biocypher._ontology.Ontology

class biocypher._ontology.Ontology(head_ontology: dict, ontology_mapping: Optional[OntologyMapping] = None, tail_ontologies: dict | None = None)

A class that represents the ontological “backbone” of a BioCypher knowledge graph. The ontology can be built from a single resource, or hybridised from a combination of resources, with one resource being the “head” ontology, while an arbitrary number of other resources can become “tail” ontologies at arbitrary fusion points inside the “head” ontology.

__init__(head_ontology: dict, ontology_mapping: Optional[OntologyMapping] = None, tail_ontologies: dict | None = None)

Initialize the Ontology class.

Args:

head_ontology (OntologyAdapter): The head ontology.

tail_ontologies (list): A list of OntologyAdapters that will be

added to the head ontology. Defaults to None.

Methods

__init__(head_ontology[, ontology_mapping, ...])	Initialize the Ontology class.
get_ancestors(node_label)	Get the ancestors of a node in the ontology.
get_dict()	Returns a dictionary compatible with a BioCypher node for compatibility with the Neo4j driver.
show_ontology_structure([to_disk, full])	Show the ontology structure using treelib or write to GRAPHML file.