1
|
Rashid R, Copelli S, Silverstein JC, Becich MJ. REDCap and the National Mesothelioma Virtual Bank-a scalable and sustainable model for rare disease biorepositories. J Am Med Inform Assoc 2023; 30:1634-1644. [PMID: 37487555 PMCID: PMC10531116 DOI: 10.1093/jamia/ocad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/16/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
OBJECTIVE Rare disease research requires data sharing networks to power translational studies. We describe novel use of Research Electronic Data Capture (REDCap), a web application for managing clinical data, by the National Mesothelioma Virtual Bank, a federated biospecimen, and data sharing network. MATERIALS AND METHODS National Mesothelioma Virtual Bank (NMVB) uses REDCap to integrate honest broker activities, enabling biospecimen and associated clinical data provisioning to investigators. A Web Portal Query tool was developed to source and visualize REDCap data in interactive, faceted search, enabling cohort discovery by public users. An AWS Lambda function behind an API calculates the counts visually presented, while protecting record level data. The user-friendly interface, quick responsiveness, automatic generation from REDCap, and flexibility to new data, was engineered to sustain the NMVB research community. RESULTS NMVB implementations enabled a network of 8 research institutions with over 2000 mesothelioma cases, including clinical annotations and biospecimens, and public users' cohort discovery and summary statistics. NMVB usage and impact is demonstrated by high website visits (>150 unique queries per month), resource use requests (>50 letter of interests), and citations (>900) to papers published using NMVB resources. DISCUSSION NMVB's REDCap implementation and query tool is a framework for implementing federated and integrated rare disease biobanks and registries. Advantages of this framework include being low-cost, modular, scalable, and efficient. Future advances to NVMB's implementations will include incorporation of -omics data and development of downstream analysis tools to advance mesothelioma and rare disease research. CONCLUSION NVMB presents a framework for integrating biobanks and patient registries to enable translational research for rare diseases.
Collapse
Affiliation(s)
- Rumana Rashid
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Medical Scientist Training Program, University of Pittsburgh-Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Susan Copelli
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jonathan C Silverstein
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael J Becich
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
2
|
Greulich L, Hegselmann S, Dugas M. An Open-Source, Standard-Compliant, and Mobile Electronic Data Capture System for Medical Research (OpenEDC): Design and Evaluation Study. JMIR Med Inform 2021; 9:e29176. [PMID: 34806987 PMCID: PMC8663450 DOI: 10.2196/29176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/13/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Medical research and machine learning for health care depend on high-quality data. Electronic data capture (EDC) systems have been widely adopted for metadata-driven digital data collection. However, many systems use proprietary and incompatible formats that inhibit clinical data exchange and metadata reuse. In addition, the configuration and financial requirements of typical EDC systems frequently prevent small-scale studies from benefiting from their inherent advantages. OBJECTIVE The aim of this study is to develop and publish an open-source EDC system that addresses these issues. We aim to plan a system that is applicable to a wide range of research projects. METHODS We conducted a literature-based requirements analysis to identify the academic and regulatory demands for digital data collection. After designing and implementing OpenEDC, we performed a usability evaluation to obtain feedback from users. RESULTS We identified 20 frequently stated requirements for EDC. According to the International Organization for Standardization/International Electrotechnical Commission (ISO/IEC) 25010 norm, we categorized the requirements into functional suitability, availability, compatibility, usability, and security. We developed OpenEDC based on the regulatory-compliant Clinical Data Interchange Standards Consortium Operational Data Model (CDISC ODM) standard. Mobile device support enables the collection of patient-reported outcomes. OpenEDC is publicly available and released under the MIT open-source license. CONCLUSIONS Adopting an established standard without modifications supports metadata reuse and clinical data exchange, but it limits item layouts. OpenEDC is a stand-alone web app that can be used without a setup or configuration. This should foster compatibility between medical research and open science. OpenEDC is targeted at observational and translational research studies by clinicians.
