Instructor Notes
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What is OMOP?
Instructor Note
Make sure everyone - has R open - has a project - has managed to connect to the database
Instructor Note
Check that everyone knows what FAIR stands for
Exploring OMOP concepts with R
Parquet files
Instructor Note
Note that the path to the data directory may be different depending on where you have stored the sample OMOP CDM dataset on your local machine.
Check the people have used the right path. Their environment should now have an entry under Data reading ‘omop List of 1’
Instructor Note
Check that everyone has been able to read in the person table and see the data.
Points worth a discussion:
the day and month of birth
gender_source_value and race_source_value are given for some rows but not others
More on concepts
Measurements and Observations
Instructor Note
Could be skipped if short of time
Instructor Note
Comment on the fact that these concepts are nonstandard and that this is an example of how local data can be mapped to OMOP concepts even if they are not part of the standard vocabulary.