utils kazu.utils.abbreviation_detector kazu.utils.build_and_test_model_packs kazu.utils.caching kazu.utils.constants kazu.utils.download_gilda_contexts kazu.utils.grouping kazu.utils.link_index kazu.utils.sapbert kazu.utils.spacy_object_mapper kazu.utils.spacy_pipeline kazu.utils.stanza_pipeline kazu.utils.string_normalizer kazu.utils.utils kazu.web kazu.web.jwtauth kazu.web.ls_web_utils kazu.web.req_id_header kazu.web.routes kazu.web.server

MolecularFunctionGeneOntologyParser (class in kazu.ontology_preprocessing.parsers) MondoOntologyParser (class in kazu.ontology_preprocessing.parsers) MultilabelSpanFinder (class in kazu.steps.ner.tokenized_word_processor) multiword() (in module kazu.ontology_preprocessing.autocuration)

N

name (kazu.data.Section attribute) name_to_parser_cfg() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager static method) namespace (kazu.data.Entity attribute) namespace() (kazu.steps.step.Step class method) new_resources_after_upgrade (kazu.ontology_preprocessing.ontology_upgrade_report.OntologyUpgradeReport property) NgramHyphenation (class in kazu.ontology_preprocessing.synonym_generation) NO_ACTION (kazu.ontology_preprocessing.curation_utils.LinkingCandidateModificationResult attribute) NO_STRATEGY (kazu.data.EquivalentIdAggregationStrategy attribute) NonContiguousEntitySplitter (class in kazu.steps.ner.entity_post_processing) NONE (kazu.ontology_preprocessing.curation_utils.AutofixStrategy attribute) normalisation_conflicts (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetConflictReport attribute) normalize() (kazu.utils.string_normalizer.StringNormalizer static method) normalize_noun_phrase() (kazu.utils.string_normalizer.AnatomyStringNormalizer static method) (kazu.utils.string_normalizer.CompanyStringNormalizer static method) (kazu.utils.string_normalizer.DefaultStringNormalizer static method) (kazu.utils.string_normalizer.DiseaseStringNormalizer static method) (kazu.utils.string_normalizer.EntityClassNormalizer static method) (kazu.utils.string_normalizer.GeneStringNormalizer static method)

normalize_symbol() (kazu.utils.string_normalizer.AnatomyStringNormalizer static method) (kazu.utils.string_normalizer.CompanyStringNormalizer static method) (kazu.utils.string_normalizer.DefaultStringNormalizer static method) (kazu.utils.string_normalizer.DiseaseStringNormalizer static method) (kazu.utils.string_normalizer.EntityClassNormalizer static method) (kazu.utils.string_normalizer.GeneStringNormalizer static method) normalizers (kazu.utils.string_normalizer.StringNormalizer attribute) NOT_CONFIGURED (kazu.steps.linking.rules_based_disambiguation.MatcherResult attribute) NOUN_PLACEHOLDER (kazu.ontology_preprocessing.synonym_generation.VerbPhraseVariantGenerator attribute) novel_df() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) nr_lowercase_rules (kazu.ontology_matching.ontology_matcher.OntologyMatcher property) nr_strict_rules (kazu.ontology_matching.ontology_matcher.OntologyMatcher property) number_finder (kazu.language.string_similarity_scorers.NumberMatchStringSimilarityScorer attribute) number_split_pattern (kazu.utils.string_normalizer.DefaultStringNormalizer attribute) NumberMatchStringSimilarityScorer (class in kazu.language.string_similarity_scorers) numeric_class_phrases (kazu.language.string_similarity_scorers.EntitySubtypeStringSimilarityScorer attribute)

O

OBOOntologyDownloader (class in kazu.ontology_preprocessing.downloads) obsolete_df() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) obsolete_resources (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetMergeReport attribute) obsolete_resources_after_upgrade (kazu.ontology_preprocessing.ontology_upgrade_report.OntologyUpgradeReport property) on_auth_error() (in module kazu.web.jwtauth) OntologyDownloader (class in kazu.ontology_preprocessing.downloads) OntologyMatcher (class in kazu.ontology_matching.ontology_matcher) OntologyMatcherConfig (class in kazu.ontology_matching.ontology_matcher) OntologyParser (class in kazu.ontology_preprocessing.base) OntologyResourceProcessor (class in kazu.ontology_preprocessing.curation_utils) OntologyResourceSetCompleteReport (class in kazu.ontology_preprocessing.curation_utils) OntologyResourceSetConflictReport (class in kazu.ontology_preprocessing.curation_utils) OntologyResourceSetMergeReport (class in kazu.ontology_preprocessing.curation_utils) OntologyStringBehaviour (class in kazu.data) OntologyStringConflictAnalyser (class in kazu.ontology_preprocessing.curation_utils) OntologyStringResource (class in kazu.data)

