Sebastian Stäubert

About Sebastian Stäubert:

I am a research associate at IMISE, Universität Leipzig.

LHA ID: 7WDQPT9398-7

Location:  Germany

Expertise: Modeling Information System Architecture, Consent Management, Data Management, medical informatics

Tools: Modeling Information System Architecture, Linux, 3LGM² Tool

ORCID: https://orcid.org/0000-0002-7221-7415

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SMITH - Smart Medical Information Technology for Healthcare
No description specified

Programme: MII - Medical Informatics Initiative

Public web page: https://www.smith.care/

Start date: 1st Jan 2018

NLP4CR - Natural Language Processing for Clinical Research

The NLP4CR project was initiated as part of Colleen Goldberg's master thesis. Medical information is not always available in a structured form, but as free text documentation. NLP techniques make it possible to analyse, annotate and extract these free texts. In this way, medical data can be made accessible for machine processing and for clinical research.

Programme: This Project is not associated with a Programme

Public web page: http://www.imise.uni-leipzig.de/Gruppen/MIG

Start date: 1st Jan 2015

Ontological Modelling and Execution of Phenotypic Queries in the Leipzig Health Atlas.
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

Sharing data is of great importance for research in medical sciences. It is the basis for reproducibility and reuse of already generated outcomes in new projects and in new contexts. FAIR data principles … are the basics for sharing data. The Leipzig Health Atlas (LHA) platform follows these principles and provides data, describing metadata, and models that have been implemented in novel software tools and are available as demonstrators. LHA reuses and extends three different major components that have been previously developed by other projects. The SEEK management platform is the foundation providing a repository for archiving, presenting and secure sharing a wide range of publication results, such as published reports, (bio)medical data as well as interactive models and tools. The LHA Data Portal manages study metadata and data allowing to search for data of interest. Finally, PhenoMan is an ontological framework for phenotype modelling. This paper describes the interrelation of these three components. In particular, we use the PhenoMan to, firstly, model and represent phenotypes within the LHA platform. Then, secondly, the ontological phenotype representation can be used to generate search queries that are executed by the LHA Data Portal. The PhenoMan generates the queries in a novel domain specific query language (SDQL), which is specific for data management systems based on CDISC ODM standard, such as the LHA Data Portal. Our approach was successfully applied to represent phenotypes in the Leipzig Health Atlas with the possibility to execute corresponding queries within the LHA Data Portal.

Authors: A. Uciteli, C. Beger, J. Wagner, A. Kiel, F. A. Meineke, S. Staubert, M. Lobe, R. Hansel, J. Schuster, T. Kirsten, H. Herre

Date Published: 24th May 2021

Publication Type: Journal article

Ontological modelling and FHIR Search based representation of basic eligibility criteria
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

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.

Authors: A. Uciteli, C. Beger, J. Wagner, T. Kirsten, F. A. Meineke, S. Staubert, M. Lobe, H. Herre

Date Published: 26th Apr 2021

Publication Type: Journal article

Problems in FAIRifying Medical Datasets.
SMITH - Smart Medical Information Technology for Healthcare

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

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

Der Leipzig Health Atlas
LHA - Leipzig Health Atlas

Abstract (Expand)

