List of omics topics in biology

Inspired by the terms genome and genomics, other words to describe complete biological datasets, mostly sets of biomolecules originating from one organism, have been coined with the suffix -ome and -omics. Some of these terms are related to each other in a hierarchical fashion. For example, the genome contains the ORFeome, which gives rise to the transcriptome, which is translated to the proteome. Other terms are overlapping and refer to the structure and/or function of a subset of proteins (e.g. glycome, kinome).

An omicist is a scientist who studies omeomics, cataloging all the “omics” subfields.^[1]

Omics.org is a Wiki that collects and alphabetically lists all the known "omes" and "omics."^[2]

List of topics

-ome	Field of study (-omics)	Collection of	Parent subject	Notes
Acetylome	Acetylomics^[3]	complete set of proteins and their corresponding lysine residues that undergo acetylation	Molecular Biology
Allergenome	Allergenomics^[4]	Proteomics of allergens	Genetics
Antibodyome	Antibodyomics	The complete set of antibodies present in an organism	Immunology
Archaeome	Archaeomics	The collective genetic material of microorganisms in archaeological samples	Microbiology
Bacteriome	Bacteriomics	Community of bacteria associated with a particular ecological niche or host organism	Microbiology
Bibliome	Bibliomics	Scientific bibliographic data
Biointeractome	Biointeractomics	The complete set of molecular interactions within a biological system	Molecular Biology
Biome		The whole set of ecological community of organisms and environments	Ecology
Cellome	Cellomics		Cellular Biology
Connectome	Connectomics	Structural and functional brain connectivity at different spatiotemporal scales	Neuroscience
Cytome	Cytomics	Cellular systems of an organism	Cytology
Editome		RNA editing sites
Embryome	Embryomics	Cell lineages of embryonic cells, genes expressed and antigens present during development	Embryology
Envirome	Enviromics	Gene related environment factors (envirome)
Environmental DNA	Environmental omics	Sequencing of ambient DNA
Epigenome	Epigenomics	Epigenetic modifications	Molecular genetics	Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, collectively known as the epigenome
Exposome (2005)	Exposomics	An individual's environmental exposures, including in the prenatal environment	Molecular genetics	A proposed term and field of study of the disease-causing effects of environmental factors (the "nurture" component of "nature vs. nurture").^[5]
Exposome (2009)		Composite occupational exposures and occupational health problems	Occupational safety and health	The proposers of this term were aware of the previous term as used above but proposed to apply the term to a new field.^[6]^[7]
Exome	Exomics	Exons in a genome	Molecular Genetics
Foodome	Foodomics	Food and Nutrition issues related to bioactivity, quality, safety and traceability of foods through the application and integration of advanced omics technologies to improve consumer's well-being, health, and confidence.	Nutrition	The term was first defined in 2009^[8]
Genome	Genomics (Classical genetics)	Genes (DNA sequences/Chromosomes)	Genetics	"Genome" refers to the set of all genes in an organism. However, "genome" was coined decades before it was discovered that most DNA is "non-coding" and not part of a gene; thus, "genome" originally referred to the entire collection of DNA within an organism. Today, both definitions are used, depending on the context.^[9]
Glycome	Glycomics	Glycans	Glycobiology
Hologenome	Hologenomics	Genomes of community members (i.e., holobionts)	Metagenomics
Humeome	Humeomics	The chemical components of soil humus	Soil science
Interferome	Interferomics	Interferons	Immunology	Also a database of the same name.^[10]
Interactome	Interactomics	All interactions		The term "interactomics" is generally not used. Instead, interactomes are considered the study of systems biology.^[11]^[12]
Ionome	Ionomics	Inorganic biomolecules	Molecular Biology
Kinome	Kinomics	Kinases	Molecular Biology	Proteins that add a phosphate group
Lipidome	Lipidomics^[13]	Lipids	Biochemistry
Mechanome	Mechanomics	The mechanical systems within an organism
Metabolome	Metabolomics	Metabolites		All products of a biological reaction (including intermediates)
Metagenome	Metagenomics	Genetic material found in an environmental sample	Molecular Biology	The genetic material is assumed to contain DNA from multiple organisms and therefore multiple genomes, hence the inclusion of the prefix meta-.
Metallome	Metallomics	Metals and metalloids
Microbiome	microbiomics	Collection of microorganisms in another organism such as an animal	Microbiology
Obesidome	Obesidomics	Obesity related proteins	Proteomics	Coined by Pardo et al., 2012.^[14]
ORFeome	ORFeomics	Open reading frames (ORFs)	Molecular Genetics
Organome	Organomics	Organ interactions	Cellular Signalling / Cell Signaling and Tissue Engineering	The study of crosstalk between organs using physiologically relevant in-vitro models
Parvome	Parvomics	Secondary metabolites	Biochemistry	Coined by Mark Martin and introduced by Julian Davies in 2008, referring to the Latin parvus for "small", and describing the "humungous microbial world of small (secreted) molecules of great structural diversity".^[15] See also ^[16]
Pharmacogenetics	Pharmacogenetics	SNPs and their effect on pharmacokinetics and pharmacodynamics	Pharmacogenomics Genomics
Pharmacogenome	Pharmacogenomics	The effect of changes on the genome on pharmacology	Pharmacogenetics Genomics
Phenome	Phenomics	Phenotypes	Genetics
Physiome	Physiomics	Physiology of an organism
Phytochemome	Phytochemomics	Phytochemicals		The term has been coined by del Castillo et al., 2013, Food Research International, [1]. Phytochemomics is a comprehensive concept aimed to increase the knowledge of phytochemicals' bioactivity which is of growing importance in agricultural, food, medicine and cosmetic sciences
Proteome	Proteomics	Proteins	Molecular Biology
Regulome	Regulomics	Transcription factors and other molecules involved in the regulation of gene expression	Molecular Biology
Researchsome		Research areas covered by an individual researcher or institution	Research	Coined by Ivan Erill at the 2011 EBM meeting^[17]
Secretome	Secretomics	Secreted proteins	Proteomics	Subset of the proteome consisting of proteins actively exported from cells.^[18]
Speechome	Speecheomics	Influences on language acquisition		Coined by the Human Speechome Project^[19]
Synthetome		A set of artificial genes in an organism	^[20]^[circular reference]
Transcriptome	Transcriptomics	All RNA molecules including mRNA, rRNA, tRNA and other ncRNAs	Molecular Biology
Trialome	Medicine	Human interventional trials data from clinical trial registries extended with trial results and links to resulting publications
Toponome	Toponomics	Cell and tissue structure	Molecular Biology
Virome	Viromics	complete set of viruses	Virology
Volatilome	Volatilomics	complete collection of volatile metabolites	Biomarkers

