Julian Sass1, Alexander Bartschke2, Moritz Lehne1, Andrea Essenwanger1, Eugenia Rinaldi2, Stefanie Rudolph2, Kai U Heitmann3, Jörg J Vehreschild4,5,6, Christof von Kalle1,2, Sylvia Thun7,8,9. 1. Berlin Institute of Health (BIH), Berlin, Germany. 2. Charité - Universitätsmedizin Berlin, Berlin, Germany. 3. HIH - Health Innovation Hub of the Federal Ministry of Health, Berlin, Germany. 4. Medical Department 2, Hematology/Oncology, University Hospital of Frankfurt, Frankfurt, Germany. 5. Department I for Internal Medicine, University Hospital Cologne, Cologne, Germany. 6. German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany. 7. Berlin Institute of Health (BIH), Berlin, Germany. sylvia.thun@charite.de. 8. Charité - Universitätsmedizin Berlin, Berlin, Germany. sylvia.thun@charite.de. 9. Hochschule Niederrhein - University of Applied Sciences, Krefeld, Germany. sylvia.thun@charite.de.
Abstract
BACKGROUND: The current COVID-19 pandemic has led to a surge of research activity. While this research provides important insights, the multitude of studies results in an increasing fragmentation of information. To ensure comparability across projects and institutions, standard datasets are needed. Here, we introduce the "German Corona Consensus Dataset" (GECCO), a uniform dataset that uses international terminologies and health IT standards to improve interoperability of COVID-19 data, in particular for university medicine. METHODS: Based on previous work (e.g., the ISARIC-WHO COVID-19 case report form) and in coordination with experts from university hospitals, professional associations and research initiatives, data elements relevant for COVID-19 research were collected, prioritized and consolidated into a compact core dataset. The dataset was mapped to international terminologies, and the Fast Healthcare Interoperability Resources (FHIR) standard was used to define interoperable, machine-readable data formats. RESULTS: A core dataset consisting of 81 data elements with 281 response options was defined, including information about, for example, demography, medical history, symptoms, therapy, medications or laboratory values of COVID-19 patients. Data elements and response options were mapped to SNOMED CT, LOINC, UCUM, ICD-10-GM and ATC, and FHIR profiles for interoperable data exchange were defined. CONCLUSION: GECCO provides a compact, interoperable dataset that can help to make COVID-19 research data more comparable across studies and institutions. The dataset will be further refined in the future by adding domain-specific extension modules for more specialized use cases.
BACKGROUND: The current COVID-19 pandemic has led to a surge of research activity. While this research provides important insights, the multitude of studies results in an increasing fragmentation of information. To ensure comparability across projects and institutions, standard datasets are needed. Here, we introduce the "German Corona Consensus Dataset" (GECCO), a uniform dataset that uses international terminologies and health IT standards to improve interoperability of COVID-19 data, in particular for university medicine. METHODS: Based on previous work (e.g., the ISARIC-WHO COVID-19 case report form) and in coordination with experts from university hospitals, professional associations and research initiatives, data elements relevant for COVID-19 research were collected, prioritized and consolidated into a compact core dataset. The dataset was mapped to international terminologies, and the Fast Healthcare Interoperability Resources (FHIR) standard was used to define interoperable, machine-readable data formats. RESULTS: A core dataset consisting of 81 data elements with 281 response options was defined, including information about, for example, demography, medical history, symptoms, therapy, medications or laboratory values of COVID-19patients. Data elements and response options were mapped to SNOMED CT, LOINC, UCUM, ICD-10-GM and ATC, and FHIR profiles for interoperable data exchange were defined. CONCLUSION: GECCO provides a compact, interoperable dataset that can help to make COVID-19 research data more comparable across studies and institutions. The dataset will be further refined in the future by adding domain-specific extension modules for more specialized use cases.
