# Introduction to OHDSI, OMOP CDM and Atlas

## OHDSI and OMOP CDM

Atlas is a tool from the Observational Health Data Sciences and Informatics [(OHDSI) program](https://www.ohdsi.org/). Besides this quick tutorial here, there are extensive tutorials available for those who are interested:

* [Atlas videos](https://www.youtube.com/playlist?list=PLpzbqK7kvfeUXjgnpNMFoff3PDOwv61lZ) by OHDSI
* [Atlas Wiki](https://github.com/OHDSI/Atlas/wiki) by OHDSI
* [The Book of OHDSI](https://ohdsi.github.io/TheBookOfOhdsi/)

Atlas is based on the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). To read more about these and data mappings to the standardized form, please see:

* [OMOP CDM](https://www.ohdsi.org/data-standardization/)
* [ATHENA tool](https://athena.ohdsi.org/search-terms/start) for exploring data mappings
* [FinnGen data mapping to the OMOP](https://finngen.github.io/ETL/) and the [coverage of mappings](https://finngen.github.io/FinOMOP_OMOP_vocabulary/StatusReport/dashboard.html#databases-coverage)
* [EHDEN Academy](https://academy.ehden.eu/login/index.php#section-0)

## Advantages of using Atlas and OMOP standards

* No coding skills required / avoiding human errors in coding when compared to building cohorts e.g. in R
* Easy string searching of terms you are looking for to quickly understand what data are available, in how many individuals, and which codes cover such data
* Your cohort and analysis are fully comparable with other OMOP studies
* Others can easily replicate your analysis
* Your algorithm is not getting ‘outdated’ so easily, for example when new drugs are coming to the market
* You can benefit from the other OHDSI software in full

## Notes on Atlas

* Atlas requires data to be mapped to OMOP, i.e. the latest data will always become available in Atlas in a slight delay
* Atlas uses only codes that can be mapped to OMOP CDM
  * E.g. A doctor in Finland may have created a subcode that does not map to any existing ICD subcode. Such codes will be included if a cohort is created e.g. in R taking the main code and all its descendants; however, such codes are not in Atlas as they cannot be mapped to OMOP CDM
* By default, Atlas uses all the registers, including primary care data whereas many endpoints are based on hospital data only
  * A quick way to compare sources of data in existing endpoints: [Risteys](https://risteys.finngen.fi/) upset plot
* Atlas is designed for creating cohorts of people based on some criteria and not for exporting any continuous values, e.g. laboratory measurement values even though they are available in Atlas to help define the group of persons based on their values

## Error reporting

* If you notice any mapping errors or other mistakes in Atlas, please email <finngen-servicedesk@helsinki.fi>

## Expectations for Atlas use

Note that starting to use Atlas and understanding the Atlas terminology and logic may take time but once you have built a cohort a few times, Atlas will quickly provide answers to many of your FinnGen data related questions. Be patient in your journey with Atlas!

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