Tag: bad omics word of the day

Good words on bad omics words: "A crisis in postgenomic nomenclature" from 2002

Just got pointed to a fun paper from 2002 “A Crisis in Postgenomic Nomenclature by Stanley Fields and Mark Johnston” by Mark Johnston himself. Their paper, in Science, is available for free on Stanley Fields website here. It is actually a hilarious tongue in cheek read where they proceed from arguing for more specificity in omics names (e.g., they go so far as to propose a EC# like system with things such as the “4.7.5.3.8ome” and also that conditions should be specified like the “37°-7.4-G1-Golgi-N-but-not- 63 O-linked glycosylome”.  And they end with a proposal to replace the term “the cell” with either the someone or the omesome.  It is definitely worth a read.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Bad omics word of the day: miRNAome

Hat tip to Rami K. Aziz on Twitter for this.

The winner of today’s Bad Omics Word of the Day is a paper in PLoS One: PLoS ONE: Characterization of the Melanoma miRNAome by Deep Sequencing

They even slipped the word into the title. I do not think the word was coined by them as I found some older references going back at least to 2005: MicroRNA Gene Expression Deregulation in Human Breast Cancer in Cancer Research.

Given that there were only 847 google hits as of today, the word clearly has not taken off, which is good.  But alas it is still being used, even in titles.  As far as I can tell, what they mean by the term is “All the miRNAs in a particular cancer class” — unclear to me why that needs an ome.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Bad omics words of the day: modomics and tRNomics

Well, just was browsing through a paper on the non coding RNAs of the model halophile Haloferax volcanii, which I study. The paper BioMed Central | Full text | RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes is quite useful. However, the terminology is icky. They use two omics terms I have never seen before, but I guess should have known were out there: tRNomics (all the tRNAs in an organism, or something like that) and modomics (the pattern of RNA modifications). These are really not needed are they? And since they are both in the same paper, today we are giving out a linked “Bad omics word of the day” award to both of these terms.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Bad omics word of the day: variome

OK – I am back. I cannot resist. The Bad Omics Word of the Day is Variome. I am not even completely sure what people mean by this, but I guess if you want to know you can go to this meeting: 3rd HVP Meeting � Paris

On the web site the seem to define this project as an attempt to “collect variation causing disease (mutations) in all genes world wide” so I guess that is what variome means to them. So – I wonder here – what is wrong with “polymorphisms”??????

HT to @ivanoransky and @boraz for pointing this out to me (by feeding my other people’s tweets).

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Oldy but baddy: bad omics word of the day – "speechome"

I know I swore to quit but I could not help myself here. I was going through old draft blog posts that I never finished and found this link to an article about the “Human Speechome Project” BBC NEWS | Science & Environment | Big brother untangles baby babble

Basically, the idea is they are recording everything a particular child hears and says and categorizing it all to create “the Human Speechome project“

“Just as the Human Genome Project illuminates the innate genetic code that shapes us, the Speechome Project is an important first step toward creating a map of how the environment shapes human development and learning,” said Frank Moss, the director of MIT’s Media Lab at the time.

In some ways – the project is eerily fascinating. But in many ways it is more on the creepy side of things. Regardless of whether one likes the project or not, the word “speechome” has just got to go. So, quite a few months late – I am still giving this my “Bad Omics Word of the Day” award.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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End (at least for while) of the bad omics word awards

Well this is it. I am declaring that I am (mostly) done with the posts about bad omics words. I will on occasion I am sure rail about one word or another with my Worst New Omics Word Award, but I will try to let ome words rest in peace, at least for a while. Mostly this is because the task is too overwhelming.  There are simply too many bad omics words out there.

I would like to note however, that as I have browsed around, I have noticed many other bloggers doing similar occasional snarky complaints about omics words here and there. That was good to see. But most amazing was that there is in fact published literature on the topic of bad omics words. See for example The Wholeness in Suffix -omics, -omes, and the Word Om and apparently[The odd omes and omics] (which is in Finnish) and many others.
My favorite published rant even has rant in the title “A rant against jargon and neologisms“. It is definitely worth a read and is free in Pubmed Central. In it, Simon Young says many things I agree with. In particular the ending

This does not mean that these terms are not useful. However, as with all new terms, they will help to promote knowledge and ideas only if their precise meaning becomes known to a broad range of researchers. Only time will tell what will become a useful scientific term and what will remain the jargon of a subgroup of researchers.

The best discussion I have seen of the issue is by none other than the great Joshua Lederberg (may he rest in peace) who wrote ‘Ome Sweet ‘Omics — A Genealogical Treasury of Words with Alexa McCray. In it they discuss the history of the word genomics, among others. They also quote Roland Brown author of “Composition of Scientific Words”

“words, when they make their debut in scientific or literary society … should be simple, euphonious, pure and mnemonically attractive.”

Clearly many of the new omics words do not meet this criteria but I am going to leave that for others to (help) judge. If you personally want to see some lists of the every growing number of omics words, check out any/all of the following:
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Bad omics word of the day: vaccinomics

The more I look at the litany of omics words, the more I fret. So let’s just get straight to the point. Todays bad omics word is “Vaccinomics” which was defined as follows:

Vaccinomics encompasses the fields of immunogenetics and immunogenomics as applied to understanding the mechanisms of heterogeneity in immune responses to vaccines

I do not like this word but if you want to learn more I guess you could look here. Not really much more to say.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Bad omics word of the day: connectome

Well, I have decided that I need to look beyond just new omic words to snark about here (I have been giving a “Worst New Omics Word Award” every once in a while”). So I am now going to post, as often as I can, a little ditty about any bad omics word that is out there. Yesterday’s winner was “phenogenomics” which I posted only to twitter.

Today’s winner is “connectome” (see for example NIH Launches the Human Connectome Project to Unravel the Brain’s Connections, July 15, 2009 News Release – National Institutes of Health (NIH)). I think it’s first major use was here but not sure. It even has a wikipedia entry which says:

A connectome is a detailed map of the full set of neurons and synapses within the nervous system of an organism. The production and study of such a map is known as connectomics.

Now I am not the first to be a bit annoyed by this word (e.g., see the Neurochannels blog post “Review of Seung’s talk at SFN”:

Incidentally, ‘connectomics’ is a cheesy mouthful of a word. Some words just weren’t meant to be biologized with the -omics suffix, and ‘connect’ is one of them. ‘Genomics,’ cool. ‘Proteomics,’ a little annoying and not very creative. ‘Connectomics,’ stop the bus I want to get off. At the very least let’s reserve the -omics for molecular biology. Thank goodness Bialek didn’t try to pull us into the world of ‘infomics.

Hat tip to Karl Broman for pointing this one out in comments here.

As with posts about other omes and omics words, I am not saying anything really at all about the science behind the word here. Just the word.

http://friendfeed.com/treeoflife/35376482/bad-omics-word-of-day-connectome?embed=1

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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