fetch_complete_omop_relationships: Fetch Relationships with Deprecated Concepts

In meerapatelmd/chariotViz: Visualize the OMOP Vocabularies

Description

The difference between this function and fetch_omop_relationships is that all concepts belonging to a vocabulary are retrieved, including deprecated concepts. In fetch_omop_relationships, concept_class_id matches on both sides are filtered out, but here, a deprecated concept may map to a valid concept within the concept concept class. For this reason, the filtering is adjusted by removing relationships where concept_ids are equal instead. Invalid relationships in the Concept Relationship table continue to be filtered out.

A new field validity_status is introduced here, which is invalid_reason with the NULL value recorded to 'V'.

Usage

fetch_complete_omop_relationships(
  ...,
  conn,
  conn_fun = "pg13::local_connect(verbose=FALSE)",
  schema = "omop_vocabulary",
  verbose = FALSE,
  render_sql = FALSE,
  version_key
)

Arguments

conn	PARAM_DESCRIPTION
conn_fun	PARAM_DESCRIPTION, Default: 'pg13::local_connect(verbose=FALSE)'
schema	PARAM_DESCRIPTION, Default: 'omop_vocabulary'
verbose	PARAM_DESCRIPTION, Default: FALSE
render_sql	PARAM_DESCRIPTION, Default: FALSE
version_key	A list object that serves as the hash for caching. Set to NULL to cache under a generic hash.
type_from	PARAM_DESCRIPTION, Default: concept_class_id

Details

The OMOP vocabularies are transformed into nodes and edges by first normalizing OMOP concepts to their associated concept classes. The distinct concept_id count is preserved to determine the extent of coverage between concept classes across relationships.

This function queries excludes invalid concepts and concept relationships as well as relationships to self.

Value

OUTPUT_DESCRIPTION

meerapatelmd/chariotViz documentation built on Dec. 21, 2021, 4:53 p.m.