Interfaces

oaklib provides a variety of interfaces that abstract away from implementation details and provide a coherent set of operations to perform on an ontology. Developers can code to the interface largely without worrying about whether the implementation is a relational database, a local file, etc.

For example, the Ubergraph Adapter implements Search Interface which has the method oaklib.interfaces.search_interface.SearchInterface.basic_search(), so you can write code like this:

>>> from oaklib import get_adapter
>>> adapter = get_adapter("sqlite:obo:uberon")
>>> for r in adapter.descendants('UBERON:0003884'):
...     print(r)

...

...

The most common operations are found in the Basic Ontology Interface

Contents:

• Basic Ontology Interface
  • BasicOntologyInterface
    • BasicOntologyInterface.strict
    • BasicOntologyInterface.autosave
    • BasicOntologyInterface.exclude_owl_top_and_bottom
    • BasicOntologyInterface.ontology_metamodel_mapper
    • BasicOntologyInterface.auto_relax_axioms
    • BasicOntologyInterface.cache_lookups
    • BasicOntologyInterface.prefix_map()
    • BasicOntologyInterface.get_prefix_map()
    • BasicOntologyInterface.converter
    • BasicOntologyInterface.set_metamodel_mappings()
    • BasicOntologyInterface.curie_to_uri()
    • BasicOntologyInterface.uri_to_curie()
    • BasicOntologyInterface.edge_index
    • BasicOntologyInterface.entailed_edge_index
    • BasicOntologyInterface.multilingual
    • BasicOntologyInterface.languages()
    • BasicOntologyInterface.default_language
    • BasicOntologyInterface.ontologies()
    • BasicOntologyInterface.ontology_curies()
    • BasicOntologyInterface.all_ontology_curies()
    • BasicOntologyInterface.obsoletes()
    • BasicOntologyInterface.obsoletes_migration_relationships()
    • BasicOntologyInterface.all_obsolete_curies()
    • BasicOntologyInterface.dangling()
    • BasicOntologyInterface.ontology_versions()
    • BasicOntologyInterface.ontology_metadata_map()
    • BasicOntologyInterface.entities()
    • BasicOntologyInterface.all_entity_curies()
    • BasicOntologyInterface.owl_types()
    • BasicOntologyInterface.owl_type()
    • BasicOntologyInterface.defined_by()
    • BasicOntologyInterface.defined_bys()
    • BasicOntologyInterface.roots()
    • BasicOntologyInterface.leafs()
    • BasicOntologyInterface.singletons()
    • BasicOntologyInterface.subsets()
    • BasicOntologyInterface.subset_curies()
    • BasicOntologyInterface.all_subset_curies()
    • BasicOntologyInterface.subset_members()
    • BasicOntologyInterface.terms_subsets()
    • BasicOntologyInterface.terms_categories()
    • BasicOntologyInterface.curies_by_subset()
    • BasicOntologyInterface.label()
    • BasicOntologyInterface.get_label_by_curie()
    • BasicOntologyInterface.labels()
    • BasicOntologyInterface.multilingual_labels()
    • BasicOntologyInterface.get_labels_for_curies()
    • BasicOntologyInterface.set_label()
    • BasicOntologyInterface.curies_by_label()
    • BasicOntologyInterface.get_curies_by_label()
    • BasicOntologyInterface.comments()
    • BasicOntologyInterface.relationships()
    • BasicOntologyInterface.relationships_metadata()
    • BasicOntologyInterface.hierarchical_parents()
    • BasicOntologyInterface.outgoing_relationship_map()
    • BasicOntologyInterface.outgoing_relationships()
    • BasicOntologyInterface.incoming_relationship_map()
    • BasicOntologyInterface.incoming_relationships()
    • BasicOntologyInterface.all_relationships()
    • BasicOntologyInterface.definition()
    • BasicOntologyInterface.definitions()
    • BasicOntologyInterface.get_definition_by_curie()
    • BasicOntologyInterface.simple_mappings_by_curie()
    • BasicOntologyInterface.simple_mappings()
    • BasicOntologyInterface.entity_aliases()
    • BasicOntologyInterface.aliases_by_curie()
    • BasicOntologyInterface.entity_alias_map()
    • BasicOntologyInterface.alias_map_by_curie()
    • BasicOntologyInterface.entity_metadata_map()
    • BasicOntologyInterface.entities_metadata_statements()
    • BasicOntologyInterface.add_missing_property_values()
    • BasicOntologyInterface.create_entity()
    • BasicOntologyInterface.delete_entity()
    • BasicOntologyInterface.query()
    • BasicOntologyInterface.save()
    • BasicOntologyInterface.clone()
    • BasicOntologyInterface.precompute_lookups()
• Search Interface
  • SearchInterface
    • SearchInterface.basic_search()
    • SearchInterface.multiterm_search()
    • SearchInterface.autosave
    • SearchInterface.exclude_owl_top_and_bottom
  • SearchConfiguration
• Subsetting
  • SubsetterInterface
    • SubsetterInterface.extract_subset_ontology()
    • SubsetterInterface.gap_fill_relationships()
    • SubsetterInterface.autosave
    • SubsetterInterface.exclude_owl_top_and_bottom
• Validator Interface
  • Schema Validation
  • LLM-based validation
    • ValidatorInterface
• Relation Graph
  • RelationGraphInterface
    • RelationGraphInterface.entailed_outgoing_relationships()
    • RelationGraphInterface.entailed_incoming_relationships()
    • RelationGraphInterface.entailed_relationships_between()
