> For the complete documentation index, see [llms.txt](https://docs.finngen.fi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas.md).

# 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](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/how-to-define-a-simple-icd-case-control-cohort-in-atlas.md)

### Cohort definition process

{% hint style="info" %}
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**.
{% endhint %}

Atlas cohorts are defined in two steps:

1. Define a [Concept Set](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/concept-sets.md) using medical codes
2. Define a cohort using [Cohort Definitions](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/cohort-definitions.md) 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.

{% hint style="info" %}
[Select the correct Finngen data release in Atlas](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/selecting-configuration-in-atlas.md) before you define your cohorts.
{% endhint %}

#### [Concept Sets](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/concept-sets.md)

* [Create Concept Sets using standard code descendants](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/concept-sets/selecting-descendants-for-a-concept-set-in-atlas.md)
* [Exclude and Remove codes from Concept Set](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/concept-sets/exclude-and-remove-codes-from-concept-set.md)
* [Simplify Concept Sets that use standard code descendants](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/concept-sets/simplify-concept-sets-that-use-standard-code-descendants.md)
* [Create Concept Sets using equivalent standard and non-standard codes](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/concept-sets/find-mapped-equivalents-for-standard-and-non-standard-codes-in-atlas.md)
* [View standard code hierarchy in Atlas](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/concept-sets/viewing-the-hierarchy-of-standard-snomed-codes-in-atlas.md)
* 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**)

#### [Cohort Definitions](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/cohort-definitions.md)

* [Using the Death register in Atlas](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/cohort-definitions/using-the-death-register-in-atlas.md)
* [Filtering by clinical registries in Atlas](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/cohort-definitions/filter-by-clinical-registries-in-atlas.md)
* [Filtering by demographic criteria in Atlas](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/cohort-definitions/filtering-by-demographic-criteria-in-atlas.md)
* [Defining exit rules for a cohort in rules](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/cohort-definitions/defining-exit-rules-for-a-cohort-in-atlas.md)
* [Selecting the correct box in Atlas for events and medical codes](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/cohort-definitions/mapping-between-atlas-registries-and-medical-codes.md)
* 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

* [How to export FinnGen IDs from Atlas](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/how-do-you-export-finngen-ids-for-an-analysis-cohort.md)
* [Downstream analyses after the Atlas cohorts are created](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/downstream-analyses-after-the-atlas-cohorts-are-created.md)