Introduction
The dsOMOPHelper package is an extension of dsOMOPClient, designed to streamline the interaction with databases in the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) format within the DataSHIELD environment. This package simplifies the process of fetching tables and integrating them into the DataSHIELD workflow, adhering to the privacy standards and disclosure control mechanisms of DataSHIELD.
By combining commands from both dsOMOPClient and dsBaseClient (which invokes standard DataSHIELD workflow operations), dsOMOPHelper significantly reduces the complexity involved in utilizing dsOMOPClient for common use cases. This is particularly beneficial for epidemiological studies that require data from an OMOP CDM database to be analyzed securely within the DataSHIELD framework.
While dsOMOPHelper significantly enhances the functionality of dsOMOPClient by catering to common research needs, it is important to note that for more specific use cases, the functions of dsOMOPHelper may not offer sufficient flexibility. In such instances, the operations of dsOMOPClient should be directly utilized to ensure the desired outcomes. For users requiring advanced functionalities, exploring the comprehensive documentation of dsOMOPClient is highly recommended to fully leverage the potential of this tool in complex research scenarios: https://github.com/isglobal-brge/dsOMOPClient.
We strongly encourage the community to contribute by creating packages similar to dsOMOPHelper that are built on top of dsOMOPClient. By leveraging the foundational capabilities of dsOMOPClient, developers can craft specialized tools that address specific needs emerging at the intersection between the OMOP CDM and DataSHIELD environments.
Installation
To install the package dsOMOPHelper, follow the steps below. This guide assumes you have R installed on your system and the necessary permissions to install R packages.
The dsOMOPHelper package can be installed directly from GitHub using the devtools package. If you do not have devtools installed, you can install it using the following command in R:
install.packages("devtools")You can then install the dsOMOPHelper package using the following command in R:
devtools::install_github('isglobal-brge/dsOMOPHelper')Once the package is installed, you can load it into your R environment using the following command:
library(dsOMOPHelper)Acknowledgements
- The development of dsOMOP has been supported by the RadGen4COPD, P4COPD, CADSET, and DATOS-CAT projects. These collaborations have not only provided essential financial backing but have also affirmed the project’s relevance and application in significant research endeavors.
- This project has received funding from the Spanish Ministry of Science and Innovation and State Research Agency through the “Centro de Excelencia Severo Ochoa 2019-2023” Program [CEX2018-000806-S] and State Research Agency and Fondo Europeo de Desarrollo Regional, UE (PID2021-122855OB-I00), and support from the Generalitat de Catalunya through the CERCA Program and Ministry of Research and Universities (2021 SGR 01563).
- This project has received funding from the “Complementary Plan for Biotechnology Applied to Health”, coordinated by the Institut de Bioenginyeria de Catalunya (IBEC) within the framework of the Recovery, Transformation, and Resilience Plan (C17.I1) - Funded by the European Union - NextGenerationEU.
- Special thanks to Xavier Escribà-Montagut for his invaluable support in the development process.
Contact
For further information or inquiries, please contact:
- Juan R González: juanr.gonzalez@isglobal.org
- David Sarrat González: david.sarrat@isglobal.org
For more details about DataSHIELD, visit https://www.datashield.org.
For more information about the Barcelona Institute for Global Health (ISGlobal), visit https://www.isglobal.org.