Josef Ingenerf | Universität zu Luebeck (original) (raw)

Papers by Josef Ingenerf

Studies in health technology and informatics, 2012

Einleitung: Die zentrale Forderung des TMF-Datenschutzkonzeptes A im Zusammenhang mit biomedizini... more Einleitung: Die zentrale Forderung des TMF-Datenschutzkonzeptes A im Zusammenhang mit biomedizinischer Forschung ist die physikalische und organisatorische Trennung der patientenidentizierenden (IDAT), der Proben-(ProbDAT) sowie der medizinischen Kontextdaten (MDAT). Eine Zusammenführung dieser[for full text, please go to the a.m. URL]

Studies in health technology and informatics, 2019

With the proliferation of digital communication in healthcare, the reuse of laboratory test data ... more With the proliferation of digital communication in healthcare, the reuse of laboratory test data entails valuable insights into clinical and scientific issues, basically enabled by semantic standardization using the LOINC coding system. In order to extend the currently limited potential for analysis, which is mainly caused by structural peculiarities of LOINC, an algorithmic transformation of relevant content into an OWL ontology was performed, which includes LOINC Terms, Parts and Hierarchies. For extending analysis capabilities, the comprehensive SNOMED CT ontology is added by transferring its contents and the recently published LOINC-related mapping data into OWL ontologies. These formalizations offer rich, computer-processable content and allow to infer additional structures and relationships, especially when used together. Consequently, various reutilizations are facilitated; an application demonstrating the dynamic visualization of fractional hierarchy structures for user-supp...

Studies in health technology and informatics, 2018

The establishment of a digital healthcare system is a national and community task. The Federal Mi... more The establishment of a digital healthcare system is a national and community task. The Federal Ministry of Education and Research in Germany is providing funding for consortia consisting of university hospitals among others participating in the "Medical Informatics Initiative". Exchange of medical data between research institutions necessitates a place where meta information for this data is made accessible. Within these consortia different metadata registry solutions were chosen. To promote interoperability between these solutions, we have examined whether the portal of Medical Data Models is eligible for managing and communicating metadata and relevant information across different data integration centres of the Medical Informatics Initiative and beyond. Apart from the MDM-portal, some ISO 11179-based systems such as Samply.MDR as well as openEHR-based solutions are going to be applyed. In this paper, we have focused on the creation of a mapping model between the CDISC O...

Studies in health technology and informatics, 2014

In many software systems to date, interactive graphical user interfaces (GUIs) are represented im... more In many software systems to date, interactive graphical user interfaces (GUIs) are represented implicitly in the source code, together with the application logic. Hence, the re-use, development, and modification of these interfaces is often very laborious. Flexible adjustments of GUIs for various platforms and devices as well as individual user preferences are furthermore difficult to realize. These problems motivate a software-based separation of content and GUI models on the one hand, and application logic on the other. In this project, a software solution for structured reporting on mobile devices is developed. Clinical content archetypes developed in a previous project serve as the content model while the Android SDK provides the GUI model. The necessary bindings between the models are specified using the Jess Rule Language.

Studies in health technology and informatics, 2019

Scientific challenges based on benchmark data enable the comparison and evaluation of different a... more Scientific challenges based on benchmark data enable the comparison and evaluation of different algorithms and take place regularly in scientific disciplines like medical image processing, text mining or genetics. The idea of a challenge is rarely applied within the eHealth community. Mappathon is a metadata mapping challenge that asks for methods to find corresponding data elements within similar datasets and to correlate data elements among each other.

Studies in Health Technology and Informatics, 2021

cBioPortal is a commonly used data warehousing solution for genomic cancer studies. The software ... more cBioPortal is a commonly used data warehousing solution for genomic cancer studies. The software is being extended for patient care application in a molecular tumor board by the MIRACUM consortium within the Medical Informatics Initiative Germany. A key feature for this use case is the ability to enter therapy recommendations for individual patients, which requires interoperability with the hospital information system. A RESTful interface between cBioPortal and an external mediation layer was selected from the different implementation options. It achieves interoperability by using a FHIR capable server to store data and applying the HL7 FHIR Genomics Reporting implementation guide. For systems not supporting the FHIR standard, the well-established HL7 Version 2 standard is available as a fallback export format.

