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Towards Implementation of OMOP in a German University Hospital Consortium

C. Maier, L. Lang, H. Storf, P. Vormstein, R. Bieber, J. Bernarding, T. Herrmann, C. Haverkamp, P. Horki, J. Laufer, F. Berger, G. Höning (+5 others)
2018 Applied Clinical Informatics  
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,  ...  Conclusion OMOP/OHDSI is a viable open source solution for data integration in a German research consortium.  ...  The authors were able to successfully implement this tools stack for the first time in a German consortium of university hospitals based on a typical dataset, although in a German flavor due to the coding  ... 
doi:10.1055/s-0037-1617452 pmid:29365340 pmcid:PMC5801887 fatcat:ttodzt7t5rdh7mwzfhz7526g4u

Moving Towards an EHR Data Quality Framework: The MIRACUM Approach

Lorenz A Kapsner, Marvin O Kampf, Susanne A Seuchter, Gaetan Kamdje-Wabo, Tobias Gradinger, Thomas Ganslandt, Sebastian Mate, Julian Gruendner, Detlef Kraska, Hans-Ulrich Prokosch
2019 Studies in Health Technology and Informatics  
DQ issues can now be systematically identified by individual hospitals to subsequently implement site- or consortium-wide feedback loops to increase data quality.  ...  Data quality (DQ) is an important prerequisite for secondary use of electronic health record (EHR) data in clinical research, particularly with regards to progressing towards a learning health system,  ...  Acknowledgement This work was funded in part by the German Federal Ministry of Education and Research (BMBF) within the Medical Informatics Initiative (MIRACUM Consortium) under the Funding Numbers FKZ  ... 
doi:10.3233/shti190834 pmid:31483279 fatcat:bjh5e5s6tfh2ddx3pxh3fvsuna

KETOS: Clinical decision support and machine learning as a service – A training and deployment platform based on Docker, OMOP-CDM, and FHIR Web Services

Julian Gruendner, Thorsten Schwachhofer, Phillip Sippl, Nicolas Wolf, Marcel Erpenbeck, Christian Gulden, Lorenz A. Kapsner, Jakob Zierk, Sebastian Mate, Michael Stürzl, Roland Croner, Hans-Ulrich Prokosch (+2 others)
2019 PLoS ONE  
The KETOS platform demonstrated in this work implements a tool for researchers allowing them to perform statistical analyses and deploy resulting models in a secure environment.  ...  To take full advantage of decision support, machine learning, and patient-level prediction models, it is important that models are not only created, but also deployed in a clinical setting.  ...  Acknowledgments The present work was performed in fulfilment of the requirements for obtaining the degree "Dr. rer. biol. hum." from the Friedrich-Alexander-Universität Erlangen-Nürnberg (JG).  ... 
doi:10.1371/journal.pone.0223010 pmid:31581246 pmcid:PMC6776354 fatcat:edsluvqr7vbmlmse47fyxxkeue

MIRACUM: Medical Informatics in Research and Care in University Medicine

Till Acker, Johannes Bernarding, Harald Binder, Martin Boeker, Melanie Boerries, Philipp Daumke, Thomas Ganslandt, Jürgen Hesser, Gunther Höning, Michael Neumaier, Kurt Marquardt, Harald Renz (+9 others)
2018 Methods of Information in Medicine  
OHDSI, PCORnet, eMerge, RD-Connect) MIRACUM is a consortium of academic and hospital partners as well as one industrial partner in eight German cities which have joined forces to create interoperable data  ...  Health System will be crucial for the acceptance and sustainability in the medical community and the MIRACUM university hospitals.  ...  Acknowledgment We are grateful to the many members of the MIRACUM team who have actively participated in the design and first implementation of the described architecture and data integration centers.  ... 
doi:10.3414/me17-02-0025 pmid:30016814 pmcid:PMC6178200 fatcat:5vgcr2psinbbdgkolpsdapqxee

Digital networks for laboratory data: potentials, barriers and current initiatives

Thomas Ganslandt, Michael Neumaier
2018 Clinical Chemistry and Laboratory Medicine  
The German Medical Informatics Initiative is presented as a current undertaking that strives to address these issues by establishing a national infrastructure for the secondary use of routine clinical  ...  Integration of these data sources opens up several potentials: a longitudinal view of laboratory findings would close the gaps between individual provider visits and allow to more closely follow disease  ...  With 10 participating university hospitals and access to data from 12 million patients, MIRACUM is currently the largest MII consortium.  ... 
doi:10.1515/cclm-2018-1131 pmid:30496134 fatcat:w4gjgsjmyvepth7qxyyynre5z4

