Detailed guide
Last updated
Was this helpful?
Last updated
Was this helpful?
This document helps you to get started using Atlas with FinnGen register data.
The Atlas is installed in the FinnGen sandbox.
Log into the sandbox:
Select the following menu option:
Applications > FinnGen > Atlas
This opens the Atlas application in a browser window
Atlas allows you to create cohorts using a web interface. Cohorts are groups of individuals who share common characteristics of interest, such as disease classifications, prescription medications or hospital procedures. Cohorts can be used to study associations between these characteristics and other data to reveal which factors increase or decrease the likelihood of developing a certain condition.
This functionality allows you to create FinnGen data release-level descriptive summary statistics.
How to view a report:
Select the Data Sources option in the left menu
Select the FinnGen data release using the first drop-down menu
Select the report using the second drop-down menu
In the example below, we have selected the FinnGen data release 11 and the Person report. This report starts with a distribution of people based on their year of birth:
This functionality allows you to search the vocabularies (codes) loaded into the Atlas and to show the number of matching records.
Make sure to select the correct FinnGen data release for both codes and the record counts when using the Search.
The Search is made against the vocabularies (codes) from one FinnGen data release while the number of matching records is shown for a potentially different FinnGen data release. These FinnGen data releases can be defined on the Configuration page using the Vocabulary Version and Record Counts columns. The FinnGen data release against which the codes are searched can also be defined on the Search page using the View record count drop-down list.
How to search codes:
Select the Search option in the left menu
Type in the search term in the text box at the top
You can change the FinnGen data release that is being searched against using the View record counts drop-down list. However, this does not affect the FinnGen data release from where the codes are selected for the search. This FinnGen data release is defined on the Configuration page.
How to view Concept Sets:
Select the Concept Sets option in the left menu
Click the Name to see which concepts (codes)are included in the Concept Set.
How to create Concept Sets:
In Atlas, people are always included in the cohort for a duration. By default, they are included for the period they belong to a Concept Set.
How to view Cohort Definitions:
Select the Cohort Definitions option in the left menu
Click the Name to see more information about the Cohort Definition
How to create Cohort Definitions:
This functionality allows you to create cohort-level descriptive summary statistics.
In the example below, we have created gender summary statistics in FinnGen data release 11:
This functionality helps you to understand the sequence of events within a cohort.
This functionality allows you to estimate incidence rates.
Atlas contains several FinnGen data releases. The Search is made against the vocabularies (codes) from one FinnGen data release while the number of matching records is shown for a potentially different FinnGen data release. These FinnGen data releases can be defined on the Configuration page using the Vocabulary Version and Record Counts columns.
In the example below, we have selected the FinnGen data release 10 in both Vocabulary Version and Record Counts columns:
The FinnGen data release is also selected when generating:
Cohort Definitions
Characterisations
Cohort Pathways
Incidence Rates
For example, Finngen does not have bone density measurements. However, you can use bisphosphonate treatments as a proxy for bone mineral density. The reason for this is that the treatment reimbursement requires a bone mineral density test and FinnGen makes the reimbursement data available from the Kela drug reimbursement register.
A quick start for defining cohorts using Atlas is available
You can create cohorts in Atlas using both . They are loaded into the OMOP-CDM data model used by Atlas from the . The loading process is explained in full detail in . In addition to mapping non-standard codes to standard codes, the ETL process resolves many register data errors, inconsistencies and anomalies.
An OHDSI tutorial for viewing Data Sources is available .
An OHDSI tutorial for using Search is available .
Click the button
In the above example, we used the 'Asthma' search term. Standard, non-standard and classification codes are shown in different colours, for example, the standard codes are in blue. More information about these codes is available .
OHDSI has tutorials for and Concept Sets.
Click the button on the right.
More information about viewing and creating Concept Sets is available .
OHDSI has a tutorial for a Cohort Definition.
Click the button on the right
More information about viewing and creating Cohort Definitions is available .
OHDSI has a on Characterizations.
More information about Characterizations is available .
OHDSI has a tutorial on Cohort Pathways .
More information about Cohort Pathways is available .
OHDSI has a on Incidence Rates.
Please follow to define the FinnGen data release for Search and for defining Concept Sets using the Search functionality**.**
You can define better cohorts if you understand the different characteristics of FinnGen and how the data is made available in the .
