Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level

Abstract A principal aim of post-genomic biology is elucidating the structures, functions and biochemical properties of all gene products in a genome. However, to adequately comprehend such a large amount of information we need new descriptions of proteins that scale to the genomic level. In short, we need a unified ontology for proteomics. Much progress has been made towards this end, including a variety of approaches to systematic structural and functional classification and initial work towards developing standardized, unified descriptions for protein properties. In relation to function, there is a particularly great diversity of approaches, involving placing a protein in structured hierarchies or more-generalized networks and a recent approach based on circumscribing a protein’s function through systematic enumeration of molecular interactions.