R Package to support quality control inspection of an OMOP-CDM instance
The European Health Data and Evidence Network (EHDEN) project has multiple yearly Open Calls for financial support for data partners to map their data to the OMOP-CDM, for more information see the EHDEN website. In addition, EHDEN is training Small and Medium-sized Enterprises in Europe to provide services to the data partners to map their data to the OMOP-CDM. A large number of these SMEs are now active all over Europe as shown in the SME Catalogue.
Quality control of the mapping is clearly important and therefore a procedure has been developed called SME Inspection in which a certified SME performs a series of tests on the CDM and produces a report that is send to the EHDEN Team for review. The goal of the inspection 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 EHDEN and OHDSI data networks and participate in research studies. If the SME that is performing the inspection was not involved in the ETL implementation we advise to use a two-stage inspection process. A first inspection report can be made to provide recommendations to the Data Partner on how to improve the ETL and processes, if necessary. Ideally, this includes a site visit of the SME after providing instructions on the content of the report. The Data Partner can share this draft report with EHDEN to obtain additional input. Once the improvements have been made the final report can be created by the SME and send to EHDEN for approval.
An example of an inspection report for the Synpuf database can be found here: link.
The CdmInspection R Package is part of this SME Inspection procedure and performs the following checks on top of the required Data Quality Dashboard step:
Vocabulary Checks
Technical Infrastructure Checks
Results Document Generation
Produces a word document in the EHDEN template that contains all the results. This template needs to be completed by the person performing the cdm inspection.
The CdmInspection package is an R package.
Requires R. Some of the packages used by CdmInspection require Java.
See the instructions here for configuring your R environment, including Java.
Make sure RohdsiWebApi is installed
remotes::install_github("OHDSI/ROhdsiWebApi")
remotes::install_github("EHDEN/CdmInspection")
You should run the cdmInspection package ideally on the same machine you will perform actual anlyses so we can test its performance.
Make sure that Achilles has run in the results schema you select when calling the cdmInspection function.
PDF versions of the documentation are available:
This package is maintained by the EHDEN consortium as part of its quality control procedures. Additions are welcome through pull requests. We suggest to first create an issue and discuss with the maintainer before implementing additional functionality.
The roadmap of this tool can be found here
CdmInspection is licensed under Apache License 2.0
CdmInspection is being developed in R Studio.
Stable Release