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281 results on '"LÖBE, Matthias"'

1. Ontological modelling and FHIR Search based representation of basic eligibility criteria

Author

Uciteli, Alexandr, Beger, Christoph, Wagner, Jonas, Kirsten, Toralf, Meineke, Frank A., Stäubert, Sebastian, Löbe, Matthias, and Herre, Heinrich

Subjects
eligibility determination, biomedical ontologies, electronic health records, health information interoperability, information storage, information retrieval, health level seven, Computer applications to medicine. Medical informatics, R858-859.7, Infectious and parasitic diseases, RC109-216
Abstract

Planning clinical studies to check medical hypotheses requires the specification of eligibility criteria in order to identify potential study participants. Electronically available patient data allows to support the recruitment of patients for studies. The Smart Medical Information Technology for Healthcare (SMITH) consortium aims to establish data integration centres to enable the innovative use of available healthcare data for research and treatment optimization. The data from the electronic health record of patients in the participating hospitals is integrated into a Health Data Storage based on the Fast Healthcare Interoperability Resources standard (FHIR), developed by HL7. In SMITH, FHIR Search is used to query the integrated data. An investigation has shown the advantages and disadvantages of using FHIR Search for specifying eligibility criteria. This paper presents an approach for modelling eligibility criteria as well as for generating and executing FHIR Search queries. Our solution is based on the Phenotype Manager, a general ontological phenotyping framework to model and calculate phenotypes using the Core Ontology of Phenotypes.

Published
2021
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4. Summary of a consensus conference on heart-liver transplantation

Author

Kobashigawa, Jon, VanWagner, Lisa B., Hall, Shelley, Ardehali, Abbas, Baran, David, Bhimaraj, Arvind, Bonham, Clark Andrew, Breda, Joao Roberto, Chen, Sharon, Czer, Lawrence, Alessandro, David D', Daugherty, Tami, De Marco, Teresa, Emamaullee, Juliet, Emerson, Dominic, Entwistle, John W., Esmailian, Fardad, Estep, Jerry, Gaber, Osama, Ganger, Daniel, Gebel, Howard, Ebel, Noelle Hanako, Harmath, Carla, Heimbach, Julie, Izzy, Manhal, Jackson, Annette, Jeevanandam, Val, Kahn, Jeffrey, Kaldas, Fady, Kamath, Patrick, Kilic, Ahmet, Kittleson, Michelle, Kuo, Alex, Kushwaha, Sudhir, Kwong, Allison, Lewis, Matthew, Loebe, Matthias, Lui, George, Madsen, Joren, McLean, Rhondalyn, Menachem, Jonathan, Mobley, Constance, Mufti, Arji, Patel, Jignesh, Pereira, Naveen, Pinney, Sean, Potter, Lisa, Sack, Jordan, Sahota, Amandeep, Schiano, Thomas D., Schlendorf, Kelly, Shingina, Alexandra, Takeda, Koji, Taner, Timucin, Te, Helen, Teuteberg, Jeffrey, Tompkins, Rose, Verna, Betsy, Wall, Anji, Jeevanandam, Valluvan, Lui, George K., Motayagheni, Negar, Patel, Nikhil, and Sani, Maryam

Published
2024
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9. Suitability of the OMOP Common Data Model for Mapping Datasets of Medical Research Studies Using the Example of a Multicenter Registry.

Author

KURTZ, Milla, WINTER, Alfred, and LÖBE, Matthias

Abstract

Common Data Models (CDM) are developed to solve integration problems that arise in the secondary use of health data. The OMOP CDM is such a model that is mainly used for healthcare data, so this paper examines whether it is also suitable for mapping research data. An exemplary research dataset is mapped to the model and the model is tested for suitability. For this purpose, an ETL process is first designed with the OHDSI tools and finally implemented with Talend Open Studio for Data Integration. The data quality is checked, and the mapping and the model, together with the tools, are evaluated. Overall, all but three data fields from the source dataset could be mapped to the OMOP model, so that the model's suitability for research data can be confirmed. [ABSTRACT FROM AUTHOR]