Hierarchy of topics

For the sake of clarity, some topics are listed more than once.

• Bibliome
• Connectome
• Cytome
• Editome
• Embryome
• Epigenome
  • Methylome^[21]
• Exposome
  • Envirome^[22]
    • Toxome^[23]
  • Foodome
  • Microbiome
  • Sociome
• Genome
  • Variome
  • Exome
    • ORFeome
      • Transcriptome
        • Proteome
          • Kinome
          • Secretome
          • Chaperome
          • Allergenome
  • Pharmacogenome
  • Regulome
• Hologenome
• Interactome
• Interferome
• Ionome
• Fluxome
• Membranome
• Metagenome
• Metallome
• Microbiome
• Moleculome
  • Glycome
  • Ionome
  • Lipidome
  • Metabolome
    • Volatilome
  • Metallome
  • Proteome
    • Acetylome
• Obesidome
• Organome
• Phenome
• Physiome
  • Connectome
    • Synaptome^[24]
  • Dynome^[25]
  • Mechanome
• Regulome
• Researchsome
• Toponome
• Trialome
• Antibodyome^[26]

References

1. Yadav SP. (2007). "The Wholeness in Suffix -omics, -omes, and the Word Om". J Biomol Tech. 18 (5): 277. PMC 2392988. PMID 18166670.
2. "Error 403(Invalid User)".
3. Wen, Siqi; Li, Jiajia; Yang, Jingru; Li, Biao; Li, Na; Zhan, Xianquan (2021). "Quantitative Acetylomics Revealed Acetylation-Mediated Molecular Pathway Network Changes in Human Nonfunctional Pituitary Neuroendocrine Tumors". Frontiers in Endocrinology. 12. doi:10.3389/fendo.2021.753606. ISSN 1664-2392. PMC 8546192.
4. Yagami T, Haishima Y, Tsuchiya T, Tomitaka-Yagami A, Kano H, Matsunaga K.; Haishima; Tsuchiya; Tomitaka-Yagami; Kano; Matsunaga (2004). "Proteomic analysis of putative latex allergens". Int Arch Allergy Immunol. 135 (1): 3–11. doi:10.1159/000080036. PMID 15286439. S2CID 35112557.{{cite journal}}: CS1 maint: multiple names: authors list (link)
5. Wild CP (2005). "Complementing the genome with an "exposome": the outstanding challenge of environmental exposure measurement in molecular epidemiology". Cancer Epidemiol. Biomarkers Prev. 14 (8): 1847–50. doi:10.1158/1055-9965.EPI-05-0456. PMID 16103423.
6. Faisandier, Laurie; De Gaudemaris, Régis; Bicout, Dominique J. (2009). "Occupational Health Problem Network : the Exposome". arXiv:0907.3410 [stat.ME].
7. Faisandier, Laurie; Bonneterre, Vincent; De Gaudemaris, Régis; Bicout, Dominique J. (2009). "A network-based approach for surveillance of occupational health exposures". arXiv:0907.3355 [stat.ME].
8. Cifuentes, A. (2009). "Food analysis and Foodomics". Journal of Chromatography A. 1216 (43): 7109. doi:10.1016/j.chroma.2009.09.018. hdl:10261/154212. PMID 19765718.
9. "genome, n". Oxford English Dictionary. March 2008.^{[dead link]}
10. "Home". interferome.org.
11. . www.the-scientist.com. Archived from the original on December 2, 2008.
