Lab 8

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Intro

In lab 5 you came up with variables for a mock observational study. In lab 6 you refined some of these into specific definitions using SQL and an OMOP CDM database. In this lab, you’ll convert them all into specific definitions using codes, thresholds, etc. I’m hoping that some of you will find challenging, interesting phenotypes that we can work through with Patrick Ryan on Tuesday.

Instructions

Create OMOP definitions of all the variables you defined in lab 5. If you have one or two definitions that you’re uncertain about, please send me an email, and we may have a chance to work through them with Patrick Ryan next class.Last year we worked through a phenotype Harry was interested in, and it was a really valuable exercise to see Patrick go through creating an OMOP definition. However, since not all of the variables you all defined are appropriate for an OMOP study, please send me what you’re struggling with before sending it to Patrick.

Please format the definitions in text or tables, as you would in a paper’s supplementary materials, not SQL.I had been hoping to use SQL, but the studies you all laid out are not all compatible with this kind of approach or the data to which I have access in an OMOP format. For example, I don’t yet have COVID-19 data in OMOP CDM format, and I only have access to data from one hospital.