How to define a cohort in Atlas
Quick start
The following tutorial is a step-by-step guide to define a simple case and "all who are not cases" control cohort:
How to define a simple ICD case-control cohort in Atlas
Cohort definition process
In Atlas, the cohort definition starts by creating a Concept Set using medical codes. The Concept Set is then used to create cohorts using additional criteria defined in Cohort Definitions.
Atlas cohorts are defined in two steps:
Define a Concept Set using medical codes
Define a cohort using Cohort Definitions using the Concept Set and additional criteria
An Atlas cohort is a set of people who satisfy one or more inclusion criteria for a period of time. A person may appear more than once in a cohort if they fulfil the inclusion criteria during multiple non-overlapping periods. For example, a cohort for pregnancy will include people from the day of conception until the day of delivery or interruption. If a person has multiple pregnancies they will appear in the cohort once per pregnancy.
Select the correct Finngen data release in Atlas before you define your cohorts.
Concept Set from standard codes and standard visit types (NO INSTRUCTIONS FOR THIS YET)
Concept Set from standard codes imported from OHDSI phenotype library (NO INSTRUCTIONS FOR THIS YET)
How to define cohort entry dates (e.g. age at the first event) (NO INSTRUCTIONS FOR THIS YET)
How to define cohort with disease onset in a time range (NO INSTRUCTIONS FOR THIS YET)
How to define cohort using medication intervals (NO INSTRUCTIONS FOR THIS YET)
How to define cohort with seasonal rules (NO INSTRUCTIONS FOR THIS YET)
Further information
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