A Generic Method and Implementation to Evaluate and Improve Data Quality in Distributed Research Networks

D. Juárez, E.E. Schmidt, S. Stahl-Toyota, F. Ückert, M. Lablans
2019 Methods of Information in Medicine  
A reference implementation for this concept has been successfully utilized at 10 sites across the German Cancer Consortium.  ...  To achieve this, we designed a quality report and the process for generating such a report. The final step was the implementation in a German research network.  ...  Acknowledgments The authors would like to acknowledge the valuable collaboration with their partners in the German Cancer Consortium (DKTK), in particular Barbara Uhl and Kristina Ihrig of the Office of  ... 
doi:10.1055/s-0039-1693685 pmid:31514209 fatcat:pjy5jtlwgvb4bobjn2algrwlzq

D8.2 Overview Document on Already Existing Data Harmonisation Tools

Sebastian Mate, Ines Leb, Christina Schüttler, Kaisa Silander, Timo Miettinen, Juha Knuuttila, Niina Eklund, Hans-Ulrich Prokosch
2016 Zenodo  
This review has been done as a deliverable of the Biobanking and Biomolecular Resources Research Infrastructure – European Research Infrastructure Consortium (BBMRI-ERIC) Common Service IT (CS-IT) as well  ...  Since data harmonisation, however, is not only an important issue in biobanking, but a key component in all data sharing/data projects, our focus is also on such projects outside the biobanking area.  ...  This may be a first step toward a larger distributed network of data archiving and dissemination services.  ... 
doi:10.5281/zenodo.165775 fatcat:gv3654h5ondpri6hbuo2hdppeq

First Steps to Evaluate an NLP Tool's Medication Extraction Accuracy from Discharge Letters [chapter]

Deniz Caliskan, Jakob Zierk, Detlef Kraska, Stefan Schulz, Philipp Daumke, Hans-Ulrich Prokosch, Lorenz A. Kapsner
2021 Studies in Health Technology and Informatics  
Methods: Ten randomly selected discharge letters were extracted from the data warehouse of the University Hospital Erlangen (UHE) and manually annotated to create a gold standard.  ...  Discussion: This proof-of-concept study is a first step towards an automated scalable evaluation system for MIRACUM's industry partner's NLP tool by using a gold standard.  ...  Acknowledgements: This work was funded in part by the German Federal Ministry of Education and Research (BMBF) within the Medical Informatics Initiative (MIRACUM Consortium) under the Funding Number FKZ  ... 
doi:10.3233/shti210073 pmid:34042898 fatcat:cywxg5b4wrcbxbcbejcxcjut7m

The French Health Data Hub and the German Medical Informatics Initiatives: Two National Projects to Promote Data Sharing in Healthcare

Marc Cuggia, Stéphanie Combes
2019 IMIA Yearbook of Medical Informatics  
The MII project is based on a bottom-up approach and relies on four consortia including academic hospitals, universities, and private partners.  ...  A Franco-German cooperation, extended to other countries of the European Union with similar initiatives, should allow sharing and strengthening efforts in a strategic area where competition from other  ...  University hospitals in the West of France have built one of the first clinical data research network in Europe [47] , which is very similar to a consortia of the German project.  ... 
doi:10.1055/s-0039-1677917 pmid:31419832 pmcid:PMC6697511 fatcat:dy4xn2kdpbf4nckd77djv72hpa

EOSC-Life Report on data standards for observational and interventional studies, and interoperability between healthcare and research data

Steve Canham, Christian Ohmann, Jan-Willem Boiten, Maria Panagiotopoulou, Nigel Hughes, Romain David, Alex Sanchez Pla, Lauren Maxwell, Jozef Aerts, Rhonda Facile, Nicolas Griffon, Gary Saunders (+2 others)
2021 Zenodo  
A conclusion summarises the report's findings and discusses possible actions to improve data interoperability in the short, medium and long term.  ...  The practicalities of interoperability, in particular with respect to making healthcare data more like interventional research data, are explored – again under the headings of outcome measures, syntactic  ...  Furthermore, OMOP is not limited to hospital data. A web page describing the mapping of a biobank's data to OMOP (at UCL in London) is available at [95] .  ... 
doi:10.5281/zenodo.5810611 fatcat:e5of54ape5bvdbv2erihu6dexi

