Abstract
Clinical Data Warehouses (DWHs) are used to provide researchers with simplified access to pseudonymized and homogenized clinical routine data from multiple primary systems. Experience with the integration of imaging and metadata from picture archiving and communication systems (PACS), however, is rare. Our goal was therefore to analyze the viability of integrating a production PACS with a research DWH to enable DWH queries combining clinical and medical imaging metadata and to enable the DWH to display and download images ad hoc. We developed an application interface that enables to query the production PACS of a large hospital from a clinical research DWH containing pseudonymized data. We evaluated the performance of bulk extracting metadata from the PACS to the DWH and the performance of retrieving images ad hoc from the PACS for display and download within the DWH. We integrated the system into the query interface of our DWH and used it successfully in four use cases. The bulk extraction of imaging metadata required a median (quartiles) time of 0.09 (0.03–2.25) to 12.52 (4.11–37.30) seconds for a median (quartiles) number of 10 (3–29) to 103 (8–693) images per patient, depending on the extraction approach. The ad hoc image retrieval from the PACS required a median (quartiles) of 2.57 (2.57–2.79) seconds per image for the download, but 5.55 (4.91–6.06) seconds to display the first and 40.77 (38.60–41.63) seconds to display all images using the pure web-based viewer. A full integration of a production PACS with a research DWH is viable and enables various use cases in research. While the extraction of basic metadata from all images can be done with reasonable effort, the extraction of all metadata seems to be more appropriate for subgroups.
Highlights
Clinical Data Warehouses (DWHs) are used to provide researchers with simplified access to pseudonymized clinical routine data from multiple primary systems
We focused on enabling the following use cases at our institution: 1. query the DWH using combinations of DICOM metadata and clinical data to discover patient cohorts, 2. extract imaging data for clinical studies, 3. query and extract imaging and clinical data for the training of neural networks, and 4. extract common and special DICOM metadata from the picture archiving and communication systems (PACS) for analysis
An example query that uses data from the PACS and other clinical data is shown in the top panel and its results in the bottom panel
Summary
Clinical Data Warehouses (DWHs) are used to provide researchers with simplified access to pseudonymized clinical routine data from multiple primary systems. DWHs can provide data from various domains that are available in structured form, semi-structured form, or narrative texts. Many clinical DWHs only integrate radiology reports [1,2,3]. The imaging data itself, stored in picture archiving and communication systems (PACS), are usually not as comprehensively integrated with DWHs as other data sources, even though they are of great interest for clinical and imaging research [4,5,6,7,8] as well as for education [9].
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