OHDSI Home | Forums | Wiki | Github

Queries to check data quality of transformed OMOP data

Implementers
#1

Hello,

I would like to run SQL queries against a source dataset that has been transformed into the OMOP model to check data quality. I have come across a list of rules that Achilles Heel uses to do exactly that. However I cannot seem to find the corresponding SQL. Firstly are these queries published and if so, from where can I get a copy?

Regards,
Vimala

#2

See the following links:

SQL
https://github.com/OHDSI/Achilles/blob/master/inst/sql/sql_server/AchillesHeel_v5.sql

Rules (and other items; overviews)

Rules - commented (view of a CSV file, in fact)

https://rawgit.com/OHDSI/Achilles/master/extras/Heel-Rules.html
https://rawgit.com/OHDSI/Achilles/master/extras/Rule-Drill-Down.html

#3

Remember, the achilles heel report is based on statistics generated in the main Achilles analysis. So be sure you run the main script here:
https://github.com/OHDSI/Achilles/blob/master/inst/sql/sql_server/Achilles_v5.sql

Then the heel will create the report of any data issues it finds.

#4

Thanks to both of you for pointing me in the right direction. By any chance is there a Postgresql version of these scripts?

Regards,
Vimala

#5

These scripts are run through a translation layer to get the appropriate dialect. If you have R, you can just install the package, and run achilles() with the parameter sqlOnly = TRUE. That will translate the sql and write it to an ‘output’ folder. You can see the line in question here:

t