├── .gitattributes ├── .github ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md └── workflows │ ├── codespell.yml │ ├── doc_pages.yaml │ ├── main.yaml │ └── pypi-publish.yaml ├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── docs ├── Makefile ├── cli.rst ├── concepts.rst ├── conf.py ├── contributing.md ├── datamodels │ ├── cross-ontology-diff │ │ ├── Boolean.md │ │ ├── Date.md │ │ ├── Datetime.md │ │ ├── Decimal.md │ │ ├── DiffCategory.md │ │ ├── Double.md │ │ ├── Float.md │ │ ├── Integer.md │ │ ├── Ncname.md │ │ ├── Nodeidentifier.md │ │ ├── Objectidentifier.md │ │ ├── Position.md │ │ ├── RelationalDiff.md │ │ ├── String.md │ │ ├── StructureDiffResultSet.md │ │ ├── Time.md │ │ ├── Uri.md │ │ ├── Uriorcurie.md │ │ ├── category.md │ │ ├── cross-ontology-diff.md │ │ ├── index.md │ │ ├── left_object_id.md │ │ ├── left_object_is_functional.md │ │ ├── left_object_name.md │ │ ├── left_predicate_id.md │ │ ├── left_predicate_name.md │ │ ├── left_subject_id.md │ │ ├── left_subject_is_functional.md │ │ ├── left_subject_name.md │ │ ├── results.md │ │ ├── right_object_id.md │ │ ├── right_object_name.md │ │ ├── right_predicate_ids.md │ │ ├── right_predicate_names.md │ │ ├── right_subject_id.md │ │ ├── right_subject_name.md │ │ └── types.md │ ├── funowl │ │ └── index.rst │ ├── index.rst │ ├── kgcl │ │ └── index.rst │ ├── lexical-index │ │ ├── Activity.md │ │ ├── Boolean.md │ │ ├── Date.md │ │ ├── Datetime.md │ │ ├── Decimal.md │ │ ├── Double.md │ │ ├── Float.md │ │ ├── Integer.md │ │ ├── LexicalGrouping.md │ │ ├── LexicalIndex.md │ │ ├── LexicalTransformation.md │ │ ├── LexicalTransformationPipeline.md │ │ ├── Ncname.md │ │ ├── Nodeidentifier.md │ │ ├── Objectidentifier.md │ │ ├── RelationshipToTerm.md │ │ ├── String.md │ │ ├── Time.md │ │ ├── TransformationType.md │ │ ├── Uri.md │ │ ├── Uriorcurie.md │ │ ├── element.md │ │ ├── element_term.md │ │ ├── groupings.md │ │ ├── index.md │ │ ├── lexical-index.md │ │ ├── lexican-index.md │ │ ├── name.md │ │ ├── params.md │ │ ├── pipeline.md │ │ ├── pipelines.md │ │ ├── predicate.md │ │ ├── relationships.md │ │ ├── source.md │ │ ├── term.md │ │ ├── transformations.md │ │ ├── type.md │ │ └── types.md │ ├── mapping-rules │ │ ├── Activity.md │ │ ├── Boolean.md │ │ ├── Date.md │ │ ├── Datetime.md │ │ ├── Decimal.md │ │ ├── Double.md │ │ ├── Float.md │ │ ├── Integer.md │ │ ├── LexicalGrouping.md │ │ ├── LexicalIndex.md │ │ ├── LexicalTransformation.md │ │ ├── LexicalTransformationPipeline.md │ │ ├── MappingRule.md │ │ ├── MappingRuleCollection.md │ │ ├── Ncname.md │ │ ├── Nodeidentifier.md │ │ ├── Objectidentifier.md │ │ ├── Postcondition.md │ │ ├── Precondition.md │ │ ├── RelationshipToTerm.md │ │ ├── String.md │ │ ├── Time.md │ │ ├── TransformationType.md │ │ ├── Uri.md │ │ ├── Uriorcurie.md │ │ ├── description.md │ │ ├── element.md │ │ ├── element_term.md │ │ ├── groupings.md │ │ ├── index.md │ │ ├── lexical-index.md │ │ ├── lexican-index.md │ │ ├── mapping-rules.md │ │ ├── mapping_source_one_of.md │ │ ├── minimum_confidence.md │ │ ├── name.md │ │ ├── object_match_field_one_of.md │ │ ├── object_source_one_of.md │ │ ├── oneway.md │ │ ├── params.md │ │ ├── pipeline.md │ │ ├── pipelines.md │ │ ├── postconditions.md │ │ ├── preconditions.md │ │ ├── predicate.md │ │ ├── predicate_id.md │ │ ├── relationships.md │ │ ├── rules.md │ │ ├── source.md │ │ ├── subject_match_field_one_of.md │ │ ├── subject_source_one_of.md │ │ ├── term.md │ │ ├── transformations.md │ │ ├── transformations_included_in.md │ │ ├── type.md │ │ ├── types.md │ │ └── weight.md │ ├── obograph │ │ ├── Axiom.md │ │ ├── BasicPropertyValue.md │ │ ├── Boolean.md │ │ ├── Date.md │ │ ├── Datetime.md │ │ ├── Decimal.md │ │ ├── DefinitionPropertyValue.md │ │ ├── DomainRangeAxiom.md │ │ ├── Double.md │ │ ├── Edge.md │ │ ├── EquivalentNodesSet.md │ │ ├── ExistentialRestrictionExpression.md │ │ ├── Float.md │ │ ├── Graph.md │ │ ├── GraphDocument.md │ │ ├── Integer.md │ │ ├── LogicalDefinitionAxiom.md │ │ ├── Meta.md │ │ ├── Ncname.md │ │ ├── Node.md │ │ ├── Nodeidentifier.md │ │ ├── Objectidentifier.md │ │ ├── PredsEnum.md │ │ ├── PropertyChainAxiom.md │ │ ├── PropertyValue.md │ │ ├── ScopesEnum.md │ │ ├── String.md │ │ ├── SynonymPropertyValue.md │ │ ├── Time.md │ │ ├── Uri.md │ │ ├── Uriorcurie.md │ │ ├── XrefPropertyValue.md │ │ ├── basicPropertyValues.md │ │ ├── comments.md │ │ ├── definition.md │ │ ├── deprecated.md │ │ ├── domainRangeAxioms.md │ │ ├── edges.md │ │ ├── equivalentNodesSets.md │ │ ├── fillerId.md │ │ ├── graphs.md │ │ ├── id.md │ │ ├── index.md │ │ ├── isExact.md │ │ ├── label.md │ │ ├── lbl.md │ │ ├── logicalDefinitionAxioms.md │ │ ├── nodeIds.md │ │ ├── nodes.md │ │ ├── obj.md │ │ ├── obographs_datamodel.md │ │ ├── obographs_linkml_model.md │ │ ├── pred.md │ │ ├── propertyChainAxioms.md │ │ ├── propertyId.md │ │ ├── representitiveNodeId.md │ │ ├── scope.md │ │ ├── sub.md │ │ ├── subsets.md │ │ ├── synonymType.md │ │ ├── synonyms.md │ │ ├── type.md │ │ ├── types.md │ │ ├── val.md │ │ ├── version.md │ │ └── xrefs.md │ ├── ontology-metadata │ │ ├── AnnotationProperty.md │ │ ├── AnnotationPropertyMixin.md │ │ ├── Anonymous.md │ │ ├── AnonymousClassExpression.md │ │ ├── Any.md │ │ ├── Axiom.md │ │ ├── Boolean.md │ │ ├── CURIELiteral.md │ │ ├── Class.md │ │ ├── ClassExpression.md │ │ ├── Datetime.md │ │ ├── Decimal.md │ │ ├── Double.md │ │ ├── Expression.md │ │ ├── Float.md │ │ ├── HasCategory.md │ │ ├── HasLifeCycle.md │ │ ├── HasMappings.md │ │ ├── HasMinimalMetadata.md │ │ ├── HasProvenance.md │ │ ├── HasSynonyms.md │ │ ├── HasUserInformation.md │ │ ├── IEDB_alternative_term.md │ │ ├── ISA_alternative_term.md │ │ ├── Integer.md │ │ ├── IriType.md │ │ ├── LabelType.md │ │ ├── NCIT_definition_source.md │ │ ├── NCIT_term_source.md │ │ ├── NCIT_term_type.md │ │ ├── NamedIndividual.md │ │ ├── NamedObject.md │ │ ├── NarrativeText.md │ │ ├── Ncname.md │ │ ├── Nodeidentifier.md │ │ ├── NotObsoleteAspect.md │ │ ├── OBO_foundry_unique_label.md │ │ ├── ObjectProperty.md │ │ ├── Objectidentifier.md │ │ ├── ObsoleteAspect.md │ │ ├── Ontology-Metadata.md │ │ ├── Ontology.md │ │ ├── Property.md │ │ ├── PropertyExpression.md │ │ ├── Restriction.md │ │ ├── String.md │ │ ├── Subset.md │ │ ├── Term.md │ │ ├── Thing.md │ │ ├── TidyString.md │ │ ├── Time.md │ │ ├── TransitiveProperty.md │ │ ├── URLLiteral.md │ │ ├── Uri.md │ │ ├── Uriorcurie.md │ │ ├── allValuesFrom.md │ │ ├── alternative_term.md │ │ ├── annotatedProperty.md │ │ ├── annotatedSource.md │ │ ├── annotatedTarget.md │ │ ├── broadMatch.md │ │ ├── cardinality.md │ │ ├── category.md │ │ ├── changeNote.md │ │ ├── closeMatch.md │ │ ├── comment.md │ │ ├── complementOf.md │ │ ├── conformsTo.md │ │ ├── consider.md │ │ ├── contributor.md │ │ ├── core_property.md │ │ ├── created.md │ │ ├── created_by.md │ │ ├── creation_date.md │ │ ├── creator.md │ │ ├── curator_note.md │ │ ├── database_cross_reference.md │ │ ├── date.md │ │ ├── date_retrieved.md │ │ ├── defaultLanguage.md │ │ ├── definition.md │ │ ├── definition_source.md │ │ ├── depicted_by.md │ │ ├── deprecated.md │ │ ├── disconnected_from.md │ │ ├── disjointWith.md │ │ ├── distinctMembers.md │ │ ├── domain.md │ │ ├── editor_note.md │ │ ├── editor_preferred_term.md │ │ ├── equivalentClass.md │ │ ├── equivalentProperty.md │ │ ├── evidence.md │ │ ├── exactMatch.md │ │ ├── example_of_usage.md │ │ ├── excluded_axiom.md │ │ ├── excluded_from_QC_check.md │ │ ├── excluded_subClassOf.md │ │ ├── excluded_synonym.md │ │ ├── external_ontology.md │ │ ├── hasValue.md │ │ ├── has_alternative_id.md │ │ ├── has_axiom_label.md │ │ ├── has_broad_synonym.md │ │ ├── has_curation_status.md │ │ ├── has_exact_synonym.md │ │ ├── has_narrow_synonym.md │ │ ├── has_obo_namespace.md │ │ ├── has_obsolescence_reason.md │ │ ├── has_ontology_root_term.md │ │ ├── has_rank.md │ │ ├── has_related_synonym.md │ │ ├── has_synonym_type.md │ │ ├── id.md │ │ ├── image.md │ │ ├── imported_from.md │ │ ├── imports.md │ │ ├── in_subset.md │ │ ├── index.md │ │ ├── informative_property.md │ │ ├── intersectionOf.md │ │ ├── inverseOf.md │ │ ├── isDefinedBy.md │ │ ├── is_a_defining_property_chain_axiom.md │ │ ├── is_a_defining_property_chain_axiom_where_second_argument_is_reflexive.md │ │ ├── is_class_level.md │ │ ├── is_cyclic.md │ │ ├── is_inferred.md │ │ ├── is_metadata_tag.md │ │ ├── is_transitive.md │ │ ├── label.md │ │ ├── license.md │ │ ├── logical_predicate.md │ │ ├── match.md │ │ ├── match_aspect.md │ │ ├── maxQualifiedCardinality.md │ │ ├── members.md │ │ ├── minCardinality.md │ │ ├── minQualifiedCardinality.md │ │ ├── narrowMatch.md │ │ ├── never_in_taxon.md │ │ ├── notes.md │ │ ├── oboInOwl_id.md │ │ ├── oboInOwl_ontology.md │ │ ├── obsoletion_related_property.md │ │ ├── omo-schema.md │ │ ├── onClass.md │ │ ├── onProperty.md │ │ ├── oneOf.md │ │ ├── ontology_term_requester.md │ │ ├── page.md │ │ ├── propertyChainAxiom.md │ │ ├── provenance_property.md │ │ ├── qualifiedCardinality.md │ │ ├── range.md │ │ ├── reification_predicate.md │ │ ├── sameAs.md │ │ ├── seeAlso.md │ │ ├── shortcut_annotation_property.md │ │ ├── shorthand.md │ │ ├── should_conform_to.md │ │ ├── someValuesFrom.md │ │ ├── source.md │ │ ├── subClassOf.md │ │ ├── synonym.md │ │ ├── temporal_interpretation.md │ │ ├── term_editor.md │ │ ├── term_replaced_by.md │ │ ├── term_tracker_item.md │ │ ├── title.md │ │ ├── type.md │ │ ├── types.md │ │ ├── unionOf.md │ │ ├── url.md │ │ ├── versionIRI.md │ │ ├── versionInfo.md │ │ └── version_property.md │ ├── search │ │ ├── Boolean.md │ │ ├── Date.md │ │ ├── Datetime.md │ │ ├── Decimal.md │ │ ├── Double.md │ │ ├── Float.md │ │ ├── Integer.md │ │ ├── Ncname.md │ │ ├── Nodeidentifier.md │ │ ├── Objectidentifier.md │ │ ├── SearchBaseConfiguration.md │ │ ├── SearchProperty.md │ │ ├── SearchResult.md │ │ ├── SearchResultSet.md │ │ ├── SearchTerm.md │ │ ├── SearchTermSyntax.md │ │ ├── String.md │ │ ├── Time.md │ │ ├── Uri.md │ │ ├── Uriorcurie.md │ │ ├── categories.md │ │ ├── configuration.md │ │ ├── cursor.md │ │ ├── include_aliases.md │ │ ├── include_definition.md │ │ ├── include_id.md │ │ ├── include_label.md │ │ ├── include_obsoletes_in_results.md │ │ ├── index.md │ │ ├── is_complete.md │ │ ├── is_partial.md │ │ ├── is_regular_expression.md │ │ ├── limit.md │ │ ├── matches_full_search_term.md │ │ ├── object_id.md │ │ ├── object_label.md │ │ ├── object_match_field.md │ │ ├── object_source.md │ │ ├── object_source_version.md │ │ ├── properties.md │ │ ├── rank.md │ │ ├── result_count.md │ │ ├── results.md │ │ ├── search-datamodel.md │ │ ├── search_terms.md │ │ ├── snippet.md │ │ ├── syntax.md │ │ └── types.md │ ├── semsql │ │ └── index.rst │ ├── similarity │ │ ├── ItemCount.md │ │ ├── NegativeLogValue.md │ │ ├── NonNegativeFloat.md │ │ ├── PairwiseSimilarity.md │ │ ├── TermPairwiseSimilarity.md │ │ ├── TermSetPairwiseSimilarity.md │ │ ├── ZeroToOne.md │ │ ├── ancestor_id.md │ │ ├── ancestor_information_content.md │ │ ├── ancestor_label.md │ │ ├── ancestor_source.md │ │ ├── dice_similarity.md │ │ ├── index.md │ │ ├── information_content.md │ │ ├── intersection_count.md │ │ ├── jaccard_similarity.md │ │ ├── object_id.md │ │ ├── object_information_content.md │ │ ├── object_label.md │ │ ├── object_source.md │ │ ├── overlap_coefficient.md │ │ ├── phenodigm_score.md │ │ ├── score.md │ │ ├── similarity.md │ │ ├── subject_id.md │ │ ├── subject_information_content.md │ │ ├── subject_label.md │ │ ├── subject_source.md │ │ ├── subsumed_by_score.md │ │ ├── subsumes_score.md │ │ ├── types.md │ │ └── union_count.md │ ├── sssom │ │ └── index.rst │ ├── summary-statistics │ │ ├── Boolean.md │ │ ├── Date.md │ │ ├── Datetime.md │ │ ├── Decimal.md │ │ ├── Double.md │ │ ├── FacetStatistics.md │ │ ├── Float.md │ │ ├── GlobalStatistics.md │ │ ├── Integer.md │ │ ├── Ncname.md │ │ ├── Nodeidentifier.md │ │ ├── Objectidentifier.md │ │ ├── String.md │ │ ├── SummaryStatisticCollection.md │ │ ├── Time.md │ │ ├── Uri.md │ │ ├── Uriorcurie.md │ │ ├── annotation_property_count.md │ │ ├── anonymous_class_expression_count.md │ │ ├── anonymous_individual_count.md │ │ ├── by_category.md │ │ ├── by_ontology.md │ │ ├── by_subset.md │ │ ├── by_taxon.md │ │ ├── class_count.md │ │ ├── class_count_excluding_deprecated.md │ │ ├── class_count_with_definitions.md │ │ ├── class_statistic_group.md │ │ ├── count_statistic.md │ │ ├── datatype_property_count.md │ │ ├── description_logic_profile.md │ │ ├── distinct_synonym_count.md │ │ ├── equivalentclasses_axiom_count.md │ │ ├── facet.md │ │ ├── index.md │ │ ├── individual_count.md │ │ ├── individual_statistic_group.md │ │ ├── mapping_count.md │ │ ├── metadata_statistic_group.md │ │ ├── named_individual_count.md │ │ ├── object_property_count.md │ │ ├── ontology_count.md │ │ ├── owl_axiom_count.md │ │ ├── owl_statistic_group.md │ │ ├── property_count.md │ │ ├── property_statistic_group.md │ │ ├── rdf_triple_count.md │ │ ├── subclass_of_axiom_count.md │ │ ├── summary-statistics.md │ │ ├── synonym_statement_count.md │ │ ├── types.md │ │ ├── unsatisfiable_class_count.md │ │ └── untyped_entity_count.md │ ├── text-annotator │ │ ├── Boolean.md │ │ ├── Date.md │ │ ├── Datetime.md │ │ ├── Decimal.md │ │ ├── Double.md │ │ ├── Float.md │ │ ├── HasSpan.md │ │ ├── Integer.md │ │ ├── Ncname.md │ │ ├── Nodeidentifier.md │ │ ├── Objectidentifier.md │ │ ├── Position.md │ │ ├── String.md │ │ ├── TextAnnotation.md │ │ ├── TextAnnotationResultSet.md │ │ ├── TextualElement.md │ │ ├── Time.md │ │ ├── TransformationType.md │ │ ├── Uri.md │ │ ├── Uriorcurie.md │ │ ├── annotations.md │ │ ├── confidence.md │ │ ├── id.md │ │ ├── index.md │ │ ├── info.md │ │ ├── is_longest_match.md │ │ ├── match_string.md │ │ ├── match_type.md │ │ ├── object_id.md │ │ ├── object_label.md │ │ ├── object_source.md │ │ ├── parent_document.md │ │ ├── predicate_id.md │ │ ├── source_text.md │ │ ├── subject_end.md │ │ ├── subject_label.md │ │ ├── subject_source.md │ │ ├── subject_start.md │ │ ├── subject_text_id.md │ │ ├── text-annotator.md │ │ ├── text.md │ │ └── types.md │ └── validation │ │ ├── Boolean.md │ │ ├── Date.md │ │ ├── Datetime.md │ │ ├── Decimal.md │ │ ├── Double.md │ │ ├── ExternalReferenceValidationResult.md │ │ ├── Float.md │ │ ├── Integer.md │ │ ├── Ncname.md │ │ ├── Nodeidentifier.md │ │ ├── Objectidentifier.md │ │ ├── SeverityOptions.md │ │ ├── String.md │ │ ├── Time.md │ │ ├── TypeSeverityKeyValue.md │ │ ├── Uri.md │ │ ├── Uriorcurie.md │ │ ├── ValidationConfiguration.md │ │ ├── ValidationReport.md │ │ ├── ValidationResult.md │ │ ├── ValidationResultType.md │ │ ├── http_response_code.md │ │ ├── index.md │ │ ├── info.md │ │ ├── instantiates.md │ │ ├── max_number_results_per_type.md │ │ ├── number_of_attempts.md │ │ ├── object.md │ │ ├── object_str.md │ │ ├── predicate.md │ │ ├── results.md │ │ ├── schema_path.md │ │ ├── severity.md │ │ ├── source.md │ │ ├── subject.md │ │ ├── time_checked.md │ │ ├── type.md │ │ ├── type_severity_map.md │ │ ├── types.md │ │ ├── url.md │ │ └── validaton-results.md ├── examples │ ├── AdHoc │ │ ├── Summarizing-with-LLMs.ipynb │ │ ├── Text-Content-Analysis.ipynb │ │ ├── ValueSets.ipynb │ │ └── index.rst │ ├── Adapters │ │ ├── LLM │ │ │ └── LLM-Tutorial.ipynb │ │ ├── Ubergraph │ │ │ ├── Ubergraph-Tutorial.ipynb │ │ │ └── output │ │ │ │ ├── ubergraph-neuron-cl-only.png │ │ │ │ └── ubergraph-neuron.png │ │ └── index.rst │ ├── Command-Line-Examples.ipynb │ ├── Commands │ │ ├── Apply.ipynb │ │ ├── Associations.ipynb │ │ ├── Crawl.ipynb │ │ ├── DiffAssociations.ipynb │ │ ├── DiffViaMappings.ipynb │ │ ├── Disjoints.ipynb │ │ ├── Enrichment.ipynb │ │ ├── GenerateSynonyms.ipynb │ │ ├── LogicalDefinitions.ipynb │ │ ├── Mappings.ipynb │ │ ├── Obsoletes.ipynb │ │ ├── Paths.ipynb │ │ ├── Prefixes.ipynb │ │ ├── Relationships.ipynb │ │ ├── Rollup.ipynb │ │ ├── Statistics.ipynb │ │ ├── TaxonConstraints.ipynb │ │ ├── TermsetSimilarity.ipynb │ │ ├── ValidateDefinitions.ipynb │ │ ├── ValidateMappings.ipynb │ │ ├── index.rst │ │ ├── input │ │ │ ├── eds-genes-hgnc.tsv │ │ │ ├── go-synonym-rules.yaml │ │ │ ├── mapping-crawler-config.yaml │ │ │ ├── test-create.kgcl.txt │ │ │ ├── test.kgcl │ │ │ ├── validate-definition-conf.yaml │ │ │ └── validate-defs-test.obo │ │ └── output │ │ │ ├── LOG │ │ │ ├── all-brain-zfa-mappings.tsv │ │ │ ├── brain-mappings.tsv │ │ │ ├── changes.kgcl │ │ │ ├── chebi.stats.tsv │ │ │ ├── chebi.stats.yaml │ │ │ ├── cl-disjoints-cell-types.tsv │ │ │ ├── cl-disjoints.obo │ │ │ ├── cl-disjoints.tsv │ │ │ ├── cl-disjoints.yaml │ │ │ ├── cl-invalid.sssom.tsv │ │ │ ├── cl-obsoletes-full.tsv │ │ │ ├── cl-obsoletes.tsv │ │ │ ├── cl.stats.grouped.tsv │ │ │ ├── eds-genes-enriched-filtered-top-5.png │ │ │ ├── eds-genes-enriched-filtered-top-5.tsv │ │ │ ├── eds-genes-enriched-filtered.tsv │ │ │ ├── eds-genes-enriched-top-5.png │ │ │ ├── eds-genes-enriched-top-5.tsv │ │ │ ├── eds-genes-enriched.tsv │ │ │ ├── eds-genes-ncbigene.tsv │ │ │ ├── eds.html │ │ │ ├── finger-relationships.tsv │ │ │ ├── go-edit-modified.obo │ │ │ ├── hpoa-query.tsv │ │ │ ├── interneuron-CA4-path.tsv │ │ │ ├── kgcl-de-novo.obo │ │ │ ├── kgcl-de-novo.ofn │ │ │ ├── nerc.png │ │ │ ├── nmbo.png │ │ │ ├── nmbo2.png │ │ │ ├── obsoleted-organelle.obo │ │ │ ├── refsum-analysis │ │ │ ├── clique_results.csv │ │ │ ├── clique_summary.csv │ │ │ └── cliques │ │ │ │ ├── GARD_4648.sssom.tsv │ │ │ │ └── GARD_6322.sssom.tsv │ │ │ ├── refsum.png │ │ │ ├── sgd-aamp-enr.tsv │ │ │ ├── sgd-aamp.txt │ │ │ ├── sgd-iba-diff.tsv │ │ │ ├── sgd-iba-diff.yaml │ │ │ ├── trigeminal-ganglion-graph.png │ │ │ ├── uberon-digit-defs-dp.tsv │ │ │ ├── uberon-digit-defs-fg.tsv │ │ │ ├── uberon-digit-defs-gd.tsv │ │ │ ├── uberon-digit-defs-gf.tsv │ │ │ ├── uberon-part-disjoint-subdivisions.tsv │ │ │ ├── uberon-zfa-diff.csv │ │ │ ├── validate-definitions.llm.yaml │ │ │ ├── validate-definitions.output.tsv │ │ │ ├── xao-invalid.sssom.tsv │ │ │ ├── zfa-bone-element-gen-disjoint.tsv │ │ │ └── zfa-skel-gen-part-disjoint.tsv │ ├── Developers-Tutorial.ipynb │ ├── Draft │ │ └── enrichment_with_OAK.ipynb │ ├── Interfaces │ │ ├── BasicOntologyInterface.ipynb │ │ ├── ClassEnrichmentCalculationInterface.ipynb │ │ ├── MappingProviderInterface.ipynb │ │ └── index.rst │ ├── Ontologies │ │ ├── CHEBI │ │ │ ├── CHEBI-Predicates.ipynb │ │ │ ├── CHEBI-Roles.ipynb │ │ │ ├── CHEBI-Slimmer.ipynb │ │ │ ├── index.rst │ │ │ └── llm │ │ │ │ └── examples │ │ │ │ └── benzenoid.py │ │ ├── CL │ │ │ ├── CL-Neuro-Tutorial.ipynb │ │ │ ├── Lung-Epithelial-Cell-Types.ipynb │ │ │ ├── images │ │ │ │ └── lung-cells-src.png │ │ │ └── index.rst │ │ ├── ENVO │ │ │ ├── ENVO-Tutorial.ipynb │ │ │ └── index.rst │ │ ├── GO │ │ │ ├── Annotation-Analysis.ipynb │ │ │ ├── Annotation-Contributions.ipynb │ │ │ ├── Edge-IC-Analysis.ipynb │ │ │ ├── Edge-Information-Analysis.ipynb │ │ │ ├── GO-EC-Structural-Diff.ipynb │ │ │ ├── GO-Subset-Analysis-OLD.ipynb │ │ │ ├── GO-Subset-Analysis.ipynb │ │ │ ├── Mapping-GO-to-Metacyc.ipynb │ │ │ ├── Pathway-Regulation.ipynb │ │ │ ├── Term-Usage-Summary.ipynb │ │ │ └── index.rst │ │ ├── HP │ │ │ ├── HP-CLI-Examples.ipynb │ │ │ └── index.rst │ │ ├── LOINC │ │ │ ├── COMPLoinc-Example.ipynb │ │ │ └── index.rst │ │ ├── MAXO │ │ │ ├── MAXO-CLI-Examples.ipynb │ │ │ └── index.rst │ │ ├── MONDO │ │ │ ├── Disease2GeneAnalysis.ipynb │ │ │ ├── Mondo-pheno-summaries.ipynb │ │ │ ├── Mondo-phenotypic-series-genes.ipynb │ │ │ ├── MondoPaperExamples.ipynb │ │ │ └── index.rst │ │ ├── NCIT │ │ │ ├── NCIT-CLI-Examples.ipynb │ │ │ └── index.rst │ │ ├── OBA │ │ │ ├── OBA-CLI-Examples.ipynb │ │ │ └── index.rst │ │ ├── OMOP │ │ │ ├── OMOP-Example.ipynb │ │ │ ├── index.rst │ │ │ └── input │ │ │ │ ├── valueset1.txt │ │ │ │ └── valueset2.txt │ │ ├── PHENIO │ │ │ ├── PhenIO-Tutorial.ipynb │ │ │ ├── Semantic-Similarity.ipynb │ │ │ ├── index.rst │ │ │ └── oak-semsimian-timing.ipynb │ │ ├── RHEA │ │ │ └── Reaction-Network.ipynb │ │ ├── SchemaDotOrg │ │ │ ├── SchemaDotOrg-Tutorial.ipynb │ │ │ └── index.rst │ │ └── index.rst │ ├── OntologyEditorsGuide │ │ ├── Edit-File-Examples.ipynb │ │ └── index.rst │ ├── Queries │ │ ├── Subsetting.ipynb │ │ ├── input │ │ │ └── water_env_local_scale.tsv │ │ └── output │ │ │ ├── cl-example-3-terms-mrca.png │ │ │ ├── cl-example-3-terms.png │ │ │ ├── cl-example-4-terms-mrca.png │ │ │ ├── cl-example-combined.png │ │ │ ├── cl-example-decomposed.png │ │ │ ├── cl-example-filtered.png │ │ │ ├── envo-water-local-filtered.png │ │ │ ├── envo-water-local-mrcas.png │ │ │ ├── envo-water-local.png │ │ │ ├── envo-water-mrcas.png │ │ │ └── envo-water.png │ ├── basic-demo-semsim.ipynb │ ├── index.rst │ └── output │ │ ├── go-enrichment-from-hp.png │ │ ├── neuron-v1.png │ │ ├── neuron-v2.png │ │ ├── ug-gap-fill1.png │ │ ├── ug-test1.png │ │ └── vacuole.png ├── faq │ ├── architecture.rst │ ├── commandline.rst │ ├── contributing.rst │ ├── general.rst │ ├── index.rst │ ├── ontologies.rst │ └── troubleshooting.rst ├── glossary.rst ├── guide │ ├── aliases.rst │ ├── associations.rst │ ├── basics.rst │ ├── curies-and-uris.rst │ ├── enrichment.rst │ ├── entailment-example-2-paths.png │ ├── entailment-example-2.png │ ├── entailment-example.png │ ├── images │ │ ├── vehicles-mrca.png │ │ └── vehicles.png │ ├── index.rst │ ├── learning-more.rst │ ├── logical-definitions.rst │ ├── mappings.rst │ ├── obsoletion.rst │ ├── primary-labels.rst │ ├── relationships-and-graphs.rst │ ├── schema-article.png │ └── similarity.rst ├── howtos │ ├── fhir-conversions.rst │ ├── index.rst │ ├── perform-lexical-matching.rst │ ├── roll-up-annotations-to-a-subset.rst │ ├── use-llms.rst │ ├── use-oak-expression-language.rst │ ├── validate-an-obo-ontology.md │ ├── visualize-ontology-subgraphs.rst │ └── write-a-plugin.rst ├── index.rst ├── intro │ ├── index.rst │ ├── tutorial01.rst │ ├── tutorial02.rst │ ├── tutorial03.rst │ ├── tutorial04.rst │ ├── tutorial05.rst │ ├── tutorial06.rst │ ├── tutorial07.rst │ ├── tutorial08.rst │ └── wing-vein.png ├── introduction.rst ├── logos │ ├── README.md │ ├── oak-logo_black-banner.png │ ├── oak-logo_black-icon.png │ └── oak-logo_black-stacked.png ├── make.bat ├── packages │ ├── architecture.rst │ ├── best-practice.rst │ ├── converters │ │ ├── data-model-converter.rst │ │ ├── index.rst │ │ ├── obo-graph-to-cx.rst │ │ ├── obo-graph-to-fhir.rst │ │ ├── obo-graph-to-obo-format.rst │ │ └── obo-graph-to-owl.rst │ ├── implementations │ │ ├── aggregator.rst │ │ ├── bioportal.rst │ │ ├── funowl.rst │ │ ├── gilda.rst │ │ ├── index.rst │ │ ├── llm.rst │ │ ├── obograph.rst │ │ ├── ols.rst │ │ ├── ontobee.rst │ │ ├── owlery.rst │ │ ├── pantherdb.rst │ │ ├── pronto.rst │ │ ├── robot-template.rst │ │ ├── simple_obo.rst │ │ ├── sparql.rst │ │ ├── sqldb.rst │ │ ├── translator.rst │ │ └── ubergraph.rst │ ├── index.rst │ ├── interfaces │ │ ├── aggregator.rst │ │ ├── association-provider.rst │ │ ├── basic.rst │ │ ├── class-enrichment.rst │ │ ├── differ.rst │ │ ├── dumper.rst │ │ ├── index.rst │ │ ├── mapping-provider.rst │ │ ├── obograph.rst │ │ ├── owl.rst │ │ ├── patcher.rst │ │ ├── relation-graph.rst │ │ ├── search.rst │ │ ├── semantic-similarity.rst │ │ ├── subsetting.rst │ │ ├── summary-statistics.rst │ │ ├── text-annotator.rst │ │ └── validator.rst │ ├── selectors.rst │ └── utilities.rst ├── rdf-owl-layering.rst └── search-syntax.rst ├── poetry.lock ├── pyproject.toml ├── src └── oaklib │ ├── __init__.py │ ├── cli.py │ ├── conf │ ├── __init__.py │ ├── go-human-input-spec.yaml │ ├── go-pombase-input-spec.yaml │ ├── hpoa-g2p-input-spec.yaml │ ├── hpoa-input-spec.yaml │ ├── lexmatch-rules-oboinowl-default.yaml │ ├── mondo-g2d-input-spec.yaml │ ├── mondo-gencc-input-spec.yaml │ ├── mondo-hpoa-g2d-input-spec.yaml │ ├── mondo-medgen-g2d-input-spec.yaml │ ├── obograph-style.json │ ├── omo-to-skos.sssom.tsv │ └── value-set-expander.conf.yaml │ ├── constants.py │ ├── converters │ ├── __init__.py │ ├── data_model_converter.py │ ├── logical_definition_flattener.py │ ├── obo_graph_to_cx_converter.py │ ├── obo_graph_to_fhir_converter.py │ ├── obo_graph_to_obo_format_converter.py │ └── obo_graph_to_rdf_owl_converter.py │ ├── datamodels │ ├── __init__.py │ ├── association.owl.ttl │ ├── association.py │ ├── association.yaml │ ├── class_enrichment.owl.ttl │ ├── class_enrichment.py │ ├── class_enrichment.yaml │ ├── cross_ontology_diff.owl.ttl │ ├── cross_ontology_diff.py │ ├── cross_ontology_diff.yaml │ ├── cx.py │ ├── cx.yaml │ ├── fhir.owl.ttl │ ├── fhir.py │ ├── fhir.yaml │ ├── input_specification.py │ ├── input_specification.yaml │ ├── item_list.py │ ├── item_list.yaml │ ├── lexical_index.owl.ttl │ ├── lexical_index.py │ ├── lexical_index.schema.json │ ├── lexical_index.yaml │ ├── mapping_cluster_datamodel.py │ ├── mapping_cluster_datamodel.yaml │ ├── mapping_rules_datamodel.owl.ttl │ ├── mapping_rules_datamodel.py │ ├── mapping_rules_datamodel.schema.json │ ├── mapping_rules_datamodel.yaml │ ├── obograph.owl.ttl │ ├── obograph.py │ ├── obograph.schema.json │ ├── obograph.yaml │ ├── ontology_metadata.owl.ttl │ ├── ontology_metadata.py │ ├── ontology_metadata.schema.json │ ├── ontology_metadata.yaml │ ├── oxo.owl.ttl │ ├── oxo.py │ ├── oxo.yaml │ ├── search.py │ ├── search_datamodel.owl.ttl │ ├── search_datamodel.py │ ├── search_datamodel.yaml │ ├── settings.py │ ├── similarity.owl.ttl │ ├── similarity.py │ ├── similarity.yaml │ ├── summary_statistics_datamodel.owl.ttl │ ├── summary_statistics_datamodel.py │ ├── summary_statistics_datamodel.schema.json │ ├── summary_statistics_datamodel.yaml │ ├── synonymizer_datamodel.py │ ├── synonymizer_datamodel.yaml │ ├── taxon_constraints.owl.ttl │ ├── taxon_constraints.py │ ├── taxon_constraints.yaml │ ├── text_annotator.owl.ttl │ ├── text_annotator.py │ ├── text_annotator.schema.json │ ├── text_annotator.yaml │ ├── validation_datamodel.owl.ttl │ ├── validation_datamodel.py │ ├── validation_datamodel.schema.json │ ├── validation_datamodel.yaml │ ├── value_set_configuration.owl.ttl │ ├── value_set_configuration.py │ ├── value_set_configuration.yaml │ └── vocabulary.py │ ├── implementations │ ├── __init__.py │ ├── aggregator │ │ ├── __init__.py │ │ └── aggregator_implementation.py │ ├── agrkb │ │ ├── __init__.py │ │ └── agrkb_implementation.py │ ├── amigo │ │ ├── __init__.py │ │ └── amigo_implementation.py │ ├── cx │ │ ├── __init__.py │ │ └── cx_implementation.py │ ├── eutils │ │ └── __init__.py │ ├── fhir │ │ └── __init__.py │ ├── funowl │ │ ├── __init__.py │ │ └── funowl_implementation.py │ ├── gilda.py │ ├── kgx │ │ ├── __init__.py │ │ └── kgx_implementation.py │ ├── llm_implementation.py │ ├── monarch │ │ ├── __init__.py │ │ └── monarch_implementation.py │ ├── ncbi │ │ ├── __init__.py │ │ ├── eutils_implementation.py │ │ ├── ncbi_gene_implementation.py │ │ └── pubmed_implementation.py │ ├── neo4j │ │ └── __init__.py │ ├── obograph │ │ ├── __init__.py │ │ └── obograph_implementation.py │ ├── ols │ │ ├── __init__.py │ │ ├── constants.py │ │ ├── ols_implementation.py │ │ └── oxo_utils.py │ ├── ontobee │ │ ├── __init__.py │ │ └── ontobee_implementation.py │ ├── ontoportal │ │ ├── __init__.py │ │ ├── agroportal_implementation.py │ │ ├── bioportal_implementation.py │ │ ├── ecoportal_implementation.py │ │ ├── matportal_implementation.py │ │ └── ontoportal_implementation_base.py │ ├── owlery │ │ ├── __init__.py │ │ └── owlery_implementation.py │ ├── pantherdb │ │ ├── __init__.py │ │ └── pantherdb_implementation.py │ ├── pronto │ │ ├── __init__.py │ │ └── pronto_implementation.py │ ├── quickgo │ │ ├── __init__.py │ │ └── quickgo_implementation.py │ ├── robot │ │ └── __init__.py │ ├── scigraph │ │ └── __init__.py │ ├── semsimian │ │ ├── __init__.py │ │ ├── profiler.py │ │ └── semsimian_implementation.py │ ├── simpleobo │ │ ├── __init__.py │ │ ├── simple_obo_implementation.py │ │ └── simple_obo_parser.py │ ├── skos │ │ └── __init__.py │ ├── solor │ │ └── __init__.py │ ├── solr │ │ └── __init__.py │ ├── sparql │ │ ├── __init__.py │ │ ├── abstract_sparql_implementation.py │ │ ├── lov_implementation.py │ │ ├── oak_metamodel_implementation.py │ │ ├── sparql_implementation.py │ │ └── sparql_query.py │ ├── sqldb │ │ ├── __init__.py │ │ ├── sql_implementation.py │ │ └── sqlite_utils.py │ ├── tabular │ │ ├── __init__.py │ │ ├── robot_template_implementation.py │ │ └── tabular_implementation.py │ ├── tccm │ │ └── __init__.py │ ├── translator │ │ ├── __init__.py │ │ └── translator_implementation.py │ ├── ubergraph │ │ ├── __init__.py │ │ └── ubergraph_implementation.py │ ├── umls │ │ └── __init__.py │ ├── uniprot │ │ ├── __init__.py │ │ └── uniprot_implementation.py │ └── wikidata │ │ ├── __init__.py │ │ └── wikidata_implementation.py │ ├── indexes │ ├── __init__.py │ └── edge_index.py │ ├── inference │ ├── __init__.py │ ├── owl_reasoner.py │ ├── reasoner.py │ └── relation_graph_reasoner.py │ ├── interfaces │ ├── __init__.py │ ├── association_provider_interface.py │ ├── basic_ontology_interface.py │ ├── class_enrichment_calculation_interface.py │ ├── differ_interface.py │ ├── dumper_interface.py │ ├── embedding_provider_interface.py │ ├── mapping_provider_interface.py │ ├── merge_interface.py │ ├── metadata_interface.py │ ├── obograph_interface.py │ ├── obolegacy_interface.py │ ├── ontology_generator_interface.py │ ├── ontology_interface.py │ ├── owl_interface.py │ ├── patcher_interface.py │ ├── rdf_interface.py │ ├── relation_graph_interface.py │ ├── search_interface.py │ ├── semsim_interface.py │ ├── skos_interface.py │ ├── subsetter_interface.py │ ├── summary_statistics_interface.py │ ├── taxon_constraint_interface.py │ ├── text_annotator_interface.py │ ├── usages_interface.py │ └── validator_interface.py │ ├── io │ ├── __init__.py │ ├── heatmap_writer.py │ ├── html_writer.py │ ├── obofoundry_markdown_writer.py │ ├── obograph_writer.py │ ├── rollup_report_writer.py │ ├── streaming_axiom_writer.py │ ├── streaming_csv_writer.py │ ├── streaming_fhir_writer.py │ ├── streaming_info_writer.py │ ├── streaming_json_lines_writer.py │ ├── streaming_json_writer.py │ ├── streaming_kgcl_writer.py │ ├── streaming_markdown_writer.py │ ├── streaming_nl_writer.py │ ├── streaming_obo_json_writer.py │ ├── streaming_obo_writer.py │ ├── streaming_owl_functional_writer.py │ ├── streaming_rdf_writer.py │ ├── streaming_writer.py │ └── streaming_yaml_writer.py │ ├── mappers │ ├── __init__.py │ ├── base_mapper.py │ └── ontology_metadata_mapper.py │ ├── parsers │ ├── __init__.py │ ├── association_parser.py │ ├── association_parser_factory.py │ ├── boomer_parser.py │ ├── gaf_association_parser.py │ ├── gencc_association_parser.py │ ├── hpoa_association_parser.py │ ├── hpoa_g2d_association_parser.py │ ├── hpoa_g2p_association_parser.py │ ├── kgx_association_parser.py │ ├── mim2gene_association_parser.py │ ├── pairwise_association_parser.py │ ├── parser_base.py │ ├── phaf_association_parser.py │ └── xaf_association_parser.py │ ├── query.py │ ├── resource.py │ ├── selector.py │ ├── transformers │ ├── __init__.py │ ├── chained_ontology_transformer.py │ ├── edge_filter_transformer.py │ ├── graph_transformer.py │ ├── node_filter_transformer.py │ ├── ontology_transformer.py │ ├── sep_transformer.py │ └── transformers_factory.py │ ├── types.py │ └── utilities │ ├── __init__.py │ ├── apikey_manager.py │ ├── associations │ ├── __init__.py │ ├── association_differ.py │ ├── association_index.py │ ├── association_queries.py │ └── edge_information_util.py │ ├── axioms │ ├── __init__.py │ ├── disjointness_axiom_analyzer.py │ ├── logical_definition_analyzer.py │ ├── logical_definition_summarizer.py │ └── logical_definition_utilities.py │ ├── basic_utils.py │ ├── caching.py │ ├── format_utilities.py │ ├── graph │ ├── __init__.py │ ├── networkx_bridge.py │ └── relationship_walker.py │ ├── identifier_utils.py │ ├── iterator_utils.py │ ├── keyval_cache.py │ ├── kgcl_utilities.py │ ├── label_utilities.py │ ├── lexical │ ├── __init__.py │ ├── lexical_indexer.py │ ├── patternizer.py │ └── synonymizer.py │ ├── mapping │ ├── __init__.py │ ├── boomer_utils.py │ ├── cross_ontology_diffs.py │ ├── mapping_crawler.py │ ├── mapping_obograph_utils.py │ ├── mapping_propagator.py │ ├── mapping_validation.py │ ├── ptable_utils.py │ └── sssom_utils.py │ ├── metrics │ ├── __init__.py │ └── text_content_analysis.py │ ├── ner_utilities.py │ ├── nlp │ ├── __init__.py │ └── natual_language_generation.py │ ├── oboformat_utils.py │ ├── obograph_utils.py │ ├── ontology_builder.py │ ├── ontology_metadata_utils.py │ ├── publication_utils │ ├── __init__.py │ ├── doi_wrapper.py │ ├── pubdb_wrapper.py │ └── pubmed_wrapper.py │ ├── queries │ ├── __init__.py │ └── dissector.py │ ├── rate_limiter.py │ ├── reasoning │ ├── __init__.py │ └── relation_graph.py │ ├── semsim │ ├── __init__.py │ └── similarity_utils.py │ ├── stats │ ├── __init__.py │ └── hypergeometric.py │ ├── subsets │ ├── __init__.py │ ├── slimmer_utils.py │ ├── subset_analysis.py │ ├── subset_validator.py │ └── value_set_expander.py │ ├── table_filler.py │ ├── taxon │ ├── __init__.py │ └── taxon_constraint_utils.py │ ├── validation │ ├── __init__.py │ ├── definition_ontology_rule.py │ ├── disjointness_rule.py │ ├── lint_utils.py │ ├── ontology_rule.py │ └── rule_runner.py │ └── writers │ ├── __init__.py │ └── change_handler.py ├── tests ├── __init__.py ├── input │ ├── AMPK-Signaling.cx │ ├── alignment-test.obo │ ├── bad-ontology.db │ ├── boomer-example.md │ ├── boomer-fake-go-example.md │ ├── cache.conf │ ├── catalog-v001.xml │ ├── cl-fbbt.sssom.tsv │ ├── cli-synonymizer-rules.yaml │ ├── dangling-node-test.obo │ ├── entailment-tutorial-2.obo │ ├── entailment-tutorial.obo │ ├── example-g2d-input-specification.yaml │ ├── example-g2d.gencc.csv │ ├── example-g2d.mim2gene.tsv │ ├── example-hpoa-g2d.tsv │ ├── exclude.txt │ ├── fbbt-cl-subset.owl.ttl │ ├── fhir_config_example.json │ ├── fill-sssom-table-relations.yaml │ ├── foo.tsv │ ├── foo_bar.obo │ ├── go-evo-gains-losses.csv │ ├── go-nucleus-ic.tsv │ ├── go-nucleus-modified.obo │ ├── go-nucleus-modified.owl.ttl │ ├── go-nucleus-simple.obo │ ├── go-nucleus-structurally-modified.obo │ ├── go-nucleus.cx │ ├── go-nucleus.db │ ├── go-nucleus.ic.tsv │ ├── go-nucleus.json │ ├── go-nucleus.obo │ ├── go-nucleus.ofn │ ├── go-nucleus.owl │ ├── go-nucleus.owl.ttl │ ├── graph_projection.db │ ├── graph_projection.omn │ ├── hp-international-test.db │ ├── hp_test.json │ ├── inst.db │ ├── inst.ofn │ ├── inst.owl.ttl │ ├── interneuron.json │ ├── interneuron.obo │ ├── interneuron.owl.ttl │ ├── lint-test.obo │ ├── mapping-predicates-test.obo │ ├── matcher-meta.yaml │ ├── matcher-test.db │ ├── matcher-test.owl │ ├── matcher-text.txt │ ├── matcher_rules.yaml │ ├── metadata-map-prefixes-test.obo │ ├── mock_ncbi_objects.py │ ├── mondo-sample-mappings.obo │ ├── mondo-sample-mappings.owl.ttl │ ├── ncbigene-1956.xml │ ├── obi-templates │ │ ├── biobank-specimens.tsv │ │ └── value-specifications.tsv │ ├── obo-compliance.obo │ ├── obo-compliance │ │ ├── alt_id │ │ │ ├── alt_id.expected.json │ │ │ ├── alt_id.expected.obo │ │ │ ├── alt_id.expected.ofn │ │ │ ├── alt_id.expected.owl │ │ │ ├── alt_id.meta.yaml │ │ │ └── alt_id.obo │ │ ├── broad_synonym │ │ │ ├── broad_synonym.expected.json │ │ │ ├── broad_synonym.expected.obo │ │ │ ├── broad_synonym.expected.ofn │ │ │ ├── broad_synonym.expected.owl │ │ │ ├── broad_synonym.meta.yaml │ │ │ └── broad_synonym.obo │ │ ├── comment │ │ │ ├── comment.expected.json │ │ │ ├── comment.expected.obo │ │ │ ├── comment.expected.ofn │ │ │ ├── comment.expected.owl │ │ │ ├── comment.meta.yaml │ │ │ └── comment.obo │ │ ├── consider-annotated │ │ │ ├── consider-annotated.expected.json │ │ │ ├── consider-annotated.expected.obo │ │ │ ├── consider-annotated.expected.ofn │ │ │ ├── consider-annotated.expected.owl │ │ │ ├── consider-annotated.meta.yaml │ │ │ └── consider-annotated.obo │ │ ├── consider │ │ │ ├── consider.expected.json │ │ │ ├── consider.expected.obo │ │ │ ├── consider.expected.ofn │ │ │ ├── consider.expected.owl │ │ │ ├── consider.meta.yaml │ │ │ └── consider.obo │ │ ├── created_by-annotated │ │ │ ├── created_by-annotated.expected.json │ │ │ ├── created_by-annotated.expected.obo │ │ │ ├── created_by-annotated.expected.ofn │ │ │ ├── created_by-annotated.expected.owl │ │ │ ├── created_by-annotated.meta.yaml │ │ │ └── created_by-annotated.obo │ │ ├── created_by │ │ │ ├── created_by.expected.json │ │ │ ├── created_by.expected.obo │ │ │ ├── created_by.expected.ofn │ │ │ ├── created_by.expected.owl │ │ │ ├── created_by.meta.yaml │ │ │ └── created_by.obo │ │ ├── creation_date-annotated │ │ │ ├── creation_date-annotated.expected.json │ │ │ ├── creation_date-annotated.expected.obo │ │ │ ├── creation_date-annotated.expected.ofn │ │ │ ├── creation_date-annotated.expected.owl │ │ │ ├── creation_date-annotated.meta.yaml │ │ │ └── creation_date-annotated.obo │ │ ├── creation_date │ │ │ ├── creation_date.expected.json │ │ │ ├── creation_date.expected.obo │ │ │ ├── creation_date.expected.ofn │ │ │ ├── creation_date.expected.owl │ │ │ ├── creation_date.meta.yaml │ │ │ └── creation_date.obo │ │ ├── default-namespace │ │ │ ├── default-namespace.expected.json │ │ │ ├── default-namespace.expected.obo │ │ │ ├── default-namespace.expected.ofn │ │ │ ├── default-namespace.expected.owl │ │ │ ├── default-namespace.meta.yaml │ │ │ └── default-namespace.obo │ │ ├── definition-annotated │ │ │ ├── definition-annotated.expected.json │ │ │ ├── definition-annotated.expected.obo │ │ │ ├── definition-annotated.expected.ofn │ │ │ ├── definition-annotated.expected.owl │ │ │ ├── definition-annotated.meta.yaml │ │ │ └── definition-annotated.obo │ │ ├── definition-xref │ │ │ ├── definition-xref.expected.json │ │ │ ├── definition-xref.expected.obo │ │ │ ├── definition-xref.expected.ofn │ │ │ ├── definition-xref.expected.owl │ │ │ ├── definition-xref.meta.yaml │ │ │ └── definition-xref.obo │ │ ├── definition │ │ │ ├── definition.expected.json │ │ │ ├── definition.expected.obo │ │ │ ├── definition.expected.ofn │ │ │ ├── definition.expected.owl │ │ │ ├── definition.meta.yaml │ │ │ └── definition.obo │ │ ├── disjoint_from-annotated │ │ │ ├── disjoint_from-annotated.expected.json │ │ │ ├── disjoint_from-annotated.expected.obo │ │ │ ├── disjoint_from-annotated.expected.ofn │ │ │ ├── disjoint_from-annotated.expected.owl │ │ │ ├── disjoint_from-annotated.meta.yaml │ │ │ └── disjoint_from-annotated.obo │ │ ├── disjoint_from │ │ │ ├── disjoint_from.expected.json │ │ │ ├── disjoint_from.expected.obo │ │ │ ├── disjoint_from.expected.ofn │ │ │ ├── disjoint_from.expected.owl │ │ │ ├── disjoint_from.meta.yaml │ │ │ └── disjoint_from.obo │ │ ├── equivalent_to-annotated │ │ │ ├── equivalent_to-annotated.expected.json │ │ │ ├── equivalent_to-annotated.expected.obo │ │ │ ├── equivalent_to-annotated.expected.ofn │ │ │ ├── equivalent_to-annotated.expected.owl │ │ │ ├── equivalent_to-annotated.meta.yaml │ │ │ └── equivalent_to-annotated.obo │ │ ├── equivalent_to │ │ │ ├── equivalent_to.expected.json │ │ │ ├── equivalent_to.expected.obo │ │ │ ├── equivalent_to.expected.ofn │ │ │ ├── equivalent_to.expected.owl │ │ │ ├── equivalent_to.meta.yaml │ │ │ └── equivalent_to.obo │ │ ├── exact_synonym │ │ │ ├── exact_synonym.expected.json │ │ │ ├── exact_synonym.expected.obo │ │ │ ├── exact_synonym.expected.ofn │ │ │ ├── exact_synonym.expected.owl │ │ │ ├── exact_synonym.meta.yaml │ │ │ └── exact_synonym.obo │ │ ├── expansion-conflict-main-idspace │ │ │ ├── expansion-conflict-main-idspace.meta.yaml │ │ │ └── expansion-conflict-main-idspace.obo │ │ ├── gci-is-a │ │ │ ├── gci-is-a.expected.json │ │ │ ├── gci-is-a.expected.obo │ │ │ ├── gci-is-a.expected.ofn │ │ │ ├── gci-is-a.expected.owl │ │ │ ├── gci-is-a.meta.yaml │ │ │ └── gci-is-a.obo │ │ ├── gci-relation │ │ │ ├── gci-relation.expected.json │ │ │ ├── gci-relation.expected.obo │ │ │ ├── gci-relation.expected.ofn │ │ │ ├── gci-relation.expected.owl │ │ │ ├── gci-relation.meta.yaml │ │ │ └── gci-relation.obo │ │ ├── intersection_of-genus-differentia-annotated │ │ │ ├── intersection_of-genus-differentia-annotated.expected.json │ │ │ ├── intersection_of-genus-differentia-annotated.expected.obo │ │ │ ├── intersection_of-genus-differentia-annotated.expected.ofn │ │ │ ├── intersection_of-genus-differentia-annotated.expected.owl │ │ │ ├── intersection_of-genus-differentia-annotated.meta.yaml │ │ │ └── intersection_of-genus-differentia-annotated.obo │ │ ├── intersection_of-genus-differentia │ │ │ ├── intersection_of-genus-differentia.expected.json │ │ │ ├── intersection_of-genus-differentia.expected.obo │ │ │ ├── intersection_of-genus-differentia.expected.ofn │ │ │ ├── intersection_of-genus-differentia.expected.owl │ │ │ ├── intersection_of-genus-differentia.meta.yaml │ │ │ └── intersection_of-genus-differentia.obo │ │ ├── intersection_of-genus-pair │ │ │ ├── intersection_of-genus-pair.expected.json │ │ │ ├── intersection_of-genus-pair.expected.obo │ │ │ ├── intersection_of-genus-pair.expected.ofn │ │ │ ├── intersection_of-genus-pair.expected.owl │ │ │ ├── intersection_of-genus-pair.meta.yaml │ │ │ └── intersection_of-genus-pair.obo │ │ ├── invalid-intersection_of-single-element │ │ │ ├── invalid-intersection_of-single-element.meta.yaml │ │ │ └── invalid-intersection_of-single-element.obo │ │ ├── invalid-name-duplicate │ │ │ ├── invalid-name-duplicate.meta.yaml │ │ │ └── invalid-name-duplicate.obo │ │ ├── invalid-owl-axioms-owl-syntax │ │ │ ├── invalid-owl-axioms-owl-syntax.meta.yaml │ │ │ └── invalid-owl-axioms-owl-syntax.obo │ │ ├── is_a-annotated-prefix │ │ │ ├── is_a-annotated-prefix.expected.json │ │ │ ├── is_a-annotated-prefix.expected.obo │ │ │ ├── is_a-annotated-prefix.expected.ofn │ │ │ ├── is_a-annotated-prefix.expected.owl │ │ │ ├── is_a-annotated-prefix.meta.yaml │ │ │ └── is_a-annotated-prefix.obo │ │ ├── is_a-annotated │ │ │ ├── is_a-annotated.expected.json │ │ │ ├── is_a-annotated.expected.obo │ │ │ ├── is_a-annotated.expected.ofn │ │ │ ├── is_a-annotated.expected.owl │ │ │ ├── is_a-annotated.meta.yaml │ │ │ └── is_a-annotated.obo │ │ ├── is_a │ │ │ ├── is_a.expected.json │ │ │ ├── is_a.expected.obo │ │ │ ├── is_a.expected.ofn │ │ │ ├── is_a.expected.owl │ │ │ ├── is_a.meta.yaml │ │ │ └── is_a.obo │ │ ├── is_anti_symmetric │ │ │ ├── is_anti_symmetric.expected.json │ │ │ ├── is_anti_symmetric.expected.obo │ │ │ ├── is_anti_symmetric.expected.ofn │ │ │ ├── is_anti_symmetric.expected.owl │ │ │ ├── is_anti_symmetric.meta.yaml │ │ │ └── is_anti_symmetric.obo │ │ ├── is_cyclic │ │ │ ├── is_cyclic.expected.json │ │ │ ├── is_cyclic.expected.obo │ │ │ ├── is_cyclic.expected.ofn │ │ │ ├── is_cyclic.expected.owl │ │ │ ├── is_cyclic.meta.yaml │ │ │ └── is_cyclic.obo │ │ ├── is_functional │ │ │ ├── is_functional.expected.json │ │ │ ├── is_functional.expected.obo │ │ │ ├── is_functional.expected.ofn │ │ │ ├── is_functional.expected.owl │ │ │ ├── is_functional.meta.yaml │ │ │ └── is_functional.obo │ │ ├── is_inverse_functional │ │ │ ├── is_inverse_functional.expected.json │ │ │ ├── is_inverse_functional.expected.obo │ │ │ ├── is_inverse_functional.expected.ofn │ │ │ ├── is_inverse_functional.expected.owl │ │ │ ├── is_inverse_functional.meta.yaml │ │ │ └── is_inverse_functional.obo │ │ ├── is_symmetric │ │ │ ├── is_symmetric.expected.json │ │ │ ├── is_symmetric.expected.obo │ │ │ ├── is_symmetric.expected.ofn │ │ │ ├── is_symmetric.expected.owl │ │ │ ├── is_symmetric.meta.yaml │ │ │ └── is_symmetric.obo │ │ ├── is_transitive │ │ │ ├── is_transitive.expected.json │ │ │ ├── is_transitive.expected.obo │ │ │ ├── is_transitive.expected.ofn │ │ │ ├── is_transitive.expected.owl │ │ │ ├── is_transitive.meta.yaml │ │ │ └── is_transitive.obo │ │ ├── name-annotated │ │ │ ├── name-annotated.expected.json │ │ │ ├── name-annotated.expected.obo │ │ │ ├── name-annotated.expected.ofn │ │ │ ├── name-annotated.expected.owl │ │ │ ├── name-annotated.meta.yaml │ │ │ └── name-annotated.obo │ │ ├── name │ │ │ ├── name.expected.json │ │ │ ├── name.expected.obo │ │ │ ├── name.expected.ofn │ │ │ ├── name.expected.owl │ │ │ ├── name.meta.yaml │ │ │ └── name.obo │ │ ├── namespace │ │ │ ├── namespace.expected.json │ │ │ ├── namespace.expected.obo │ │ │ ├── namespace.expected.ofn │ │ │ ├── namespace.expected.owl │ │ │ ├── namespace.meta.yaml │ │ │ └── namespace.obo │ │ ├── narrow_synonym │ │ │ ├── narrow_synonym.expected.json │ │ │ ├── narrow_synonym.expected.obo │ │ │ ├── narrow_synonym.expected.ofn │ │ │ ├── narrow_synonym.expected.owl │ │ │ ├── narrow_synonym.meta.yaml │ │ │ └── narrow_synonym.obo │ │ ├── obsolete-annotated │ │ │ ├── obsolete-annotated.expected.json │ │ │ ├── obsolete-annotated.expected.obo │ │ │ ├── obsolete-annotated.expected.ofn │ │ │ ├── obsolete-annotated.expected.owl │ │ │ ├── obsolete-annotated.meta.yaml │ │ │ └── obsolete-annotated.obo │ │ ├── obsolete │ │ │ ├── obsolete.expected.json │ │ │ ├── obsolete.expected.obo │ │ │ ├── obsolete.expected.ofn │ │ │ ├── obsolete.expected.owl │ │ │ ├── obsolete.meta.yaml │ │ │ └── obsolete.obo │ │ ├── owl-axioms-ObjectInverseOf │ │ │ ├── owl-axioms-ObjectInverseOf.expected.json │ │ │ ├── owl-axioms-ObjectInverseOf.expected.obo │ │ │ ├── owl-axioms-ObjectInverseOf.expected.ofn │ │ │ ├── owl-axioms-ObjectInverseOf.expected.owl │ │ │ ├── owl-axioms-ObjectInverseOf.meta.yaml │ │ │ └── owl-axioms-ObjectInverseOf.obo │ │ ├── prefixes-conflict-main-idspace │ │ │ ├── prefixes-conflict-main-idspace.meta.yaml │ │ │ └── prefixes-conflict-main-idspace.obo │ │ ├── prefixes-conflict-oio │ │ │ ├── prefixes-conflict-oio.expected.json │ │ │ ├── prefixes-conflict-oio.expected.obo │ │ │ ├── prefixes-conflict-oio.expected.ofn │ │ │ ├── prefixes-conflict-oio.expected.owl │ │ │ ├── prefixes-conflict-oio.meta.yaml │ │ │ └── prefixes-conflict-oio.obo │ │ ├── prefixes-conflict-skos │ │ │ ├── prefixes-conflict-skos.expected.json │ │ │ ├── prefixes-conflict-skos.expected.obo │ │ │ ├── prefixes-conflict-skos.expected.ofn │ │ │ ├── prefixes-conflict-skos.expected.owl │ │ │ ├── prefixes-conflict-skos.meta.yaml │ │ │ └── prefixes-conflict-skos.obo │ │ ├── prefixes-created_by │ │ │ ├── prefixes-created_by.expected.json │ │ │ ├── prefixes-created_by.expected.obo │ │ │ ├── prefixes-created_by.expected.ofn │ │ │ ├── prefixes-created_by.expected.owl │ │ │ ├── prefixes-created_by.meta.yaml │ │ │ └── prefixes-created_by.obo │ │ ├── prefixes-xref │ │ │ ├── prefixes-xref.expected.json │ │ │ ├── prefixes-xref.expected.obo │ │ │ ├── prefixes-xref.expected.ofn │ │ │ ├── prefixes-xref.expected.owl │ │ │ ├── prefixes-xref.meta.yaml │ │ │ └── prefixes-xref.obo │ │ ├── prefixes │ │ │ ├── prefixes.expected.json │ │ │ ├── prefixes.expected.obo │ │ │ ├── prefixes.expected.ofn │ │ │ ├── prefixes.expected.owl │ │ │ ├── prefixes.meta.yaml │ │ │ └── prefixes.obo │ │ ├── property_value-anyURI │ │ │ ├── property_value-anyURI.expected.json │ │ │ ├── property_value-anyURI.expected.obo │ │ │ ├── property_value-anyURI.expected.ofn │ │ │ ├── property_value-anyURI.expected.owl │ │ │ ├── property_value-anyURI.meta.yaml │ │ │ └── property_value-anyURI.obo │ │ ├── property_value-float │ │ │ ├── property_value-float.expected.json │ │ │ ├── property_value-float.expected.obo │ │ │ ├── property_value-float.expected.ofn │ │ │ ├── property_value-float.expected.owl │ │ │ ├── property_value-float.meta.yaml │ │ │ └── property_value-float.obo │ │ ├── property_value-id-tag │ │ │ ├── property_value-id-tag.expected.json │ │ │ ├── property_value-id-tag.expected.obo │ │ │ ├── property_value-id-tag.expected.ofn │ │ │ ├── property_value-id-tag.expected.owl │ │ │ ├── property_value-id-tag.meta.yaml │ │ │ └── property_value-id-tag.obo │ │ ├── property_value-object-annotated │ │ │ ├── property_value-object-annotated.expected.json │ │ │ ├── property_value-object-annotated.expected.obo │ │ │ ├── property_value-object-annotated.expected.ofn │ │ │ ├── property_value-object-annotated.expected.owl │ │ │ ├── property_value-object-annotated.meta.yaml │ │ │ └── property_value-object-annotated.obo │ │ ├── property_value-object │ │ │ ├── property_value-object.expected.json │ │ │ ├── property_value-object.expected.obo │ │ │ ├── property_value-object.expected.ofn │ │ │ ├── property_value-object.expected.owl │ │ │ ├── property_value-object.meta.yaml │ │ │ └── property_value-object.obo │ │ ├── property_value-skos-object │ │ │ ├── property_value-skos-object.expected.json │ │ │ ├── property_value-skos-object.expected.obo │ │ │ ├── property_value-skos-object.expected.ofn │ │ │ ├── property_value-skos-object.expected.owl │ │ │ ├── property_value-skos-object.meta.yaml │ │ │ └── property_value-skos-object.obo │ │ ├── property_value-string-annotated │ │ │ ├── property_value-string-annotated.expected.json │ │ │ ├── property_value-string-annotated.expected.obo │ │ │ ├── property_value-string-annotated.expected.ofn │ │ │ ├── property_value-string-annotated.expected.owl │ │ │ ├── property_value-string-annotated.meta.yaml │ │ │ └── property_value-string-annotated.obo │ │ ├── property_value-string │ │ │ ├── property_value-string.expected.json │ │ │ ├── property_value-string.expected.obo │ │ │ ├── property_value-string.expected.ofn │ │ │ ├── property_value-string.expected.owl │ │ │ ├── property_value-string.meta.yaml │ │ │ └── property_value-string.obo │ │ ├── related_synonym │ │ │ ├── related_synonym.expected.json │ │ │ ├── related_synonym.expected.obo │ │ │ ├── related_synonym.expected.ofn │ │ │ ├── related_synonym.expected.owl │ │ │ ├── related_synonym.meta.yaml │ │ │ └── related_synonym.obo │ │ ├── relationship-annotated │ │ │ ├── relationship-annotated.expected.json │ │ │ ├── relationship-annotated.expected.obo │ │ │ ├── relationship-annotated.expected.ofn │ │ │ ├── relationship-annotated.expected.owl │ │ │ ├── relationship-annotated.meta.yaml │ │ │ └── relationship-annotated.obo │ │ ├── relationship-non-logical │ │ │ ├── relationship-non-logical.expected.json │ │ │ ├── relationship-non-logical.expected.obo │ │ │ ├── relationship-non-logical.expected.ofn │ │ │ ├── relationship-non-logical.expected.owl │ │ │ ├── relationship-non-logical.meta.yaml │ │ │ └── relationship-non-logical.obo │ │ ├── relationship-skos-object │ │ │ ├── relationship-skos-object.expected.json │ │ │ ├── relationship-skos-object.expected.obo │ │ │ ├── relationship-skos-object.expected.ofn │ │ │ ├── relationship-skos-object.expected.owl │ │ │ ├── relationship-skos-object.meta.yaml │ │ │ └── relationship-skos-object.obo │ │ ├── relationship │ │ │ ├── relationship.expected.json │ │ │ ├── relationship.expected.obo │ │ │ ├── relationship.expected.ofn │ │ │ ├── relationship.expected.owl │ │ │ ├── relationship.meta.yaml │ │ │ └── relationship.obo │ │ ├── replaced_by-annotated │ │ │ ├── replaced_by-annotated.expected.json │ │ │ ├── replaced_by-annotated.expected.obo │ │ │ ├── replaced_by-annotated.expected.ofn │ │ │ ├── replaced_by-annotated.expected.owl │ │ │ ├── replaced_by-annotated.meta.yaml │ │ │ └── replaced_by-annotated.obo │ │ ├── replaced_by │ │ │ ├── replaced_by.expected.json │ │ │ ├── replaced_by.expected.obo │ │ │ ├── replaced_by.expected.ofn │ │ │ ├── replaced_by.expected.owl │ │ │ ├── replaced_by.meta.yaml │ │ │ └── replaced_by.obo │ │ ├── skos-xref-duplicate │ │ │ ├── skos-xref-duplicate.expected.json │ │ │ ├── skos-xref-duplicate.expected.obo │ │ │ ├── skos-xref-duplicate.expected.ofn │ │ │ ├── skos-xref-duplicate.expected.owl │ │ │ ├── skos-xref-duplicate.meta.yaml │ │ │ └── skos-xref-duplicate.obo │ │ ├── subset-annotated │ │ │ ├── subset-annotated.expected.json │ │ │ ├── subset-annotated.expected.obo │ │ │ ├── subset-annotated.expected.ofn │ │ │ ├── subset-annotated.expected.owl │ │ │ ├── subset-annotated.meta.yaml │ │ │ └── subset-annotated.obo │ │ ├── subset │ │ │ ├── subset.expected.json │ │ │ ├── subset.expected.obo │ │ │ ├── subset.expected.ofn │ │ │ ├── subset.expected.owl │ │ │ ├── subset.meta.yaml │ │ │ └── subset.obo │ │ ├── synonym-with-multiple_xrefs │ │ │ ├── synonym-with-multiple_xrefs.expected.json │ │ │ ├── synonym-with-multiple_xrefs.expected.obo │ │ │ ├── synonym-with-multiple_xrefs.expected.ofn │ │ │ ├── synonym-with-multiple_xrefs.expected.owl │ │ │ ├── synonym-with-multiple_xrefs.meta.yaml │ │ │ └── synonym-with-multiple_xrefs.obo │ │ ├── synonym-with-scope-and-xref │ │ │ ├── synonym-with-scope-and-xref.expected.json │ │ │ ├── synonym-with-scope-and-xref.expected.obo │ │ │ ├── synonym-with-scope-and-xref.expected.ofn │ │ │ ├── synonym-with-scope-and-xref.expected.owl │ │ │ ├── synonym-with-scope-and-xref.meta.yaml │ │ │ └── synonym-with-scope-and-xref.obo │ │ ├── synonym-with-type │ │ │ ├── synonym-with-type.expected.json │ │ │ ├── synonym-with-type.expected.obo │ │ │ ├── synonym-with-type.expected.ofn │ │ │ ├── synonym-with-type.expected.owl │ │ │ ├── synonym-with-type.meta.yaml │ │ │ └── synonym-with-type.obo │ │ ├── synonym-with-xref │ │ │ ├── synonym-with-xref.expected.json │ │ │ ├── synonym-with-xref.expected.obo │ │ │ ├── synonym-with-xref.expected.ofn │ │ │ ├── synonym-with-xref.expected.owl │ │ │ ├── synonym-with-xref.meta.yaml │ │ │ └── synonym-with-xref.obo │ │ ├── synonym-without-scope │ │ │ ├── synonym-without-scope.meta.yaml │ │ │ └── synonym-without-scope.obo │ │ ├── synonymtypedef-definition │ │ │ ├── synonymtypedef-definition.expected.json │ │ │ ├── synonymtypedef-definition.expected.obo │ │ │ ├── synonymtypedef-definition.expected.ofn │ │ │ ├── synonymtypedef-definition.expected.owl │ │ │ ├── synonymtypedef-definition.meta.yaml │ │ │ └── synonymtypedef-definition.obo │ │ ├── typedef-declaration │ │ │ ├── typedef-declaration.expected.json │ │ │ ├── typedef-declaration.expected.obo │ │ │ ├── typedef-declaration.expected.ofn │ │ │ ├── typedef-declaration.expected.owl │ │ │ ├── typedef-declaration.meta.yaml │ │ │ └── typedef-declaration.obo │ │ ├── typedef-def │ │ │ ├── typedef-def.expected.json │ │ │ ├── typedef-def.expected.obo │ │ │ ├── typedef-def.expected.ofn │ │ │ ├── typedef-def.expected.owl │ │ │ ├── typedef-def.meta.yaml │ │ │ └── typedef-def.obo │ │ ├── typedef-domain │ │ │ ├── typedef-domain.expected.json │ │ │ ├── typedef-domain.expected.obo │ │ │ ├── typedef-domain.expected.ofn │ │ │ ├── typedef-domain.expected.owl │ │ │ ├── typedef-domain.meta.yaml │ │ │ └── typedef-domain.obo │ │ ├── typedef-inverse_of │ │ │ ├── typedef-inverse_of.expected.json │ │ │ ├── typedef-inverse_of.expected.obo │ │ │ ├── typedef-inverse_of.expected.ofn │ │ │ ├── typedef-inverse_of.expected.owl │ │ │ ├── typedef-inverse_of.meta.yaml │ │ │ └── typedef-inverse_of.obo │ │ ├── typedef-is_a-metadata │ │ │ ├── typedef-is_a-metadata.expected.json │ │ │ ├── typedef-is_a-metadata.expected.obo │ │ │ ├── typedef-is_a-metadata.expected.ofn │ │ │ ├── typedef-is_a-metadata.expected.owl │ │ │ ├── typedef-is_a-metadata.meta.yaml │ │ │ └── typedef-is_a-metadata.obo │ │ ├── typedef-is_a │ │ │ ├── typedef-is_a.expected.json │ │ │ ├── typedef-is_a.expected.obo │ │ │ ├── typedef-is_a.expected.ofn │ │ │ ├── typedef-is_a.expected.owl │ │ │ ├── typedef-is_a.meta.yaml │ │ │ └── typedef-is_a.obo │ │ ├── typedef-is_class_level │ │ │ ├── typedef-is_class_level.expected.json │ │ │ ├── typedef-is_class_level.expected.obo │ │ │ ├── typedef-is_class_level.expected.ofn │ │ │ ├── typedef-is_class_level.expected.owl │ │ │ ├── typedef-is_class_level.meta.yaml │ │ │ └── typedef-is_class_level.obo │ │ ├── typedef-is_metadata_tag-is_class_level │ │ │ ├── typedef-is_metadata_tag-is_class_level.expected.json │ │ │ ├── typedef-is_metadata_tag-is_class_level.expected.obo │ │ │ ├── typedef-is_metadata_tag-is_class_level.expected.ofn │ │ │ ├── typedef-is_metadata_tag-is_class_level.expected.owl │ │ │ ├── typedef-is_metadata_tag-is_class_level.meta.yaml │ │ │ └── typedef-is_metadata_tag-is_class_level.obo │ │ ├── typedef-is_metadata_tag │ │ │ ├── typedef-is_metadata_tag.expected.json │ │ │ ├── typedef-is_metadata_tag.expected.obo │ │ │ ├── typedef-is_metadata_tag.expected.ofn │ │ │ ├── typedef-is_metadata_tag.expected.owl │ │ │ ├── typedef-is_metadata_tag.meta.yaml │ │ │ └── typedef-is_metadata_tag.obo │ │ ├── typedef-name │ │ │ ├── typedef-name.expected.json │ │ │ ├── typedef-name.expected.obo │ │ │ ├── typedef-name.expected.ofn │ │ │ ├── typedef-name.expected.owl │ │ │ ├── typedef-name.meta.yaml │ │ │ └── typedef-name.obo │ │ ├── typedef-range │ │ │ ├── typedef-range.expected.json │ │ │ ├── typedef-range.expected.obo │ │ │ ├── typedef-range.expected.ofn │ │ │ ├── typedef-range.expected.owl │ │ │ ├── typedef-range.meta.yaml │ │ │ └── typedef-range.obo │ │ ├── typedef-transitive_over │ │ │ ├── typedef-transitive_over.expected.json │ │ │ ├── typedef-transitive_over.expected.obo │ │ │ ├── typedef-transitive_over.expected.ofn │ │ │ ├── typedef-transitive_over.expected.owl │ │ │ ├── typedef-transitive_over.meta.yaml │ │ │ └── typedef-transitive_over.obo │ │ ├── typedef-xref-anyiri-ann │ │ │ ├── typedef-xref-anyiri-ann.expected.json │ │ │ ├── typedef-xref-anyiri-ann.expected.obo │ │ │ ├── typedef-xref-anyiri-ann.expected.ofn │ │ │ ├── typedef-xref-anyiri-ann.expected.owl │ │ │ ├── typedef-xref-anyiri-ann.meta.yaml │ │ │ └── typedef-xref-anyiri-ann.obo │ │ ├── typedef-xref-anyiri │ │ │ ├── typedef-xref-anyiri.expected.json │ │ │ ├── typedef-xref-anyiri.expected.obo │ │ │ ├── typedef-xref-anyiri.expected.ofn │ │ │ ├── typedef-xref-anyiri.expected.owl │ │ │ ├── typedef-xref-anyiri.meta.yaml │ │ │ └── typedef-xref-anyiri.obo │ │ ├── typedef-xref-ro │ │ │ ├── typedef-xref-ro.expected.json │ │ │ ├── typedef-xref-ro.expected.obo │ │ │ ├── typedef-xref-ro.expected.ofn │ │ │ ├── typedef-xref-ro.expected.owl │ │ │ ├── typedef-xref-ro.meta.yaml │ │ │ └── typedef-xref-ro.obo │ │ ├── typedef-xref │ │ │ ├── typedef-xref.expected.json │ │ │ ├── typedef-xref.expected.obo │ │ │ ├── typedef-xref.expected.ofn │ │ │ ├── typedef-xref.expected.owl │ │ │ ├── typedef-xref.meta.yaml │ │ │ └── typedef-xref.obo │ │ ├── union_of-annotated │ │ │ ├── union_of-annotated.expected.json │ │ │ ├── union_of-annotated.expected.obo │ │ │ ├── union_of-annotated.expected.ofn │ │ │ ├── union_of-annotated.expected.owl │ │ │ ├── union_of-annotated.meta.yaml │ │ │ └── union_of-annotated.obo │ │ ├── union_of │ │ │ ├── union_of.expected.json │ │ │ ├── union_of.expected.obo │ │ │ ├── union_of.expected.ofn │ │ │ ├── union_of.expected.owl │ │ │ ├── union_of.meta.yaml │ │ │ └── union_of.obo │ │ ├── xref-annotated │ │ │ ├── xref-annotated.expected.json │ │ │ ├── xref-annotated.expected.obo │ │ │ ├── xref-annotated.expected.ofn │ │ │ ├── xref-annotated.expected.owl │ │ │ ├── xref-annotated.meta.yaml │ │ │ └── xref-annotated.obo │ │ └── xref │ │ │ ├── xref.expected.json │ │ │ ├── xref.expected.obo │ │ │ ├── xref.expected.ofn │ │ │ ├── xref.expected.owl │ │ │ ├── xref.meta.yaml │ │ │ └── xref.obo │ ├── obsoletion_test.db │ ├── obsoletion_test.json │ ├── obsoletion_test.obo │ ├── obsoletion_test.owl │ ├── obsoletion_test_pre.obo │ ├── soil-profile.skos.nt │ ├── sort-test.obo │ ├── ssn.db │ ├── ssn.owl │ ├── synonym-test.obo │ ├── synonym-test.owl │ ├── taxon-constraint-test.obo │ ├── test-create.kgcl.txt │ ├── test-pairwise-associations.tsv │ ├── test-uniprot.gaf │ ├── test.hpoa.tsv │ ├── test.hpoa_g2p.tsv │ ├── test.phaf.tsv │ ├── test_ic.tsv │ ├── test_import_root.obo │ ├── test_import_root.owl │ ├── test_imported_ontology.obo │ ├── test_imported_ontology.owl │ ├── test_simpleobo.obo │ ├── three-way-mapping.obo │ ├── three-way-mapping.owl.ttl │ ├── uniprot-P12345.json │ ├── unreciprocated-mapping-test.expected.bidi.diff.yaml │ ├── unreciprocated-mapping-test.expected.l2r.diff.yaml │ ├── unreciprocated-mapping-test.obo │ ├── unreciprocated-mapping-test.owl │ ├── unreciprocated-mapping-test.sssom.tsv │ └── value_set_example.yaml ├── integration_tests │ ├── __init__.py │ └── test_sqlite_full.py ├── output │ └── README.md ├── test_cli.py ├── test_converters │ ├── __init__.py │ ├── test_logical_definition_flattener_converter.py │ ├── test_obo_format.py │ ├── test_obo_graph_to_cx.py │ ├── test_obo_graph_to_fhir.py │ ├── test_obo_graph_to_obo_format.py │ └── test_obo_graph_to_rdf_owl_converter.py ├── test_datamodels │ ├── __init__.py │ ├── test_obograph_datamodel.py │ ├── test_ontology_metadata_datamodel.py │ ├── test_search_datamodel.py │ ├── test_text_annotator_datamodel.py │ └── test_validation_datamodel.py ├── test_implementations │ ├── __init__.py │ ├── test_aggregator.py │ ├── test_amigo.py │ ├── test_bioportal.py │ ├── test_cx.py │ ├── test_funowl.py │ ├── test_gilda.py │ ├── test_ncbigene.py │ ├── test_obograph.py │ ├── test_ols.py │ ├── test_ontobee.py │ ├── test_pantherdb.py │ ├── test_pronto.py │ ├── test_pubmed.py │ ├── test_robot_template.py │ ├── test_semsimian_implementation.py │ ├── test_simple_obo.py │ ├── test_sparql.py │ ├── test_sqldb.py │ ├── test_translator.py │ ├── test_ubergraph.py │ ├── test_uniprot.py │ └── test_wikidata.py ├── test_indexes │ ├── __init__.py │ └── test_edge_index.py ├── test_inference │ ├── __init__.py │ └── test_relation_graph_reasoner.py ├── test_parsers │ ├── __init__.py │ ├── test_boomer_parser.py │ ├── test_gaf_association_parser.py │ ├── test_gencc_association_parser.py │ ├── test_hpoa_association_parser.py │ ├── test_hpoa_g2d_association_parser.py │ ├── test_hpoa_g2p_association_parser.py │ ├── test_mim2gene_association_parser.py │ ├── test_obojson_parser.py │ ├── test_pairwise_association_parser.py │ ├── test_phaf_association_parser.py │ └── test_xaf_association_parser.py ├── test_pv_syntax_expander.py ├── test_selector.py ├── test_utilities │ ├── __init__.py │ ├── test_association_diffs.py │ ├── test_association_index.py │ ├── test_boomer_utils.py │ ├── test_caching.py │ ├── test_chunker.py │ ├── test_cross_ontology_diff.py │ ├── test_disjointness_analysis.py │ ├── test_kgcl_utilities.py │ ├── test_lexical_index.py │ ├── test_logical_definition_summarizer.py │ ├── test_mapping_validation.py │ ├── test_networkx_bridge.py │ ├── test_obograph_utils.py │ ├── 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