Edges

omop_graph.graph.edges

Definitions for graph edges and predicates.

This module defines the lightweight data structures representing the relationships (edges) between concepts in the OMOP Knowledge Graph.

It focuses on data definitions and classification logic, not graph traversal algorithms.

Supported Relationships

• Mapping: Semantic equivalence (e.g., source code to standard concept).
• Versioning: Lifecycle tracking (e.g., 'replaced by', 'is a').
• Ontological: Hierarchical structure (e.g., 'is a', 'subsumes').
• Attribute: Descriptive properties (e.g., 'has dose form').
• Metadata: Administrative or low-semantic value connections.

EdgeView dataclass

A lightweight, immutable view of an edge in the Knowledge Graph.

Parameters:

Name	Type	Description	Default
subject_id	int	The OMOP Concept ID of the source.	required
predicate_id	str	The relationship ID (e.g., 'is a', 'mapped from').	required
object_id	int	The OMOP Concept ID of the target.	required
valid_start_date	date	The date the relationship became valid.	required
valid_end_date	date	The date the relationship became invalid.	required
invalid_reason	str	The reason for invalidation (e.g., 'D' for deleted), if applicable.	required

pretty(kg)

Return a human-readable string representation of the edge using concept names.

Parameters:

Name	Type	Description	Default
kg	KnowledgeGraph	The graph instance used to look up concept names.	required

Returns:

Type	Description
str	A string in the format 'Subject Name -[predicate]-> Object Name'.

Predicate dataclass

Definition of a Relationship Type in the OMOP CDM.

Parameters:

Name	Type	Description	Default
relationship_id	str	The unique string identifier (e.g. maps to).	required
name	str	The human-readable label (e.g. Non-standard to Standard Mapping).	required
reverse_id	str	The relationship_id of the inverse relationship (e.g. mapped from).	required
is_hierarchical	bool	Whether OMOP defines this as a hierarchical relationship.	required
anc_up	bool	Whether this relationship defines 'defines_ancestry' upwards (deprecated logic).	required
anc_down	bool	Whether this relationship defines 'defines_ancestry' downwards (deprecated logic).	required

defines_ancestry property

Check if this predicate is involved in defining ancestry.

is_active(start, end, invalid_reason, *, on=None)

Check if a relationship is active on a given date.

Parameters:

Name	Type	Description	Default
start	date	The start date of the relationship.	required
end	date	The end date of the relationship.	required
invalid_reason	str	The invalid reason code (e.g. 'D', 'U'). None implies valid.	required
on	date	The reference date to check against. If None, only checks invalid_reason.	None

Returns:

Type	Description
bool	True if the relationship is active, False otherwise.