Terminologien und Ordnungssysteme in der Medizin, 2015

Informations- und Wissensverarbeitung in den Sozialwissenschaften, 1994

itit, 1987

Es werden zunächst allgemeine Bemerkungen über den Nutzen von Typen insbesondere in funktionalen ... more Es werden zunächst allgemeine Bemerkungen über den Nutzen von Typen insbesondere in funktionalen Programmiersprachen vorgestellt. Sodann folgt eine Erörterung der Grundideen der polymorphen Typisierung, wie sie in ML erfolgt, und wozu man sie benutzen kann. Dies wird in einer etwas detaillierteren Erörterung des Sprachumfanges vom ML vertieft. Neben verschiedenen Variationsmöglichkeiten und historischen Aspekten von ML schließen sich sowohl hinweisende wie auch einschränkende Ratschläge an.

Bundesgesundheitsblatt - Gesundheitsforschung - Gesundheitsschutz, 2007

Page 1. J. Ingenerf Institut für Medizinische Informatik, Universität zu Lübeck, BRD Terminologie... more Page 1. J. Ingenerf Institut für Medizinische Informatik, Universität zu Lübeck, BRD Terminologien oder Klassifikationen Was bringt die Zukunft? Bundesgesundheitsbl - Gesundheitsforsch - Gesundheitsschutz 2007 · 50:1070 ...

Dokumentation als ein zentrales Aufgabengebiet in der Medizin beinhaltet definitionsgemäß die Sam... more Dokumentation als ein zentrales Aufgabengebiet in der Medizin beinhaltet definitionsgemäß die Sammlung und Erfassung, Erschließung und Ordnung sowie Speicherung und Wieder- Nutzbarmachung (unter evtl. neuen Gesichtspunkten) von Information, insbesondere von sprachlich repräsentierter Information. Die medizinische Fachsprache ist noch vor Bildern und Meßdaten das vorherrschende Ausdrucksmittel, in dem zu dokumentierende Sachverhalte vorliegen. Von besondere Wichtigkeit sind Beschreibungen diagnostischer und therapeutischer Sachverhalte. Eigenschaften einer solchen Fachsprache wie Mehrdeutigkeit, begriffliche Unschärfe sowie zahlreiche synonymen Umschreibungsmöglichkeiten machen sie für Dokumentationszwecke nur bedingt brauchbar. Durch die Nutzung von begrifflichen Ordnungssystemen, in denen die für die Dokumentation zugelassenen Begriffe taxonomisch angeordnet sind, erreicht man eine kontrollierte, d.h. vergleichbare inhaltliche Erschließung der zu dokumentierenden Sachverhalte. Die ...

Applied Sciences

Expressive clinical terminologies are of utmost importance for achieving a semantically interoper... more Expressive clinical terminologies are of utmost importance for achieving a semantically interoperable data exchange and reuse in healthcare. SNOMED CT, widely respected as the most comprehensive terminology in medicine, provides formal concept definitions based on description logic which not only allows for advanced querying of SNOMED-CT-coded data but also for flexibly augmenting its 350,000 concepts by allowing a controlled combination of these. This ability for postcoordination largely increases the expressivity of the terminology but correlates with an intrinsic complexity. Complicated by the current lack of tooling support, postcoordination is widely either ignored or applied in an error-prone way. To help facilitate the adoption of postcoordination, we implemented a web application that guides users through the creation of postcoordinated expressions (PCEs) while ensuring adherence to syntactic and semantic constraints. Our approach was largely facilitated by making use of the...

