Appendix:Suffixes -ome and -omics

See also: -nomics

The English-language neologism omics informally refers to a field of study in biology ending in -omics, such as genomics or proteomics. The related neologism omes addresses the objects of study of such fields, such as the genome or proteome respectively.

The suffix -ome- as used in molecular biology refers to a totality of some sort; it is an example of a "neo-suffix" formed by abstraction from various Greek terms in -ωμα (-ōma), a sequence that does not form an identifiable suffix in Greek.

Origin

The Oxford English Dictionary (OED) distinguishes three different fields of application for the -ome- suffix:

1. in medicine, forming nouns with the sense "swelling, tumour"
2. in botany or zoology, forming nouns in the sense "a part of an animal or plant with a specified structure"
3. in cellular and molecular biology, forming nouns with the sense "all constituents considered collectively".

The -ome- suffix originates as a variant of -oma-, and became productive in the last quarter of the 19th century. It was originally found in terms like carcinome, sclerome, rhizome. All of these are terms are derived from Greek words in -ωμα (-ōma), a sequence that is not a single suffix, but analyzable as -ω-μα (-ō-ma), the -ω- (-ō-) belonging to the word stem, usually a verb, and the -μα (-ma) being a genuine Greek suffix forming abstract nouns.

OED suggests that suffix -ome- in sense 3. originated as a back-formation from mitome, later also reinforced by chromosome. Early attestations include biome (1916) and genome (first coined as German Genom in 1920).

The association with chromosome in molecular biology is by false etymology. The word chromosome derives from the Greek stems χρωμ(ατ)- (khrōm(at)-) "colour" and σωμ(ατ)- (sōm(at)-) "body".. While σωμα (sōma) "body" genuinely contains the -μα (-ma) suffix, the preceding -ω- (-ō-) is not a stem-forming suffix but part of the word's root. Because genome refers to the complete genetic makeup of an organism, a neo-suffix -ome- suggested itself as referring to "wholeness" or "completion".

Bioinformaticians and molecular biologists figured amongst the first scientists to start to apply the "-ome" suffix widely. Some early advocates were bioinformaticians in Cambridge, UK, where there were many early bioinformatics labs such as the MRC centre, w:Sanger centre, and EBI (w:European Bioinformatics Institute). For example, the w:MRC centre is where the first genome and proteome projects were carried out.

Current usage

Many “omes” beyond the original “genome” have become useful and have been widely adopted by research scientists. “Proteomics” has become well-established as a term for studying proteins at a large scale. "Omes" can provide an easy short-hand to encapsulate a field; for example, an interactomics study is clearly recognisable as relating to large-scale analyses of gene-gene, protein-protein, or protein-ligand interactions. Researchers are rapidly taking up omes and omics, as shown by the explosion of the use of these terms in w:PubMed since the mid '90s.

List of "omes"

Established usage

• The transcriptome, the mRNA complement of an entire organism, tissue type, or cell; with its associated field transcriptomics^[2]
• The proteome, the protein complement of an entire organism, tissue type, or cell; with its associated field proteomics^[3]
• The metabolome, the totality of metabolites in an organism; with its associated field metabolomics^[4]
• The metallome, the totality of metal and metalloid species; with its associated field metallomics
• The lipidome, the totality of lipids; with its associated field lipidomics ^[5]
• The glycome, the totality of glycans, carbohydrate structures of an organism, a cell or tissue type; with its associated field glycomics
• The interactome, the totality of the molecular interactions in an organism^[6]; a once proposed field of interactomics^[7] has generally become known as systems biology
• The spliceome (see spliceosome), the totality of the alternative splicing protein isoforms;^[8] with its associated field spliceomics.
• The ORFeome refers to the totality of DNA sequences that begin with the initiation codon ATG, end with a nonsense codon, and contain no stop codon. Such sequences may therefore encode part or all of a protein.^[9][10]
• The speechome. (BBC article on the Speechome Project)
• The mechanome refers to the force and mechanical systems at work within an organism.
• The phenome - the organism itself. The phenome is to the phenotype what the genome is to the gene. The phenome can also be the complete list of phenotypic mutants available for a species.
• The exposome - the collection of an individual's environmental exposures.

Nonce coinages

• ubiquitome: The complement of ubiquitin conjugated proteins within the proteome.
• receptorome: The portion of the genome encoding receptors
• kinome: The totality of protein kinases in a cell. Kinomics: The study of the kinome.
• physiome: Related to physiology. Physiomics: The associated field of study.
• neurome: The complete neural makeup of an organism. A word which a neurobiologist might utter in the future. Neuromics: The study of the neurome. ([11])
  • Note: Neurome^[12] and Neuromics^[13] are also the names of Biotech companies. The term 'Neurome' has been used by NeuronBank.org^[14], which is an attempt to develop an approach to catalog the Neurome.
• cytome: The cellular composition of a tissue. This term is associated to cell sorting techniques.
• predictome: A complete set of predictions.^[15]
• reactome: A knowledge base of biological processes.^[16]
• connectome: The connections between neurons. A Technicolour Approach to the Connectome (Nature)
• translatomics: Analysis of actively transcribed mRNA molecules. ^[17]
• transferome: the complete set of genes within a genome that were acquired through horizontal gene transfer

Unrelated words in -omics

See also: -nomics

The word “comic” does not use the "omics" suffix; it derives from Greek “κωμ(ο)-” (merriment) + “-ικ(ο)-” (an adjectival suffix), rather than presenting a truncation of “σωμ(ατ)-”.

Similarly, the word “economy” is assembled from Greek “οικ(ο)-” (household) + “νομ(ο)-” (law or custom), and “economic(s)” from “οικ(ο)-” + “νομ(ο)-” + “-ικ(ο)-”. The suffix -omics is sometimes used to create portmanteau words to refer to schools of economics such as Reaganomics.

External links

• Omics.org — The omics wiki site. A comprehensive omics list on the internet.
• List of omics — Lists far more than this page, with references/origins. Maintained by the (CHI) Cambridge Health Institute. One of the earliest lists.
• Omics World — Resources and information for omics research
• Lederberg J, McCray A. 'Ome Sweet 'Omics — A Genealogical Treasury of Words PDF (2 pages). w:The Scientist 15[7]:8, Apr. 2, 2001. Commentary.