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Cohort definitions

A cohort (also called a phenotype) is a set of persons who fulfil inclusion and exclusion criteria for a duration of time. A cohort definition describes these criteria. Because a cohort is defined independently of a single study, you can reuse it across studies and data sources.

Data2Evidence offers two ways to work with cohorts:

  • Cohort Definitions, the ATLAS cohort builder described on this page. Use it for precise, reusable cohort definitions that you generate on one or more data sources and use in analyses.
  • Data Exploration, an interactive way to filter persons and see the results right away. You can turn an exploration into an ATLAS cohort definition.

Create a cohort definition​

  1. Select Cohort Definitions in the navigation bar. The list shows the cohort definitions you can see. Use the search box to find one by name or description.
  2. Select New Cohort, enter a name and select Create.
  3. Define the cohort in three steps:
    1. Cohort Entry Events: the event that brings a person into the cohort, for example the first diagnosis of a condition from a concept set.
    2. Inclusion Criteria: rules a person must also meet, for example "at least one year of observation before entry" or "no prior exposure to drug X".
    3. Exit & Eras: when a person leaves the cohort, for example at the end of continuous drug exposure or at the end of observation.
  4. Select Save.

To add concept sets to the cohort, open the Concept Sets dialog from the toolbar of the cohort builder, or pick an existing concept set while you define a criterion.

Live counts​

While you edit the inclusion criteria, the cohort builder can show how many persons each rule keeps. Choose the data source for these counts in the header of the inclusion rules. A status next to it shows whether the counts are available:

  • Ready: the counts are current.
  • Stale or Building: the counts may be outdated or appear shortly.
  • Not Built or Error: counts are not available for this data source. Ask your administrator.

Generate a cohort​

Generating a cohort runs its definition against a data source and stores the persons it finds.

  1. Open the cohort definition and expand the Generation section at the top.
  2. Select Generate in the row of the data source you want to use. You can only generate cohorts on data sources you have access to.
  3. Wait until the status changes to COMPLETED.
  4. Open the Inclusion report of that row to see how many persons each rule kept.

From the generation results you can also look at sample persons and open their profiles, a timeline of a single person's records. Use profiles to check whether the persons in your cohort really have the condition you are looking for.

Share and reuse a cohort​

  • Use the Configure access button (lock icon) in the toolbar to give other users read or write access to your cohort definition.
  • Use Export to download the cohort definition as JSON, and Import on the list page to import one.
  • Use Duplicate on the list page to start a new cohort from an existing one.

More in the ATLAS user manual​

  • Chapter 3 "A first phenotype: end-to-end": a complete example, from concept sets to cohort generation and review.
  • Chapter 7 "Cohort definitions": all parts of the cohort builder, generation, samples, export and sharing.
  • Chapter 12 "Profiles": the person timeline and phenotype validation.
  • Chapter 14 "Versions": previewing and restoring earlier versions of a cohort definition.