There are hundreds of English-language biomedical vocabularies, but only a minor part has been tr... more There are hundreds of English-language biomedical vocabularies, but only a minor part has been translated into other languages. We performed a survey of localized German content in biomedical vocabularies, based on the authors' past experiences, web search, and analysis of the UMLS Metathesaurus. As a result we found German versions for fourteen medical terminologies in a strict sense. ICD 10 (International Classification of Diseases) for disease and OPS (Operationenund Prozedurenschlussel) for procedure encoding play a prominent role, as both are used in the German patient classification system. Interestingly they exceed in content and coverage the international sources they had been derived from. German content is also available for ICD-O (oncology), the Medical Subject Headings (MeSH), the Medical Dictionary for Regulatory Activities (MedDRA), the Logical Observation Identifiers Names and Codes (LOINC), the Anatomical Therapeutic Chemical Classification System (ATC), and the ...

International Journal of Medical Informatics, 2001

Studies in Health Technology and Informatics, 2021

To ensure semantic interoperability within healthcare systems, using common, curated terminologic... more To ensure semantic interoperability within healthcare systems, using common, curated terminological systems to identify relevant concepts is of fundamental importance. The HL7 FHIR standard specifies means of modelling terminological systems and appropriate ways of accessing and querying these artefacts within a terminology server. Hence, initiatives towards healthcare interoperability like IHE specify not only software interfaces, but also common codes in the form of value sets and code systems. The way in which these coding tables are provided is not necessarily compatible to the current version of the HL7 FHIR specification and therefore cannot be used with current HL7 FHIR-based terminology servers. This work demonstrates a conversion of terminological resources specified by the Integrating the Healthcare Initiative in the ART-DECOR platform, partly available in HL7 FHIR, to ensure that they can be used within a HL7 FHIR-based terminological server. The approach itself can be us...

Studies in health technology and informatics

The parallel use of different versions of classifications and terminologies complicates the compa... more The parallel use of different versions of classifications and terminologies complicates the comparability of coded patient data. Annual adaptations of classifications like ICD-10 can be dealt with by using simple conversion tables. Terminologies like SNOMED CT have a much more complicate structure and biannual versions in different languages are offered in at least four representation formats. A version management system, called Terminology Version (TV) Manager, has been developed for searching and navigating in synchronized presentations of selected versions of SNOMED CT. Several functions for qualitative and quantitative comparisons of subtrees of interest are extended by accessing external software systems.

Studies in health technology and informatics, 2012

Einleitung: Die zentrale Forderung des TMF-Datenschutzkonzeptes A im Zusammenhang mit biomedizini... more Einleitung: Die zentrale Forderung des TMF-Datenschutzkonzeptes A im Zusammenhang mit biomedizinischer Forschung ist die physikalische und organisatorische Trennung der patientenidentizierenden (IDAT), der Proben-(ProbDAT) sowie der medizinischen Kontextdaten (MDAT). Eine Zusammenführung dieser[for full text, please go to the a.m. URL]

Studies in health technology and informatics, 2019

With the proliferation of digital communication in healthcare, the reuse of laboratory test data ... more With the proliferation of digital communication in healthcare, the reuse of laboratory test data entails valuable insights into clinical and scientific issues, basically enabled by semantic standardization using the LOINC coding system. In order to extend the currently limited potential for analysis, which is mainly caused by structural peculiarities of LOINC, an algorithmic transformation of relevant content into an OWL ontology was performed, which includes LOINC Terms, Parts and Hierarchies. For extending analysis capabilities, the comprehensive SNOMED CT ontology is added by transferring its contents and the recently published LOINC-related mapping data into OWL ontologies. These formalizations offer rich, computer-processable content and allow to infer additional structures and relationships, especially when used together. Consequently, various reutilizations are facilitated; an application demonstrating the dynamic visualization of fractional hierarchy structures for user-supp...

Studies in health technology and informatics, 2018

The establishment of a digital healthcare system is a national and community task. The Federal Mi... more The establishment of a digital healthcare system is a national and community task. The Federal Ministry of Education and Research in Germany is providing funding for consortia consisting of university hospitals among others participating in the "Medical Informatics Initiative". Exchange of medical data between research institutions necessitates a place where meta information for this data is made accessible. Within these consortia different metadata registry solutions were chosen. To promote interoperability between these solutions, we have examined whether the portal of Medical Data Models is eligible for managing and communicating metadata and relevant information across different data integration centres of the Medical Informatics Initiative and beyond. Apart from the MDM-portal, some ISO 11179-based systems such as Samply.MDR as well as openEHR-based solutions are going to be applyed. In this paper, we have focused on the creation of a mapping model between the CDISC O...

