INDRA CoGEx Representation (indra_cogex.representation)

This documentation goes over helper functions and the python objects that represent Neo4j Nodes and Relations.

Representations for nodes and relations to upload to Neo4j.

class Node(db_ns, db_id, labels, data=None)[source]

Representation for a node.

Initialize the node.

Parameters:

  • db_ns (str) – The namespace associated with the node. Uses the INDRA standard.

  • db_id (str) – The identifier within the namespace associated with the node. Uses the INDRA standard.

  • labels (Collection[str]) – A collection of labels for the node.

  • data (Optional[Mapping[str, Any]]) – An optional data dictionary associated with the node.

grounding()[source]

Get the grounded namespace and identifier for this node as a tuple

Return type:

Tuple[str, str]

Returns:

A tuple of the namespace and identifier for the node.

classmethod standardized(*, db_ns, db_id, name=None, labels)[source]

Initialize the node, but first standardize the prefix/identifier/name.

Parameters:

  • db_ns (str) – The namespace associated with the node.

  • db_id (str) – The identifier within the namespace associated with the node.

  • name (Optional[str]) – An optional name for the node.

  • labels (Collection[str]) – A collection of labels for the node.

Return type:

Node

Returns:

A node with standardized prefix/identifier/name.

to_json()[source]

Serialize the node to JSON.

Return type:

Dict[str, Union[Collection[str], Dict[str, Any]]]

Returns:

A JSON representation of the node.

class Relation(source_ns, source_id, target_ns, target_id, rel_type, data=None)[source]

Representation for a relation.

Initialize the relation.

Parameters:

  • source_ns (str) – The namespace associated with the source node.

  • source_id (str) – The identifier within the namespace associated with the source node.

  • target_ns (str) – The namespace associated with the target node.

  • target_id (str) – The identifier within the namespace associated with the target node.

  • rel_type (str) – The type of relation.

  • data (Optional[Mapping[str, Any]]) – An optional data dictionary associated with the relation.

to_json()[source]

Serialize the relation to JSON format.

Return type:

Dict[str, Union[Mapping[str, Any], Dict]]

Returns:

A JSON representation of the relation.

indra_stmts_from_relations(rels)[source]

Convert a list of relations to INDRA Statements.

Any relations that aren’t representing an INDRA Statement are skipped.

Parameters:

rels (Iterable[Relation]) – A list of Relations.

Return type:

List[Statement]

Returns:

A list of INDRA Statements.

norm_id(db_ns, db_id)[source]

Normalize an identifier.

Parameters:

  • db_ns – The namespace of the identifier.

  • db_id – The identifier.

Return type:

str

Returns:

The normalized identifier.