Collapse
Affiliation(s)
- Leonard Greulich
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Stefan Hegselmann
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
3
|
Berger A, Rustemeier AK, Göbel J, Kadioglu D, Britz V, Schubert K, Mohnike K, Storf H, Wagner TOF. How to design a registry for undiagnosed patients in the framework of rare disease diagnosis: suggestions on software, data set and coding system. Orphanet J Rare Dis 2021; 16:198. [PMID: 33933089 PMCID: PMC8088651 DOI: 10.1186/s13023-021-01831-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/20/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND About 30 million people in the EU and USA, respectively, suffer from a rare disease. Driven by European legislative requirements, national strategies for the improvement of care in rare diseases are being developed. To improve timely and correct diagnosis for patients with rare diseases, the development of a registry for undiagnosed patients was recommended by the German National Action Plan. In this paper we focus on the question on how such a registry for undiagnosed patients can be built and which information it should contain. RESULTS To develop a registry for undiagnosed patients, a software for data acquisition and storage, an appropriate data set and an applicable terminology/classification system for the data collected are needed. We have used the open-source software Open-Source Registry System for Rare Diseases (OSSE) to build the registry for undiagnosed patients. Our data set is based on the minimal data set for rare disease patient registries recommended by the European Rare Disease Registries Platform. We extended this Common Data Set to also include symptoms, clinical findings and other diagnoses. In order to ensure findability, comparability and statistical analysis, symptoms, clinical findings and diagnoses have to be encoded. We evaluated three medical ontologies (SNOMED CT, HPO and LOINC) for their usefulness. With exact matches of 98% of tested medical terms, a mean number of five deposited synonyms, SNOMED CT seemed to fit our needs best. HPO and LOINC provided 73% and 31% of exacts matches of clinical terms respectively. Allowing more generic codes for a defined symptom, with SNOMED CT 99%, with HPO 89% and with LOINC 39% of terms could be encoded. CONCLUSIONS With the use of the OSSE software and a data set, which, in addition to the Common Data Set, focuses on symptoms and clinical findings, a functioning and meaningful registry for undiagnosed patients can be implemented. The next step is the implementation of the registry in centres for rare diseases. With the help of medical informatics and big data analysis, case similarity analyses could be realized and aid as a decision-support tool enabling diagnosis of some undiagnosed patients.
Collapse
Affiliation(s)
- Alexandra Berger
- Frankfurt Reference Centre for Rare Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
| | - Anne-Kathrin Rustemeier
- Medical Clinic II, University Hospital Gießen and Marburg, Klinikstraße 33, 35392, Gießen, Germany
| | - Jens Göbel
- Medical Informatics Group Frankfurt, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Dennis Kadioglu
- Medical Informatics Group Frankfurt, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Vanessa Britz
- Frankfurt Reference Centre for Rare Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Katharina Schubert
- Central-German Network for rare diseases, University Hospital Magdeburg A.Ö.R, Leipziger Straße 44, 39120, Magdeburg, Germany
| | - Klaus Mohnike
- Central-German Network for rare diseases, University Hospital Magdeburg A.Ö.R, Leipziger Straße 44, 39120, Magdeburg, Germany
| | - Holger Storf
- Medical Informatics Group Frankfurt, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Thomas O F Wagner
- Frankfurt Reference Centre for Rare Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| |
Collapse
|
4
|
Schaaf J, Sedlmayr M, Sedlmayr B, Prokosch HU, Storf H. Evaluation of a clinical decision support system for rare diseases: a qualitative study. BMC Med Inform Decis Mak 2021; 21:65. [PMID: 33602191 PMCID: PMC7890997 DOI: 10.1186/s12911-021-01435-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/10/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Rare Diseases (RDs) are difficult to diagnose. Clinical Decision Support Systems (CDSS) could support the diagnosis for RDs. The Medical Informatics in Research and Medicine (MIRACUM) consortium developed a CDSS for RDs based on distributed clinical data from eight German university hospitals. To support the diagnosis for difficult patient cases, the CDSS uses data from the different hospitals to perform a patient similarity analysis to obtain an indication of a diagnosis. To optimize our CDSS, we conducted a qualitative study to investigate usability and functionality of our designed CDSS. METHODS We performed a Thinking Aloud Test (TA-Test) with RDs experts working in Rare Diseases Centers (RDCs) at MIRACUM locations which are specialized in diagnosis and treatment of RDs. An instruction sheet with tasks was prepared that the participants should perform with the CDSS during the study. The TA-Test was recorded on audio and video, whereas the resulting transcripts were analysed with a qualitative content analysis, as a ruled-guided fixed procedure to analyse text-based data. Furthermore, a questionnaire was handed out at the end of the study including the System Usability Scale (SUS). RESULTS A total of eight experts from eight MIRACUM locations with an established RDC were included in the study. Results indicate that more detailed information about patients, such as descriptive attributes or findings, can help the system perform better. The system was rated positively in terms of functionality, such as functions that enable the user to obtain an overview of similar patients or medical history of a patient. However, there is a lack of transparency in the results of the CDSS patient similarity analysis. The study participants often stated that the system should present the user with an overview of exact symptoms, diagnosis, and other characteristics that define two patients as similar. In the usability section, the CDSS received a score of 73.21 points, which is ranked as good usability. CONCLUSIONS This qualitative study investigated the usability and functionality of a CDSS of RDs. Despite positive feedback about functionality of system, the CDSS still requires some revisions and improvement in transparency of the patient similarity analysis.
