Operations¶

This module provides a set of operations that are supported by KGX.

Clique Merge¶

class kgx.operations.clique_merge.CliqueMerge(prefix_prioritization_map: dict = None)[source]¶

Bases: object

build_cliques(target_graph: networkx.classes.multidigraph.MultiDiGraph)[source]¶

Builds a clique graph from same_as edges in target_graph.

Parameters: target_graph (networkx.MultiDiGraph) – A MultiDiGraph that contains nodes and edges
Returns: The clique graph with only same_as edges
Return type: networkx.Graph

consolidate_edges() → networkx.classes.multidigraph.MultiDiGraph[source]¶

Move all edges from nodes in a clique to the clique leader.

Returns: The target graph where all edges from nodes in a clique are moved to clique leader
Return type: nx.MultiDiGraph

get_category_from_equivalence(node: str, attributes: dict) → str[source]¶

Get category for a node based on its equivalent nodes in a graph.

Parameters

Returns

Category for the node

Return type

str

get_leader_by_annotation(clique: list) → Tuple[Optional[str], Optional[str]][source]¶

Get leader by searching for leader annotation property in any of the nodes in a given clique.

Parameters: clique (list) – A list of nodes from a clique
Returns: A tuple containing the node that has been elected as the leader, and the election strategy
Return type: tuple[Optional[str], Optional[str]]

get_leader_by_prefix_priority(clique: list, prefix_priority_list: list) → Tuple[Optional[str], Optional[str]][source]¶

Get leader from clique based on a given prefix priority.

Parameters

Returns

A tuple containing the node that has been elected as the leader, and the election strategy

Return type

tuple[Optional[str], Optional[str]]

get_leader_by_sort(clique: list) → Tuple[Optional[str], Optional[str]][source]¶

Get leader from clique based on the first selection from an alphabetical sort of the node id prefixes.

Parameters: clique (list) – A list of nodes that correspond to a clique
Returns: A tuple containing the node that has been elected as the leader, and the election strategy
Return type: tuple[Optional[str], Optional[str]]

get_the_most_specific_category(categories: list) → Tuple[str, list][source]¶

From a list of categories, it tries to fetch ancestors for all. The category with the longest ancestor is considered to be the most specific.

Parameters: categories (list) – A list of categories
Returns: A tuple of the most specific category and a list of ancestors of that category
Return type: tuple[str, list]

update_categories(clique: list)[source]¶

For a given clique, get category for each node in clique and validate against BioLink Model, mapping to BioLink Model category where needed.

Ex.: If a node has gene as its category, then this method adds all of its ancestors.

validate_categories(clique: list) → Tuple[str, list][source]¶

For nodes in a clique, validate the category for each node to make sure that all nodes in a clique are of the same type.