# 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) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. 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