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Genomics categories & taxonomy
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions? 
Mary Chitty MSLS mchitty@healthtech.com
Last revised January 09, 2020

agricultural genomics: Agricultural biotechnology continues to benefit from the insights being developed during the era of the Human Genome Project. The proliferation of mapping, genotyping, and diagnostic methodologies has rapidly expanded the analytical tools available to crop scientists for the analysis and utilization of plant genomes.  Related terms: crop genomics, environmental genomics, food genomics, nutritional genomics, plant genomics; Model & other organisms glossary Arabidopsis

Agricultural genomics links: 
AgBioTech Infonet, Ecologic, Inc. http://www.agbiotech.net/  Genetic engineering applications, impacts and implications. 
Biotechnology in Food and Agriculture, FAO, 2002 http://www.fao.org/biotech/doc.asp
FAO Glossary of Biotechnology for Food and Agriculture , Food and Agricultural Organization, http://www.fao.org/biotech/index_glossary.asp

applied genomics: Applications are at varying stages of development and include clinical genomics, pharmacogenomics, plant and animal breeding, drug discovery and development and microbial genomics. 

combinatorial genomics:  Similar in concept to required for recognition of all items in long- term memory combinatorial chemistry, this technology shuffles portions of genes to give a vast number of new combinations, which are then screened for a desired function. Enhanced function, or even new functions, can be generated by repeating the cycle circuits many times to "evolve" optimized recombinants in vitro. [Department of Defense Critical Technologies Part III: Developing Critical Technologies Section 3: Biological Technology, July 1999]   Related terms: Combinatorial libraries & synthesis glossary combinatorial chemistry; 

crop genomics: Molecular technologies, techniques and breeding strategies associated with plants of agricultural importance. Related terms: agricultural genomics, plant genomics, nutritional genomics

environmental genomics: This programme will apply genomics to the natural environment, using sequence data to advance and test evolutionary and ecological theory, and so provide a better understanding of ecosystem function in the context of biodiversity (intraspecific genetic variation, species richness and perceived redundancy).  Related terms: ecological genomics, plant genomics; Pharmacogenomics glossary toxicogenomics

forward genetics:  the approach of determining the genetic basis responsible for a phenotype. This was initially done by using naturally occurring mutations or inducing mutants with radiation, chemicals, or insertional mutagenesis  (e.g. transposable elements). Subsequent breeding takes place, mutant individuals are isolated, and then the gene is mapped. Forward genetics can be thought of as a counter to reverse genetics, which determines the function of a gene by analyzing the phenotypic effects of altered DNA sequences.[1]  Wikipedia accessed 2018 Nov   https://en.wikipedia.org/wiki/Forward_genetics  

The traditional approach to genetics, which starts with a phenotype and then identifies genetic mutations or variations that control or cause that trait.  Related term: positional cloning.  Compare reverse genetics 

forward genomics:  Given the advances in next-generation sequencing, a veritable zoo of genomic data from hundreds of animals have now been sequenced, allowing scientists unprecedented insights into how DNA changes may underlie the differences between species and the diversity of life on Earth. When viewed through the prism of evolution, these DNA changes either discard ancestral traits or gain entirely new ones, for example, in key senses like vision, speech and hearing. Now, in a new study, Prudent et al. (2016) have developed new computational approaches, called “Forward Genomics” which can hone in on key genomic locations amongst the millions of DNA changes that occurred between different species. Joseph Caspermeyer; New “Forward Genomics” Approach to Identify Keys to Loss of Vision in Blind Mammals, Molecular Biology and Evolution, Volume 33, Issue 8, 1 August 2016, Pages 2175,  https://doi.org/10.1093/molbev/msw136 https://academic.oup.com/mbe/article/33/8/2175/2579436   Narrower terms: Post-Transcriptional Gene Silencing PTGS, RNA silencing; Related term: epigenetics

genomics: The systematic study of the complete DNA sequences (GENOME) of organisms. [MeSH, 2001]  More under genomics: Genomics glossary  Basic genetics & genomics (tries to) answer the question of what the difference between genetics and genomics is. 