Die Notwendigkeit des Managements von Forschungsdaten ist von der Forschungscommunity erkannt – Sponsoren, Gesetzgeber, Verlage erwarten und fördern die Einhaltung der guten wissenschaftlichen Praxis, … was nicht nur die Archivierung umfasst, sondern auch die Verfügbarkeit von Forschungsdaten- und ergebnissen im Sinne der FAIR-Prinzipien. Der Leipzig Health Atlas (LHA) ist ein Projekt zur Präsentation und zum Austausch eines breiten Spektrums von Publikationen, (bio) medizinischen Daten (z.B. klinisch, epidemiologisch, molekular), Modellen und Tools z.B. zur Risikoberechnung in der Gesundheitsforschung. Die Verbundpartner decken hierbei einen breiten Bereich wissenschaftlicher Disziplinen ab, beginnend von medizinischer Systembiologie über klinische und epidemiologische Forschung bis zu ontologischer und dynamischer Modellierung. Derzeit sind 18 Forschungskonsortien beteiligt (u.a. zu den Domänen Lymphome, Gliome, Sepsis, Erblicher Darm- und Brustkrebs), die Daten aus klinischen Studien, Patientenkohorten, epidemiologischen Kohorten, teilweise mit umfangreichen molekularen und genetischen Profilen, sammeln. Die Modellierung umfasst algorithmische Phänotypklassifizierung, Risikovorhersage und Krankheitsdynamik. Wir konnten in einer ersten Entwicklungsphase zeigen, dass unsere webbasierte Plattform geeignet ist, um (1) Methoden zur Verfügung zu stellen, um individuelle Patientendaten aus Publikationen für eine Weiternutzung zugänglich zu machen, (2) algorithmische Werkzeuge zur Phänotypisierung und Risikoprofilerstellung zu präsentieren, (3) Werkzeuge zur Durchführung dynamischer Krankheits- und Therapiemodelle interaktiv verfügbar zu machen und (4) strukturierte Metadaten zu quantitativen und qualitativen Merkmalen bereit zu stellen. Die semantische Datenintegration liefert hierzu die Technologien (Ontologien und Datamining Werkzeuge) für die (semantische) Datenintegration und Wissensanreicherung. Darüber hinaus stellt sie Werkzeuge zur Verknüpfung eigener Daten, Analyseergebnisse, öffentlich zugänglicher Daten- und Metadaten-Repositorien sowie zur Verdichtung komplexer Daten zur Verfügung. Eine Arbeitsgruppe zur Applikationsentwicklung und –validierung entwickelt innovative paradigmatische Anwendungen für (1) die klinische Entscheidungsfindung für Krebsstudien, die genetische Beratung, für Risikovorhersagemodelle sowie Gewebe- und Krankheitsmodelle und (2) Anwendungen (sog. Apps), die sich auf die Charakterisierung neuer Phänotypen (z.B. ‚omics‘-Merkmale, Körpertypen, Referenzwerte) aus epidemiologischen Studien konzentrieren. Diese Anwendungen werden gemeinsam mit klinischen Experten, Genetikern, Systembiologen, Biometrikern und Bioinformatikern spezifiziert. Der LHA stellt Integrationstechnologie bereit und implementiert die Anwendungen für die User Communities unter Verwendung verschiedener Präsentationswerkzeuge bzw. Technologien (z.B. R-Shiny, i2b2, Kubernetes, SEEK). Dazu ist es erforderlich, die Daten und Metadaten vor dem Hochladen zu kuratieren, Erlaubnisse der Datenbesitzer einzuholen, die erforderlichen Datenschutzkriterien zu berücksichtigen und semantische Annotationen zu überprüfen. Zudem werden die zugelieferten Modellalgorithmen in einer qualitätsgesicherten Weise aufbereitet und, soweit anwendbar, online interaktiv zur Verfügung gestellt. Der LHA richtet sich insbesondere an die Zielgruppen Kliniker, Epidemiologen, Molekulargenetiker, Humangenetiker, Pathologen, Biostatistiker und Modellierer ist aber unter www.healthatlas.de öffentlich zugänglich – aus rechtlichen Gründen erfordert der Zugriff auf bestimmte Applikationen und Datensätze zusätzliche Autorisierung. Das Projekt wird über das BMBF Programm i:DSem (Integrative Datensemantik für die Systemmedizin, Förderkennzeichen 031L0026) gefördert.

Authors: F. A. Meineke, Sebastian Stäubert, Matthias Löbe, C. Beger, René Hänsel, A. Uciteli, H. Binder, T. Kirsten, M. Scholz, H. Herre, C. Engel, Markus Löffler

Date Published: 19th Sep 2019

Publication Type: Misc

Design and Concept of the SMITH Phenotyping Pipeline.
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

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 … working on the implementation of a phenotyping pipeline. to extract, structure and normalize information from the EHR data of the hospital information systems of the participating sites; to automatically apply complex algorithms and models and to enrich the data within the research data warehouses of the distributed data integration centers with the computed results. Here we present the overall picture and essential building blocks and workflows of this concept.

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

Date Published: 3rd Sep 2019

Publication Type: Journal article

Design of Metadata Services for Clinical Data Interoperability in Germany.
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

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 … paper describes the concept of the SMITH consortium that includes conventions, processes, and tools for describing and managing metadata using common standards for semantic interoperability. It deals in particular with the chain of processing steps of data from existing information systems and provides an overview of the planned use of metadata, medical terminologies, and semantic services in the consortium.

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

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 … and medical faculties in order to provide medical informatics solutions for health data integration and cross-institutional communication. In this paper, we focus on requirements elicitation and management for extracting clinical data from heterogeneous subsystems and data integration based on eHealth standards such as HL7 FHIR and IHE profiles.

