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 “126.96.36.199.8ome” 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.
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.
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.
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”??????
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.
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.
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.
“words, when they make their debut in scientific or literary society … should be simple, euphonious, pure and mnemonically attractive.”
- Omes Table, Gerstein Lab
- The best place is “Alphabetically ordered list of omes and omic words” at omics.org
Vaccinomics encompasses the fields of immunogenetics and immunogenomics as applied to understanding the mechanisms of heterogeneity in immune responses to vaccines
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.
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.
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.