genome transplantation: As a step toward propagation of synthetic genomes, we completely replaced the genome of a bacterial cell with one from another species by transplanting a whole genome as naked DNA. Carole Lartigue ¹, John I. Glass ^1*, Nina Alperovich ¹, Rembert Pieper ¹, Prashanth P. Parmar ¹, Clyde A. Hutchison III ¹, Hamilton O. Smith ¹, J. Craig Venter , Genome Transplantation in Bacteria: Changing One Species to Another, Science Published Online June 28, 2007, Science DOI: 10.1126/science.1144622 

genomic library: Gene categories

high-throughput genomics:  Genomic studies are now approaching "industrial" speed and scale, thanks to advances in gene sequencing and the increasing availability of high- throughput methods for studying genes, the proteins they encode, and the pathways in which they are involved. Data can now be acquired on many genes at once, either sequentially or in parallel. It is also possible to expand the range of genomic effects being examined. The abundance of new data available means that more targets should now be identifiable, but the key to finding such new targets will be to use the right combination of technologies and have them ideally integrated. Related terms: Bioinformatics high throughput Drug discovery & development target validation. 

industrial genomics:  Genomics scaled up to industrial strength and throughput.  Related term: high throughput genomics

integrative genomics: According to PubMed, published research studies involving integrated analysis of multiple ‘omic data types have witnessed a nearly 10-fold increase over the past decade. The reasons for the surge in integrative genomics studies are both biological – fueled by an increasing understanding that the development and progression of complex diseases are due to the confluence of alterations in the genome, epigenome, transcriptome, proteome, etc. (and their complex interactions) – and logistical – while large-scale integrative ‘omic studies were once economically infeasible, the declining cost of high-throughput technologies for interrogating the ‘ome have opened the door for such studies to become a reality. Koestler DC, Jones MJ, Kobor MS. The era of integrative genomics: more data or better methods? Epigenomics. 2014;6(5):463-7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414242/

intergenomics: The bioinformatics competence center "Intergenomics" in Braunschweig has the scientific goal to develop bioinformatic tools for modeling of the interactivity of genome- driven bacterial infection processes in mammals and plants. Bioinformatics research and education in Germany. Dietmar Schomburg, Martin Vingron, In Silico Biology 2, 0015, 2002  http://www.bioinfo.de/isb/2002/02/0015/main.html 

metagenome: Historically, biotechnology has missed up to 99% of existing microbial resources by using traditional screening techniques. Strategies of directly cloning 'environmental DNA' comprising the genetic blueprints of entire microbial consortia (the so-called 'metagenome') provide molecular sequence space that along with ingenious in vitro evolution technologies will act synergistically to bring a maximum of available sequence- space into biocatalytic application. Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Lorenz P, Liebeton K, Niehaus F, Eck J. Curr Opin Biotechnol 2002 Dec;13(6): 572- 577    Related terms: microbiome

metagenomics: is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While  traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods.^[1] … The term "metagenomics" was first used by Jo Handelsman, Jon Clardy, Robert M. Goodman, Sean F. Brady, and others, and first appeared in publication in 1998.^[4]The term metagenome referenced the idea that a collection of genes sequenced from the environment could be analyzed in a way analogous to the study of a single genome. Recently, Kevin Chen and Lior Pachter (researchers at the University of California, Berkeley) defined metagenomics as "the application of modern genomics technique without the need for isolation and lab cultivation of individual species".^[5] Wikipedia http://en.wikipedia.org/wiki/Metagenomics    accessed Oct 19 2017

The committee will convene a workshop and other appropriate information gathering activities in order to define the scope of metagenomics, understand how it is being used now in various disciplines, the technical approaches being used by different groups, and how metagenomics may develop in the future. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet, Board on Life Sciences , National Academies Press, 2007 http://books.nap.edu/openbook.php?record_id=11902&page=151 

microbial genomics:  Genome, Microbial: The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA. MeSH Year introduced: 2014 Related term:  Omes & omics glossary microbiome

paleogenomics: The complete sequence of the human and other vertebrate and nonvertebrate genomes provide a wealth of information on the organization, relationships and evolution of the metazoans. … In the absence of fossil DNA, this knowledge will forever remain a yearning for dreamy molecular biologists. And yet, will not the power of deduction and reconstitution of information gained through man's sophisticated technologies one day recreate a "virtual" metazoan ancestor? D Birnbaum, F Coulier, MJ Pebusque, P Pontarotti "Paleogenomics": looking in the past to the future, J Exp Zool. 288(1): 21- 22, April 15, 2000 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10750049&query_hl=8