Collapse
Affiliation(s)
- Jannik Schaaf
- Medical Informatics Group (MIG), University Hospital Frankfurt, Frankfurt, Germany.
| | - Martin Sedlmayr
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technical University of Dresden, Dresden, Germany
| | - Brita Sedlmayr
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technical University of Dresden, Dresden, Germany
| | - Hans-Ulrich Prokosch
- Department of Medical Informatics, Biometrics and Epidemiology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Holger Storf
- Medical Informatics Group (MIG), University Hospital Frankfurt, Frankfurt, Germany
| |
Collapse
|
5
|
Rohde F, Franke M, Sehili Z, Lablans M, Rahm E. Optimization of the Mainzelliste software for fast privacy-preserving record linkage. J Transl Med 2021; 19:33. [PMID: 33451317 PMCID: PMC7809773 DOI: 10.1186/s12967-020-02678-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Data analysis for biomedical research often requires a record linkage step to identify records from multiple data sources referring to the same person. Due to the lack of unique personal identifiers across these sources, record linkage relies on the similarity of personal data such as first and last names or birth dates. However, the exchange of such identifying data with a third party, as is the case in record linkage, is generally subject to strict privacy requirements. This problem is addressed by privacy-preserving record linkage (PPRL) and pseudonymization services. Mainzelliste is an open-source record linkage and pseudonymization service used to carry out PPRL processes in real-world use cases. METHODS We evaluate the linkage quality and performance of the linkage process using several real and near-real datasets with different properties w.r.t. size and error-rate of matching records. We conduct a comparison between (plaintext) record linkage and PPRL based on encoded records (Bloom filters). Furthermore, since the Mainzelliste software offers no blocking mechanism, we extend it by phonetic blocking as well as novel blocking schemes based on locality-sensitive hashing (LSH) to improve runtime for both standard and privacy-preserving record linkage. RESULTS The Mainzelliste achieves high linkage quality for PPRL using field-level Bloom filters due to the use of an error-tolerant matching algorithm that can handle variances in names, in particular missing or transposed name compounds. However, due to the absence of blocking, the runtimes are unacceptable for real use cases with larger datasets. The newly implemented blocking approaches improve runtimes by orders of magnitude while retaining high linkage quality. CONCLUSION We conduct the first comprehensive evaluation of the record linkage facilities of the Mainzelliste software and extend it with blocking methods to improve its runtime. We observed a very high linkage quality for both plaintext as well as encoded data even in the presence of errors. The provided blocking methods provide order of magnitude improvements regarding runtime performance thus facilitating the use in research projects with large datasets and many participants.