Entities:
Keywords:
COVID-19; FHIR; Interoperability; Standard dataset
Authors: Clement J McDonald; Stanley M Huff; Jeffrey G Suico; Gilbert Hill; Dennis Leavelle; Raymond Aller; Arden Forrey; Kathy Mercer; Georges DeMoor; John Hook; Warren Williams; James Case; Pat Maloney Journal: Clin Chem Date: 2003-04 Impact factor: 8.327
Authors: Martin Dugas; Philipp Neuhaus; Alexandra Meidt; Justin Doods; Michael Storck; Philipp Bruland; Julian Varghese Journal: Database (Oxford) Date: 2016-02-11 Impact factor: 3.451
Authors: Annemarie B Docherty; Ewen M Harrison; Christopher A Green; Hayley E Hardwick; Riinu Pius; Lisa Norman; Karl A Holden; Jonathan M Read; Frank Dondelinger; Gail Carson; Laura Merson; James Lee; Daniel Plotkin; Louise Sigfrid; Sophie Halpin; Clare Jackson; Carrol Gamble; Peter W Horby; Jonathan S Nguyen-Van-Tam; Antonia Ho; Clark D Russell; Jake Dunning; Peter Jm Openshaw; J Kenneth Baillie; Malcolm G Semple Journal: BMJ Date: 2020-05-22
Authors: J L Raisaro; Francesco Marino; Juan Troncoso-Pastoriza; Raphaelle Beau-Lejdstrom; Riccardo Bellazzi; Robert Murphy; Elmer V Bernstam; Henry Wang; Mauro Bucalo; Yong Chen; Assaf Gottlieb; Arif Harmanci; Miran Kim; Yejin Kim; Jeffrey Klann; Catherine Klersy; Bradley A Malin; Marie Méan; Fabian Prasser; Luigia Scudeller; Ali Torkamani; Julien Vaucher; Mamta Puppala; Stephen T C Wong; Milana Frenkel-Morgenstern; Hua Xu; Baba Maiyaki Musa; Abdulrazaq G Habib; Trevor Cohen; Adam Wilcox; Hamisu M Salihu; Heidi Sofia; Xiaoqian Jiang; J P Hubaux Journal: J Am Med Inform Assoc Date: 2020-11-01 Impact factor: 4.497
Authors: Florian Kurth; Maria Roennefarth; Charlotte Thibeault; Victor M Corman; Holger Müller-Redetzky; Mirja Mittermaier; Christoph Ruwwe-Glösenkamp; Katrin M Heim; Alexander Krannich; Saskia Zvorc; Sein Schmidt; Lucie Kretzler; Chantip Dang-Heine; Matthias Rose; Michael Hummel; Andreas Hocke; Ralf H Hübner; Bastian Opitz; Marcus A Mall; Jobst Röhmel; Ulf Landmesser; Burkert Pieske; Samuel Knauss; Matthias Endres; Joachim Spranger; Frank P Mockenhaupt; Frank Tacke; Sascha Treskatsch; Stefan Angermair; Britta Siegmund; Claudia Spies; Steffen Weber-Carstens; Kai-Uwe Eckardt; Dirk Schürmann; Alexander Uhrig; Miriam S Stegemann; Thomas Zoller; Christian Drosten; Norbert Suttorp; Martin Witzenrath; Stefan Hippenstiel; Christof von Kalle; Leif Erik Sander Journal: Infection Date: 2020-06-13 Impact factor: 3.553
Authors: Melissa A Haendel; Christopher G Chute; Tellen D Bennett; David A Eichmann; Justin Guinney; Warren A Kibbe; Philip R O Payne; Emily R Pfaff; Peter N Robinson; Joel H Saltz; Heidi Spratt; Christine Suver; John Wilbanks; Adam B Wilcox; Andrew E Williams; Chunlei Wu; Clair Blacketer; Robert L Bradford; James J Cimino; Marshall Clark; Evan W Colmenares; Patricia A Francis; Davera Gabriel; Alexis Graves; Raju Hemadri; Stephanie S Hong; George Hripscak; Dazhi Jiao; Jeffrey G Klann; Kristin Kostka; Adam M Lee; Harold P Lehmann; Lora Lingrey; Robert T Miller; Michele Morris; Shawn N Murphy; Karthik Natarajan; Matvey B Palchuk; Usman Sheikh; Harold Solbrig; Shyam Visweswaran; Anita Walden; Kellie M Walters; Griffin M Weber; Xiaohan Tanner Zhang; Richard L Zhu; Benjamin Amor; Andrew T Girvin; Amin Manna; Nabeel Qureshi; Michael G Kurilla; Sam G Michael; Lili M Portilla; Joni L Rutter; Christopher P Austin; Ken R Gersing Journal: J Am Med Inform Assoc Date: 2021-03-01 Impact factor: 7.942