Published
2024
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10. A Formal Model for the FAIR4Health Information Architecture

Author

Perbix, Mona, primary, Löbe, Matthias, additional, Stäubert, Sebastian, additional, Sinaci, A. Anil, additional, Gencturk, Mert, additional, Quintero, Miriam, additional, Martinez-Garcia, Alicia, additional, Alvarez-Romero, Celia, additional, Parra-Calderon, Carlos L., additional, and Winter, Alfred, additional

Published
2022
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14. COVID-19 in hospitalized lung and non-lung solid organ transplant recipients: A comparative analysis from a multicenter study

Author

Heldman, Madeleine R., Kates, Olivia S., Safa, Kassem, Kotton, Camille N., Georgia, Sarah J., Steinbrink, Julie M., Alexander, Barbara D., Hemmersbach-Miller, Marion, Blumberg, Emily A., Crespo, Maria M., Multani, Ashrit, Lewis, Angelica V., Eugene Beaird, Omer, Haydel, Brandy, La Hoz, Ricardo M., Moni, Lisset, Condor, Yesabeli, Flores, Sandra, Munoz, Carlos G., Guitierrez, Juan, Diaz, Esther I., Diaz, Daniela, Vianna, Rodrigo, Guerra, Giselle, Loebe, Matthias, Rakita, Robert M., Malinis, Maricar, Azar, Marwan M., Hemmige, Vagish, McCort, Margaret E., Chaudhry, Zohra S., Singh, Pooja, Hughes, Kailey, Velioglu, Arzu, Yabu, Julie M., Morillis, Jose A., Mehta, Sapna A., Tanna, Sajal D., Ison, Michael G., Tomic, Rade, Candace Derenge, Ariella, van Duin, David, Maximin, Adrienne, Gilbert, Carlene, Goldman, Jason D., Sehgal, Sameep, Weisshaar, Dana, Girgis, Reda E., Nelson, Joanna, Lease, Erika D., Limaye, Ajit P., and Fisher, Cynthia E.

Published
2021
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18. Collaborative Semantic Annotation Tooling (CoAT) to Improve Efficiency and Plug-and-Play Semantic Interoperability in the Secondary Use of Medical Data: Concept, Implementation, and First Cross-Institutional Experiences

Author

Wiktorin, Thomas, primary, Grigutsch, Daniel, additional, Erdfelder, Felix, additional, Heidel, Andrew J., additional, Bloos, Frank, additional, Ammon, Danny, additional, Löbe, Matthias, additional, and Zenker, Sven, additional

Published
2024
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20. End User Evaluation of the FAIR4Health Data Curation Tool

Author

Gencturk, Mert, primary, Teoman, Alper, additional, Alvarez-Romero, Celia, additional, Martinez-Garcia, Alicia, additional, Parra-Calderon, Carlos Luis, additional, Poblador-Plou, Beatriz, additional, Löbe, Matthias, additional, and Sinaci, A. Anil, additional

Published
2021
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23. Using Health IT Standards to Facilitate Metadata Exchange Between Research Data Management Systems.

Author

LÖBE, Matthias, Xiaoming HU, and KLOPFENSTEIN, Sophie A. I.

Abstract

The National Research Data Infrastructure for Personal Health Data (NFDI4Health) uses Local Data Hubs (LDHs) to manage locally research studies, documents and sensitive personal data to support controlled data sharing. While research data management (RDM) systems facilitate the storage and preparation of data and metadata as well as organizational access, they often lack support for interoperability standards of the application domain. To support the exchange with external registries of research studies, we chose 17 attributes to characterize the most relevant aspects of clinical trials (in the following named “metadata profile”). We implemented the metadata profile in the RDM system FAIRDOM SEEK using core attributes and SEEK’s extended metadata feature and created a mapping conforming to the Health Level 7 Fast Healthcare Interoperability Resources (FHIR) standard version R4. Finally, we implemented a prototype application interface for exports in FHIR-JSON format. We plan to extend the interface to serve central registries and support specific FHIR Implementation Guides from various use cases. [ABSTRACT FROM AUTHOR]

