-omics

The English-language neologism omics informally refers to a field of study in biology ending in the suffix "-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. Users of the suffix “"-om-"” frequently take it as referring to "totality" of some sort.

Origin

The suffix “"-om-"” originated as a "back-formation" from “genome”, a word formed in analogy with “chromosome”.Coleridge, H.; "et alii". "The Oxford English Dictionary"] The word “chromosome” comes from the Greek stems “χρωμ(ατ)-” ("colour") and “σωμ(ατ)-” ("body").. Because “genome” refers to the "complete" genetic makeup of an organism, some people have made the inference that there exists some root, *“"-ome-"”, of Greek origin referring to "wholeness" or to "completion", but such root is unknown to most or all scholars.Liddell,, H.G.; Scott, R.; "et alii". "A Greek-English Lexicon" [1996] . ( [http://www.perseus.tufts.edu/cgi-bin/resolveform?lang=greek Search at Perseus Project.] )] .

Because of the success of large-scale genome sequencing, the suffix "-om-" has been picked up by a wide array of other large-scale quantitative biology fields.

Early adopters of "omes"

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, Sanger centre, and EBI (European Bioinformatics Institute). For example, the MRC centre is where the first genome and proteome projects were carried out.

Acceptance

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 PubMed since the mid '90s [ [http://bioinfo.mbb.yale.edu/what-is-it/omes/omes.html Omes Table, Gerstein Lab] ] .

Established "omes"

* The "transcriptome", the mRNA complement of an entire organism, tissue type, or cell; with its associated field "transcriptomics" ^{[http://www.affymetrix.com/transcriptome/index.affx]}
* The "metabolome", the totality of metabolites in an organism; with its associated field "metabolomics" ^{[http://www.metabolomicssociety.org/about.html]}
* 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" ^{[http://doi.wiley.com/10.1002/ejlt.200390101]}
* 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 ^{[http://www.the-scientist.com/article/display/14769/]} "; a once proposed field of interactomics" ^{[http://interactomics.org/]} has generally become known as systems biology
* The "spliceome" (see spliceosome), the totality of the alternative splicing protein isoforms; ^{[http://publications.nigms.nih.gov/genetics/glossary/spliceosome.html]} 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. ^{[http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-O/open_reading_frame.html] [http://www.medterms.com/script/main/art.asp?articlekey=4644]}
* The "speechome". ( [http://news.bbc.co.uk/2/hi/science/nature/4987880.stm 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.cite journal |author=Wild CP |title=Complementing the genome with an "exposome": the outstanding challenge of environmental exposure measurement in molecular epidemiology |journal=Cancer Epidemiol. Biomarkers Prev. |volume=14 |issue=8 |pages=1847–50 |year=2005 |pmid=16103423 |doi=10.1158/1055-9965.EPI-05-0456]

Newer "omics" and "omes"

* "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.
** Note: Neurome ^{[http://Neurome.com]} and Neuromics ^{[http://neuromics.com]} are now the names of Biotech companies. The term 'Neurome' has been used by NeuronBank.org ^{[http://NeuronBank.org]} , 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. ^{[http://predictome.bu.edu/]}
* "Reactome": A knowledge base of biological processes. ^{[http://www.reactome.org/]}
*"Connectome": The connections between neurons. [http://www.nature.com/nrn/journal/vaop/ncurrent/abs/nrn2391.html A Technicolour Approach to the Connectome (Nature)]

Unrelated "-omics"

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.

References

See also

* -ome
* List of omics topics in biology

External links

* [http://omics.org Omics.org] — The omics wiki site. A comprehensive omics list on the internet.
* [http://www.genomicglossaries.com/content/omes.asp List of omics] — Lists far more than this page, with references/origins. Maintained by the (CHI) Cambridge Health Institute. One of the earliest lists.
* [http://www.omicsworld.com/ Omics World] — Resources and information for omics research
* Lederberg J, McCray A. [http://lhncbc.nlm.nih.gov/lhc/docs/published/2001/pub2001047.pdf 'Ome Sweet 'Omics — A Genealogical Treasury of Words] PDF (2 pages). The Scientist 15 [7] :8, Apr. 2, 2001. Commentary.