Abstract
| Original language | English |
|---|---|
| Article number | 105104 |
| Journal | International Journal of Medical Informatics |
| Volume | 176 |
| DOIs | |
| Publication status | Published - 1 Aug 2023 |
Keywords
- EHDEN
- FAIR
- FAIR assessment
- OHDSI
- OMOP CDM
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In: International Journal of Medical Informatics, Vol. 176, 105104, 01.08.2023.
Research output: Contribution to journal › Article › Academic › peer-review
TY - JOUR
T1 - Assessing the FAIRness of databases on the EHDEN portal
T2 - A case study on two Dutch ICU databases
AU - Puttmann, Daniel
AU - de Groot, Rowdy
AU - de Keizer, Nicolette
AU - Cornet, Ronald
AU - Elbers, Paul W. G.
AU - Dongelmans, Dave
AU - Bakhshi-Raiez, Ferishta
N1 - Funding Information: The Dutch ICU Data Sharing Against COVID-19 Collaborators:, Diederik Gommers, MD, PhD, Department of Intensive Care, Erasmus Medical Center, Rotterdam, The Netherlands. Olaf L. Cremer, MD, PhD, Intensive Care, UMC Utrecht, Utrecht, The Netherlands. Rob J. Bosman, MD, ICU, OLVG, Amsterdam, The Netherlands. Sander Rigter, MD, Department of Anesthesiology and Intensive Care, St. Antonius Hospital, Nieuwegein, The Netherlands. Evert-Jan Wils, MD, PhD, Department of Intensive Care, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands. Tim Frenzel, MD, PhD, Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, The Netherlands. Dave A. Dongelmans, MD, PhD, Department of Intensive Care Medicine, Amsterdam UMC, Amsterdam, The Netherlands. Remko de Jong, MD, Intensive Care, Bovenij Ziekenhuis, Amsterdam, The Netherlands. Marco A.A. Peters, MD, Intensive Care, Canisius Wilhelmina Ziekenhuis, Nijmegen, The Netherlands. Marlijn J.A Kamps, MD, Intensive Care, Catharina Ziekenhuis Eindhoven, Eindhoven, The Netherlands. Dharmanand Ramnarain, MD, Department of Intensive Care, ETZ Tilburg, Tilburg, The Netherlands. Ralph Nowitzky, MD, Intensive Care, HagaZiekenhuis, Den Haag, The Netherlands. Fleur G.C.A. Nooteboom, MD, Intensive Care, Laurentius Ziekenhuis, Roermond, The Netherlands. Wouter de Ruijter, MD, PhD, Department of Intensive Care Medicine, Northwest Clinics, Alkmaar, The Netherlands. Louise C. Urlings-Strop, MD, PhD, Intensive Care, Reinier de Graaf Gasthuis, Delft, The Netherlands. Ellen G.M. Smit, MD, Intensive Care, Spaarne Gasthuis, Haarlem en Hoofddorp, The Netherlands. D. Jannet Mehagnoul-Schipper, MD, PhD, Intensive Care, VieCuri Medisch Centrum, Venlo, The Netherlands. Tom Dormans, MD, PhD, Intensive care, Zuyderland MC, Heerlen, The Netherlands. Cornelis P.C. de Jager, MD, PhD, Department of Intensive Care, Jeroen Bosch Ziekenhuis, Den Bosch, The Netherlands. Stefaan H.A. Hendriks, MD, Intensive Care, Albert Schweitzerziekenhuis, Dordrecht, The Netherlands. Sefanja Achterberg, MD, PhD, ICU, Haaglanden Medisch Centrum, Den Haag, The Netherlands. Evelien Oostdijk, MD, PhD, ICU, Maasstad Ziekenhuis Rotterdam, Rotterdam, The Netherlands. Auke C. Reidinga, MD, ICU, BWC, Martiniziekenhuis, Groningen. Barbara Festen-Spanjer, MD, Intensive Care, Ziekenhuis Gelderse Vallei, Ede, The Netherlands. Gert B. Brunnekreef, MD, Department of Intensive Care, Ziekenhuisgroep Twente, Almelo, The Netherlands. Alexander D. Cornet, MD, PhD, FRCP, Department of Intensive Care, Medisch Spectrum Twente, Enschede, The Netherlands. Walter van den Tempel, MD, Department of Intensive Care, Ikazia Ziekenhuis Rotterdam, Rotterdam, The Netherlands. Age D. Boelens, MD, Anesthesiology, Antonius Ziekenhuis Sneek, Sneek, The Netherlands. Peter Koetsier, MD, Intensive Care, Medisch Centrum Leeuwarden, Leeuwarden, The Netherlands. Judith Lens, MD, ICU, IJsselland Ziekenhuis, Capelle aan den IJssel, The Netherlands. Harald J. Faber, MD, ICU, WZA, Assen, The Netherlands. A. Karakus, MD, Department of Intensive Care, Diakonessenhuis Hospital, Utrecht, The Netherlands. Robert Entjes, MD, Department of Intensive Care, Adrz, Goes, The Netherlands. Paul de Jong, MD, Department of Anesthesia and Intensive Care, Slingeland Ziekenhuis, Doetinchem, The Netherlands. Thijs C.D. Rettig, MD, PhD, Department of Anesthesiology, Intensive Care and Pain Medicine, Amphia Ziekenhuis, Breda, The Netherlands. Sesmu Arbous, MD, PhD, Department of Intensive Care, LUMC, Leiden, The Netherlands. Tariq A. Dam, MD, Department of Intensive Care Medicine, Laboratory