Publications

85 Publications visible to you, out of a total of 85

Abstract (Expand)

Despite their young age, the FAIR principles are recognised as important guidelines for research data management. Their generic design, however, leaves much room for interpretation in domain-specific application. Based on practical experience in the operation of a data repository, this article addresses problems in FAIR provisioning of medical data for research purposes in the use case of the Leipzig Health Atlas project and shows necessary future developments.

Authors: M. Lobe, F. Matthies, S. Staubert, F. A. Meineke, A. Winter

Date Published: 16th Jun 2020

Publication Type: Journal article

Abstract (Expand)

We here describe the evolution of annotation guidelines for major clinical named entities, namely Diagnosis, Findings and Symptoms, on a corpus of approximately 1,000 German discharge letters. Due to their intrinsic opaqueness and complexity, clinical annotation tasks require continuous guideline tuning, beginning from the initial definition of crucial entities and the subsequent iterative evolution of guidelines based on empirical evidence. We describe rationales for adaptation, with focus on several metrical criteria and task-centered clinical constraints.

Authors: C. Lohr, L. Modersohn, J. Hellrich, T. Kolditz, U. Hahn

Date Published: 16th Jun 2020

Publication Type: InProceedings

Abstract (Expand)

BACKGROUND: The aim of the German Medical Informatics Initiative is to establish a national infrastructure for integrating and sharing health data. To this, Data Integration Centers are set up at university medical centers, which address data harmonization, information security and data protection. To capture patient consent, a common informed consent template has been developed. It consists of different modules addressing permissions for using data and biosamples. On the technical level, a common digital representation of information from signed consent templates is needed. As the partners in the initiative are free to adopt different solutions for managing consent information (e.g. IHE BPPC or HL7 FHIR Consent Resources), we had to develop an interoperability layer. METHODS: First, we compiled an overview of data items required to reflect the information from the MII consent template as well as patient preferences and derived permissions. Next, we created entity-relationship diagrams to formally describe the conceptual data model underlying relevant items. We then compared this data model to conceptual models describing representations of consent information using different interoperability standards. We used the result of this comparison to derive an interoperable representation that can be mapped to common standards. RESULTS: The digital representation needs to capture the following information: (1) version of the consent, (2) consent status for each module, and (3) period of validity of the status. We found that there is no generally accepted solution to represent status information in a manner interoperable with all relevant standards. Hence, we developed a pragmatic solution, comprising codes which describe combinations of modules with a basic set of status labels. We propose to maintain these codes in a public registry called ART-DECOR. We present concrete technical implementations of our approach using HL7 FHIR and IHE BPPC which are also compatible with the open-source consent management software gICS. CONCLUSIONS: The proposed digital representation is (1) generic enough to capture relevant information from a wide range of consent documents and data use regulations and (2) interoperable with common technical standards. We plan to extend our model to include more fine-grained status codes and rules for automated access control.

Authors: R. Bild, M. Bialke, K. Buckow, T. Ganslandt, K. Ihrig, R. Jahns, A. Merzweiler, S. Roschka, B. Schreiweis, S. Staubert, S. Zenker, F. Prasser

Date Published: 5th Jun 2020

Publication Type: Journal article

Abstract (Expand)

BACKGROUND: The aim of the German Medical Informatics Initiative is to establish a national infrastructure for integrating and sharing health data. To this, Data Integration Centers are set up at university medical centers, which address data harmonization, information security and data protection. To capture patient consent, a common informed consent template has been developed. It consists of different modules addressing permissions for using data and biosamples. On the technical level, a common digital representation of information from signed consent templates is needed. As the partners in the initiative are free to adopt different solutions for managing consent information (e.g. IHE BPPC or HL7 FHIR Consent Resources), we had to develop an interoperability layer. METHODS: First, we compiled an overview of data items required to reflect the information from the MII consent template as well as patient preferences and derived permissions. Next, we created entity-relationship diagrams to formally describe the conceptual data model underlying relevant items. We then compared this data model to conceptual models describing representations of consent information using different interoperability standards. We used the result of this comparison to derive an interoperable representation that can be mapped to common standards. RESULTS: The digital representation needs to capture the following information: (1) version of the consent, (2) consent status for each module, and (3) period of validity of the status. We found that there is no generally accepted solution to represent status information in a manner interoperable with all relevant standards. Hence, we developed a pragmatic solution, comprising codes which describe combinations of modules with a basic set of status labels. We propose to maintain these codes in a public registry called ART-DECOR. We present concrete technical implementations of our approach using HL7 FHIR and IHE BPPC which are also compatible with the open-source consent management software gICS. CONCLUSIONS: The proposed digital representation is (1) generic enough to capture relevant information from a wide range of consent documents and data use regulations and (2) interoperable with common technical standards. We plan to extend our model to include more fine-grained status codes and rules for automated access control.

Authors: Raffael Bild, Martin Bialke, Karoline Buckow, Thomas Ganslandt, Kristina Ihrig, Roland Jahns, Angela Merzweiler, Sybille Roschka, Björn Schreiweis, Sebastian Stäubert, Sven Zenker, Fabian Prasser

Date Published: 1st Jun 2020

Publication Type: Journal article

Abstract (Expand)

Despite their young age, the FAIR principles are recognised as important guidelines for research data management. Their generic design, however, leaves much room for interpretation in domain-specific application. Based on practical experience in the operation of a data repository, this article addresses problems in FAIR provisioning of medical data for research purposes in the use case of the Leipzig Health Atlas project and shows necessary future developments.

Authors: Matthias Löbe, Franz Matthies, Sebastian Stäubert, Frank A Meineke, Alfred Winter

Date Published: 1st Jun 2020

Publication Type: Journal article

Abstract (Expand)

We here describe the evolution of annotation guidelines for major clinical named entities, namely Diagnosis, Findings and Symptoms, on a corpus of approximately 1,000 German discharge letters. Due to their intrinsic opaqueness and complexity, clinical annotation tasks require continuous guideline tuning, beginning from the initial definition of crucial entities and the subsequent iterative evolution of guidelines based on empirical evidence. We describe rationales for adaptation, with focus on several metrical criteria and task-centered clinical constraints.

Authors: Christina Lohr, Luise Modersohn, Johannes Hellrich, Tobias Kolditz, Udo Hahn

Date Published: 1st Jun 2020

Publication Type: Journal article

Abstract

Not specified

Authors: Erik Faessler, L. Modersohn, C. Lohr, U. Hahn

Date Published: 11th May 2020

Publication Type: InProceedings

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