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
- 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
- Subsetting
- Validator Interface
- Relation Graph
- 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()
- 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
- Summary Statistics
- Differ Interface
- Patcher Interface
- 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.load_information_content_scores()
SemanticSimilarityInterface.set_information_content_scores()
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