The Health Atlas - Local Data Hub/Leipzig

9 items tagged with 'medical informatics'.

Integrating Heterogeneous Data Sources for Cross-Institutional Data Sharing: Requirements Elicitation and Management in SMITH.

SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

The digitization of health records and cross-institutional data sharing is a necessary precondition to improve clinical research and patient care. The SMITH project unites several university hospitals …

Authors: K. Tahar, C. Muller, A. Durschmid, S. Haferkamp, K. Saleh, P. Jurs, S. Staubert, J. E. Gewehr, S. Zenker, D. Ammon, T. Wendt

Date Published: 21st Aug 2019

Publication Type: Journal article

PubMed ID: 31438343

Citation: Stud Health Technol Inform. 2019 Aug 21;264:1785-1786. doi: 10.3233/SHTI190647.

Created: 29th Jul 2020 at 08:27, Last updated: 7th Dec 2021 at 17:58

Design and Concept of the SMITH Phenotyping Pipeline.

SMITH - Smart Medical Information Technology for Healthcare

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Phenotyping means the determination of clinical relevant phenotypes, e.g. by classification or calculation based on EHR data. Within the German Medical Informatics Initiative, the SMITH consortium is …

Authors: F. A. Meineke, S. Staubert, M. Lobe, A. Uciteli, M. Loffler

Date Published: 3rd Sep 2019

Publication Type: Journal article

PubMed ID: 31483269

Citation: Stud Health Technol Inform. 2019 Sep 3;267:164-172. doi: 10.3233/SHTI190821.

Created: 29th Jul 2020 at 08:25, Last updated: 7th Dec 2021 at 17:58

Design of Metadata Services for Clinical Data Interoperability in Germany.

SMITH - Smart Medical Information Technology for Healthcare

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Secondary use of electronic health record (EHR) data requires a detailed description of metadata, especially when data collection and data re-use are organizationally and technically far apart. This …

Authors: M. Lobe, O. Beyan, S. Staubert, F. Meineke, D. Ammon, A. Winter, S. Decker, M. Loffler, T. Kirsten

Date Published: 21st Aug 2019

Publication Type: Journal article

PubMed ID: 31438215

Citation: Stud Health Technol Inform. 2019 Aug 21;264:1528-1529. doi: 10.3233/SHTI190518.

Created: 29th Jul 2020 at 08:23, Last updated: 7th Dec 2021 at 17:58

Towards a comprehensive and interoperable representation of consent-based data usage permissions in the German medical informatics initiative.

SMITH - Smart Medical Information Technology for Healthcare

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

PubMed ID: 32503529

Citation: BMC Med Inform Decis Mak. 2020 Jun 5;20(1):103. doi: 10.1186/s12911-020-01138-6.

Created: 29th Jul 2020 at 08:18, Last updated: 7th Dec 2021 at 17:58

Smart Medical Information Technology for Healthcare (SMITH).

SMITH - Smart Medical Information Technology for Healthcare

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Abstract (Expand)