Published
2024
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27. Techniques for Inflow Cannula Placement

Author

Brozzi, Nicolas A., Loforte, Antonio, Loebe, Matthias, Montalto, Andrea, editor, Loforte, Antonio, editor, Musumeci, Francesco, editor, Krabatsch, Thomas, editor, Slaughter, Mark S., editor, and Amarelli, Cristiano, With contrib. by

Published
2017
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30. FAIR4Health: Findable, Accessible, Interoperable and Reusable data to foster Health Research

Author

European Commission, Instituto de Salud Carlos III, Álvarez-Romero, Celia [0000-0001-8647-9515], Sinaci, A. Anil [0000-0003-4397-3382], Gencturk, Mert [0000-0003-2697-5722], Méndez-Rodríguez, Eva [0000-0002-5337-4722], Hernández-Pérez, Tony [0000-0001-8404-9247], Angioletti, Carmen [0000-0002-0341-1679], Löbe, Matthias [0000-0002-2344-0426], Ganapathy, Nagarajan [0000-0002-3743-5388], Almada, Marta [0000-0001-6575-1698], Costa, Elisio [0000-0003-1158-1480], Chronaki, Catherine [0000-0001-6638-8448], Cornet, Ronald0000-0002-1704-5980, Poblador-Plou, Beatriz0000-0002-5119-5093, Carmona-Pírez, Jonás0000-0002-6268-8803, Gaudet-Blavignac, Christophe [0000-0001-6527-5898], Lovis, Christian [0000-0002-2681-8076], Ashley, Kevin [0000-0001-7546-5978], Horton, Laurence [0000-0003-2742-6434], Parra-Calderón, Carlos Luis [0000-0003-2609-575X], Álvarez-Romero, Celia, Martínez-García, Alicia, Sinaci, A. Anil, Gencturk, Mert, Méndez-Rodríguez, Eva, Hernández-Pérez, Tony, Liperoti, Rosa, Angioletti, Carmen, Löbe, Matthias, Ganapathy, Nagarajan, Deserno, Thomas, Almada, Marta, Costa, Elisio, Chronaki, Catherine, Cangioli, Giorgio, Cornet, Ronald, Poblador-Plou, Beatriz, Carmona-Pírez, Jonás, Gimeno-Miguel, Antonio, Poncel-Falcó, Antonio, Prados-Torres, Alexandra, Kovacevic, Tomi, Zaric, Bojan, Bokan, Darijo, Hromis, Sanja, Djekic Malbasa, Jelena, Rapallo Fernández, Carlos, Velázquez Fernández, Teresa, Rochat, Jessica, Gaudet-Blavignac, Christophe, Lovis, Christian, Weber, Patrick, Quintero, Miriam, Pérez-Pérez, Manuel M., Ashley, Kevin, Horton, Laurence, Parra-Calderón, Carlos Luis, European Commission, Instituto de Salud Carlos III, Álvarez-Romero, Celia [0000-0001-8647-9515], Sinaci, A. Anil [0000-0003-4397-3382], Gencturk, Mert [0000-0003-2697-5722], Méndez-Rodríguez, Eva [0000-0002-5337-4722], Hernández-Pérez, Tony [0000-0001-8404-9247], Angioletti, Carmen [0000-0002-0341-1679], Löbe, Matthias [0000-0002-2344-0426], Ganapathy, Nagarajan [0000-0002-3743-5388], Almada, Marta [0000-0001-6575-1698], Costa, Elisio [0000-0003-1158-1480], Chronaki, Catherine [0000-0001-6638-8448], Cornet, Ronald0000-0002-1704-5980, Poblador-Plou, Beatriz0000-0002-5119-5093, Carmona-Pírez, Jonás0000-0002-6268-8803, Gaudet-Blavignac, Christophe [0000-0001-6527-5898], Lovis, Christian [0000-0002-2681-8076], Ashley, Kevin [0000-0001-7546-5978], Horton, Laurence [0000-0003-2742-6434], Parra-Calderón, Carlos Luis [0000-0003-2609-575X], Álvarez-Romero, Celia, Martínez-García, Alicia, Sinaci, A. Anil, Gencturk, Mert, Méndez-Rodríguez, Eva, Hernández-Pérez, Tony, Liperoti, Rosa, Angioletti, Carmen, Löbe, Matthias, Ganapathy, Nagarajan, Deserno, Thomas, Almada, Marta, Costa, Elisio, Chronaki, Catherine, Cangioli, Giorgio, Cornet, Ronald, Poblador-Plou, Beatriz, Carmona-Pírez, Jonás, Gimeno-Miguel, Antonio, Poncel-Falcó, Antonio, Prados-Torres, Alexandra, Kovacevic, Tomi, Zaric, Bojan, Bokan, Darijo, Hromis, Sanja, Djekic Malbasa, Jelena, Rapallo Fernández, Carlos, Velázquez Fernández, Teresa, Rochat, Jessica, Gaudet-Blavignac, Christophe, Lovis, Christian, Weber, Patrick, Quintero, Miriam, Pérez-Pérez, Manuel M., Ashley, Kevin, Horton, Laurence, and Parra-Calderón, Carlos Luis