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

An integrative web platform for user-friendly application of risk prediction models in hereditary cancer predisposition
GC-HBOC - German Consortium for Hereditary Breast and Ovarian Cancer

Abstract (Expand)

Background and Objective: Predicting individual mutation and cancer risks is essential to assist genetic counsellors in clinical decision making for patients with a hereditary cancer predisposition. … Worldwide a variety of statistical models and empirical data for risk prediction have been developed and published for hereditary breast and ovarian cancer (HBOC), and hereditary non-polyposis colorectal cancer (HNPCC / Lynch syndrome, LS). However, only few models have so far been implemented in convenient and easy-to-use computer applications. We therefore aimed to develop user-friendly applications of selected HBOC and LS risk prediction models, and to make them available through the "Leipzig Health Atlas" (LHA), a web-based multifunctional platform to share research data, novel ontologies, models and software tools with the medical and scientific community. LHA is a project funded within the BMBF initiative "i:DSem – Integrative data semantics in system medicine". Methods and Results: We selected a total of six statistical models and empirical datasets relevant for HBOC and LS: 1) the Manchester Scoring System, 2) the "Mutation Frequency Explorer" of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC), 3) an extended version of the Claus model, 4) MMRpredict, 5) PREMM1,2,6, and 6) PREMM5. The Manchester Scoring System allows calculation of BRCA1/2 mutation probabilities based on aggregated family history. The "Mutation Frequency Explorer" allows flexible assessment of mutation risks in BRCA1/2 and other genes for different sets of familial cancer histories based on a large dataset from the GC-HBOC. The extended Claus model (as implemented in the commercial predigree drawing software Cyrillic 2.1.3, which is no longer supported and no longer works on newer operating systems) predicts both mutation and breast cancer risks based on structured pedigree data. MMRpredict, PREMM 1,2,6, and PREMM 5 predict mutation risks in mismatch repair genes for patients from families suspected of having LS. All models were implemented using the statistical software "R" and the R-package "Shiny". "Shiny" allows the development of interactive applications by incorporating "R" with HTML and other web technologies. The Shiny apps are accessible on the website of the "Leipzig Health Atlas" (https://www.health-atlas.de) for registered researchers and genetic counselors. Conclusions: The risk prediction apps allow convenient calculation of mutation or cancer risks for an advice-seeking individual based on pedigree data or aggregated information on the familial cancer history. Target users should be specialized health professionals (physicians and genetic counselors) and scientists to ensure correct handling of the tools and careful interpretation of results.

Authors: Silke Zachariae, Sebastian Stäubert, C. Fischer, Markus Löffler, Christoph Engel

Date Published: 8th Mar 2019

Publication Type: InProceedings

Human Diseases: hereditary breast ovarian cancer syndrome, Lynch syndrome, colorectal cancer

Continouus Annotation Quality Control, Support for Hierarchically Structured Label Sets and Long-Segment Annotation with WAT-SL 2.0
SMITH - Smart Medical Information Technology for Healthcare

Abstract

Not specified

Authors: Matthias Löbe, O. Beyan, Sebastian Stäubert, Frank A. Meineke, D. Ammon, Alfred Winter, S. Deckert, Markus Löffler, Toralf Kirsten

Date Published: 2019

Publication Type: InProceedings

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

Poster: Der Leipzig Health Atlas
LHA - Leipzig Health Atlas

The need to manage research data is recognised by the research community - sponsors, legislators, publishers expect and encourage good scientific practice, which not only includes archiving, but also the availability of research data and results in line with FAIR principles. The publication gives a brief overview of the Leipzig Health Atlas (LHA), which is a project for the presentation and exchange of a wide range of publications, (bio) medical data (e.g. clinical, epidemiological, molecular), ...

Creators: René Hänsel, Matthias Löbe, Sebastian Stäubert, Christoph Beger

Submitter: Christoph Beger

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Abstract: Der Leipzig Health Atlas
LHA - Leipzig Health Atlas

The need to manage research data is recognised by the research community - sponsors, legislators, publishers expect and encourage good scientific practice, which not only includes archiving, but also the availability of research data and results in line with FAIR principles. The publication gives a brief overview of the Leipzig Health Atlas (LHA), which is a project for the presentation and exchange of a wide range of publications, (bio) medical data (e.g. clinical, epidemiological, molecular), ...

Creators: René Hänsel, Matthias Löbe, Sebastian Stäubert, Christoph Beger

Submitter: Christoph Beger

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MII - Medical Informatics Initiative

The medical informatics initiative was created to close the gap between research and healthcare. All of Germany’s university hospitals have joined forces with research institutions, businesses, health insurers, and patient advocacy groups to create a framework that harnesses research findings to the direct benefit of patients. The German Federal Ministry of Education and Research (BMBF) is investing around 160 million euros in the programme through 2021. The digitisation of medicine is creating ...

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

Web page: https://www.medizininformatik-initiative.de/en

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Health Atlas

The Health Atlas is an alliance of medical ontologists, medical systems biologists and clinical trials groups to design and implement a multi-functional and quality-assured atlas. It provides models, data and metadata on specific use cases from medical research fields.

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