History of Omics

From Omics.org

The History of Omics: as a generic name for various omics and a standalone biology disciplines.

 Jong Bhak

Korean Genomics Center (KOGIC), UNIST, Ulsan, South Korea



There are perhaps over a thousand omics fields in biology by 2016. Researchers are organizing the life science disciplines to be more efficient and easy to understand for the humans and computers. The main contribution of omics is to make humans work better with computers by generating well-defined systematic data types, databases, and data representations. Biology is the ultimate fusion of mathematics, physics, chemistry, mechanics, and informatics, and such a catergorization of subfields has produced a large number of offspring which have their own methodologies and knowledge domains. Here, I present the initiation, advancement, and propagation of ome and omics fields in the early 1990s and onwards. Omics has occurred a result of independent and distributed unconscious networking of biologists all over the world although there were key advocates as well as sceptics. 


In a broad philosophical perspective, the concept and origin of omics (and omes) is perhaps as long as human history. It is a natural knowledge cotegorization process as we see in chemistry, biology, physics, and mathematics which are orginally fused with various other knowledge seeking discipline. Broadly, the largest term can be philosophy. The term biology has been invented independently in history by several people while the most modern usesage was etablished by researchers in 1700s~1800s. They include Carl Linnaeus, Gottfried Reinhold Treviranus, and Jean-Baptistae Lamarck.


Logy versus Omics

Instead of using 'logy' which was probably used frequently to differentiate science fields from previous less scientific researches such as arts and religious studies by putting mathematical "logi" in the names. For example, physiology is not just a research field of collecting facts and knowledge, but is based on logical and scientific principles. While logy is a reductionist word, ome and omics are more organic and synthetive terms.

Darwinian logy and omics
Logy represents Darwinian objects and objects that select the objects. A dichotomic view of the universe. On the other hand, ome and omics apply systems theories to the problems regarding the problem domains as complex mutually interactive information systems that have to be understood by not only logics, but also with components' interactions and dynamics using computers. The involvement of computation or information processing is the most representative of omics revolution in biology, socialogy, physical sciences, mathematics and philosophy. Omics can be the last discipline of science that solves all the problems of the universe in terms of information processing. In omics paradigms, the universe and life are the research objects that are all derived from the primordial and ultimate starting point of information processing before the big bang of the universe. Therefore, omics is an attempt to understand the whole universe from biological principles. I.e., biological principles on Earth is perhaps the most filtered essence of the universe that tells us what the universe really is: information and its structures ramified from it.


The prime ome and omics: genome and genomics.

The omics fields in biology in modern world are also old. Perhaps the core of many biological omes is the genome. The word Genome was coined in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany, as a portmanteau of the words gene and chromosome.  The word genomics is said to be appeared in the 1980s and became widely used in the 1990s.

The term genomics is supposedly coined by Tom Roderick in a bar in 1986. The term proteomics is supposedly coined by a few people on the internet. There is, however, an accuracy problem in finding the first person who coined a term. This author's own experience shows that most term coinage claims are wrong. For example, after coining a term such as Absuromics and searching in Yahoo, Google, and Webcrawler to check who listed the term and possibly with definitions and finding that no one has uploaded, mentioned, or listed it, the later media and journals and writers put down wrong people as the originators. The first pattern is that people only acknowdge the originator when he/she has published a paper with the name on it. The second is people show bias and prejudice against less privilaged and less known people. For example, a Chinese name who claims to have coined the term "Secretomics" would find it harder to be accepted.


Practical benefit is not clear in finding the originators

This phenomenon is observed in a more open knowledge base, Wikipedia, where if a foreign name enlists a definition, it is criticized and erased rapidly while more established and western author names are accepted readily even with similar content and quality with the foreign ones. This is not uncommon in academia where the same researcher with different national affiliation may result in different acceptance rate of research papers. Hostility to new ideas and newcomers exist even in science. It is not necessarily all adverse evolutionarily. Such resistance can have a critical benefit to the system.

Finding the very first user or originator does not necessarily bring any practical benefit either and may result in advocating more selfish and egoistic proponents. As a competition, this may accelerate the systemization of biology although the side-effect and purpose-disorientation of such competition may nullify the benefits.


Generating omes and omics using Perl scripts automatically

From mid 1997 to 1999, this author has generated tens of thousand of -omes and -omics terms including Functome and Functomics, for example. Bibliome and Bibliomics are other examples. A perl program was used to attach ome and omics suffices to all the common English names such as car, bus, bio, man, human, medical, god, and book as well as latin and roman word stems such as chem-, mathe-, med-, bio-, and phen. The results were over 10,000s of omes and omics words that could possibly used in the future. I predicted that biologists will use -omes and -omics as not because of it is fancy but because it is practical to describe their research area succinctly without having to provide a lengthy description of it. When those terms searched in Yahoo and Google, most terms were unlisted resulting in blank or mis-searched page with a similarly spelled terms. However, even in 1997, there were already researchers who came up with ome and omics terms.


Acceptance of the -omes and -omics

In early 2000s, when this author listed some words on Wikipedia, the curators immediately erased the terms. One example was "exome" and "exomics". Later in 2009, someone else accompanied with a research paper reference, it was listed as a proper entry on Wikipedia, although exome was coined by this author independently and has been used in everyday resarch since mid 1990s. I am certain that some other people  in a research lab have jokingly and seriously coined it around the same time I have coined it. Interactome is an example. It is probably coined by at least three different research groups. One is by this author at George Church's lab at Harvard Medical School as a lab project. The other is by Albert Barabasi group who was then in the University of Notre Dame. Also, Leroy Hood and/or Trey Ideker group is one of the first groups. It is not clear who used the term first and it will perhaps never be known as in many other ome and omics terms. One early advocate of ome and omics is Keith Robison who has been a bioinformatist and been running a blog site of omics for cecades.

