We will develop an ontology, OncoCL, to describe cancer cells that will provide a framework for consistent annotation of cancer-associated genetic and genomic data. OncoCL will capture the spatiotemporal properties of cancer cell changes and provide a framework for the representation of cancer development and progression. The existing Cell Ontology (CL) is a representation of normal in vivo and in vitro cell types from all f biology and includes cell lineage descriptions. However, the CL was not designed to capture the pathology of cancer cells and the molecular changes involved in tumorigenesis. OncoCL will fill this gap. The conceptual basis of our approach is that cancer cell genotypes derive from the succession of alterations as described by Hanahan and Weinberg: self-sufficiency in growth signals, insensitivity to antigrowth signals, evasion of apoptosis, limitless replicative potential sustained angiogenesis, tissue invasion and metastasis, as well as reprogramming of energy metabolism, evading immune destruction, genomic instability and mutation, and tumor-promoting inflammation. Project deliverables for the research proposed here include a preliminary OncoCL ontology that will allow the integration and analysis of genome-scale data that depend on cancer cell lineage, the relation to normal cells, and the temporal aspects of development from one cell type to another.
The results of this work will help provide a mechanism for the synthesis of complex, heterogeneous genome- scale data leading to a more cohesive representation of the cellular processes that lead to cancer, a leading cause of human mortality. OncoCL will provide the specific framework to capture the molecular data and facilitate the design of better and earlier diagnosis and treatment.