# Define a simple ICD Concept Set in Atlas

This example shows how to build a simple Concept Set using the Finnish-specific H81 ICD10fi codes.

In Atlas, a cohort definition starts by creating a **Concept Set** of medical codes of interest. The Concept Set is then used to create case and control cohorts using additional criteria defined in **Cohort Definitions**.

### **Step 1:** [Select 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)

### Step 2: Create an empty Concept Set

* Select the **Concept Sets** option on the left menu.

<div align="left"><figure><img src="/files/s6tA4GBaEWpTxVzywO5i" alt=""><figcaption></figcaption></figure></div>

* Click the **New Concept Set** button on the right.

<div align="left"><figure><img src="/files/VGwWXxomEo07xVC3GYES" alt=""><figcaption></figcaption></figure></div>

* **Name the Concept Set** by replacing the "New Concept Set" text at the top of the page. The name should correspond to the medical codes you use to define the Concept Set followed by your initials (e.g. MyPhenotypeCodeSet\[MN]). The most important aspect of the name is that you can find it later easily.
* You can **Save the Concept Set** by clicking the save button <img src="/files/mnwt5JQuUzWerumFz7S6" alt="" data-size="line">
* You can **Close the Concept Set** by clicking the close button <img src="/files/hmCaLGOctsy74ZZJxTCa" alt="" data-size="line">
* You can **Re-open the Concept Set** by selecting the **Concept Sets** option on the left menu and selecting your Concept Set from the list.

Note that the **Concept Sets** shopping cart icon changes its color\*\*:\*\*

* Red: you have unsaved Concept Set edits
* Green: you have saved your Concept Set

### Step 3: Search medical codes to add to the Concept Set

* Select the **Concept Sets** option on the left menu.
* Make sure that you have a Concept Set open. You can select one from the list or create a new one.
* Click the **Add Concepts** button that will activate the **Search** left menu option. You can also select the **Search** menu option directly.

<figure><img src="/files/w7v3fqC937oqAEK6UKJI" alt=""><figcaption></figcaption></figure>

* **Search the codes** to add to the Concept Set by writing your search terms in the text box at the top. In the example below, we have used the "H81" text as the search term:

<figure><img src="/files/QmpW0tlkJ7VguRocZLmF" alt=""><figcaption></figcaption></figure>

Typical search terms are medical codes and disease or condition names. You can filter the search results using the Filter text box on the right. You can sort the results by clicking the column headings.

#### Standard and non-standard codes

The search results may show red results in the **Name** column. These results are non-standard codes from Finnish health registries. In this example above, we see only non-standard (red) results for the Finnish-specific H81 ICD10fi code. For more information about standard and non-standard codes please see [Standard and non-standard medical codes in Atlas](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/code-sets-in-atlas.md).

**Result columns**

* **Code**: medical code
* **Name**
  * blue: standard codes
  * red: non-standard Finnish codes
* **Class**: the medical code class
* **RC**: record count (usually different than the number of people)
* **DRC**: descendant record count
  * Available only for standard codes
  * DRC is a record count for the given code and all of it's lower level descendant codes.
* **PC**: person count
  * Available only for standard codes
  * 0 for non-standard codes
* **DPC**: descendant person count
  * Available only for standard codes
  * 0 for non-standard codes
* **Vocabulary**: the vocabulary from where the code originates

{% hint style="info" %}
Sometimes the results can be empty (RC = 0). See instructions on [how to select only codes with RC](/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).
{% endhint %}

{% hint style="info" %}
Not sure if you found all relevant codes for your cohort? You can also use [code hierarchy](/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) to find relevant codes for your Concept Set.
{% endhint %}

### Step 4: Add medical codes to the Concept Set

* **Select the codes** using the check boxes on the left of the **Id** column. You can select all results at once using the topmost check box.
* **Add the selected codes** to the Concept Set by clicking the **Add To Concept Set** button. The name of the Concept Set is shown in the blue drop-down list (e.g. MyPhenotypeCodeSet\[MN]). If you have opened more than one Concept Set, you can use the blue drop-down list to select the correct one.

In the example below, we have select all H81 IDC10fi codes:

<figure><img src="/files/LBqPDJXhdl22PfH5cOJT" alt=""><figcaption></figcaption></figure>

The **Concept Sets** shopping cart icon will turn red to show that you have edited but not saved your Concept Set:

<figure><img src="/files/8zgSGK8pyLdh88W2oyyE" alt=""><figcaption></figcaption></figure>

* Select the **Concept Sets** option on the left menu:

<figure><img src="/files/9hAC1TMFIyTJbVATheeJ" alt=""><figcaption></figcaption></figure>

* **Save** the Concept Set by clicking the save button <img src="/files/mnwt5JQuUzWerumFz7S6" alt="" data-size="line">

You have now defined a Concept Set for all Finnish-specific H81 IDC10fi codes.

### Next steps

* [Define a simple ICD case 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/define-a-simple-icd-case-cohort-in-atlas.md)
* [Define a simple ICD 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/define-a-simple-icd-control-cohort-in-atlas.md)


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