Name: OMOPV4_PCORNetV1_ETL
Owner: Observational Health Data Sciences and Informatics
Description: ETL script to transform data from OMOP v4 CDM to PCORNet V1 CDM
Created: 2014-09-17 20:04:11.0
Updated: 2017-11-30 14:53:12.0
Pushed: 2014-11-05 20:36:14.0
Homepage: null
Size: 474
Language: null
GitHub Committers
User | Most Recent Commit | # Commits |
---|---|---|
Toan Ong | 2014-10-29 13:40:16.0 | 11 |
Ritu Khare | 2014-10-15 14:08:04.0 | 27 |
Other Committers
User | Most Recent Commit | # Commits | |
---|---|---|---|
toanong | chitoan@challena-e5430.ucdenver.pvt | 2014-09-17 20:20:56.0 | 1 |
toanong | chitoan@hiens-air.ucdenver.pvt | 2014-09-22 18:57:38.0 | 3 |
toanong | chitoan@hiens-macbook-air.local | 2014-10-29 14:51:54.0 | 5 |
toanong | chitoan@spa-lsc440h-m.ucdenver.pvt | 2014-10-09 16:27:26.0 | 3 |
toanong | chitoan@wrls-guest-165-158.ucdenver.edu | 2014-10-10 20:52:00.0 | 1 |
This repository contains the documentation and source code to transform an instance of OMOP CDM v4 to an instance of PCORnet CDM v1. The documentation and source code (in PostgreSQL) are designed for the PEDSnet project but may also be useful for other CDRNs.
This document contains the mappings from OMOP vocabulary to PCORnet vocabulary. Each column in this file denotes the following:
This document describes all the assumptions made for the transformation process.
This document describes the ETL process to populate each field of the PCORnet model.
The pdf version of the ETL process description document
This document contains the DDL script to create the source-to-concept mapping table (i.e. OMOP->PCORnet vocabulary mapping) into database. In addition, each site is required to manually load the omop_pcornet_mappings.csv file into this table. The PostgreSQL setting for importing the file include: format=csv, header=check.
This is the script to generate the pcornet schema in a PostgreSQL database. For this script to run without errors, the 'rosita' username must be replaced by the name of the user of your OMOP database. Important: running this script will permanently erase all data in the existing pcornet schema.
This file contains the complete ETL source code, i.e. table-wise SQL queries to extract the PCORnet instance from a given OMOP instance and the source-to-concept mapping table
This document describes changes made to each version of the repository