OntologyUpdateForm (class in kazu.krt.ontology_update_editor.components) OntologyUpdateManager (class in kazu.krt.ontology_update_editor.utils) OntologyUpgradeReport (class in kazu.ontology_preprocessing.ontology_upgrade_report) openapi_no_auth() (in module kazu.web.server) OpenTargetsDiseaseOntologyParser (class in kazu.ontology_preprocessing.parsers) OpenTargetsMoleculeOntologyParser (class in kazu.ontology_preprocessing.parsers) OpenTargetsOntologyDownloader (class in kazu.ontology_preprocessing.downloads) OpenTargetsTargetOntologyParser (class in kazu.ontology_preprocessing.parsers) OpsinStep (class in kazu.steps.ner.opsin) OPTIMISTIC (kazu.krt.string_editor.utils.CaseConflictResolutionRequest attribute) (kazu.ontology_preprocessing.curation_utils.AutofixStrategy attribute) original_synonyms (kazu.data.OntologyStringResource attribute) OT_PREFIX (kazu.ontology_preprocessing.downloads.OpenTargetsOntologyDownloader attribute) other_subs (kazu.utils.string_normalizer.DefaultStringNormalizer attribute) OwlOntologyDownloader (class in kazu.ontology_preprocessing.downloads) oxo_url (kazu.steps.linking.post_processing.xref_manager.OxoCrossReferenceManager attribute) OxoCrossReferenceManager (class in kazu.steps.linking.post_processing.xref_manager)

P

parse_oxo_dump() (kazu.steps.linking.post_processing.xref_manager.OxoCrossReferenceManager method) parse_result() (kazu.steps.ner.llm_ner.LLMModel static method) parse_to_dataframe() (kazu.ontology_preprocessing.base.OntologyParser method) (kazu.ontology_preprocessing.parsers.ATCDrugClassificationParser method) (kazu.ontology_preprocessing.parsers.CellosaurusOntologyParser method) (kazu.ontology_preprocessing.parsers.ChemblOntologyParser method) (kazu.ontology_preprocessing.parsers.ChemblParquetOntologyParser method) (kazu.ontology_preprocessing.parsers.GeneOntologyParser method) (kazu.ontology_preprocessing.parsers.HGNCGeneFamilyParser method) (kazu.ontology_preprocessing.parsers.HGNCGeneOntologyParser method) (kazu.ontology_preprocessing.parsers.JsonLinesOntologyParser method) (kazu.ontology_preprocessing.parsers.MeddraOntologyParser method) (kazu.ontology_preprocessing.parsers.MondoOntologyParser method) (kazu.ontology_preprocessing.parsers.RDFGraphParser method) (kazu.ontology_preprocessing.parsers.TabularOntologyParser method) parse_to_graph() (kazu.ontology_preprocessing.parsers.GeneOntologyParser static method) (kazu.ontology_preprocessing.parsers.RDFGraphParser static method) parser_behaviour() (kazu.data.GlobalParserActions method) parser_count() (kazu.krt.resource_manager.ResourceManager method) parser_name (kazu.data.LinkingCandidate attribute) (kazu.data.Mapping attribute) parser_name_to_entity_type (kazu.ontology_matching.ontology_matcher.OntologyMatcher property) (kazu.ontology_matching.ontology_matcher.OntologyMatcherConfig attribute) PARSER_SELECTOR (kazu.krt.components.ParserSelector attribute) parser_to_target_id_mappings (kazu.data.ParserAction attribute) ParserAction (class in kazu.data) ParserBehaviour (class in kazu.data) ParserDependentStep (class in kazu.steps.step) ParserSelector (class in kazu.krt.components) parseString() (kazu.steps.ner.opsin.OpsinStep method) PESSIMISTIC (kazu.krt.string_editor.utils.CaseConflictResolutionRequest attribute) (kazu.ontology_preprocessing.curation_utils.AutofixStrategy attribute)

