Joshua P. Wiedekopf

selected publications

1. MIMIC-IV on FHIR: converting a decade of in-patient data into an exchangeable, interoperable format

   Bennett, Alex M, Ulrich, Hannes, Damme, Philip,  Wiedekopf, Joshua, and Johnson, Alistair E W

   Journal of the American Medical Informatics Association Jan 2023

   DOI Abs Bib

   Convert the Medical Information Mart for Intensive Care (MIMIC)-IV database into Health Level 7 Fast Healthcare Interoperability Resources (FHIR). Additionally, generate and publish an openly available demo of the resources, and create a FHIR Implementation Guide to support and clarify the usage of MIMIC-IV on FHIR.FHIR profiles and terminology system of MIMIC-IV were modeled from the base FHIR R4 resources. Data and terminology were reorganized from the relational structure into FHIR according to the profiles. Resources generated were validated for conformance with the FHIR profiles. Finally, FHIR resources were published as newline delimited JSON files and the profiles were packaged into an implementation guide.The modeling of MIMIC-IV in FHIR resulted in 25 profiles, 2 extensions, 35 ValueSets, and 34 CodeSystems. An implementation guide encompassing the FHIR modeling can be accessed at mimic.mit.edu/fhir/mimic. The generated demo dataset contained 100 patients and over 915 000 resources. The full dataset contained 315 000 patients covering approximately 5 840 000 resources. The final datasets in NDJSON format are accessible on PhysioNet.Our work highlights the challenges and benefits of generating a real-world FHIR store. The challenges arise from terminology mapping and profiling modeling decisions. The benefits come from the extensively validated openly accessible data created as a result of the modeling work.The newly created MIMIC-IV on FHIR provides one of the first accessible deidentified critical care FHIR datasets. The extensive real-world data found in MIMIC-IV on FHIR will be invaluable for research and the development of healthcare applications.

   @article{bennett_mimicfhir_2023,
     doi = {10.1093/jamia/ocad002},
     selected = {true},
     url = {https://doi.org/10.1093/jamia/ocad002},
     year = {2023},
     month = jan,
     publisher = {Oxford University Press ({OUP})},
     author = {Bennett, Alex M and Ulrich, Hannes and van Damme, Philip and Wiedekopf, Joshua and Johnson, Alistair E W},
     title = {{MIMIC}-{IV} on {FHIR}: converting a decade of in-patient data into an exchangeable, interoperable format},
     journal = {Journal of the American Medical Informatics Association}
   }

2. TerminoDiff – Detecting Semantic Differences in HL7 FHIR CodeSystems

   Wiedekopf, Joshua, Drenkhahn, Cora, Rosenau, Lorenz, Ulrich, Hannes, Kock-Schoppenhauer, Ann-Kristin, and Ingenerf, Josef

   Journal of the American Medical Informatics Association May 2022

   DOI Abs Bib

   While HL7 FHIR and its terminology package have seen a rapid uptake by the research community, in no small part due to the wide availability of tooling and resources, there are some areas where tool availability is still lacking. In particular, the comparison of terminological resources, which supports the work of terminologists and implementers alike, has not yet been sufficiently addressed. Hence, we present TerminoDiff, an application to semantically compare FHIR R4 CodeSystem resources. Our tool considers differences across all levels required, i.e. metadata and concept differences, as well as differences in the edge graph, and surfaces them in a visually digestible fashion.

   @incollection{wiedekopf_terminodiff_2022,
     selected = {true},
     author = {Wiedekopf, Joshua and Drenkhahn, Cora and Rosenau, Lorenz and Ulrich, Hannes and Kock-Schoppenhauer, Ann-Kristin and Ingenerf, Josef},
     booktitle = {Studies in Health Technology and Informatics},
     publisher = {{IOS} Press},
     title = {{TerminoDiff} {\textendash} Detecting Semantic Differences in {HL}7 {FHIR} {CodeSystems}},
     year = {2022},
     month = may,
     doi = {10.3233/shti220475}
   }

3. Medical Data Engineering – Theory and Practice

   Kock-Schoppenhauer, Ann-Kristin, Schreiweis, Björn, Ulrich, Hannes, Reimer, Niklas,  Wiedekopf, Joshua, Kinast, Benjamin, Busch, Hauke, Bergh, Björn, and Ingenerf, Josef

   Advances in Model and Data Engineering in the Digitalization Era Oct 2021

   DOI Abs Bib

   Data integration and exchange are becoming more crucial with the increasing amount of distributed systems and ever-growing amounts of data. This need is also widely known in medical research and not yet comprehensively solved. Practical implementation steps will demonstrate the different challenges in the context of the National Medical Informatics Initiative in Germany. Top-down versus bottom-up approaches as general methods of standard-based data integration in healthcare will be discussed and illustrated in the process of building up Medical Data Integration Centers. As practical examples, the use cases Infection Control, Cardiology, and Molecular Tumor Board, will be presented. Finally, limitations that prevent the use of theoretically recommended data integration methods in the particular field of medical informatics are illustrated.

   @article{kockschopp_medical_2021,
     selected = {true},
     location = {Cham},
     title = {Medical Data Engineering – Theory and Practice},
     volume = {1481},
     isbn = {978-3-030-87656-2 978-3-030-87657-9},
     url = {https://link.springer.com/10.1007/978-3-030-87657-9_21},
     pages = {269--284},
     journal = {Advances in Model and Data Engineering in the Digitalization Era},
     publisher = {Springer International Publishing},
     author = {Kock-Schoppenhauer, Ann-Kristin and Schreiweis, Björn and Ulrich, Hannes and Reimer, Niklas and Wiedekopf, Joshua and Kinast, Benjamin and Busch, Hauke and Bergh, Björn and Ingenerf, Josef},
     editor = {Bellatreche, Ladjel and Chernishev, George and Corral, Antonio and Ouchani, Samir and Vain, Jüri},
     year = {2021},
     month = oct,
     langid = {english},
     doi = {10.1007/978-3-030-87657-9_21},
     note = {Series Title: Communications in Computer and Information Science}
   }