INTRODUCTION: This article is part of the Focus Theme of Methods of Information in Medicine on the German Medical Informatics Initiative. "Smart Medical Information Technology for Healthcare … (SMITH)" is one of four consortia funded by the German Medical Informatics Initiative (MI-I) to create an alliance of universities, university hospitals, research institutions and IT companies. SMITH's goals are to establish Data Integration Centers (DICs) at each SMITH partner hospital and to implement use cases which demonstrate the usefulness of the approach. OBJECTIVES: To give insight into architectural design issues underlying SMITH data integration and to introduce the use cases to be implemented. GOVERNANCE AND POLICIES: SMITH implements a federated approach as well for its governance structure as for its information system architecture. SMITH has designed a generic concept for its data integration centers. They share identical services and functionalities to take best advantage of the interoperability architectures and of the data use and access process planned. The DICs provide access to the local hospitals' Electronic Medical Records (EMR). This is based on data trustee and privacy management services. DIC staff will curate and amend EMR data in the Health Data Storage. METHODOLOGY AND ARCHITECTURAL FRAMEWORK: To share medical and research data, SMITH's information system is based on communication and storage standards. We use the Reference Model of the Open Archival Information System and will consistently implement profiles of Integrating the Health Care Enterprise (IHE) and Health Level Seven (HL7) standards. Standard terminologies will be applied. The SMITH Market Place will be used for devising agreements on data access and distribution. 3LGM(2) for enterprise architecture modeling supports a consistent development process.The DIC reference architecture determines the services, applications and the standardsbased communication links needed for efficiently supporting the ingesting, data nourishing, trustee, privacy management and data transfer tasks of the SMITH DICs. The reference architecture is adopted at the local sites. Data sharing services and the market place enable interoperability. USE CASES: The methodological use case "Phenotype Pipeline" (PheP) constructs algorithms for annotations and analyses of patient-related phenotypes according to classification rules or statistical models based on structured data. Unstructured textual data will be subject to natural language processing to permit integration into the phenotyping algorithms. The clinical use case "Algorithmic Surveillance of ICU Patients" (ASIC) focusses on patients in Intensive Care Units (ICU) with the acute respiratory distress syndrome (ARDS). A model-based decision-support system will give advice for mechanical ventilation. The clinical use case HELP develops a "hospital-wide electronic medical record-based computerized decision support system to improve outcomes of patients with blood-stream infections" (HELP). ASIC and HELP use the PheP. The clinical benefit of the use cases ASIC and HELP will be demonstrated in a change of care clinical trial based on a step wedge design. DISCUSSION: SMITH's strength is the modular, reusable IT architecture based on interoperability standards, the integration of the hospitals' information management departments and the public-private partnership. The project aims at sustainability beyond the first 4-year funding period.

Authors: A. Winter, S. Staubert, D. Ammon, S. Aiche, O. Beyan, V. Bischoff, P. Daumke, S. Decker, G. Funkat, J. E. Gewehr, A. de Greiff, S. Haferkamp, U. Hahn, A. Henkel, T. Kirsten, T. Kloss, J. Lippert, M. Lobe, V. Lowitsch, O. Maassen, J. Maschmann, S. Meister, R. Mikolajczyk, M. Nuchter, M. W. Pletz, E. Rahm, M. Riedel, K. Saleh, A. Schuppert, S. Smers, A. Stollenwerk, S. Uhlig, T. Wendt, S. Zenker, W. Fleig, G. Marx, A. Scherag, M. Loffler

Date Published: 18th Jul 2018

Publication Type: Journal article

PubMed ID: 30016815

Citation: Methods Inf Med. 2018 Jul;57(S 01):e92-e105. doi: 10.3414/ME18-02-0004. Epub 2018 Jul 17.

Created: 29th Jul 2020 at 07:54, Last updated: 7th Dec 2021 at 17:58

NLP for Clinical Research Tool

NLP4CR - Natural Language Processing for Clinical Research

Motivation: By using the NLP4CR tool, medical facts (e.g. diagnoses, laboratory values) can be extracted from German medical full texts.

Description: The NLP4CR tool is a prototype that demonstrates the applicability of Apache UIMA and cTakes to medical full texts in German language.

Creators: Sebastian Stäubert, Matthias Löbe, Colleen Goldberg

Submitter: Christoph Beger

Model type: Not specified

Model format: Not specified

Environment: Not specified

Organism: Not specified

Human Disease: Not specified

Investigations: No Investigations

Studies: No Studies

Resources: No Resources

Created: 6th May 2019 at 13:59, Last updated: 14th Dec 2020 at 14:43

Danny Ammon

Projects: SMITH - Smart Medical Information Technology for Healthcare, POLAR - Polypharmacy, Drug Interactions, Risks

Institutions: Universitätsklinikum Jena

https://orcid.org/0000-0001-8960-7316

Expertise: data sharing, Interoperability, data integration, medical informatics

Tools: fhir, IHE, HL7, 3LGM² Tool

As head of the Data Integration Center at Jena University Hospital, Dr. Danny Ammon is active in the areas of standardization, processing and communication of medical documentation for healthcare and biomedical research.

Jens Przybilla