12. Main Page – Interactomics July 6, 2008, at the Wayback Machine
13. Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, Cotter D, Dinasarapu AR, Maurya MR (2011). "Bioinformatics and Systems Biology of the Lipidome". Chemical Reviews. 111 (10): 6452–6490. doi:10.1021/cr200295k. PMC 3383319. PMID 21939287.
14. Pardo, Maria; Roca-Rivada, Arturo; Seoane, Luisa Maria; Casanueva, Felipe F. (2012). "Obesidomics: Contribution of adipose tissue secretome analysis to obesity research". Endocrine. 41 (3): 374–383. doi:10.1007/s12020-012-9617-z. PMID 22434412. S2CID 20503653.
15. Schaechter M (2014-05-15). "Of Terms in Biology: The Parvome". Small Things Considered. Retrieved 2020-04-21.
16. Davies J, Ryan KS (2012). "Introducing the parvome: bioactive compounds in the microbial world". ACS Chemical Biology. 7 (2): 252–259. doi:10.1021/cb200337h. PMID 22074935.
17. (2011) "15th EBM PROGRAM" 2016-01-26 at the Wayback Machine Evolutionary Biology Meeting at Marseilles. Retrieved December 14, 2011.
18. Dov Greenbaum; Nicholas M. Luscombe; Ronald Jansen; et al. (2001). "Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function". Genome Research. 11 (9): 1463–1468. doi:10.1101/gr.207401. PMID 11544189.
19. BBC article on the Speechome Project
20. Synthetome
21. Carlson, Scott M.; Gozani, Or (2014-10-09). "Emerging technologies to map the protein methylome". Journal of Molecular Biology. 426 (20): 3350–3362. doi:10.1016/j.jmb.2014.04.024. ISSN 1089-8638. PMC 4177301. PMID 24805349.
22. Huser, V.; Cimino, J. J. (2012). "Precision and Negative Predictive Value of Links between ClinicalTrials.gov and PubMed". AMIA Annual Symposium Proceedings. 2012: 400–408. PMC 3540528. PMID 23304310.
23. Bouhifd, Mounir; Andersen, Melvin E.; Baghdikian, Christina; Boekelheide, Kim; Crofton, Kevin M.; Fornace, Albert J.; Kleensang, Andre; Li, Henghong; Livi, Carolina (2015-01-01). "The human toxome project". ALTEX. 32 (2): 112–124. doi:10.14573/altex.1502091. ISSN 1868-596X. PMC 4778566. PMID 25742299.
24. DeFelipe, Javier (2010-11-26). "From the Connectome to the Synaptome: An Epic Love Story". Science. 330 (6008): 1198–1201. Bibcode:2010Sci...330.1198D. doi:10.1126/science.1193378. ISSN 0036-8075. PMID 21109663. S2CID 33348231.
25. Kopell, Nancy J.; Gritton, Howard J.; Whittington, Miles A.; Kramer, Mark A. (2014-09-17). "Beyond the connectome: the dynome". Neuron. 83 (6): 1319–1328. doi:10.1016/j.neuron.2014.08.016. ISSN 1097-4199. PMC 4169213. PMID 25233314.
26. Dimitrov, DS (May–Jun 2010). "Therapeutic antibodies, vaccines and antibodyomes". mAbs. 2 (3): 347–56. doi:10.4161/mabs.2.3.11779. PMC 2881260. PMID 20400863.