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 2: Create an empty Concept Set
Select the Concept Sets option on the left menu.
Click the New Concept Set button on the right.
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 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.
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:
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.
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
Sometimes the results can be empty (RC = 0). See instructions on how to select only codes with RC.
Not sure if you found all relevant codes for your cohort? You can also use code hierarchy to find relevant codes for your Concept Set.
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:
The Concept Sets shopping cart icon will turn red to show that you have edited but not saved your Concept Set:
Select the Concept Sets option on the left menu:
You have now defined a Concept Set for all Finnish-specific H81 IDC10fi codes.
Next steps
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