We have chosen to construct a network of connections between genes based on how strongly they are coupled in the literature, rather than whether there is extractable information supporting a physical interaction between them. There are two advantages to this approach. First, relevant connections between proteins may be non-physical. For example, genes that are involved in the same complex disease may not directly interact, or even be in the same local pathway, but may never-the-less interact in terms of affecting disease susceptibility. Second, the text mining procedure will capture considerably more information than is currently in any database, or that can be easily formalized in a simple cause and effect pathway description. In this sense, the KnowledgeNet expands on existing pathways descriptions by linking genes with conceptual relationships.