Collapse
Affiliation(s)
- Florens Rohde
- Database Group, University of Leipzig, Leipzig, Germany.
| | - Martin Franke
- Database Group, University of Leipzig, Leipzig, Germany
| | - Ziad Sehili
- Database Group, University of Leipzig, Leipzig, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Erhard Rahm
- Database Group, University of Leipzig, Leipzig, Germany
| |
Collapse
|
6
|
Scheible R, Kadioglu D, Ehl S, Blum M, Boeker M, Folz M, Grimbacher B, Göbel J, Klein C, Nieters A, Rusch S, Kindle G, Storf H. Enabling External Inquiries to an Existing Patient Registry by Using the Open Source Registry System for Rare Diseases: Demonstration of the System Using the European Society for Immunodeficiencies Registry. JMIR Med Inform 2020; 8:e17420. [PMID: 33026355 PMCID: PMC7578818 DOI: 10.2196/17420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/13/2020] [Accepted: 03/22/2020] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The German Network on Primary Immunodeficiency Diseases (PID-NET) utilizes the European Society for Immunodeficiencies (ESID) registry as a platform for collecting data. In the context of PID-NET data, we show how registries based on custom software can be made interoperable for better collaborative access to precollected data. The Open Source Registry System for Rare Diseases (Open-Source-Registersystem für Seltene Erkrankungen [OSSE], in German) provides patient organizations, physicians, scientists, and other parties with open source software for the creation of patient registries. In addition, the necessary interoperability between different registries based on the OSSE, as well as existing registries, is supported, which allows those registries to be confederated at both the national and international levels. OBJECTIVE Data from the PID-NET registry should be made available in an interoperable manner without losing data sovereignty by extending the existing custom software of the registry using the OSSE registry framework. METHODS This paper describes the following: (1) the installation and configuration of the OSSE bridgehead, (2) an approach using a free toolchain to set up the required interfaces to connect a registry with the OSSE bridgehead, and (3) the decentralized search, which allows the formulation of inquiries that are sent to a selected set of registries of interest. RESULTS PID-NET uses the established and highly customized ESID registry software. By setting up a so-called OSSE bridgehead, PID-NET data are made interoperable according to a federated approach, and centrally formulated inquiries for data can be received. As the first registry to use the OSSE bridgehead, the authors introduce an approach using a free toolchain to efficiently implement and maintain the required interfaces. Finally, to test and demonstrate the system, two inquiries are realized using the graphical query builder. By establishing and interconnecting an OSSE bridgehead with the underlying ESID registry, confederated queries for data can be received and, if desired, the inquirer can be contacted to further discuss any requirements for cooperation. CONCLUSIONS The OSSE offers an infrastructure that provides the possibility of more collaborative and transparent research. The decentralized search functionality includes registries into one search application while still maintaining data sovereignty. The OSSE bridgehead enables any registry software to be integrated into the OSSE network. The proposed toolchain to set up the required interfaces consists of freely available software components that are well documented. The use of the decentralized search is uncomplicated to use and offers a well-structured, yet still improvable, graphical user interface to formulate queries.
Collapse
Affiliation(s)
- Raphael Scheible
- Institute of Medical Biometry and Statistics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dennis Kadioglu
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marco Blum
- Institute of Medical Biometry and Statistics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Boeker
- Institute of Medical Biometry and Statistics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Folz
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- RESIST, Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
| | - Jens Göbel
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr von Hauner Children's Hospital, University Hospital, Ludwig Maximilians Universität München, München, Germany
| | - Alexandra Nieters
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- FREEZE Biobank, Center for Biobanking, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Rusch
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- FREEZE Biobank, Center for Biobanking, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gerhard Kindle
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- FREEZE Biobank, Center for Biobanking, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Holger Storf
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt am Main, Germany
| |
Collapse
|
7
|
Schaaf J, Prokosch HU, Boeker M, Schaefer J, Vasseur J, Storf H, Sedlmayr M. Interviews with experts in rare diseases for the development of clinical decision support system software - a qualitative study. BMC Med Inform Decis Mak 2020; 20:230. [PMID: 32938448 PMCID: PMC7493382 DOI: 10.1186/s12911-020-01254-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/09/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Patients with rare diseases (RDs) are often diagnosed too late or not at all. Clinical decision support systems (CDSSs) could support the diagnosis in RDs. The MIRACUM (Medical Informatics in Research and Medicine) consortium, which is one of four funded consortia in the German Medical Informatics Initiative, will develop a CDSS for RDs based on distributed clinical data from ten university hospitals. This qualitative study aims to investigate (1) the relevant organizational conditions for the operation of a CDSS for RDs when diagnose patients (e.g. the diagnosis workflow), (2) which data is necessary for decision support, and (3) the appropriate user group for such a CDSS. METHODS Interviews were carried out with RDs experts. Participants were recruited from staff physicians at the Rare Disease Centers (RDCs) at the MIRACUM locations, which offer diagnosis and treatment of RDs. An interview guide was developed with a category-guided deductive approach. The interviews were recorded on an audio device and then transcribed into written form. We continued data collection until all interviews were completed. Afterwards, data analysis was performed using Mayring's qualitative content analysis approach. RESULTS A total of seven experts were included in the study. The results show that medical center guides and physicians from RDC B-centers (with a focus on different RDs) are involved in the diagnostic process. Furthermore, interdisciplinary case discussions between physicians are conducted. The experts explained that RDs exist which cannot be fully differentiated, but rather described only by their overall symptoms or findings: diagnosis is dependent on the disease or disease group. At the end of the diagnostic process, most centers prepare a summary of the patient case. Furthermore, the experts considered both physicians and experts from the B-centers to be potential users of a CDSS. The experts also have different experiences with CDSS for RDs. CONCLUSIONS This qualitative study is a first step towards establishing the requirements for the development of a CDSS for RDs. Further research is necessary to create solutions by also including the experts on RDs.