Studies in health technology and informatics, 2014

In many software systems to date, interactive graphical user interfaces (GUIs) are represented im... more In many software systems to date, interactive graphical user interfaces (GUIs) are represented implicitly in the source code, together with the application logic. Hence, the re-use, development, and modification of these interfaces is often very laborious. Flexible adjustments of GUIs for various platforms and devices as well as individual user preferences are furthermore difficult to realize. These problems motivate a software-based separation of content and GUI models on the one hand, and application logic on the other. In this project, a software solution for structured reporting on mobile devices is developed. Clinical content archetypes developed in a previous project serve as the content model while the Android SDK provides the GUI model. The necessary bindings between the models are specified using the Jess Rule Language.

Studies in health technology and informatics, 2019

Scientific challenges based on benchmark data enable the comparison and evaluation of different a... more Scientific challenges based on benchmark data enable the comparison and evaluation of different algorithms and take place regularly in scientific disciplines like medical image processing, text mining or genetics. The idea of a challenge is rarely applied within the eHealth community. Mappathon is a metadata mapping challenge that asks for methods to find corresponding data elements within similar datasets and to correlate data elements among each other.

Studies in Health Technology and Informatics, 2021

cBioPortal is a commonly used data warehousing solution for genomic cancer studies. The software ... more cBioPortal is a commonly used data warehousing solution for genomic cancer studies. The software is being extended for patient care application in a molecular tumor board by the MIRACUM consortium within the Medical Informatics Initiative Germany. A key feature for this use case is the ability to enter therapy recommendations for individual patients, which requires interoperability with the hospital information system. A RESTful interface between cBioPortal and an external mediation layer was selected from the different implementation options. It achieves interoperability by using a FHIR capable server to store data and applying the HL7 FHIR Genomics Reporting implementation guide. For systems not supporting the FHIR standard, the well-established HL7 Version 2 standard is available as a fallback export format.

Terminologien und Ordnungssysteme in der Medizin, 2015

Informations- und Wissensverarbeitung in den Sozialwissenschaften, 1994

itit, 1987

Es werden zunächst allgemeine Bemerkungen über den Nutzen von Typen insbesondere in funktionalen ... more Es werden zunächst allgemeine Bemerkungen über den Nutzen von Typen insbesondere in funktionalen Programmiersprachen vorgestellt. Sodann folgt eine Erörterung der Grundideen der polymorphen Typisierung, wie sie in ML erfolgt, und wozu man sie benutzen kann. Dies wird in einer etwas detaillierteren Erörterung des Sprachumfanges vom ML vertieft. Neben verschiedenen Variationsmöglichkeiten und historischen Aspekten von ML schließen sich sowohl hinweisende wie auch einschränkende Ratschläge an.

Bundesgesundheitsblatt - Gesundheitsforschung - Gesundheitsschutz, 2007

Page 1. J. Ingenerf Institut für Medizinische Informatik, Universität zu Lübeck, BRD Terminologie... more Page 1. J. Ingenerf Institut für Medizinische Informatik, Universität zu Lübeck, BRD Terminologien oder Klassifikationen Was bringt die Zukunft? Bundesgesundheitsbl - Gesundheitsforsch - Gesundheitsschutz 2007 · 50:1070 ...