Pipeline (class in kazu.pipeline) PipelineValueError PLACEHOLDER_RESOURCE (kazu.krt.components.PlaceholderResource attribute) PlaceholderResource (class in kazu.krt.components) PLURAL_CAPS_S_PATTERN (kazu.utils.string_normalizer.GildaUtils attribute) populate_databases() (kazu.ontology_preprocessing.base.OntologyParser method) (kazu.ontology_preprocessing.parsers.GeneOntologyParser method) populate_metadata_db_and_resolve_string_resources() (kazu.ontology_preprocessing.base.OntologyParser method) POSSIBLE (kazu.data.DisambiguationConfidence attribute) (kazu.data.MentionConfidence attribute) (kazu.data.StringMatchConfidence attribute) precision (kazu.annotation.acceptance_test.AggregatedAccuracyResult property) PreferDefaultLabelMatchDisambiguationStrategy (class in kazu.steps.linking.post_processing.disambiguation.strategies) PreferNearestEmbeddingToDefaultLabelDisambiguationStrategy (class in kazu.steps.linking.post_processing.disambiguation.strategies) prefilter_docs() (kazu.pipeline.Pipeline method) prepare() (kazu.steps.linking.post_processing.disambiguation.strategies.AnnotationLevelDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.DefinedElsewhereInDocumentDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.DisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.GildaTfIdfDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.PreferDefaultLabelMatchDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.PreferNearestEmbeddingToDefaultLabelDisambiguationStrategy method) (kazu.steps.linking.post_processing.disambiguation.strategies.TfIdfDisambiguationStrategy method) (kazu.steps.linking.post_processing.mapping_strategies.strategies.MappingStrategy method) PROBABLE (kazu.data.DisambiguationConfidence attribute) (kazu.data.MentionConfidence attribute) (kazu.data.StringMatchConfidence attribute) process_batch() (kazu.utils.spacy_pipeline.SpacyPipelines method) process_next_word() (kazu.steps.ner.tokenized_word_processor.MultilabelSpanFinder method) (kazu.steps.ner.tokenized_word_processor.SimpleSpanFinder method) process_single() (kazu.utils.spacy_pipeline.SpacyPipelines method) profile() (kazu.pipeline.Pipeline method) project_id (kazu.annotation.label_studio.LabelStudioManager property)

R

RapidFuzzStringSimilarityScorer (class in kazu.language.string_similarity_scorers) raw_synonyms (kazu.data.LinkingCandidate attribute) RDFGraphParser (class in kazu.ontology_preprocessing.parsers) re_subs (kazu.utils.string_normalizer.DefaultStringNormalizer attribute) re_subs_2 (kazu.utils.string_normalizer.DefaultStringNormalizer attribute) read() (kazu.ontology_preprocessing.parsers.JsonLinesOntologyParser method) recall (kazu.annotation.acceptance_test.AggregatedAccuracyResult property) relevant_text (kazu.steps.linking.entity_class_disambiguation.DisambiguationEntry attribute) reload_at (kazu.utils.spacy_pipeline.SpacyPipelines attribute) reload_model() (kazu.utils.spacy_pipeline.SpacyPipelines method) remove_non_alphanum() (kazu.utils.string_normalizer.DefaultStringNormalizer static method) remove_trailing_s_if_otherwise_capitalised() (kazu.utils.string_normalizer.GeneStringNormalizer static method) replace_greek() (kazu.utils.string_normalizer.DefaultStringNormalizer static method) replace_substrings() (kazu.utils.string_normalizer.DefaultStringNormalizer static method) report_tested_dependencies() (kazu.utils.build_and_test_model_packs.ModelPackBuilder method) request_with_retry() (in module kazu.steps.linking.post_processing.xref_manager) requires_base_config (kazu.utils.build_and_test_model_packs.BuildConfiguration attribute) requires_resources (kazu.utils.build_and_test_model_packs.BuildConfiguration attribute) reset() (in module kazu.krt.resource_discrepancy_editor.components) (in module kazu.krt.string_editor.components) (kazu.pipeline.Pipeline method) (kazu.steps.linking.post_processing.strategy_runner.ConfidenceLevelStrategyExecution method)