for Critical Care Computational Intelligence, Amsterdam Medical Data Science, Amsterdam UMC,. Sebastiaan J.J. Vonk, MSc, Pacmed, Amsterdam, The Netherlands. Tomas Machado, Pacmed, Amsterdam, The Netherlands. Willem E. Herter, BSc, Pacmed, Amsterdam, The Netherlands. From collaborating hospitals having shared data:, Julia Koeter, MD, Intensive Care, Canisius Wilhelmina Ziekenhuis, Nijmegen, The Netherlands. Roger van Rietschote, Business Intelligence, Haaglanden MC, Den Haag, The Netherlands. M.C. Reuland, MD, Department of Intensive Care Medicine, Amsterdam UMC, Universiteit van Amsterdam, Amsterdam, The Netherlands. Laura van Manen, MD, Department of Intensive Care, BovenIJ Ziekenhuis, Amsterdam, The Netherlands. Leon Montenij, MD, PhD, Department of Anesthesiology, Pain Management and Intensive Care, Catharina Ziekenhuis Eindhoven, Eindhoven, The Netherlands. Jasper van Bommel, MD, PhD, Department of Intensive Care, Erasmus Medical Center, Rotterdam, The Netherlands. Roy van den Berg, Department of Intensive Care, ETZ Tilburg, Tilburg, The Netherlands. Ellen van Geest, Department of ICMT, Haga Ziekenhuis, Den Haag, The Netherlands. Anisa Hana, MD, PhD, Intensive Care, Laurentius Ziekenhuis, Roermond, The Netherlands. B. van den Bogaard, MD, PhD, ICU, OLVG, Amsterdam, The Netherlands. Prof. Peter Pickkers, Department of Intensive Care Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands. Pim van der Heiden, MD, PhD, Intensive Care, Reinier de Graaf Gasthuis, Delft, The Netherlands. Claudia (C.W.) van Gemeren, MD, Intensive Care, Spaarne Gasthuis, Haarlem en Hoofddorp, The Netherlands. Arend Jan Meinders, MD, Department of Internal Medicine and Intensive Care, St Antonius Hospital, Nieuwegein, The Netherlands. Martha de Bruin, MD, Department of Intensive Care, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands. Emma Rademaker, MD, MSc, Department of Intensive Care, UMC Utrecht, Utrecht, The Netherlands. Frits H.M. van Osch, PhD, Department of Clinical Epidemiology, VieCuri Medisch Centrum, Venlo, The Netherlands. Martijn de Kruif, MD, PhD, Department of Pulmonology, Zuyderland MC, Heerlen, The Netherlands. Nicolas Schroten, MD, Intensive Care, Albert Schweitzerziekenhuis, Dordrecht, The Netherlands. Klaas Sierk Arnold, MD, Anesthesiology, Antonius Ziekenhuis Sneek, Sneek, The Netherlands. J.W. Fijen, MD, PhD, Department of Intensive Care, Diakonessenhuis Hospital, Utrecht, The Netherland. Jacomar J.M. van Koesveld, MD, ICU, IJsselland Ziekenhuis, Capelle aan den IJssel, The Netherlands. Koen S. Simons, MD, PhD, Department of Intensive Care, Jeroen Bosch Ziekenhuis, Den Bosch, The Netherlands. Joost Labout, MD, PhD, ICU, Maasstad Ziekenhuis Rotterdam, The Netherlands. Bart van de Gaauw, Martini ziekenhuis, Groningen, The Netherlands. Michael Kuiper, Intensive Care, Medisch Centrum Leeuwarden, Leeuwarden, The Netherlands. Albertus Beishuizen, MD, PhD, Department of Intensive Care, Medisch Spectrum Twente, Enschede, The Netherlands. Dennis Geutjes, Department of Information Technology, Slingeland Ziekenhuis, Doetinchem, The Netherlands. Johan Lutisan, MD, ICU, WZA, Assen, The Netherlands. Bart P. Grady, MD, PhD, Department of Intensive Care, Ziekenhuisgroep Twente, Almelo, The Netherlands. Remko van den Akker, Intensive Care, Adrz, Goes, The Netherlands. Tom A. Rijpstra, MD, Department of Anesthesiology, Intensive Care and Pain Medicine, Amphia Ziekenhuis, Breda, The Netherlands. Wim G. Boersma, MD, PhD, Department of Pulmonology, Northwest Clinics, Alkmaar, The Netherlands. From collaborating hospitals having signed the data sharing agreement:, Daniël Pretorius, MD, Department of Intensive Care Medicine, Hospital St Jansdal, Harderwijk, The Netherlands. Menno Beukema, MD, Department of Intensive Care, Streekziekenhuis Koningin Beatrix, Winterswijk, The Netherlands. Bram Simons, MD, Intensive Care, Bravis Ziekenhuis, Bergen op Zoom en Roosendaal, The Netherlands. A.A. Rijkeboer, MD, ICU, Flevoziekenhuis, Almere, The Netherlands. Marcel Aries, MD, PhD, MUMC+, University Maastricht, Maastricht, The Netherlands. Niels C. Gritters van den Oever, MD, Intensive Care, Treant Zorggroep, Emmen, The Netherlands. Martijn van Tellingen, MD, EDIC, Department of Intensive Care Medicine, afdeling Intensive Care, ziekenhuis Tjongerschans, Heerenveen, The Netherlands. Annemieke Dijkstra, MD, Department of Intensive Care Medicine, Het Van Weel-Bethesda Ziekenhuis, Dirksland, The Netherlands. Rutger van Raalte, Department of Intensive Care, Tergooi hospital, Hilversum, The Netherlands. Publisher Copyright: © 2023 The Author(s)
