Motivation: The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development and tumourigenesis. However, methods for translating these high-level hallmarks concepts into data level-links between individual genes and individual cancer hallmarks varies widely between studies. When we examine different strategies for linking and mapping cancer hallmarks in detail, we see significant differences, but also consensus.
Results: Here we compare hallmark mapping schemes from multiple studies and explore the consensus knowledge from these different approaches, in order to help us better understand the core biological processes and pathways that are associated with the hallmarks of cancer. We also explore the differences between mapping schemes and identify which differences represent changes in our understanding of cancer, changes in our understanding of biological processes in the non-disease state, or the accumulation of more experimental evidence over time.
Conclusions: Mapping strategies rely on intermediate knowledge resources, such as biological pathway databases like KEGG or the Gene Ontology. The structure and annotations of these intermediate resources also change over time. The results of this study therefore highlight the challenges of integrating accumulated, distributed and changing biological knowledge in bioinformatics.