Collapse
Affiliation(s)
- Jannik Schaaf
- Medical Informatics Group (MIG), University Hospital Frankfurt, Frankfurt, Germany.
| | - Hans-Ulrich Prokosch
- Chair of Medical Informatics, Department of Medical Informatics, Biometrics and Epidemiology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Martin Boeker
- Institute of Medical Biometry and Statistics, Medical Faculty and Medical Centre - University of Freiburg, Freiburg, Germany
| | - Johanna Schaefer
- Medical Informatics Group (MIG), University Hospital Frankfurt, Frankfurt, Germany
| | - Jessica Vasseur
- Medical Informatics Group (MIG), University Hospital Frankfurt, Frankfurt, Germany
| | - Holger Storf
- Medical Informatics Group (MIG), University Hospital Frankfurt, Frankfurt, Germany
| | - Martin Sedlmayr
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine Technical University of Dresden, Dresden, Germany
| |
Collapse
|
8
|
Storf H, Stausberg J, Kindle G, Quadder B, Schlangen M, Walter MC, Ückert F, Wagner TOF. [Patient registries for rare diseases in Germany: concept paper of the NAMSE strategy group]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2020; 63:761-770. [PMID: 32424556 DOI: 10.1007/s00103-020-03151-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The National Action Plan for People with Rare Diseases contains 52 concrete actions, including in the fields of care, research, diagnosis, and information management. With the aim of improving the quality and interoperability of national registries in the long term, action 28 proposed the establishment of a "Rare Diseases Registry" strategy group. The strategy group began its work in 2016. In this report, the group takes into account developments at the national and international level in order to develop recommendations for national initiatives.In addition to this, the group reports on consent and implementation as well as on the adaptation of a minimal dataset for use in rare disease registries and mapping the used data elements and schemata in a metadata repository. This position paper was created by the strategy group together with additional authors. The paper reached a consensus within the strategy group and can be seen as a concept paper of the Rare Diseases Registry strategy group.
Collapse
Affiliation(s)
- Holger Storf
- Medical Informatics Group (MIG), Universitätsklinikum Frankfurt, Haus 33C 2. OG, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Deutschland. .,Datenintegrationszentrum (DIZ), Dezernat 7 - Informations- und Kommunikationstechnologie (DICT), Universitätsklinikum Frankfurt, Frankfurt am Main, Deutschland.
