Subnetwork Client (indra_cogex.client.subnetwork)

Queries that generate statement subnetworks.

indra_mediated_subnetwork(nodes, *, client, order_by_ev_count=False)[source]

Return the INDRA Statement subnetwork induced pairs of statements between the given nodes.

For example, if gene A and gene B are given as the query, find statements mediated by X such that A -> X -> B.

Parameters:

  • client (Neo4jClient) – The Neo4j client.

  • nodes (Iterable[Tuple[str, str]]) – The nodes to query.

  • order_by_ev_count (bool) – Whether to order the statements by evidence count in descending order.

Return type:

List[Statement]

Returns:

The subnetwork induced by the given nodes.

indra_subnetwork(nodes, *, client, include_db_evidence=True, order_by_ev_count=False, return_source_counts=False)[source]

Return the INDRA Statement subnetwork induced by the given nodes.

Parameters:

  • client (Neo4jClient) – The Neo4j client.

  • nodes (Iterable[Tuple[str, str]]) – The nodes to query.

  • include_db_evidence (bool) – Whether to include statements with database evidence.

  • order_by_ev_count (bool) – Whether to order the statements by evidence count in the query.

  • return_source_counts (bool) – Whether to return source counts as well as statements.

Return type:

Union[List[Statement], Tuple[List[Statement], Dict[int, Dict[str, int]]]]

Returns:

The subnetwork induced by the given nodes.

indra_subnetwork_go(go_term, *, client, include_indirect=False, mediated=False, upstream_controllers=False, downstream_targets=False, include_db_evidence=True, order_by_ev_count=False, return_source_counts=False)[source]

Return the INDRA Statement subnetwork induced by the given GO term.

Parameters:

  • include_db_evidence (bool) – Whether to include database evidence or not.

  • go_term (Tuple[str, str]) – The GO term to query. Example: ("GO", "GO:0006915")

  • client (Neo4jClient) – The Neo4j client.

  • include_indirect (bool) – Should ontological children of the given GO term be queried as well? Defaults to False.

  • mediated (bool) – Should relations A->X->B be included for X not associated to the given GO term? Defaults to False.

  • upstream_controllers (bool) – Should relations A<-X->B be included for upstream controller X not associated to the given GO term? Defaults to False.

  • downstream_targets (bool) – Should relations A->X<-B be included for downstream target X not associated to the given GO term? Defaults to False.

  • order_by_ev_count (bool) – Should the statements be ordered by evidence count? Defaults to False.

  • return_source_counts (bool) – Whether to return source counts as well as statements.

Return type:

Union[List[Statement], Tuple[List[Statement], Dict[int, Dict[str, int]]]]

Returns:

The INDRA statement subnetwork induced by GO term.

indra_subnetwork_relations(nodes, *, client, include_db_evidence=True)[source]

Return the subnetwork induced by the given nodes as a set of Relations.

Parameters:

  • client (Neo4jClient) – The Neo4j client.

  • nodes (Iterable[Tuple[str, str]]) – The nodes to query.

  • include_db_evidence (bool) – Whether to include statements with database evidence.

Return type:

List[Relation]

Returns:

The subnetwork induced by the given nodes represented as Relation objects.

indra_subnetwork_tissue(nodes, tissue, *, client)[source]

Return the INDRA Statement subnetwork induced by the given nodes and expressed in the given tissue.

Parameters:
Return type:

List[Statement]

Returns:

The subnetwork induced by the given nodes and expressed in the given tissue.