Pathway research defines or refines our understanding of interactions between molecules within and between cells, primarily to identify molecular targets for disease therapies. Pathways interact to form networks. Pathways and networks should be understood as a concrete series of chemical reactions, but as abstract probabilistic models of molecular behavior. The past decade has witnessed exceptional growth in research involving the study of biological pathways and corresponding growth in bioinformatics tools to support it. Evolving concepts in the field are not always understood consistently, increasing the risk of misinterpreted or lost research. It is therefore imperative to bioinformaticians that possible areas of confusion be identified and clarified.