omop.omop_models

source

Concept

class Concept(
  concept_id = Column(Integer, primary_key=True)
  concept_name = Column(String)
  vocabulary_id = Column(String)
  concept_code = Column(String)
  standard_concept = Column(String)
)

This class represents an ORM mapping to the OMOP concept table

ConceptSynonym

class ConceptSynonym(
  concept_id = Column(Integer, primary_key=True)
  concept_synonym_name = Column(String)
  language_concept_id = Column(Integer)
)

This class represents an ORM mapping to the OMOP concept_synonym table

build_query

def build_query(
	search_term: str
	vocabulary_id: 
	concept_synonym: bool
)

Builds an OMOP query to search for concepts

Uses the ORM models for the concept and concept_synonym tables to build a query

Parameters

search_term: str The term to use when searching the relevant tables for concepts

vocabulary_id: list[str] A list of vocabulary_ids in the concepts table. The returned concepts will have one of these vocabulary_ids

concept_synonym: str If true, then the query is expanded to find matches using the concept_synonym table

Returns

Select An SQLAlchemy Select for the desired query