History of Omics

From Omics.org

Jump to: navigation, search

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

 Jong Bhak

 Director of The Genomics Institute, UNIST, Ulsan, South Korea

jongbhak@genomics.org


Abstract

There are perhaps over 1000 omics fields in biology today. They 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, such a catergorization of subfields have produced a large number of offspring which have their own methodologies and knowledge domains. Here, I present the initiation, advancement, and propagation of 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.

 

Background
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 but is based on logical and scientific principles. While logy is reductionist word, ome and omics are more organic and synthetive terms. They apply systems theories to the problems regarding the problem domains as complex systems to be understood by not only logics, but also with components' interactions and dynamics using computers.

 

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. My 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 known people. For example, a Chinese name who claims to have coined the term "Secretomics" would find it harder to be accepted.

 

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.

 

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.

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 terms that have never been used before, probably never in other parts of the world. 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 very 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.

 

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.

 

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.

 http://omics.org/index.php/Omics_classification

 

 

References

Bibliotheca botanica, Carl Linnaeus, 1736

http://jnci.oxfordjournals.org/content/90/2/93.long

 

Yadav, S. P. (2007). "The wholeness in suffix -omics, -omes, and the word om". Journal of biomolecular techniques : JBT 18 (5): 277.PMC 2392988. PMID 18166670

Personal tools
Google AdSense