resolve_conflicts_form() (kazu.krt.string_editor.components.StringConflictForm static method) RESOLVED_BY_SIMILARITY (kazu.data.EquivalentIdAggregationStrategy attribute) RESOLVED_BY_XREF (kazu.data.EquivalentIdAggregationStrategy attribute) resource_sort_key() (kazu.ontology_preprocessing.curation_utils.OntologyResourceProcessor class method) resource_to_df() (in module kazu.krt.utils) ResourceConflict (class in kazu.krt.string_editor.utils) ResourceConflictManager (class in kazu.krt.string_editor.utils) ResourceDiscrepancyManger (class in kazu.krt.resource_discrepancy_editor.utils) ResourceDiscrepancyResolutionForm (class in kazu.krt.resource_discrepancy_editor.components) ResourceEditor (class in kazu.krt.components) ResourceManager (class in kazu.krt.resource_manager) resources (kazu.utils.build_and_test_model_packs.BuildConfiguration attribute) resources_with_discrepancies (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetMergeReport attribute) Ret (class in kazu.utils.caching) retry_wiki_with_maxlag() (in module kazu.utils.download_gilda_contexts) RulesBasedEntityClassDisambiguationFilterStep (class in kazu.steps.linking.rules_based_disambiguation) run_acceptance_tests (kazu.utils.build_and_test_model_packs.BuildConfiguration attribute) run_acceptance_tests() (kazu.utils.build_and_test_model_packs.ModelPackBuilder method) run_conjunction_rules() (kazu.steps.ner.entity_post_processing.SplitOnConjunctionPattern method) run_consistency_checks (kazu.utils.build_and_test_model_packs.BuildConfiguration attribute)

S

sanity_test_strings (kazu.utils.build_and_test_model_packs.BuildConfiguration attribute) SapBertHelper (class in kazu.utils.sapbert) SapbertStringSimilarityScorer (class in kazu.language.string_similarity_scorers) save() (in module kazu.krt.components) (kazu.krt.resource_manager.ResourceManager method) schema_extra (kazu.web.server.DocumentCollection.Config attribute) (kazu.web.server.SectionedWebDocument.Config attribute) (kazu.web.server.SimpleWebDocument.Config attribute) score (kazu.steps.linking.entity_class_disambiguation.ScoredContext attribute) score_and_group_ids() (kazu.ontology_preprocessing.base.OntologyParser method) (kazu.ontology_preprocessing.parsers.CellosaurusOntologyParser method) (kazu.ontology_preprocessing.parsers.OpenTargetsDiseaseOntologyParser method) (kazu.ontology_preprocessing.parsers.OpenTargetsTargetOntologyParser method) score_entity_context() (kazu.steps.linking.entity_class_disambiguation.EntityClassTfIdfScorer method) score_sections() (in module kazu.annotation.acceptance_test) ScoredContext (class in kazu.steps.linking.entity_class_disambiguation) search() (kazu.utils.link_index.DictionaryIndex method) search_and_edit_synonyms_form() (kazu.krt.string_editor.components.StringConflictForm static method) search_score (kazu.data.LinkingMetrics attribute) Section (class in kazu.data) section (kazu.steps.ner.gliner.GliNERBatchItem attribute) section_frames_to_tokenised_words() (kazu.steps.ner.hf_token_classification.TransformersModelForTokenClassificationNerStep method) SectionedWebDocument (class in kazu.web.server) SectionedWebDocument.Config (class in kazu.web.server) sections (kazu.data.Document attribute) (kazu.web.server.SectionedWebDocument attribute) SectionScorer (class in kazu.annotation.acceptance_test) select_preferred_entity() (kazu.steps.other.merge_overlapping_ents.MergeOverlappingEntsStep method) Self (class in kazu.steps.step) sentence (kazu.steps.ner.gliner.GliNERBatchItem attribute) sentence_context_for_entity() (kazu.steps.linking.entity_class_disambiguation.EntityClassDisambiguationStep static method) sentence_spans (kazu.data.Section property) SeparatorExpansion (class in kazu.ontology_preprocessing.synonym_generation) set_context_matchers() (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) set_download_completed_or_skipped() (kazu.krt.ontology_update_editor.components.OntologyUpdateForm static method) set_labels() (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) set_safety_settings() (kazu.steps.ner.llm_ner.VertexLLMModel method) SethStep (class in kazu.steps.ner.seth) short_form_filter() (in module kazu.utils.abbreviation_detector) show_reset_button() (in module kazu.krt.components) show_save_button() (in module kazu.krt.components) simple_document_from_sents() (kazu.data.Document class method) simple_stanza_init() (in module kazu.utils.stanza_pipeline) SimpleOntologyDownloader (class in kazu.ontology_preprocessing.downloads) SimpleSpanFinder (class in kazu.steps.ner.tokenized_word_processor) SimpleWebDocument (class in kazu.web.server) SimpleWebDocument.Config (class in kazu.web.server) SingleEntityDocumentConverter (class in kazu.web.server) Singleton (class in kazu.utils.utils) SKOSXLGraphParser (class in kazu.ontology_preprocessing.parsers) sort_then_group() (in module kazu.utils.grouping) source (kazu.data.Mapping attribute) sources (kazu.data.EquivalentIdSet property) SpacyNerStep (class in kazu.steps.ner.spacy_ner) SpacyPipelines (class in kazu.utils.spacy_pipeline) span_continue_condition() (kazu.steps.ner.tokenized_word_processor.MultilabelSpanFinder method) (kazu.steps.ner.tokenized_word_processor.SimpleSpanFinder method) span_in_FP_context() (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) span_in_FP_coocc() (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) span_in_TP_context() (kazu.ontology_matching.ontology_matcher.OntologyMatcher method)