In conclusion, the finding of the term originator is not only inaccurate but also will end up listing people who have certain bias in listing them up in public literature. Therefore, in this paper, I will describe the history of omes and omics terms claiming no exact originators but the trends of the terms. Usually, the most advanced research labs in the field tend to bring up new terms that are propagated even if the exact terms were coined by other people somewhere else. Although the word genomics was claimed to be coined in a bar, I suspect that people in MRC Cambridge, UK, where who first sequenced the genomes might have used unconsciously when there were trying to analyze the first viral, mitochondrial, and human genomes since 1980s. 


Self-reinforcement of the term in a circle of researchers.

As a Ph.D. student in MRC Centre from 1994, I personally used and coined many combination terms that have never been used before, probably never in other parts of the world. Well-known early examples are Bio-Perl, Bio-Java, Bio-Python, and Bio-PHP. However, no one in the research labs are usually interested in what terms are shared as long as they can effectively communicate with each other. When, they suddenly hear the word from outside, for example, "exome" on a news or a research paper in the field, they will probably assume that it has been around and they may even think that they previously used the term as they heard it some time in the past of their lives even if they were actually the very first people and some visiting scientists to their lab heard and wrote a paper with the term assuming that that term was common as the very first researchers who used the term used to be influential in the community.


Resistence to omes and omics

In around 1998, there were some active advocates of new omes and omics. They include Mark Gerstein, George Church, and this author. These people not only actively using the terms, but also advocating them to organize the biology with new terms. It is mainly because the above people were bioinformatists who had to organize heterogeneous bio-data. It was not just a convenience but a must. Creating a big SNP database and calling them with specific name may not deliver the concept and principles efficiently. Instead, bioinformatists can coin human 'Variome' and indicate that dbSNP database is a variome database. A repeat database is a useful tool while "repeatome" is a small discipline which deals with various research aspsects of repeat detection, filtering, analyses, prediction, finding biological functions of repeats, repeat masking algorithms, and even generating new repeats for therapies.

However, the initial response to the ome and omics name pioneers were frequently hostile. Some responded to those with sinicism, aggression, and ridicules. As time went, it became a fashion wagon to jump on and if one could not coin a reasonable term in his/her field of research such as 'Neurome' and 'Neuromics', perhaps he/she was not doing the state of the art research in neuro-science. This trend was observable after around 2003. This was also helped by the advance of new sequencing and bioinformatics DBs and tools. In 2005, it became wide spread that most biological fields have some names with omes and omics.


Acceptance by mainstream media.

The main stream media who started covering ome- and omics terms was CHI group. It was followed by Nature group who opened an Omics portal. This somewhat legitimized the useage of strange and unusual ome terms and later generations probably took it as a normality to coin ome- related terms in labs and on the internet.


The future of omes and omics.

The key in modern biology is how one can find geno- and pheno-type associations definitely. This involves a very large scale data generation and analyses. It means, computers are the key researchers. Most biological resources are managed these days by robots and computer software as if almost all the banks of the worlds are run by computer software. As computers cannot understand ambiguous terms, more precise definitions and categorizations will be essential for future biology. In the future, systematic and automatic classification of omes will be used to process tagged data in computers. Continous differentiation of biology will be the main trend using omes and omics.


More omes and omics

This author predicts that there will be ome and omics for virtually all biological fields, chunk of coherent data, groups of concepts, species, and company names and products. For example, for studying bats, people will use 'chiropteromics' as well as chiropterology to express its computer and data driven more systems biology oriented research with rich -ome data such as proteome, genome, and metabolome. Chiropteromics has not been used by anyone by May 2016. This phenomenon of putting ome and omics to even an individual species will cross over the boundary of biology to other fields in the far future. The future research of humans can be humanomics as well as humanity studies. As Johnathan Eisen pointed out, not all ome and omics terms are useful nor meaningful. There will be selection processes of the terms as in everything in biology under the light of evolution.


Democratization of science.

The usage of many omics terms have a democracy element. Traditionally science has been a specialized academic field. In biology, the propagation of omics terms has an interesting aspect of involving common people. Partly confused with 'Economics', some people use omics as their company suffices. It is comparable to -gen trend in biotech company names in the past decades. Omics also has an affinity to UNIX. Its association with computing might have contributed to information technology people to adopt the biological omics concept to biomedical data analyses and healthcare.




Hierarchy of Omics and Omes.

Omics is about systematic, automated, organic, computer based, data-driven discipline and it is not strange to map out all the possible omes and omics by computers ahead of time. Omics.org is one of such a fast and systematic generation and archiving ome and omics terms.





Bibliotheca botanica, Carl Linnaeus, 1736


Nature Group's Omics web: http://www.nature.com/omics/index.html 

'Ome Sweet 'Omics-- A Genealogical Treasury of Words: http://www.the-scientist.com/?articles.view/articleNo/13313/title/-Ome-Sweet--Omics---A-Genealogical-Treasury-of-Words

Yadav, S. P. (2007). "The wholeness in suffix -omics, -omes, and the word om"Journal of biomolecular techniques : JBT 18 (5): 277.

Badomics words and the power and peril of the ome-meme: https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-6

Ome- and Omics Glossary and Taxonomy: http://www.genomicglossaries.com/content/omes.asp

Keith Robison's Omics Omics: http://omicsomics.blogspot.kr/

Badomics by Johnathan Eisen: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617454/


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