title: Toward a Taxonomy for Multi-Omics Science? Terminology Development for Whole Genome Study Approaches by Omics Technology and Hierarchy.
abstract: Omics is a form of high-throughput systems science. However, taxonomies for omics studies are limited, inviting us to rethink new ways in which we classify, prioritize, and rank various omics systems science studies. In this overarching context, the genome-wide study approaches have proliferated in number and popularity over the past decade. However, their hierarchy is not well organized and the development of attendant terminology is not controlled. In the present study, we searched the literature in PubMed and the Web of Science databases published from March 1999 to September 2016 using the keywords, including genome-wide, association, whole genome, transcriptome-wide, metabolome, epigenome, and phenome. We identified the whole genome study approaches and sorted them according to the omics technology types (genomics, proteomics, and so on) and hierarchy. Thirty-four studies from over 90 publications were sorted into 10 omics groups: DNA level, transcriptomics, proteomics, interactomics, metabolomics, epigenomics, miRNomics/ncRNomics, phenomics, environmental omics, and pharmacogenomics. We suggest here modifications of terminology for study approaches, which share the same acronyms such as EWAS for epigenome-wide association and environment-wide association studies, and MWAS for methylome-wide association and metabolome-wide association studies. Taken together, our study presented here provides the first systematic review and analyses of whole genome approaches and presents a baseline for further controlled terminology development, with a view to a new taxonomy for omics and multi-omics studies in the future. Finally, we call for greater dialogue and collaboration across diverse omics knowledge domains and applications, for example, across plants, animals, clinical medicine, and ecology.
authors.affiliation: Department of Animal Science, Biotechnical Faculty, University of Ljubljana , Domzale, Slovenia .
authors.forename: Nina
authors.initials: N
authors.lastname: Pirih
authors.affiliation: Department of Animal Science, Biotechnical Faculty, University of Ljubljana , Domzale, Slovenia .
authors.forename: Tanja
authors.initials: T
authors.lastname: Kunej
mesh_terms: D035843:Biomedical Research / Q000379:methods*; D057890:Epigenomics / Q000379:methods; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D055432:Metabolomics / Q000379:methods; D040901:Proteomics / Q000379:methods
keywords: environment; epigenome; genome-wide association study; interactions; metabolome; multi-omics; network; pathway; phenome; transcriptome; whole genome analysis