Abstract

Due to the nature of health data, its sharing and reuse for research are limited by ethical, legal and technical barriers. The FAIR4Health project facilitated and promoted the application of FAIR principles in health research data, derived from the publicly funded health research initiatives to make them Findable, Accessible, Interoperable, and Reusable (FAIR). To confirm the feasibility of the FAIR4Health solution, we performed two pathfinder case studies to carry out federated machine learning algorithms on FAIRified datasets from five health research organizations. The case studies demonstrated the potential impact of the developed FAIR4Health solution on health outcomes and social care research. Finally, we promoted the FAIRified data to share and reuse in the European Union Health Research community, defining an effective EU-wide strategy for the use of FAIR principles in health research and preparing the ground for a roadmap for health research institutions. This scientific report presents a general overview of the FAIR4Health solution: from the FAIRification workflow design to translate raw data/metadata to FAIR data/metadata in the health research domain to the FAIR4Health demonstrators' performance.

Published
2022

31. A Data Transformation Methodology to Create Findable, Accessible, Interoperable, and Reusable Health Data: Software Design, Development, and Evaluation Study

Author

European Commission, Sinaci, A. Anil, Gencturk, Mert, Teoman, Huseyin Alper, Laleci Erturkmen, Gokce Banu, Álvarez-Romero, Celia, Martínez-García, Alicia, Poblador-Plou, Beatriz, Carmona-Pírez, Jonás, Löbe, Matthias, Parra-Calderón, Carlos Luis, European Commission, Sinaci, A. Anil, Gencturk, Mert, Teoman, Huseyin Alper, Laleci Erturkmen, Gokce Banu, Álvarez-Romero, Celia, Martínez-García, Alicia, Poblador-Plou, Beatriz, Carmona-Pírez, Jonás, Löbe, Matthias, and Parra-Calderón, Carlos Luis