Dokumentation als ein zentrales Aufgabengebiet in der Medizin beinhaltet definitionsgemäß die Sam... more Dokumentation als ein zentrales Aufgabengebiet in der Medizin beinhaltet definitionsgemäß die Sammlung und Erfassung, Erschließung und Ordnung sowie Speicherung und Wieder- Nutzbarmachung (unter evtl. neuen Gesichtspunkten) von Information, insbesondere von sprachlich repräsentierter Information. Die medizinische Fachsprache ist noch vor Bildern und Meßdaten das vorherrschende Ausdrucksmittel, in dem zu dokumentierende Sachverhalte vorliegen. Von besondere Wichtigkeit sind Beschreibungen diagnostischer und therapeutischer Sachverhalte. Eigenschaften einer solchen Fachsprache wie Mehrdeutigkeit, begriffliche Unschärfe sowie zahlreiche synonymen Umschreibungsmöglichkeiten machen sie für Dokumentationszwecke nur bedingt brauchbar. Durch die Nutzung von begrifflichen Ordnungssystemen, in denen die für die Dokumentation zugelassenen Begriffe taxonomisch angeordnet sind, erreicht man eine kontrollierte, d.h. vergleichbare inhaltliche Erschließung der zu dokumentierenden Sachverhalte. Die ...

Applied Sciences

Expressive clinical terminologies are of utmost importance for achieving a semantically interoper... more Expressive clinical terminologies are of utmost importance for achieving a semantically interoperable data exchange and reuse in healthcare. SNOMED CT, widely respected as the most comprehensive terminology in medicine, provides formal concept definitions based on description logic which not only allows for advanced querying of SNOMED-CT-coded data but also for flexibly augmenting its 350,000 concepts by allowing a controlled combination of these. This ability for postcoordination largely increases the expressivity of the terminology but correlates with an intrinsic complexity. Complicated by the current lack of tooling support, postcoordination is widely either ignored or applied in an error-prone way. To help facilitate the adoption of postcoordination, we implemented a web application that guides users through the creation of postcoordinated expressions (PCEs) while ensuring adherence to syntactic and semantic constraints. Our approach was largely facilitated by making use of the...

There are hundreds of English-language biomedical vocabularies, but only a minor part has been tr... more There are hundreds of English-language biomedical vocabularies, but only a minor part has been translated into other languages. We performed a survey of localized German content in biomedical vocabularies, based on the authors' past experiences, web search, and analysis of the UMLS Metathesaurus. As a result we found German versions for fourteen medical terminologies in a strict sense. ICD 10 (International Classification of Diseases) for disease and OPS (Operationenund Prozedurenschlussel) for procedure encoding play a prominent role, as both are used in the German patient classification system. Interestingly they exceed in content and coverage the international sources they had been derived from. German content is also available for ICD-O (oncology), the Medical Subject Headings (MeSH), the Medical Dictionary for Regulatory Activities (MedDRA), the Logical Observation Identifiers Names and Codes (LOINC), the Anatomical Therapeutic Chemical Classification System (ATC), and the ...

International Journal of Medical Informatics, 2001

Studies in Health Technology and Informatics, 2021

To ensure semantic interoperability within healthcare systems, using common, curated terminologic... more To ensure semantic interoperability within healthcare systems, using common, curated terminological systems to identify relevant concepts is of fundamental importance. The HL7 FHIR standard specifies means of modelling terminological systems and appropriate ways of accessing and querying these artefacts within a terminology server. Hence, initiatives towards healthcare interoperability like IHE specify not only software interfaces, but also common codes in the form of value sets and code systems. The way in which these coding tables are provided is not necessarily compatible to the current version of the HL7 FHIR specification and therefore cannot be used with current HL7 FHIR-based terminology servers. This work demonstrates a conversion of terminological resources specified by the Integrating the Healthcare Initiative in the ART-DECOR platform, partly available in HL7 FHIR, to ensure that they can be used within a HL7 FHIR-based terminological server. The approach itself can be us...

Studies in health technology and informatics

The parallel use of different versions of classifications and terminologies complicates the compa... more The parallel use of different versions of classifications and terminologies complicates the comparability of coded patient data. Annual adaptations of classifications like ICD-10 can be dealt with by using simple conversion tables. Terminologies like SNOMED CT have a much more complicate structure and biannual versions in different languages are offered in at least four representation formats. A version management system, called Terminology Version (TV) Manager, has been developed for searching and navigating in synchronized presentations of selected versions of SNOMED CT. Several functions for qualitative and quantitative comparisons of subtrees of interest are extended by accessing external software systems.