Ontology-based Annotation, Management and Visualisation of Microarray data

me

Dipl. Biol. Daniel Schober

Max-Delbrück-Center for Molecular Medicine
Room 7, Walter Friedrich Building  DNA
Robert-Rössle-Str. 10
13125 Berlin, Germany
Fax:  (+49 30) 9406 2834
Phone:  (+49 30) 9406 3125
e-mail: schober-at-mdc-berlin.de (where "-at-" == "@")
  • Current Project: Currently I am finishing my Ph.D. with the title "Ein Repräsentationsformat zur standardisierten Beschreibung und wissensbasierten Modellierung genomischer Expressionsdaten". Its about using an object-oriented, ontology-based knowledge model and Protege-2000 as Laboratory Information Management System (LIMS) for annotating, querying and visualising Affymetrix Probe set ids, their annotation and expression data.
  • I use and extend the Protege-2000 Knowledge Base Editor API. The Gandr (Gene annotation data representation)-Knowledgebase allows associative browsing, semantic complex ontological querying and an integrated frame-based view on Affymetrix Microarray expression- & context data (human and rat chips). Besides, it allows the lab bench user to annotate his data in a domain-dependent, but still formal way which allows visualisations of gene relations with graph and spring layout display tools. For an overview of the GandrKB, look at the poster displayed at the 7th protege conference or have a look at the short summary (English).
  • The GandrKB is free for use and can be downloaded at the GandrKB project site.
  • You can alternatively browse a prototype of the GandrKB as a webapplication (use mozilla or netscape browsers).
  • Former Projects: Development of a distributed, agent-based in silico Model of the Toll/NFkB-signaling pathway in mus musculus under verification of DNA-Microarray generated expression data (poster). Slides of a talk at MDC (intern) "Multiagent-basierte Modellierung von Signaltransduktionsnetzen" (german). In this context I also implemented a prototype of an ontology that can be used to structure basic knowledge-ideoms for use in a multiagent-based simulation of signal transduction (see poster for details).
  • Recources: A very short introduction to DNA-microarrays (german). Slides of a talk entitled "Ontologien - Wissensrepräsentation für biologische Datenbanken" (German). Slides of a talk entitled "Annotating microarray data with gene ontology terms" (English).
  • I wrote an Introduction to ontologies (German) which contains also an overview on existing bioontology projects.
  • An overview on websites providing context-information and services for microarray data analysis.
  • Some websites providing free software-tools for microarray data analysis.
  • Background: Diploma in molecular neurobiology in the group of Prof. D. Richter in the Institute for Cellbiochemistry and Clinical Neurobiology at the Universitätsklinikum Eppendorf, Hamburg. Thesis: Investigation of the expression of synapse-associated proteins in the brain of rattus norvegicus through radioactive in situ hybridisation (German).
  • Scientific interests: Expression analysis, gene data management, ontologies, signaltransduction-simulation, knowledge representation, Protege-2000, multiagent-based modeling, object oriented programming concepts, JAVA. 
  • Current position: Guest at the MDC Bioinformatics group under Prof. Jens Reich.
  • Other interests:  I´ve fiddled around with Google Maps a bit and have checked an area near Hoisdorf/Hamburg for potential archaeological landmarks (big PDF).
  • Check the MATRIX.
  • This is what I am going to do when I`ve finished my Ph.D. ... and sure I`ll take my brother with me.
  • A little lesson on working morality. All these funny flash movies were created by the famous Evilzug!
    [MDC-Bioinformatics Page]
    Last updated on November, 2005
    E-Mail: schober-at-mdc-berlin.de (where "-at-" == "@")