Authors: Christoph Spinner; Jörg Janne Vehreschild; Carolin E M Jakob; Stefan Borgmann; Fazilet Duygu; Uta Behrends; Martin Hower; Uta Merle; Anette Friedrichs; Lukas Tometten; Frank Hanses; Norma Jung; Siegbert Rieg; Kai Wille; Beate Grüner; Hartwig Klinker; Nicole Gersbacher-Runge; Kerstin Hellwig; Lukas Eberwein; Sebastian Dolff; Dominic Rauschning; Michael von Bergwelt-Baildon; Julia Lanznaster; Richard Strauß; Janina Trauth; Katja de With; Maria Ruethrich; Catherina Lueck; Jacob Nattermann; Lene Tscharntke; Lisa Pilgram; Sandra Fuhrmann; Annika Classen; Melanie Stecher; Maximilian Schons Journal: Infection Date: 2020-10-01 Impact factor: 7.455
Authors: Stephany N Duda; Nan Kennedy; Douglas Conway; Alex C Cheng; Viet Nguyen; Teresa Zayas-Cabán; Paul A Harris Journal: J Am Med Inform Assoc Date: 2022-08-16 Impact factor: 7.942
Authors: Lorenz A Kapsner; Marvin O Kampf; Susanne A Seuchter; Julian Gruendner; Christian Gulden; Sebastian Mate; Jonathan M Mang; Christina Schüttler; Noemi Deppenwiese; Linda Krause; Daniela Zöller; Julien Balig; Timo Fuchs; Patrick Fischer; Christian Haverkamp; Martin Holderried; Gerhard Mayer; Holger Stenzhorn; Ana Stolnicu; Michael Storck; Holger Storf; Jochen Zohner; Oliver Kohlbacher; Adam Strzelczyk; Jürgen Schüttler; Till Acker; Martin Boeker; Udo X Kaisers; Hans A Kestler; Hans-Ulrich Prokosch Journal: Front Public Health Date: 2021-01-13
Authors: Lorenz Rosenau; Raphael W Majeed; Josef Ingenerf; Alexander Kiel; Björn Kroll; Thomas Köhler; Hans-Ulrich Prokosch; Julian Gruendner Journal: JMIR Med Inform Date: 2022-04-27
Authors: Alexander Kiel; Raphael W Majeed; Julian Gruendner; Noemi Deppenwiese; Michael Folz; Thomas Köhler; Björn Kroll; Hans-Ulrich Prokosch; Lorenz Rosenau; Mathias Rühle; Marc-Anton Scheidl; Christina Schüttler; Brita Sedlmayr; Alexander Twrdik Journal: JMIR Med Inform Date: 2022-05-25
Authors: Maximilian Schons; Lisa Pilgram; Jens-Peter Reese; Melanie Stecher; Gabriele Anton; Katharina S Appel; Thomas Bahmer; Alexander Bartschke; Carla Bellinghausen; Inga Bernemann; Markus Brechtel; Folke Brinkmann; Clara Brünn; Christine Dhillon; Cornelia Fiessler; Ramsia Geisler; Eckard Hamelmann; Stefan Hansch; Frank Hanses; Sabine Hanß; Susanne Herold; Ralf Heyder; Anna-Lena Hofmann; Sina Marie Hopff; Anna Horn; Carolin Jakob; Steffi Jiru-Hillmann; Thomas Keil; Yascha Khodamoradi; Mirjam Kohls; Monika Kraus; Dagmar Krefting; Sonja Kunze; Florian Kurth; Wolfgang Lieb; Lena Johanna Lippert; Roberto Lorbeer; Bettina Lorenz-Depiereux; Corina Maetzler; Olga Miljukov; Matthias Nauck; Daniel Pape; Valentina Püntmann; Lennart Reinke; Christoph Römmele; Stefanie Rudolph; Julian Sass; Christian Schäfer; Jens Schaller; Mario Schattschneider; Christian Scheer; Margarete Scherer; Sein Schmidt; Julia Schmidt; Kristina Seibel; Dana Stahl; Fridolin Steinbeis; Stefan Störk; Maike Tauchert; Johannes Josef Tebbe; Charlotte Thibeault; Nicole Toepfner; Kathrin Ungethüm; Istvan Vadasz; Heike Valentin; Silke Wiedmann; Thomas Zoller; Eike Nagel; Michael Krawczak; Christof von Kalle; Thomas Illig; Stefan Schreiber; Martin Witzenrath; Peter Heuschmann; Jörg Janne Vehreschild Journal: Eur J Epidemiol Date: 2022-07-29 Impact factor: 12.434
Authors: Carina Nina Vorisek; Moritz Lehne; Sophie Anne Ines Klopfenstein; Paula Josephine Mayer; Alexander Bartschke; Thomas Haese; Sylvia Thun Journal: JMIR Med Inform Date: 2022-07-19