lnmylos / cdmonboarding

R Package to support the onboarding process of new CDMs in the DARWIN EU Data Network

CdmOnboarding

R Package to support the onboarding process of new CDMs in the DARWIN EU Data Network

Introduction

The DARWIN EU Coordination Center (CC) is resposonsible for building a data network to support EMA and stakeholders to answer regulatory research questions. To support the onboarding process of data sources, the CdmOnboarding R package will generate an onboarding document that is used by the CC and EMA to assess the quality and readiness of the CDM for participating in regulatory studies.

The goal of the onboarding report is to provide insight into the completeness, transparency and quality of the performed Extraction Transform, and Load (ETL) process and the readiness of the data partner to be onboarded in the DARWIN EU® data network and participate in research studies.

An example of an onboarding report for a OMOP Synthea database can be found in extras/CdmOnboarding-Synthea.docx.

Main repository on DARWIN-EU/CdmOnboarding.

CdmOnboarding Checks

The CdmOnboarding R Package performs the following checks on top of the required Data Quality Dashboard step.

Data table counts

• Extraction of the CDM Source table
• The number of records and persons per OMOP table
• Achilles data density plots are inserted
• For each domain, the distinct concepts per person
• Observation Period length
• Type concepts
• Date ranges per domain

Vocabulary counts

• For each domain generate mapping completeness statistics with the number of unmapped codes and and unmapped records
• For each domain extract the top 25 mapped and unmapped codes (counts are round up to the nearest 100)
• Extract the number of records in all vocabulary tables
• Count of concepts per vocabulary by standard, classification and non-standard
• Mapping levels of drugs (Clinical Drug etc.)
• Extracts the source_to_concept map

Technical Infrastructure Checks

• Extract the timings of the Achilles queries (Achilles results need to be present in the database)
• Checks on the number of CPUs, memory available in R
• Extract the versions of all installed R packages, checks if core HADES packages are installed
• Check if ATLAS is installed and WebAPI is running

Data Quality Dashboard

• Overview of number of passed/failed checks

Drug Exposure Diagnostics

• Summary for set of 11 ingredients:

  Concept ID	Drug name (ATLAS)
  1125315	acetaminophen
  1139042	acetylcysteine
  1703687	acyclovir
  1119119	adalimumab
  1154343	albuterol
  528323	hepatitis B surface antigen vaccine
  954688	latanoprost
  968426	mesalamine
  1550557	prednisolone
  1140643	sumatriptan
  40225722	ulipristal

Results Document Generation

Produces a word document in a DARWIN EU template that contains all the results and can be added as Annex 1 to the DARWIN-EU© Onboarding document.

Technology

The CdmOnboarding package is an R package.

System Requirements

Requires R. Some of the packages used by CdmOnboarding require Java.

Installation

1. See the instructions here for configuring your R environment, including Java.

2. Make sure dependencies from Github are installed:

remotes::install_github("OHDSI/ROhdsiWebApi")
remotes::install_github("DARWIN-EU/CDMConnector")
remotes::install_github("DARWIN-EU/DrugExposureDiagnostics")

3. Use the following commands to download and install CdmOnboarding:

remotes::install_github("DARWIN-EU/CdmOnboarding")

Execution instructions

Performing the checks and exporting the CdmOnboarding results is done by executing the cdmOnboarding(...) function. Ideally, run the CdmOnboarding package on the same machine you will perform actual analyses so we can test its performance.

Make sure that Achilles has run in the results schema you select when calling the cdmOnboarding function. Ideally, all Achilles analyses are run before running CdmOnboarding. However, the following Achilles analyses are required for CdmOnboarding to create a complete report: analysisIds = c(105, 110, 111, 117, 220, 420, 502, 620, 720, 820, 920, 1020, 1820, 2102, 2120, 203, 403, 603, 703, 803, 903, 920, 1003, 1020, 1320, 1411, 1803, 1820)

For a template execution script, see extras/CodeToRun.R.

User documentation

PDF versions of the documentation are available:

• Package manual: Link
• CodeToRun Example: Link
• Report Example: Link

Support and contributing

This package is maintained by the Darwin EU Coordination Centre as part of its quality control procedures. We use the GitHub issue tracker for all bugs/issues/enhancements/questions/feedback Additions are welcome through pull requests. We suggest to first create an issue and discuss with the maintainer before implementing additional functionality.

License

CdmOnboarding is licensed under Apache License 2.0

Development

CdmOnboarding is being developed in R Studio.

Acknowledgements

• The package is build upon the CdmInspection R package used and developed by The European Health Data & Evidence Network has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 806968. The JU receives support from the European Union’s Horizon 2020 research
• We also like to thank the contributors of the OHDSI community for their fantastic work