| | - Jürgen Stausberg
- Institut für Medizinische Informatik, Biometrie und Epidemiologie (IMIBE), Universitätsklinikum Essen, Essen, Deutschland
| | - Gerhard Kindle
- Institut für Immundefizienz, Centrum für Chronische Immundefizienz (CCI), Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Freiburg, Deutschland.,Zentrum für Biobanking, FREEZE-Biobank, Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Freiburg, Deutschland
| | - Bernd Quadder
- Allianz Chronischer Seltener Erkrankungen ACHSE e. V., Berlin, Deutschland.,Deutsche Sarkoidose-Vereinigung e. V., Meerbusch, Deutschland
| | - Miriam Schlangen
- Geschäftsstelle des Nationalen Aktionsbündnisses für Menschen mit Seltenen Erkrankungen, Bonn, Deutschland
| | - Maggie C Walter
- Friedrich-Baur-Institut, Neurologische Klinik und Poliklinik, Ludwig-Maximilians-Universität München, München, Deutschland
| | - Frank Ückert
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Heidelberg, Deutschland
| | - Thomas O F Wagner
- Frankfurter Referenzzentrum für Seltene Erkrankungen (FRZSE), Universitätsklinikum Frankfurt, Frankfurt am Main, Deutschland
| | | |
Collapse
|
9
|
Mate S, Kampf M, Rödle W, Kraus S, Proynova R, Silander K, Ebert L, Lablans M, Schüttler C, Knell C, Eklund N, Hummel M, Holub P, Prokosch HU. Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC. Appl Clin Inform 2019; 10:679-692. [PMID: 31509880 PMCID: PMC6739205 DOI: 10.1055/s-0039-1695793] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background
High-quality clinical data and biological specimens are key for medical research and personalized medicine. The Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) aims to facilitate access to such biological resources. The accompanying ADOPT BBMRI-ERIC project kick-started BBMRI-ERIC by collecting colorectal cancer data from European biobanks.
Objectives
To transform these data into a common representation, a uniform approach for data integration and harmonization had to be developed. This article describes the design and the implementation of a toolset for this task.
Methods
Based on the semantics of a metadata repository, we developed a lexical bag-of-words matcher, capable of semiautomatically mapping local biobank terms to the central ADOPT BBMRI-ERIC terminology. Its algorithm supports fuzzy matching, utilization of synonyms, and sentiment tagging. To process the anonymized instance data based on these mappings, we also developed a data transformation application.
Results
The implementation was used to process the data from 10 European biobanks. The lexical matcher automatically and correctly mapped 78.48% of the 1,492 local biobank terms, and human experts were able to complete the remaining mappings. We used the expert-curated mappings to successfully process 147,608 data records from 3,415 patients.
Conclusion
A generic harmonization approach was created and successfully used for cross-institutional data harmonization across 10 European biobanks. The software tools were made available as open source.
Collapse
Affiliation(s)
- Sebastian Mate
- Medical Centre for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Marvin Kampf
- Medical Centre for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Wolfgang Rödle
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Stefan Kraus
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Rumyana Proynova
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Kaisa Silander
- Genomics and Biobank Unit, Finnish National Institute for Health and Welfare, Helsinki, Finland
| | - Lars Ebert
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Christina Schüttler
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christian Knell
- Medical Centre for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Niina Eklund
- Genomics and Biobank Unit, Finnish National Institute for Health and Welfare, Helsinki, Finland
| | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Biobanking and BioMolecular Resources Research Infrastructure (BBMRI-ERIC), Graz, Austria
| | - Petr Holub
- Biobanking and BioMolecular Resources Research Infrastructure (BBMRI-ERIC), Graz, Austria
| | - Hans-Ulrich Prokosch
- Medical Centre for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany.,Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| |
Collapse
|
10
|
Prokosch HU, Acker T, Bernarding J, Binder H, Boeker M, Boerries M, Daumke P, Ganslandt T, Hesser J, Höning G, Neumaier M, Marquardt K, Renz H, Rothkötter HJ, Schade-Brittinger C, Schmücker P, Schüttler J, Sedlmayr M, Serve H, Sohrabi K, Storf H. MIRACUM: Medical Informatics in Research and Care in University Medicine. Methods Inf Med 2018; 57:e82-e91. [PMID: 30016814 PMCID: PMC6178200 DOI: 10.3414/me17-02-0025] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/13/2018] [Indexed: 01/05/2023]
Abstract
