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.