Graph Utils#

Utility methods for working with graphs.

kgx.utils.graph_utils#

kgx.utils.graph_utils.curie_lookup(curie: str) → Optional[str][source]#

Given a CURIE, find its label.

This method first does a lookup in predefined maps. If none found, it makes use of CurieLookupService to look for the CURIE in a set of preloaded ontologies.

Parameters:

curie (str) – A CURIE

Returns:

The label corresponding to the given CURIE

Return type:

Optional[str]

kgx.utils.graph_utils.get_ancestors(graph: BaseGraph, node: str, relations: Optional[List[str]] = None) → List[str][source]#

Return all ancestors of specified node, filtered by relations.

Parameters:
Returns:

A list of ancestor nodes

Return type:

List[str]

kgx.utils.graph_utils.get_category_via_superclass(graph: BaseGraph, curie: str, load_ontology: bool = True) → Set[str][source]#

Get category for a given CURIE by tracing its superclass, via subclass_of hierarchy, and getting the most appropriate category based on the superclass.

Parameters:

  • graph (kgx.graph.base_graph.BaseGraph) – Graph to traverse

  • curie (str) – Input CURIE

  • load_ontology (bool) – Determines whether to load ontology, based on CURIE prefix, or to simply rely on subclass_of hierarchy from graph

Returns:

A set containing one (or more) category for the given CURIE

Return type:

Set[str]

kgx.utils.graph_utils.get_parents(graph: BaseGraph, node: str, relations: Optional[List[str]] = None) → List[str][source]#

Return all direct parents of a specified node, filtered by relations.

Parameters:
Returns:

A list of parent node(s)

Return type:

List[str]