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Author: Franz Matthies3
Towards an ontology-based phenotypic query model
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

Clinical research based on data from patient or study data management systems plays an important role in transferring basic findings into the daily practices of physicians. To support study recruitment, … diagnostic processes, and risk factor evaluation, search queries for such management systems can be used. Typically, the query syntax as well as the underlying data structure vary greatly between different data management systems. This makes it difficult for domain experts (e.g., clinicians) to build and execute search queries. In this work, the Core Ontology of Phenotypes is used as a general model for phenotypic knowledge. This knowledge is required to create search queries that determine and classify individuals (e.g., patients or study participants) whose morphology, function, behaviour, or biochemical and physiological properties meet specific phenotype classes. A specific model describing a set of particular phenotype classes is called a Phenotype Specification Ontology. Such an ontology can be automatically converted to search queries on data management systems. The methods described have already been used successfully in several projects. Using ontologies to model phenotypic knowledge on patient or study data management systems is a viable approach. It allows clinicians to model from a domain perspective without knowing the actual data structure or query language.

Authors: Christoph Beger, Franz Matthies, Ralph Schäfermeier, Toralf Kirsten, Heinrich Herre, Alexandr Uciteli

Date Published: 1st May 2022

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

Date Published: 1st Jun 2020

Publication Type: Journal article

3000PA-Towards a National Reference Corpus of German Clinical Language
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We introduce 3000PA, a clinical document corpus composed of 3,000 EPRs from three different clinical sites, which will serve as the backbone of a national reference language resource for German clinical … NLP. We outline its design principles, results from a medication annotation campaign and the evaluation of a first medication information extraction prototype using a subset of 3000PA.

Authors: U. Hahn, F. Matthies, C. Lohr, Markus Löffler

Date Published: 24th Apr 2018

Publication Type: InProceedings

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