A Proposal for a Gene Functions Wiki

  • Robert Hoehndorf
  • Kay Prüfer
  • Michael Backhaus
  • Heinrich Herre
  • Janet Kelso
  • Frank Loebe
  • Johann Visagie
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4277)


Large knowledge bases integrating different domains can provide a foundation for new applications in biology such as data mining or automated reasoning. The traditional approach to the construction of such knowledge bases is manual and therefore extremely time consuming. The ubiquity of the internet now makes large-scale community collaboration for the construction of knowledge bases, such as the successful online encyclopedia “Wikipedia”, possible.

We propose an extension of this model to the collaborative annotation of molecular data. We argue that a semantic wiki provides the functionality required for this project since this can capitalize on the existing representations in biological ontologies. We discuss the use of a different relationship model than the one provided by RDF and OWL to represent the semantic data. We argue that this leads to a more intuitive and correct way to enter semantic content in the wiki. Furthermore, we show how formal ontologies could be used to increase the usability of the software through type-checking and automatic reasoning.


Gene Ontology Semantic Relation Semantic Content Description Logic Biomedical Ontology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Robert Hoehndorf
    • 1
    • 2
    • 3
  • Kay Prüfer
    • 2
  • Michael Backhaus
    • 1
    • 2
  • Heinrich Herre
    • 1
    • 3
  • Janet Kelso
    • 2
  • Frank Loebe
    • 1
    • 3
  • Johann Visagie
    • 2
  1. 1.Research Group Ontologies in Medicine, Institute for Medical Informatics, Statistics and EpidemiologyUniversity of Leipzig 
  2. 2.Department of Evolutionary GeneticsMax-Planck-Institute for Evolutionary Anthropology 
  3. 3.Institute for InformaticsUniversity of Leipzig 

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