Abstract

[Background] Sharing health data is challenging because of several technical, ethical, and regulatory issues. The Findable, Accessible, Interoperable, and Reusable (FAIR) guiding principles have been conceptualized to enable data interoperability. Many studies provide implementation guidelines, assessment metrics, and software to achieve FAIR-compliant data, especially for health data sets. Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) is a health data content modeling and exchange standard., [Objective] Our goal was to devise a new methodology to extract, transform, and load existing health data sets into HL7 FHIR repositories in line with FAIR principles, develop a Data Curation Tool to implement the methodology, and evaluate it on health data sets from 2 different but complementary institutions. We aimed to increase the level of compliance with FAIR principles of existing health data sets through standardization and facilitate health data sharing by eliminating the associated technical barriers., [Methods] Our approach automatically processes the capabilities of a given FHIR end point and directs the user while configuring mappings according to the rules enforced by FHIR profile definitions. Code system mappings can be configured for terminology translations through automatic use of FHIR resources. The validity of the created FHIR resources can be automatically checked, and the software does not allow invalid resources to be persisted. At each stage of our data transformation methodology, we used particular FHIR-based techniques so that the resulting data set could be evaluated as FAIR. We performed a data-centric evaluation of our methodology on health data sets from 2 different institutions., [Results] Through an intuitive graphical user interface, users are prompted to configure the mappings into FHIR resource types with respect to the restrictions of selected profiles. Once the mappings are developed, our approach can syntactically and semantically transform existing health data sets into HL7 FHIR without loss of data utility according to our privacy-concerned criteria. In addition to the mapped resource types, behind the scenes, we create additional FHIR resources to satisfy several FAIR criteria. According to the data maturity indicators and evaluation methods of the FAIR Data Maturity Model, we achieved the maximum level (level 5) for being Findable, Accessible, and Interoperable and level 3 for being Reusable., [Conclusions] We developed and extensively evaluated our data transformation approach to unlock the value of existing health data residing in disparate data silos to make them available for sharing according to the FAIR principles. We showed that our method can successfully transform existing health data sets into HL7 FHIR without loss of data utility, and the result is FAIR in terms of the FAIR Data Maturity Model. We support institutional migration to HL7 FHIR, which not only leads to FAIR data sharing but also eases the integration with different research networks.

Published
2023

35. A Data Transformation Methodology to Create Findable, Accessible, Interoperable, and Reusable Health Data: Software Design, Development, and Evaluation Study

Author

Sinaci, A Anil, primary, Gencturk, Mert, additional, Teoman, Huseyin Alper, additional, Laleci Erturkmen, Gokce Banu, additional, Alvarez-Romero, Celia, additional, Martinez-Garcia, Alicia, additional, Poblador-Plou, Beatriz, additional, Carmona-Pírez, Jonás, additional, Löbe, Matthias, additional, and Parra-Calderon, Carlos Luis, additional

Published
2023
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39. A Semantic Representation of the NFDI4Health Metadata Schema Utilizing the CEDAR Workbench - Poster

Author

Löbe, Matthias, Shutsko, Aliaksandra, Schmidt, Carsten, Darms, Johannes, Klopfenstein, Sophie, Vorisek, Carina, Hu, Xioaming, Golebiewski, Martin, and Fluck, Juliane

Subjects
Metadata Schema, CEDAR, BioPortal, Dublin Core, RDF, Clinical Trial Registries, DataCite, DCAT
Abstract

Rich metadata is required for a comprehensive description of research assets. We developed a metadata schema for clinical and epidemiological research studies based on existing generic and domain-specific metadata vocabularies. It forms the basis for various search and data management services. Interoperability remains a challenge, as various health research standards are to be supported in the medium term. At the same time, embedding our infrastructure in national and international initiatives requires the use of overarching syntactic and semantic standards and vocabularies. In this paper we present a prototypical implementation in CEDAR Workbench. This not only provides a graphical web interface for collaboration and a possibility for form-based data entry for testing purposes. CEDAR also enables the use of standard vocabularies, annotation of concepts with medical terminologies, and a serialization in an RDF-JSON format.

Published
2023
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44. Bringing Communities Together: Mapping the Investigation-Study-Assay-Model (ISA) to Fast Healthcare Interoperability Resources (FHIR).

Author

KLOPFENSTEIN, Sophie A. I., SASS, Julian, VORISEK, Carina N., JORCZIK, Felix, SCHMIDT, Carsten Oliver, LÖBE, Matthias, GOLEBIEWSKI, Martin, ABAZA, Haitham, and THUN, Sylvia

Abstract

Adhering to FAIR principles (findability, accessibility, interoperability, reusability) ensures sustainability and reliable exchange of data and metadata. Research communities need common infrastructures and information models to collect, store, manage and work with data and metadata. The German initiative NFDI4Health created a metadata schema and an infrastructure integrating existing platforms based on different information models and standards. To ensure system compatibility and enhance data integration possibilities, we mapped the Investigation-Study-Assay (ISA) model to Fast Healthcare Interoperability Resources (FHIR). We present the mapping in FHIR logical models, a resulting FHIR resources' network and challenges that we encountered. Challenges mainly related to ISA's genericness, and to different structures and datatypes used in ISA and FHIR. Mapping ISA to FHIR is feasible but requires further analyses of example data and adaptations to better specify target FHIR elements, and enable possible automatized conversions from ISA to FHIR. [ABSTRACT FROM AUTHOR]

Published
2023
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45. Modeling the Application of IHE QRPH Profiles in Data Integration Centers: A Practical Approach with 3LGM2.

