Introduction to OWL-Ontologies and Protégé

This workshop gives an introduction to ontologies in the life sciences. It introduces the current standard ontologies for computational biology (e.g., GO, ChEBI) and computational neuroscience (e.g., NIFSTD, CNO). It furthermore introduces crucial guidelines for the development of own ontologies. On the second day, it explains in more detail the Web Ontology Language (OWL) format and how ontologies can be encoded using OWL. A software tool for the implementation of ontologies, Protégé, will be introduced in a hands-on session.

The workshop is targeted at researchers who seek an introduction to computational ontologies, their applications in the life sciences, and who like to get some background information on how these ontologies can be encoded and developed on the computer.

Participation is free of charge. Please register beforehand with Dagmar Waltemath (


THU 24th of January 2013  
9:00am – 10:30am Introduction to Ontologies in Computer Science
  (Dagmar Waltemath)
10:45am – 11:00am Requirements for Application in Computational Neuroscience
  (Lars Schwabe)
11:00am – 12:30pm Sample Ontologies in Bio-Medicine and Neuroscience
  (Dagmar Waltemath)
12:30pm – 2:00pm Lunch break
2:00pm – 2:15pm Official Opening of the German Node of the Web Intelligence Consortium
  (Lars Schwabe)
2:15 – 4 pm Guidelines for Ontology Design
  (Ludger Jansen & Johannes Röhl)
open end Discussion & finger food
FRI 25th of January 2013  
9:00am – 10:30 am Introduction to OWL & Protégé
  (Dagmar Waltemath)
10:45am – 12:15pm Practical Lecture: Building Ontologies in Protégé
  (Dagmar Waltemath)
  Please bring your own laptop with Protégé (preferably release 4.1) installed, if
12:15pm – 13:30pm Lunch break
open end Practical Lecture cont‘d
  (Lars Schwabe)


Dr. Dagmar Waltemath
Dagmar Waltemath leads the research group SEMS at the Department of Systems Biology and Bioinformatics, University of Rostock. Her research interests focus around the reusability of computational models of biological systems, and on the reproducible encoding of research results, in particular simulation results.

Prof. Dr. rer. nat. Lars Schwabe
Lars Schwabe works as a junior professor at the University of Rostock where he leads the Department for Adaptive and Regenerative Systems.


PD Dr. habil. Ludger Jansen
Ludger Jansen teaches philosophy at the University of Rostock. His research interests center around metaphysics and the philosophy of science, including applied ontology. His is editor, together with Barry Smith, of the first introduction to biomedical ontology in German, and principal investigator of the DFG-project "Good Ontology Design".

M.A. Johannes Röhl
Johannes Röhl works as a research staff at the Institute of Philosophy, University of Rostock. His research interest is on Formal Ontology and ontology design.