An Updated Taxonomy and a Graphical Summary Tool for Optimal Classification and Comprehension of Omics Research

Omics : a Journal of Integrative Biology
Nina Pirih, Tanja Kunej

Abstract

The volume of publications and the type of research approaches used in omics system sciences are vast and continue to expand rapidly. This increased complexity and heterogeneity of omics data are challenging data extraction, sensemaking, analyses, knowledge translation, and interpretation. An extended and dynamic taxonomy for the classification and summary of omics studies are essential. We present an updated taxonomy for classification of omics research studies based on four criteria: (1) type and number of genomic loci in a research study, (2) number of species and biological samples, (3) the type of omics technology (e.g., genomics, transcriptomics, and proteomics) and omics technology application type (e.g., pharmacogenomics and nutrigenomics), and (4) phenotypes. In addition, we present a graphical summary approach that enables the researchers to define the main characteristics of their study in a single figure, and offers the readers to rapidly grasp the published study and omics data. We searched the PubMed and the Web of Science from 09/2002 to 02/2018, including research and review articles, and identified 90 scientific publications. We propose a call toward omics studies' standardization for reporting in scientific li...Continue Reading

References

Sep 20, 2002·BioTechniques·Mario F Fraga, Manel Esteller
Jan 17, 2003·Genome Research·Kelly A FrazerRoss C Hardison
Oct 19, 1957·Journal of the American Medical Association·A G MOTULSKY
Jul 9, 2004·Genome Biology·Xianghong Jasmine Zhou, Greg Gibson
Aug 12, 2005·Science in China. Series C, Life Sciences·Xiangqing SunYanda Li
Jan 1, 2008·Computational Biology and Chemistry·Donggen ZhouYuping Luo
Jul 17, 2008·Comparative and Functional Genomics·Karen Eilbeck, Suzanna E Lewis
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Aug 27, 2009·Bioinformatics·Kim-Anh Lê CaoSébastien Déjean
Dec 9, 2009·Methods : a Companion to Methods in Enzymology·Stefaan DerveauxJan Hellemans
Jul 22, 2010·The New England Journal of Medicine·Teri A Manolio
Aug 13, 2010·Journal of Proteome Research·Marc Chadeau-HyamMaria De Iorio
Nov 19, 2010·Nature Reviews. Genetics·Kai WangHakon Hakonarson
Sep 22, 2011·Wiley Interdisciplinary Reviews. RNA·Robert B Darnell
Jul 5, 2012·Human Genetics·Hugues AschardKristel Van Steen
Dec 4, 2012·Cancer Letters·Eun-Joon LeeHuidong Shi
May 10, 2013·BMC Genetics·Radhika PatnalaJyotsna Batra
Jul 3, 2013·Journal of Child Psychology and Psychiatry, and Allied Disciplines·Stacey J Winham, Joanna M Biernacka
Jul 9, 2013·Genome Biology and Evolution·Tatiana TatarinovaMatteo Pellegrini
Aug 14, 2013·Journal of Biomedical Semantics·Carissa A ParkJames M Reecy
Jan 16, 2014·BMC Bioinformatics·Hyunjung KangWankyu Kim
Jan 25, 2014·Omics : a Journal of Integrative Biology·Eugene KolkerGregory Yandl
May 6, 2014·Mitochondrion·Ozgur GuneyHikmet Hakan Aydin
Jun 24, 2014·Molecular Therapy : the Journal of the American Society of Gene Therapy·Marinee K ChuahThierry VandenDriessche
Jun 25, 2014·Neurobiology of Aging·Elena S GusarevaKristel Van Steen
Aug 29, 2014·BioMed Research International·Mengmeng Wu, Rui Jiang
Sep 25, 2014·Molecular Genetics and Genomics : MGG·Quanwei ZhangXingxu Zhao
Nov 26, 2014·Methods in Molecular Biology·James M Flanagan
Apr 16, 2015·Journal of Genomics·Minja ZorcTanja Kunej

❮ Previous
Next ❯

Citations

Aug 25, 2020·Omics : a Journal of Integrative Biology·Nicholas Ekow ThomfordCharles Awortwe
Feb 26, 2019·Frontiers in Pediatrics·Natalia Hernandez-PachecoCarlos Flores
Apr 3, 2019·Human Reproduction Update·Rivka KoedooderSam Schoenmakers
Jun 22, 2018·Omics : a Journal of Integrative Biology·Matija PecakTanja Kunej

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
immunoprecipitation

Software Mentioned

miRNomics
MultiOmics Analysis
GWEI
GWISS
Omics Discovery Index
Cytoscan HD
Iatromics

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.