INTRODUCTION This article is part of the Focus Theme of Methods of Information in Medicine on the German Medical Informatics Initiative. Similar to other large international data sharing networks (e.g. 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 integration centres (DIC) and make data within those DIC available for innovative new IT solutions in patient care and medical research. OBJECTIVES Sharing data shall be supported by common interoperable tools and services, in order to leverage the power of such data for biomedical discovery and moving towards a learning health system. This paper aims at illustrating the major building blocks and concepts which MIRACUM will apply to achieve this goal. GOVERNANCE AND POLICIES Besides establishing an efficient governance structure within the MIRACUM consortium (based on the steering board, a central administrative office, the general MIRACUM assembly, six working groups and the international scientific advisory board), defining DIC governance rules and data sharing policies, as well as establishing (at each MIRACUM DIC site, but also for MIRACUM in total) use and access committees are major building blocks for the success of such an endeavor. ARCHITECTURAL FRAMEWORK AND METHODOLOGY The MIRACUM DIC architecture builds on a comprehensive ecosystem of reusable open source tools (MIRACOLIX), which are linkable and interoperable amongst each other, but also with the existing software environment of the MIRACUM hospitals. Efficient data protection measures, considering patient consent, data harmonization and a MIRACUM metadata repository as well as a common data model are major pillars of this framework. The methodological approach for shared data usage relies on a federated querying and analysis concept. USE CASES MIRACUM aims at proving the value of their DIC with three use cases: IT support for patient recruitment into clinical trials, the development and routine care implementation of a clinico-molecular predictive knowledge tool, and molecular-guided therapy recommendations in molecular tumor boards. RESULTS Based on the MIRACUM DIC release in the nine months conceptual phase first large scale analysis for stroke and colorectal cancer cohorts have been pursued. DISCUSSION Beyond all technological challenges successfully applying the MIRACUM tools for the enrichment of our knowledge about diagnostic and therapeutic concepts, thus supporting the concept of a Learning Health System will be crucial for the acceptance and sustainability in the medical community and the MIRACUM university hospitals.
Collapse
Affiliation(s)
- Hans-Ulrich Prokosch
- Chair of Medical Informatics, Department of Medical Informatics, Biometrics and Epidemiology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Till Acker
- Institute of Neuropathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Johannes Bernarding
- Chair of Medical Informatics, Institute for Biometry and Medical Informatics, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Harald Binder
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Medical Biometry and Statistics, Medical Faculty and Medical Center – University of Freiburg, Freiburg, Germany
| | - Martin Boeker
- Institute of Medical Biometry and Statistics, Medical Faculty and Medical Center – University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Molecular Medicine and Cell Research and Comprehensive Cancer Center Freiburg (CCCF), University Medical Center, Faculty of Medicine, University of Freiburg; German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) partner site Freiburg, Freiburg, Germany
| | | | - Thomas Ganslandt
- Chair of Medical Informatics, Department of Medical Informatics, Biometrics and Epidemiology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Department of Biomedical Informatics, University Medicine Mannheim, Ruprecht-Karls-University Heidelberg, Mannheim, Germany
| | - Jürgen Hesser
- Experimental Radiation Oncology Department, University Medical Center Mannheim, Central Institute for Scientific Computing (IWR), Central Institute for Computer Engineering (ZITI), Heidelberg University, Mannheim, Germany
| | - Gunther Höning
- Department of Information Technology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Michael Neumaier
- Chair for Clinical Chemistry, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Kurt Marquardt
- University Hospital of Giessen and Marburg, Giessen, Germany
| | - Harald Renz
- Chair for Clinical Chemistry, Philipps University Marburg, Medical Director of the University Clinic Marburg, Marburg, Germany
| | - Hermann-Josef Rothkötter
- Institute of Anatomy, Otto-von-Guericke-University Magdeburg, Dean of the Medical Faculty, Magdeburg, Germany
| | - Carmen Schade-Brittinger
- Chair of the Coordinating Centre for Clinical Trials, Philipps University Marburg, Marburg, Germany
| | - Paul Schmücker
- University of Applied Sciences Mannheim, Institute for Medical Informatics, Mannheim, Germany
| | - Jürgen Schüttler
- Department of Anesthesiology, University of Erlangen-Nürnberg, Dean of the Medical Faculty, Erlangen, Germany
| | - Martin Sedlmayr
- Chair of Medical Informatics, Department of Medical Informatics, Biometrics and Epidemiology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Institute of Medical Informatics and Biometrics, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Hubert Serve
- Department of Hematology and Oncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Keywan Sohrabi
- Faculty of Health Sciences, University of Applied Sciences – THM, Giessen, Germany
| | - Holger Storf
- Medical Informatics Group, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| |
Collapse
|