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Repository for SQL used to create OMOP and I2B2 views given a PCORnet CDM loaded to Snowflake

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Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
i2b2_views		i2b2_views
omop_views		omop_views
setup		setup
README.md		README.md

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PCORnet to OMOP and I2B2 Views

This directory contains all SQL logic used to create OMOP and I2B2 Views on top of PCORnet CDM data within Snowflake.

Prerequisites:

A PCORnet modeled CDM loaded into a Snowflake database

Process:

(setup folder) Create a set of de-identified (deid) PCORnet Tables. Patid, encounterid, facilityid, and providerid are made stable beforehand in corresponding map_id tables. All ids for deid tables are conveted to integers.
(setup folder) Create and load data into OMOP vocabulary tables and additional mapping tables
(omop_views folder) Create a view for each OMOP table using the deid PCORnet tables and mapping tables. Any OMOP table that does not have a view mapping will have an empty table created.
(i2b2_views folder) Create a view for each I2B2 table using the deid PCORnet tables and mapping tables. Each obervation_fact domain has it's own view created in the format "domain_fact."

Notes:

Database and schema names are generalized in code and may need to be changed. Names are as follows in code:

database - "database"
source pcornet cdm data schema - "schema_pcornet"
Deid PCORnet CDM data dchema - "schema_pcornet_deid"
OMOP data views schema - "schema_omop"
I2B2 data views schema - "schema_i2b2"