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.
An erratum to this chapter can be found at http://dx.doi.org/10.1007/11915034_125.