Friday, May 3, 2013

Trendy and inspirational: the suffixes -ome and -omics

In the beginning there was the word genome for the complete set of genetic material present in a cell or organism. The German botanist Hans Winkler came up with this term in 1920 [1]. It is a portmanteau blending the words gene and chromosome. An Oxford Dictionary of 2002 further tells us that [2]:

a  couple of terms have been formed on its model [the portmanteau genome]: proteome, the complete set of proteins produced from the instructions coded in a cell's genetic material, and metabolome (from metabolism), the complete set of metabolic processes within a cell. These seem to have been created partly by blending and partly by analogy with the older sense of the ending.

The older sense of -ome is the meaning of having a specified nature; for example, rhizome for the subterranean roots and shoots of a plant [2].

Now, ten years later, there are hundreds or even thousands of words derived by following the nomenclatural model creating the established terms genome, proteome and metabolome. The word transcriptome refers to the set of RNA molecules expressed from the genome. Emerging terms include variome for the set of genetic variation across a population of a species, epigenome for the set of chemical compounds involved in not-DNA-encoded gene expression, interactome for the set of molecular interactions in a biological system such as a cell, and fluxome for the set of small molecules changing along metabolic pathways in a dynamic system (due to flux responses resulting from both genetic and metabolic regulation). Terms you certainly will find more often in future publications include phenome for the set of physical descriptions that can ideally be related to genotype, regulome for the set of regulatory compounds in a cell, integrome for unions of 'omics data sets, omnisciome for the entirety of knowledge about a cell, organism or system, toxome for the set of cellular processes responsive to small molecules and involved in their toxicological activities, and lipidome for the set of all fatty molecules in an organism [3].

The name of a scientific field associated with an ome-ending word is typically built by replacing the suffix -ome with -omics. Genomics, proteomics, and metabolomics are well known examples. Transcriptomics, variomics, epigenomics, interactomics, fluxomics, phenomics, regulomics, integromics and lipidomics are emerging names and disciplines of scientific study. Omnisciomics and toxomics may follow. Data and knowledge within these fields have not all been derived from recent studies, some insight has been accumulated over decades. But recent advances, driven by modern analytical devices and high-throughput technology, are accelerating application and impact of these fields. Dedicated to the integration of  'omics domains is a peer-reviewed journal with the name OMICS [4].

And then there is the ending -etics, as in genetics. The distinction between 'omics and 'etics may seem confusing for outsiders. Let's conclude this with the description of the fine line between epigenomics and epigenitcs [5]: “Epigenetics focuses on processes that regulate how and when certain genes are turned on and turned off, while epigenomics pertains to analysis of epigenetic changes across many genes in a cell or entire organism.”

Keywords: biochemistry, linguistics, nomenclature, terminology, meta-data, integrative research.

References and more to explore
[1] Where the Word 'Genome' Came From [].
[2] Michael Quinion: Ologies and Ismas. A Dictionary of Word Beginnings and Endings. Oxford University Press, Oxford and New York, 2002..
[3] Monya Baker: The 'omes puzzle. Nature February 28, 2013, 494, pp.416-419. doi: 10.1038/494416a
[4] OMICS: A Journal of Integrative Biology [].
[5] National Cancer Institute: Epigenomics and Epigenetics Research [].

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