Author

DRAEGER, Christian, STÄUBERT, Sebastian, KUNTZ, Alessandra, HENKE, Christian, WINTER, Alfred, SAX, Ulrich, and LÖBE, Matthias

Abstract

The Data Integration Centers (DICs), all part of the German Medical Informatics Initiative (MII), prepare routine care data captured in university hospitals to enable its reuse in clinical research. Tackling this challenging task requires them to maintain multiple data stores, implement the necessary transformation processes, and provide the required terminology services, all while also addressing the use case specific needs researchers might have. An MII wide application of the standardized profiles defined in the IHE QRPH domain might therefore be able to drastically reduce the overhead at any one DIC. The MII DIC reference model built in 3LGM², a method to describe complex information system architectures, serves as a starting point to evaluate whether such an application is possible. We first extend the IHE modeling capabilities of 3LGM² to also support the five profiles from the QRPH domain that our experts evaluated as relevant in the MII DIC context. We then expand the DIC reference model by some IHE QRPH actors and transactions, showing that their application could be beneficial in the MII DIC context, provided they surpass their trial status. [ABSTRACT FROM AUTHOR]

Published
2023
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46. FAIR4Health - Public resources

Author

Martinez-Garcia, Alicia, Hernández, Tony, Sinaci, A. Anil, Chronaki, Catherine, Cornet, Ronald, Méndez, Eva, Gencturk, Mert, Calderón, Carlos, Kovacevic, Tomi, Bokan, Darijo, Cangioli, Giorgio, angioletti, carmen, Löbe, Matthias, Rochat, Jessica, Hörbst, Alexander, Weber, Patrick, Venkataraman, Shanmugasundaram, Gimeno-Miguel, Antonio, Correro, Carlos, Schweitzer, Marco, Matthies, Franz, Fernandez, Teresa, Teoman, Alper, Naranjo-Saucedo, Ana, Sveinsdottir, Thordis, Alvarez, Celia, Hernández, Iván, Quintero, Miriam, Monteau, Sophie, Mateos, David, Poblador-Plou, Beatriz, Carmona-Pirez, Jonas, Inau, Esther, Horton, Laurence, Aso, Santiago, Villarán, Esther, Goldman, Jean-Philippe, and Ganapathy, Nagarajan

Abstract

Here we'll post the public documents of the project, including deliverables and dissemination materials, among others

Published
2022
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47. A glimpse at representing data quality rules for their collaborative governance in the Medical Informatics Initiative

Author

Tute, Erik, Draeger, Christian, Gierend, Kerstin, Löbe, Matthias, Palm, Julia, and Schmidt, Carsten Oliver

Subjects
ddc: 610, Medicine and health, data quality, medical informatics
Abstract

Introduction: The Medical Informatics Initiative (MII) supports multicenter data usage in research as well as in clinical use cases. Both involve cross-site multidisciplinary teams. This implies a need to support collaborative governance of methods for checking the data usages’ data quality [for full text, please go to the a.m. URL]

Published
2022

48. A Data Transformation Methodology to Create Findable, Accessible, Interoperable, and Reusable Health Data: Software Design, Development, and Evaluation Study (Preprint)

Author

Sinaci, A Anil, primary, Gencturk, Mert, additional, Teoman, Huseyin Alper, additional, Laleci Erturkmen, Gokce Banu, additional, Alvarez-Romero, Celia, additional, Martinez-Garcia, Alicia, additional, Poblador-Plou, Beatriz, additional, Carmona-Pírez, Jonás, additional, Löbe, Matthias, additional, and Parra-Calderon, Carlos Luis, additional

Published
2022
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