PY - 2023/8/1
Y1 - 2023/8/1
N2 - Objective: To address the growing need for effective data reuse in health research, healthcare institutions need to make their data Findable, Accessible, Interoperable, and Reusable (FAIR). A prevailing method to model databases for interoperability is the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM), developed by the Observational Health Data Sciences and Informatics (OHDSI) initiative. A European repository for OMOP CDM-converted databases called the “European Health Data & Evidence Network (EHDEN) portal” was developed, aiming to make these databases Findable and Accessible. This paper aims to assess the FAIRness of databases on the EHDEN portal. Materials and methods: Two researchers involved in the OMOP CDM conversion of separate Dutch Intensive Care Unit (ICU) research databases each manually assessed their own database using seventeen metrics. These were defined by the FAIRsFAIR project as a list of minimum requirements for a database to be FAIR. Each metric is given a score from zero to four based on how well the database adheres to the metric. The maximum score for each metric varies from one to four based on the importance of the metric. Results: Fourteen out of the seventeen metrics were unanimously rated: seven were rated the highest score, one was rated half of the highest score, and five were rated the lowest score. The remaining three metrics were assessed differently for the two use cases. The total scores achieved were 15.5 and 12 out of a maximum of 25. Conclusion: The main omissions in supporting FAIRness were the lack of globally unique identifiers such as Uniform Resource Identifiers (URIs) in the OMOP CDM and the lack of metadata standardization and linkage in the EHDEN portal. By implementing these in future updates, the EHDEN portal can be more FAIR.
AB - Objective: To address the growing need for effective data reuse in health research, healthcare institutions need to make their data Findable, Accessible, Interoperable, and Reusable (FAIR). A prevailing method to model databases for interoperability is the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM), developed by the Observational Health Data Sciences and Informatics (OHDSI) initiative. A European repository for OMOP CDM-converted databases called the “European Health Data & Evidence Network (EHDEN) portal” was developed, aiming to make these databases Findable and Accessible. This paper aims to assess the FAIRness of databases on the EHDEN portal. Materials and methods: Two researchers involved in the OMOP CDM conversion of separate Dutch Intensive Care Unit (ICU) research databases each manually assessed their own database using seventeen metrics. These were defined by the FAIRsFAIR project as a list of minimum requirements for a database to be FAIR. Each metric is given a score from zero to four based on how well the database adheres to the metric. The maximum score for each metric varies from one to four based on the importance of the metric. Results: Fourteen out of the seventeen metrics were unanimously rated: seven were rated the highest score, one was rated half of the highest score, and five were rated the lowest score. The remaining three metrics were assessed differently for the two use cases. The total scores achieved were 15.5 and 12 out of a maximum of 25. Conclusion: The main omissions in supporting FAIRness were the lack of globally unique identifiers such as Uniform Resource Identifiers (URIs) in the OMOP CDM and the lack of metadata standardization and linkage in the EHDEN portal. By implementing these in future updates, the EHDEN portal can be more FAIR.
KW - EHDEN
KW - FAIR
KW - FAIR assessment
KW - OHDSI
KW - OMOP CDM
UR - http://www.scopus.com/inward/record.url?scp=85160661757&partnerID=8YFLogxK
U2 - https://doi.org/10.1016/j.ijmedinf.2023.105104
DO - https://doi.org/10.1016/j.ijmedinf.2023.105104
M3 - Article
C2 - 37267810
SN - 1386-5056
VL - 176
JO - International Journal of Medical Informatics
JF - International Journal of Medical Informatics
M1 - 105104
ER -