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Auflistung nach Autor:in "Kirsten, Toralf"

1 - 10 von 11
  • Konferenzbeitrag
    Comparative evaluation of microarray-based gene expression databases
    (BTW 2003 – Datenbanksysteme für Business, Technologie und Web, Tagungsband der 10. BTW Konferenz, 2003) Do, Hong Hai; Kirsten, Toralf; Rahm, Erhard
    Microarrays make it possible to monitor the expression of thousands of genes in parallel thus generating huge amounts of data. So far, several databases have been developed for managing and analyzing this kind of data but the current state of the art in this field is still early stage. In this paper, we comprehensively analyze the requirements for microarray data management. We consider the various kinds of data involved as well as data preparation, integration and analysis needs. The identified requirements are then used to comparatively evaluate eight existing microarray databases described in the literature. In addition to providing an overview of the current state of the art we identify problems that should be addressed in the future to obtain better solutions for managing and analyzing microarray data.
  • Zeitschriftenartikel
    Das E-Assessment-Tool DMT
    (Datenbank-Spektrum: Vol. 21, No. 1, 2021) Thor, Andreas; Kirsten, Toralf
    Die Bearbeitung von Übungsaufgaben ist ein wichtiges Element in der Datenbank-Lehre. Lösungen der Studierenden lassen sich dabei häufig in strukturierten Ergebnisformaten festhalten, wie z. B. SQL-Anfragen oder die Spezifikation von Schemata und Relationen. Dieser Beitrag stellt das E‑Assessment-Tool DMT (Data Management Tester) vor, das sowohl eine automatische Bewertung als auch eine automatische Feedback-Generierung solcher strukturierter Lösungen ermöglicht. Es soll dabei insbesondere Studierende unterstützen, nicht ganz korrekte Lösungen zielgerichtet überarbeiten zu können. Dieser Betrag skizziert Konzept und Architektur von DMT und erläutert den Einsatz an der HTWK Leipzig und der Hochschule Mittweida.
  • Konferenzbeitrag
    An evolution-based approach for assessing ontology mappings - A case study in the life sciences
    (Datenbanksysteme in Business, Technologie und Web (BTW) – 13. Fachtagung des GI-Fachbereichs "Datenbanken und Informationssysteme" (DBIS), 2009) Thor, Andreas; Hartung, Michael; Gross, Anika; Kirsten, Toralf; Rahm, Erhard
    Ontology matching has been widely studied. However, the resulting ontology mappings can be rather unstable when the participating ontologies or utilized secondary sources (e.g., instance sources, thesauri) evolve. We propose an evolution-based approach fo
  • Konferenzbeitrag
    Hybride Integration von molekularbiologischen Annotationsdaten
    (Datenbanksysteme in Business, Technologie und Web, 11. Fachtagung des GIFachbereichs “Datenbanken und Informationssysteme” (DBIS), 2005) Körner, Christine; Kirsten, Toralf; Do, Hong-Hai; Rahm, Erhard
    Wir präsentieren einen Ansatz, um Annotationsdaten von molekularbiologischen Objekten wie Genen, Proteinen und Pathways aus öffentlichen Datenquellen für datenintensive Expressionsanalysen verwendbar zu machen. Die Expressionsdaten sind mit Experimentbeschreibungen physisch in einem Data Warehouse integriert, um schnelle Auswertungen zu unterstützen. Die öffentlichen Annotationsdaten werden virtuell über einen Mediatoransatz integriert und bedarfsgesteuert für Analysen abgerufen. Für die einheitliche Anbindung der Datenquellen wird das verbreitete Tool SRS (Sequence Retrieval System) der Fa. LION bioscience genutzt. Die Kopplung zwischen dem Warehouse und SRS erfolgt über einen Query-Mediator unter Nutzung explizit gespeicherter Beziehungen (Mappings) zwischen den Instanzen der öffentlichen Datenquellen. Dieser hybride In- tegrationsansatz wurde als Erweiterung des Leipziger Data Warehouse für Genexpressionsdaten (http://www.izbi.de/GEWARE) implementiert und wird für die Einbindung von GeneOntology, LocusLink und Ensemble in Analysen eingesetzt. Neben der Darstellung des Integrationskonzepts und seiner Realisierung werden auch Ergebnisse erster Performanzmessungen präsentiert.
  • Konferenzbeitrag
    Instance-based matching of hierarchical ontologies
    (Datenbanksysteme in Business, Technologie und Web (BTW 2007) – 12. Fachtagung des GI-Fachbereichs "Datenbanken und Informationssysteme" (DBIS), 2007) Thor, Andreas; Kirsten, Toralf; Rahm, Erhard
    We study an instance-based approach for matching hierarchical ontolo- gies, such as product catalogs. The motivation for utilizing instances is that meta-data-based match approaches often suffer from semantic heterogeneity, e.g. ambiguous concept names, different concept granularities or incomparable categorizations. Our instance-based match approach matches categories based on the instances (e.g. products) assigned to them. This way we partly translate the ontology match problem into an instance match problem which is often easier to solve, especially when instances carry globally unique object ids. Since concepts of different ontologies rarely match 1:1 we propose to determine correspondences between sets of concepts. We experimentally evaluate the match approaches for real product catalogs.