International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium

Gabriel A. Brat, Griffin M. Weber, Nils Gehlenborg, Paul Avillach, Nathan P. Palmer, Luca Chiovato, James Cimino, Lemuel R. Waitman, Gilbert S. Omenn, Alberto Malovini, Jason H. Moore, Brett K. Beaulieu-Jones (+75 others)
2020 npj Digital Medicine  
To do this, we formed an international consortium (4CE) of 96 hospitals across five countries (www.covidclinical.net).  ...  Laboratory tests at the time of diagnosis showed hospital-level differences equivalent to country-level variation across the consortium partners.  ...  Hospitals in Italy, in contrast, did not see a dramatic rise in creatinine in their hospitalized population, while the small percentage of French and German patients remaining in the hospital for 2 weeks  ... 
doi:10.1038/s41746-020-00308-0 pmid:32864472 pmcid:PMC7438496 fatcat:kfanlgxygfaxhghsmadytwgmea

International Electronic Health Record-Derived COVID-19 Clinical Course Profile: The 4CE Consortium [article]

Gabriel A Brat, Griffin M Weber, Nils Gehlenborg, Paul Avillach, Nathan P Palmer, Luca Chiovato, James Cimino, Lemuel R Waitman, Gilbert S Omenn, Alberto Malovini, Jason H Moore, Brett K Beaulieu-Jones (+73 others)
2020 medRxiv   pre-print
METHODS: A consortium of international hospital systems of different sizes utilizing Informatics for Integrating Biology and the Bedside (i2b2) and Observational Medical Outcomes Partnership (OMOP) platforms  ...  RESULTS: 96 hospitals in the US, France, Italy, Germany, and Singapore contributed data to the consortium for a total of 27,927 COVID-19 cases and 187,802 performed laboratory values.  ...  Hospitals in Italy, in contrast, did not see a dramatic rise in creatinine in their hospitalized population, while the small percentage of French and German patients remaining in the hospital for two weeks  ... 
doi:10.1101/2020.04.13.20059691 fatcat:3fnicc3ayncdnozy7tgvbcp2di

Information Technology for Clinical, Translational and Comparative Effectiveness Research

C. Daniel, R. Choquet
2015 IMIA Yearbook of Medical Informatics  
Acknowledgement We would like to acknowledge the support of Martina Hutter and the reviewers in the selection process of the IMIA Yearbook.  ...  The authors selected five sites from a portfolio of German University Hospitals runing EHR implementations and evaluated within these sites the existence of modules or tools, which can readily be applied  ...  The authors analysed in five sites' hospital information system environments in Germany the possibility of implementing a patient recruitment process and provided recommendations for the development of  ... 
doi:10.15265/iy-2015-030 pmid:26293866 pmcid:PMC4587062 fatcat:xhhh6mfzdnbr3lr43hjinrwtge

B1MG D3.7 - Documented best practices in sharing and linking phenotypic and genetic data - 1v0

Jeroen Belien, Catia Pinto, Maarten Ligtvoet, Milena Urbini, Pim Volkert, Wei Gu, Michela Tebaldi, Attila Patocs, K.Joeri van der Velde, Marielle E van Gijn, Jan O Korbel, Antonella Padella (+5 others)
2021 Zenodo  
This is the first version of documented best practices in sharing and linking phenotypic and genetic data.  ...  It identifies and describes best practices on sharing and linking phenotypic and genetic data in both the healthcare sector and in the research setting.  ...  Documented best practices in sharing and linking phenotypic and genetic dataChampion: Medical Informatics Hospital Clínic-University of Barcelona; Doce de Octubre University Hospital, Madrid, Telemedicine  ... 
doi:10.5281/zenodo.5018520 fatcat:5riuzciexnbypgdvmeumdxvyim

B1MG D3.7 - Documented best practices in sharing and linking phenotypic and genetic data - 1v0

Jeroen Belien, Catia Pinto, Maarten Ligtvoet, Milena Urbini, Pim Volkert, Wei Gu, Michela Tebaldi, Attila Patocs, K.Joeri van der Velde, Marielle E van Gijn, Jan O Korbel, Antonella Padella (+5 others)
2021 Zenodo  
This is the first version of documented best practices in sharing and linking phenotypic and genetic data.  ...  It identifies and describes best practices on sharing and linking phenotypic and genetic data in both the healthcare sector and in the research setting.  ...  sharing and linking phenotypic and genetic data -1v0 19 Champion: Medical Informatics Hospital Clínic-University of Barcelona; Doce de Octubre University Hospital, Madrid, Telemedicine and Information  ... 
doi:10.5281/zenodo.4819148 fatcat:emq7g3lcinbxjcsqjokjw3ehpa
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