    • RelationGraphInterface.autosave
    • RelationGraphInterface.exclude_owl_top_and_bottom
• Mapping Provider Interface
  • MappingProviderInterface
    • MappingProviderInterface.sssom_mappings()
    • MappingProviderInterface.sssom_mappings_by_source()
    • MappingProviderInterface.all_sssom_mappings()
    • MappingProviderInterface.get_sssom_mappings_by_curie()
    • MappingProviderInterface.get_transitive_mappings_by_curie()
    • MappingProviderInterface.normalize()
    • MappingProviderInterface.normalize_prefix()
    • MappingProviderInterface.create_normalization_map()
    • MappingProviderInterface.autosave
    • MappingProviderInterface.exclude_owl_top_and_bottom
• OboGraph Interface
  • OboGraphInterface
    • OboGraphInterface.enable_transitive_query_cache()
    • OboGraphInterface.disable_transitive_query_cache()
    • OboGraphInterface.node()
    • OboGraphInterface.nodes()
    • OboGraphInterface.edges()
    • OboGraphInterface.synonym_map_for_curies()
    • OboGraphInterface.direct_graph()
    • OboGraphInterface.ancestor_graph()
    • OboGraphInterface.descendant_graph()
    • OboGraphInterface.non_redundant_entailed_relationships()
    • OboGraphInterface.ancestors()
    • OboGraphInterface.descendants()
    • OboGraphInterface.descendant_count()
    • OboGraphInterface.subgraph_from_traversal()
    • OboGraphInterface.extract_graph()
    • OboGraphInterface.relationships_to_graph()
    • OboGraphInterface.walk_up_relationship_graph()
    • OboGraphInterface.paths()
    • OboGraphInterface.logical_definitions()
    • OboGraphInterface.disjoint_class_expressions_axioms()
    • OboGraphInterface.add_metadata()
    • OboGraphInterface.as_obograph()
    • OboGraphInterface.load_graph()
  • TraversalConfiguration
• Text Annotator Interface
  • TextAnnotatorInterface
    • TextAnnotatorInterface.lexical_index
    • TextAnnotatorInterface.cache_directory
    • TextAnnotatorInterface.rule_collection
    • TextAnnotatorInterface.annotate_text()
    • TextAnnotatorInterface.annotate_file()
    • TextAnnotatorInterface.annotate_tabular_file()
  • TextAnnotation
• Summary Statistics
  • SummaryStatisticsInterface
    • SummaryStatisticsInterface.global_summary_statistics()
    • SummaryStatisticsInterface.branch_summary_statistics()
    • SummaryStatisticsInterface.metadata_property_summary_statistics()
    • SummaryStatisticsInterface.summary_statistic_description()
• Differ Interface
  • DifferInterface
    • DifferInterface.grouped_diff()
    • DifferInterface.diff()
    • DifferInterface.diff_summary()
    • DifferInterface.compare_ontology_term_lists()
    • DifferInterface.autosave
    • DifferInterface.exclude_owl_top_and_bottom
• Patcher Interface
  • PatcherInterface
    • PatcherInterface.auto_add_contributor_using
    • PatcherInterface.ignore_invalid_changes
    • PatcherInterface.apply_patch()
    • PatcherInterface.migrate_curies()
    • PatcherInterface.save()
    • PatcherInterface.expand_changes()
    • PatcherInterface.expand_change()
    • PatcherInterface.undo()
    • PatcherInterface.reverse_changes()
• Semantic Similarity Interface
  • SemanticSimilarityInterface
    • SemanticSimilarityInterface.cached_information_content_map
    • SemanticSimilarityInterface.most_recent_common_ancestors()
    • SemanticSimilarityInterface.setwise_most_recent_common_ancestors()
    • SemanticSimilarityInterface.multiset_most_recent_common_ancestors()
    • SemanticSimilarityInterface.common_ancestors()
    • SemanticSimilarityInterface.get_information_content()
    • SemanticSimilarityInterface.information_content_scores()
    • SemanticSimilarityInterface.pairwise_similarity()
    • SemanticSimilarityInterface.all_by_all_pairwise_similarity()
• Association Provider Interface
  • AssociationProviderInterface
    • AssociationProviderInterface.associations()
    • AssociationProviderInterface.associations_subjects()
    • AssociationProviderInterface.associations_subject_search()
    • AssociationProviderInterface.association_pairwise_coassociations()
    • AssociationProviderInterface.add_associations()
    • AssociationProviderInterface.association_counts()
    • AssociationProviderInterface.association_subject_counts()
    • AssociationProviderInterface.map_associations()
    • AssociationProviderInterface.normalize_associations()
    • AssociationProviderInterface.normalize_association()
• Class Enrichment Calculation Interface
• Dumper Interface
• OWL Interface
  • OwlInterface
    • OwlInterface.subclass_axioms()
    • OwlInterface.equivalence_axioms()
    • OwlInterface.annotation_assertion_axioms()
    • OwlInterface.disjoint_pairs()
    • OwlInterface.is_disjoint()
    • OwlInterface.is_satisfiable()
    • OwlInterface.reasoner_configurations()
    • OwlInterface.axiom_is_about()
    • OwlInterface.axiom_references()
    • OwlInterface.property_characteristics()
    • OwlInterface.transitive_object_properties()
    • OwlInterface.simple_subproperty_of_chains()

Note

Some interfaces may not be “pure” interfaces is that they may provide a default implementation, which may or may not be overridden by an implementation