span_in_TP_coocc() (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) span_key (kazu.ontology_matching.ontology_matcher.OntologyMatcher property) (kazu.ontology_matching.ontology_matcher.OntologyMatcherConfig attribute) SpanFinder (class in kazu.steps.ner.tokenized_word_processor) spangrouped_ent_section_pairs() (kazu.steps.linking.entity_class_disambiguation.EntityClassDisambiguationStep method) spans (kazu.data.Entity attribute) spans_to_entities() (kazu.steps.ner.tokenized_word_processor.TokenizedWordProcessor method) spelling (kazu.ontology_preprocessing.synonym_generation.GreekSymbolSubstitution attribute) SpellingVariationReplacement (class in kazu.ontology_preprocessing.synonym_generation) split_on_dashes_or_space() (kazu.utils.string_normalizer.GildaUtils class method) split_on_numbers() (kazu.utils.string_normalizer.DefaultStringNormalizer static method) SplitOnConjunctionPattern (class in kazu.steps.ner.entity_post_processing) SplitOnNumericalListPatternWithPrefix (class in kazu.steps.ner.entity_post_processing) StanzaStep (class in kazu.steps.other.stanza) start (kazu.data.CharSpan attribute) (kazu.data.Entity attribute) start() (in module kazu.web.server) start_span (kazu.steps.ner.gliner.GliNERBatchItem attribute) start_span() (kazu.steps.ner.tokenized_word_processor.MultilabelSpanFinder method) (kazu.steps.ner.tokenized_word_processor.SimpleSpanFinder method) state_key() (kazu.krt.resource_discrepancy_editor.components.ResourceDiscrepancyResolutionForm static method) StatoParser (class in kazu.ontology_preprocessing.parsers) Step (class in kazu.steps.step) stop() (in module kazu.web.server) StopWordRemover (class in kazu.ontology_preprocessing.synonym_generation) StrategyRunner (class in kazu.steps.linking.post_processing.strategy_runner) STRING_CONFLICT_BATCH_APPLY (kazu.krt.string_editor.components.StringConflictForm attribute) string_match_confidence (kazu.data.Mapping attribute) string_match_strategy (kazu.data.Mapping attribute) StringConflictForm (class in kazu.krt.string_editor.components) StringMatchConfidence (class in kazu.data) StringNormalizer (class in kazu.utils.string_normalizer) StringReplacement (class in kazu.ontology_preprocessing.synonym_generation) StringSimilarityScorer (class in kazu.language.string_similarity_scorers) StripMappingURIsAction (class in kazu.steps.other.cleanup) StrongMatchMappingStrategy (class in kazu.steps.linking.post_processing.mapping_strategies.strategies) StrongMatchWithEmbeddingConfirmationStringMatchingStrategy (class in kazu.steps.linking.post_processing.mapping_strategies.strategies) sub_greek_char_abbreviations() (kazu.utils.string_normalizer.DefaultStringNormalizer static method) submit_form_and_clear_state() (kazu.krt.components.ParserSelector static method) submit_form_and_keep_state() (kazu.krt.components.ParserSelector static method) submit_form_for_addition() (kazu.krt.components.ResourceEditor static method) suffixes (kazu.utils.spacy_pipeline.KazuCustomEnglishDefaults attribute) SuffixReplacement (class in kazu.ontology_preprocessing.synonym_generation) summary_df() (kazu.krt.resource_discrepancy_editor.utils.ResourceDiscrepancyManger method) (kazu.krt.string_editor.utils.ResourceConflictManager method) superfluous_resources (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetMergeReport attribute) SymbolicToCaseSensitiveAction (class in kazu.ontology_preprocessing.autocuration) SymbolMatchMappingStrategy (class in kazu.steps.linking.post_processing.mapping_strategies.strategies) SYN (in module kazu.ontology_preprocessing.constants) syn_column_keys (kazu.ontology_preprocessing.parsers.HGNCGeneFamilyParser attribute) syn_norm_for_linking() (kazu.data.OntologyStringResource method) sync_resources() (kazu.krt.resource_manager.ResourceManager method) sync_resources_for_resolved_resource_conflict_and_find_new_conflicts() (kazu.krt.string_editor.utils.ResourceConflictManager method) SynNormIsSubStringMappingStrategy (class in kazu.steps.linking.post_processing.mapping_strategies.strategies) Synonym (class in kazu.data) SYNONYM_IS_AMBIGUOUS (kazu.data.EquivalentIdAggregationStrategy attribute) synonym_norm (kazu.data.LinkingCandidate attribute) SynonymDatabase (class in kazu.database.in_memory_db) SynonymDiscrepancy (class in kazu.krt.resource_discrepancy_editor.utils) SynonymGenerator (class in kazu.ontology_preprocessing.synonym_generation)

