Alchemist / Critical Care

Documentation on the data exchange format for HIC Critical Care and the Alchemist ingestion pipeline.

Attribute Definition

The ATTRIBUTE_DEFINITION table contains records defining Attributes, or covariates, to members of a Cohort through an associated description and syntax and upon instantiation (execution of the algorithm) placed into the COHORT_ATTRIBUTE table. Attributes are derived elements that can be selected or calculated for a subject in a Cohort. The ATTRIBUTE_DEFINITION table provides a standardized structure for maintaining the rules governing the calculation of covariates for a subject in a Cohort, and can store operational programming code to instantiate the Attributes for a given Cohort within the OMOP Common Data Model.

Field Required Type FK Table Description
attribute_definition_id Yes bigint   A unique identifier for each Attribute.
attribute_name Yes varchar(255)   A short description of the Attribute.
attribute_description No text   A complete description of the Attribute definition.
attribute_type_concept_id Yes bigint CONCEPT Type defining what kind of Attribute Definition the record represents and how the syntax may be executed.
attribute_syntax No text   Syntax or code to operationalize the Attribute definition.

Conventions

  • Like the definition syntax field for the COHORT_DEFINITION table, the attribute_definition_syntax does not prescribe any specific syntax or programming language. Typically, it would be any flavor SQL, or a cohort definition language, or a free-text description of the algorithm.
  • The Attribute Definition is generic and not necessarily related to a specific Cohort Definition, however the instantiated Attribute is linked to the Cohort records (see the COHORT table). For example, the Attribute “Age” can be defined as the amount of time between the cohort_start_date of the COHORT table and the year_of_birth , month_of_birth and day_of_birth of the PERSON table. Thus, such an Attribute Definition can be applied and instantiated with any Cohort, as long as it is applied to a Cohort of the same Domain (Person in this case), as it is defined in the subject_concept_id in the COHORT_DEFINITION table.