Large-scale sequencing of mammoth DNA. "We sequenced 28 million base pairs of DNA in a metagenomics approach using a woolly mammoth (Mammuthus primigenius) sample from Siberia … The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.^" Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA, Hendrik N. Poinar ^1*, Carsten Schwarz ², Ji Qi ³, Beth Shapiro ⁴, Ross D. E. MacPhee ⁵, Bernard Buigues ⁶, Alexei Tikhonov ⁷, Daniel Huson ⁸, Lynn P. Tomsho ³, Alexander Auch ³, Markus Rampp ⁹, Webb Miller ³, Stephan C. Schuster ^3* 

phage genomics: The Age of Genomics dawned only gradually for bacteriophages. It was 1977 when the genome of phage phi X174 was published and 1983 when the "large" genome of phage lambda hit the streets. More recently, the pace has quickened, so that we now have over 100 complete phage genomes and can expect thousands in a very few years. These sequences have been marvelously informative for the biology of the individual phages, but with the advent of high volume sequencing technology, the real excitement for phage biology is that it is now possible to analyze the sequences together and thereby address -- for the first time at whole genome resolution -- a set of fundamental biological questions related to populations. H. Brussow, RW Hendrix, Phage genomics: small is beautiful, Cell 108 (1) : 13- 16, Jan. 11, 2002    Related terms: Functional genomics glossary bacteriophage, phage, phage display?

quantitative genomics: An offshoot of quantitative genetics, includes QTL mapping, gene expression data analysis.  Related terms:  SNPs & Genetic variations; Model organisms

subtractive genomics: One of the recently adopted strategies is based on a subtractive genomics approach, in which the subtraction dataset between the host and pathogen genome provides information for a set of genes that are likely to be essential to the pathogen but absent in the host. This approach has been used successfully in recent times to identify essential genes in Pseudomonas aeruginosa. Anirban Dutta¹, Shashi Kr. Singh¹, Payel Ghosh¹, Runni Mukherjee¹, Sayak Mitter¹ and Debashis Bandyopadhyay^2, In silico identification of potential therapeutic targets in the human pathogen Helicobacter pylori, In Silico Biology 6, 0005 (2006); ©2006, Bioinformation Systems e.V. http://www.bioinfo.de/isb/2006/06/0005/main.html 

Genomics resources
DOE, Genome Glossary, Genome Science Program   http://doegenomestolife.org/glossary/index.shtml
FAO Glossary of Biotechnology for Food and Agriculture: Revised and augmented edition, Food and Agricultural Organization, https://www.amazon.com/Glossary-Biotechnology-Agriculture-Research-Technology/dp/9251046832 Not just for food or agriculture. 
NCBI, Commonly used Genome Terms  https://www.ncbi.nlm.nih.gov/projects/genome/glossary.shtml
NCBI Genomes and Maps https://www.ncbi.nlm.nih.gov/guide/genomes-maps/
NCBI Variations https://www.ncbi.nlm.nih.gov/guide/variation/
NHGRI (National Human Genome Research Institute), Glossary of Genetic Terms, 250+ definitions. Includes extended audio definitions. https://www.genome.gov/genetics-glossary

All about the Human Genome Project, NHGRI, NIH, US, 2005  http://www.genome.gov/10001772 
Human Genome Project Working Draft Univ. of California Santa Cruz, US, http://genome.ucsc.edu/
International Human Genome Sequencing Consortium special issue: Nature 409 (6822) 15 Feb., 2001  http://www.nature.com/genomics/human/papers/analysis.html 
Celera Genomics special issue: Science 291 (5507) Feb. 16, 2001

Genomics Conferences http://www.healthtech.com/conferences/upcoming.aspx?s=GENS

How to look for other unfamiliar  terms

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.