  • Zeitschriftenartikel
    Integration and visualization of spatial data in LIFE
    (it - Information Technology: Vol. 59, No. 5, 2017) Lin, Ying-Chi; Groß, Anika; Kirsten, Toralf
    It is usually a challenging task to integrate and analyze huge amounts of heterogeneous data in large medical research projects. Often meaningful new insights can be achieved by visualizing medical data on geographical maps. For instance in epidemiological studies, data is often explored on a spatial dimension. LIFE is a large epidemiological study, managed by the LIFE Research Center for Civilization Diseases at Leipzig University. The study investigates the health-related states of the local population, e.g. by looking at the role of lifestyle factors on major civilization diseases. To allow for an effective data exploration, the development of sophisticated data analysis and spatial visualization techniques is necessary. Here, we present the interactive web application LIFE Spatial Data Visualization System (LIFE-SDVS) that adds a geographical facet to the data integration and analysis workflow of the LIFE research project.
  • Konferenzbeitrag
    Metadata Management for Data Integration in Medical Sciences
    (Datenbanksysteme für Business, Technologie und Web (BTW 2017), 2017) Kirsten, Toralf; Kiel, Alexander; Rühle, Mathias; Wagner, Jonas
    Clinical and epidemiological studies are commonly used in medical sciences. They typically collect data by using different input forms and information systems. Metadata describing input forms, database schemas and input systems are used for data integration but are typically distributed over different software tools; each uses portions of metadata, such as for loading (ETL), data presentation and analysis. In this paper, we describe an approach managing metadata centrally and consistently in a dedicated Metadata Repository (MDR). Metadata can be provided to different tools. Moreover, the MDR includes a matching component creating schema mappings as a prerequisite to integrate captured medical data. We describe the approach, the MDR infrastructure and provide algorithms for creating schema mappings. Finally, we show selected evaluation results. The MDR is fully operational and used to integrate data from a multitude of input forms and systems in the epidemiological study LIFE.
  • Konferenzbeitrag
    Ontology-based registration of entities for data integration in large biomedical research projects
    (INFORMATIK 2010. Service Science – Neue Perspektiven für die Informatik. Band 1, 2010) Kirsten, Toralf; Kiel, Alexander
    Large biomedical projects often include workflows running across institutional borders. In these workflows, data describing biomedical entities, such as patients, bio-materials but also processes itself, is typically produced, modified and analyzed at different locations and by several systems. Therefore, both tracking entities within inter-organizational workflows and data integration are often crucial steps. To address these problems, we centrally register entities and their relationships by using a multi-layered model. The model utilizes an ontology and a typed system graph to semantically describe and classify entities and their relationships but also to access entity data on demand in their original source. Moreover, this integration approach allows to centrally track entities along the project workflows and can be used in explorative data analyses as well as by other data integration approaches using the registered entity relationships. We describe the model, the utilized ontology, and a system implementing this approach, which is applied in a large biomedical research project.
  • Konferenzbeitrag
    Ontology-based retrieval of scientific data in LIFE
    (Datenbanksysteme für Business, Technologie und Web (BTW 2015) - Workshopband, 2015) Uciteli, Alexandr; Kirsten, Toralf
    LIFE is an epidemiological study determining thousands of Leipzig inhabitants with a wide spectrum of interviews, questionnaires, and medical investigations. The heterogeneous data are centrally integrated into a research database and are analyzed by specific analysis projects. To semantically describe the large set of data, we have developed an ontological framework. Applicants of analysis projects and other interested people can use the LIFE Investigation Ontology (LIO) as central part of the framework to get insights, which kind of data is collected in LIFE. Moreover, we use the framework to generate queries over the collected scientific data in order to retrieve data as requested by each analysis project. A query generator transforms the ontological specifications using LIO to database queries which are implemented as project-specific database views. Since the requested data is typically complex, a manual query specification would be very timeconsuming, error-prone, and is, therefore, unsuitable in this large project. We present the approach, overview LIO and show query formulation and transformation. Our approach runs in production mode for two years in LIFE.
  • Textdokument
    Selecting, Packaging, and Granting Access for Sharing Study Data
    (INFORMATIK 2017, 2017) Kirsten, Toralf; Kiel, Alexander; Wagner, Jonas; Rühle, Mathias; Löffler, Markus
    Data in medical studies and research projects are captured, curated and analyzed, often, with a substantial personal and financial effort. Such study data are typically managed by institutions and groups who are involved in these studies and projects. Often, they are refrained by these institutions and, thus, not shared with other scientists who are interested in similar medical topics or hypotheses. Open the data for other scientists will speed up medical insights, enable analyzes which currently lacks data amount either by enlarge the set size of study objects and by finding suitable controls, and allow to validate published results taking data from other studies into account. In this paper, we introduce the data sharing approach we use at the LIFE Research Center for Civilization Diseases, University Leipzig. Our approach is influenced by the OAIS reference model for archiving and distributing data to a designated community. We highlight several aspects of this approach, sketch the process and describe the supporting IT infrastructure. In particular, we outline the LIFE Data Portal and the LIFE Proposal Manager allowing to find, access, and reuse metadata and study data for dedicated analysis projects.