T

TabularOntologyParser (class in kazu.ontology_preprocessing.parsers) tasks_for_fn() (kazu.annotation.acceptance_test.AggregatedAccuracyResult method) tasks_for_fp() (kazu.annotation.acceptance_test.AggregatedAccuracyResult method) text (kazu.data.Section attribute) (kazu.data.Synonym attribute) (kazu.web.server.SimpleWebDocument attribute) tfidf_document (kazu.steps.linking.entity_class_disambiguation.TfIdfDisambiguationEntry attribute) tfidf_score() (kazu.steps.linking.entity_class_disambiguation.EntityClassTfIdfScorer static method) tfidf_vectorizer (kazu.steps.linking.entity_class_disambiguation.TfIdfDisambiguationEntry attribute) TfIdfDisambiguationEntry (class in kazu.steps.linking.entity_class_disambiguation) TfIdfDisambiguationStrategy (class in kazu.steps.linking.post_processing.disambiguation.strategies) TfIdfScorer (class in kazu.steps.linking.post_processing.disambiguation.context_scoring) thresh (kazu.steps.linking.entity_class_disambiguation.DisambiguationEntry attribute) (kazu.steps.linking.entity_class_disambiguation.ScoredContext attribute) (kazu.steps.linking.entity_class_disambiguation.TfIdfDisambiguationEntry attribute) to_dict() (kazu.data.Document method) (kazu.data.OntologyStringResource method)

to_disk() (kazu.ontology_matching.ontology_matcher.OntologyMatcher method) to_json() (kazu.data.Document method) (kazu.data.OntologyStringResource method) to_kazu_document() (kazu.web.server.SectionedWebDocument method) (kazu.web.server.SimpleWebDocument method) tok_words (kazu.steps.ner.tokenized_word_processor.TokWordSpan attribute) token_confidences (kazu.steps.ner.tokenized_word_processor.TokenizedWord attribute) token_ids (kazu.steps.ner.tokenized_word_processor.TokenizedWord attribute) token_offsets (kazu.steps.ner.tokenized_word_processor.TokenizedWord attribute) TokenizedWord (class in kazu.steps.ner.tokenized_word_processor) TokenizedWordProcessor (class in kazu.steps.ner.tokenized_word_processor) tokenizer_exceptions (kazu.utils.spacy_pipeline.KazuCustomEnglishDefaults attribute) TokenListReplacementGenerator (class in kazu.ontology_preprocessing.synonym_generation) tokens (kazu.steps.ner.tokenized_word_processor.TokenizedWord attribute) TokWordSpan (class in kazu.steps.ner.tokenized_word_processor) tp (kazu.annotation.acceptance_test.AggregatedAccuracyResult attribute) TransformersModelForTokenClassificationNerStep (class in kazu.steps.ner.hf_token_classification)

