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Knowledge Representation and Ontology: Semantic Web for Sciences

In this lecture we provide first insights into diverse ontological knowledge representation formalisms of different semantic expressivity. The most prominent applications of ontologies will be introduced via examples from the biomedical domain. Specificly we will briefly tackle the following topics:

  • Roots of the term ‘Ontology’
  • Basic compounds of ontologies
  • Ontology Editors (Protégé)
  • Ontological semantics
    • The semantic continuum (of increasing expressivity) in examples
    • Terminologies (SNOMED)
    • Controlled Vocabularies (MSI Standards)
    • Thesauri (UMLS)
    • Ontologies (GO, FMA, UMLS Metathesaurus)
    • Ontologies in description logics (DCO, OBI)
  • Ontological Syntax
    • 'Semantic Web Stack’
    • Owl, Obo,
  • Classes vs. Instances
  • Reference terminologies and the metaterminological blur
  • Top level Ontologies (BioTop, DOLCE, SUMO, BFO, ro, …)
  • Ontology engineering methods
  • Ontology metadata formats (Dublin Core, Skos, …)
  • Ontologie-Portals and libraries (NCBO BioPortal, OBO-Foundry, OLS)
  • Ontology visualisations (Graph-based, text-based)
  • Ontological querying with SPARQL
  • Applications and examples
    • Ontological data annotation: Semantic Web
    • Format exchange syntax
    • Decision Support
    • Reasoning models (Logic-based, rule-based and probablistic reasoning)
    • Simulations
    • Minimal Journal Reporting Requirements (e.g. MIBBI - Minimum Information for Biological and Biomedical Investigations)


  • Berners-Lee, Tim, Hendler, James, and Lassila Ora, “The Semantic Web”, Scientific American Magazine, 2008
  • Noy NF, McGuinness DL, “Ontology Development 101: A Guide to Creating Your First Ontology”, 2001, Technical Report,
  • Sematic Web Consortium, "Semantic web best practices and deployment group, Ontology Engineering and Patterns Task Force", 2008, from
  • Cote, R. G., P. Jones, et al. "The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.", 2008, Nucleic Acids Res 36 Web Server issue): W372-6.
  • Harris, M. A. "Developing an ontology." 2008, Methods Mol Biol 452: 111-24.
  • Schober, D., B. Smith, et al. "Naming Conventions for OBO Foundry Ontology engineering", 2009, BMC Bioinformatics 10(125).