Abstract
Background In 2015, the German Federal Ministry of Education and Research initiated a large
data integration and data sharing research initiative to improve the reuse of data
from patient care and translational research. The Observational Medical Outcomes Partnership
(OMOP) common data model and the Observational Health Data Sciences and Informatics
(OHDSI) tools could be used as a core element in this initiative for harmonizing the
terminologies used as well as facilitating the federation of research analyses across
institutions.
Objective To realize an OMOP/OHDSI-based pilot implementation within a consortium of eight
German university hospitals, evaluate the applicability to support data harmonization
and sharing among them, and identify potential enhancement requirements.
Methods The vocabularies and terminological mapping required for importing the fact data
were prepared, and the process for importing the data from the source files was designed.
For eight German university hospitals, a virtual machine preconfigured with the OMOP
database and the OHDSI tools as well as the jobs to import the data and conduct the
analysis was provided. Last, a federated/distributed query to test the approach was
executed.
Results While the mapping of ICD-10 German Modification succeeded with a rate of 98.8% of
all terms for diagnoses, the procedures could not be mapped and hence an extension
to the OMOP standard terminologies had to be made.
Overall, the data of 3 million inpatients with approximately 26 million conditions,
21 million procedures, and 23 million observations have been imported.
A federated query to identify a cohort of colorectal cancer patients was successfully
executed and yielded 16,701 patient cases visualized in a Sunburst plot.
Conclusion OMOP/OHDSI is a viable open source solution for data integration in a German research
consortium. Once the terminology problems can be solved, researchers can build on
an active community for further development.
Keywords
data integration - secondary use - OMOP - OHDSI