U

UberonOntologyParser (class in kazu.ontology_preprocessing.parsers) UNAMBIGUOUS (kazu.data.EquivalentIdAggregationStrategy attribute) update() (kazu.steps.ner.gliner.ConflictScorer method) update_candidates_lookup_cache() (kazu.utils.caching.EntityLinkingLookupCache method) update_failed_docs() (kazu.pipeline.Pipeline method)

update_tasks() (kazu.annotation.label_studio.LabelStudioManager method) update_view() (kazu.annotation.label_studio.LabelStudioManager method) UPDATES_SAVED (kazu.krt.ontology_update_editor.components.OntologyUpdateForm attribute) upgrade_ontology_version() (kazu.ontology_preprocessing.base.OntologyParser method) upper_greek_letter (kazu.ontology_preprocessing.synonym_generation.GreekSymbolSubstitution attribute)

V

VERB_PLACEHOLDER (kazu.ontology_preprocessing.synonym_generation.VerbPhraseVariantGenerator attribute) VerbPhraseVariantGenerator (class in kazu.ontology_preprocessing.synonym_generation) verify_resource_set_integrity() (kazu.ontology_preprocessing.curation_utils.OntologyStringConflictAnalyser method) version() (kazu.ontology_preprocessing.downloads.ChemblParquetOntologyDownloader method) (kazu.ontology_preprocessing.downloads.OBOOntologyDownloader method) (kazu.ontology_preprocessing.downloads.OntologyDownloader method) (kazu.ontology_preprocessing.downloads.OpenTargetsOntologyDownloader method) (kazu.ontology_preprocessing.downloads.OwlOntologyDownloader method) (kazu.ontology_preprocessing.downloads.SimpleOntologyDownloader method)

VertexLLMModel (class in kazu.steps.ner.llm_ner)

W

wait_for_model_pack_completion() (in module kazu.utils.build_and_test_model_packs) wiki_gene_ids (kazu.utils.download_gilda_contexts.WikipediaEnsemblMapping attribute) wiki_gene_urls_to_text (kazu.utils.download_gilda_contexts.WikipediaEnsemblMapping attribute) wiki_protein_ids (kazu.utils.download_gilda_contexts.WikipediaEnsemblMapping attribute) wiki_protein_urls_to_text (kazu.utils.download_gilda_contexts.WikipediaEnsemblMapping attribute) WikipediaEnsemblMapping (class in kazu.utils.download_gilda_contexts) with_default_colours() (kazu.annotation.label_studio.LabelStudioAnnotationView static method) word_char_end (kazu.steps.ner.tokenized_word_processor.TokenizedWord attribute)

word_char_start (kazu.steps.ner.tokenized_word_processor.TokenizedWord attribute) word_id (kazu.steps.ner.tokenized_word_processor.TokenizedWord attribute) word_is_valid() (in module kazu.utils.utils) write_new_defaults_to_model_pack() (kazu.krt.ontology_update_editor.utils.OntologyUpdateManager method) write_normalisation_conflict_report() (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetConflictReport method) write_ontology_merge_report() (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetMergeReport method) write_report() (kazu.ontology_preprocessing.ontology_upgrade_report.OntologyUpgradeReport method) write_reports_for_parser() (kazu.ontology_preprocessing.curation_utils.OntologyResourceSetCompleteReport method)

X

xref_db (kazu.steps.linking.post_processing.xref_manager.CrossReferenceManager attribute)

xref_source_parser_name (kazu.data.Mapping attribute)

Z

zip_model_pack() (kazu.utils.build_and_test_model_packs.ModelPackBuilder method)