Tag: Worst New Omics Word Award

Cool paper, & winner of "worst new omics word award": Predatosome

ResearchBlogging.org
And the bad new omics words keep streaming in. Today’s winner of the “Worst New Omics Word Award” is going to Carey Lambert, Chien-Yi Chang, Michael J. Capeness and R. Elizabeth Sockett from Nottingham for their use/ invention of “Predatosome”. They use this term in the title of their new PLoS One paper: The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio. Here is the very long sentence where the define it:

The gene products required for the initial invasive predatory processes have not been extensively studied but the genome sequencing of B. bacteriovorus HD100 [1] revealed a genome of 3.85Mb, including a core genome similar to that of non-predatory bacteria and some 40% of the genome comprising a potential predicted “predatosome” of genes, encoding both hydrolytic products that may be employed in prey degradation, and genes that may be required specifically for host predation and thus are not conserved across the Proteobacteria.

The paper is actually quite interesting. They use genomic approaches to characterize a fascinating organism – the bacterial species Bdellovibrio bacteriovorus. This bug is a predatory organism – eating other bacteria. Since it eats them from the inside out, some, including these authors, refer to this organism as a pathogen of other bacteria and their is some discussion here and elsewhere for its potential to serve as a “living antibiotic” in much the same way people are trying to use bacterial viruses (a.k.a. phage).

The paper overall is quite nice on first read. They used microarray studies to characterize gene expression patterns in different phases of the life cycle (see Figure above for the life cycle outline). They backed up this work by quantitative PCR studies and regular RT PCR. And based upon their analysis they found some genes that are “Up-Regulated in Predatory, but Not HI” phase (HI stands for host-independent). And here is where they really tell us what they mean by predatosome:

This category of 240 genes are very interesting as they potentially exclude those genes simply involved with release from attack-phase into growth, namely they should be part of the “predatosome” of predatorily specific genes.

It seems to me this terminology is completely unnecessary. All they need to do is say they are studying the genes related to the predatory phase. To assign these genes to the “predatosome” is a bit much. They continue in the paper to report some really interesting stuff. For example, they also examine another predatory bacterial species, and look at whether there are genes conserved in the process between species. They made some really nice figures by the way about the different phases of hte life cycle in this organism and which genes are expressed:

Anyway – the science in the paper is nice. However, the invention of yet another omics word is a bit much. And thus Lambert et al. are winners of the highly coveted “Worst New Omics Word Award” for their invention of “predatosome“. Details on the paper are below – and that is where the figures come from too. (Hat tip to Bora for letting me know about the paper, and the word).

Lambert, C., Chang, C., Capeness, M., & Sockett, R. (2010). The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008599

Friendfeed comments below:
http://friendfeed.com/treeoflife/9262afad/cool-paper-winner-of-worst-new-omics-word-award?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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Worst new omics word award: Negatome

Last week I asked for people to post suggestions for bad new omics words as candidates for my “Worst new omics word award”. And there were some great ones posted there by MAT kinase (physiomics, orfeomics), Mr. Gunn (degradomics, though he noticed it was already suggested), anonymous (incidentalome), Karl Broman (human connectome), Paul (splicome), blJOg (Systemomics), Farhat Habib (resourceome), Rosie Redfield (sewa-genomics), Marmaduke (Microbial paleomics), and many others.

But by far and away, the worst of the worst, the most negative of all new omics words I have seen in a while, is the negatome suggested by multiple people. Yes, indeed, a group ( Pawel Smialowski, Philipp Pagel, Philip Wong, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Thomas Rattei, Dmitrij Frishman and Andreas Ruepp ) has written about, and even created a database for the negatome (for an excellent description about what the negatome is about, see The ‘negatome’ – a database of negative information… « mental indigestion (from Dr. Jim).

The concept of the negatome is good – it- “is a collection of protein and domain pairs that are unlikely to be engaged in direct physical interactions”. It is meant in many ways as a database for testing various interaction measuring methods. And it could end up being quite useful. See Dr. Jim for more on its uses at the link in the previous paragraph.

But the name. Oh the name. It hurts to see. It hurts to say.

And thus,
… as suggested by GenomeWeb “Just watch out for Jonathan Eisen’s Worst New Omics Award.”
…and Iddo Friedberg on Twitter (@phylogenomics is going to love this one. The Negatome. Actually, quite useful.)
…and PSI Wavefunction on my blog) …
…and contrary to the suggestion by Ed Winstead on twitter who misinterpreted my twitter post about Iddo’s post when he said “Liked “The ‘negatome’ – a database of negative information” http://bit.ly/5ht98d even got the nod from @phylogenomics”

…  Negatome the word is a winner of my coveted “Worst New Omics Word Award“.

Previous winners were:

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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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Wanted – Bad New Omics Words

Blogger in need of material while taking a little break for medical reasons needs help. Seeking bad new “omics” words to give “Worst New Omics Word Award” to. Junkome from PZ Myers already under consideration. Please post suggestions here.

Previous winners are

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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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Worst new omics word award: material degradomics

And the bad omics words just keep getting worse. This one really takes the cake. A story from BBC News Online (Sniff test to preserve old books)
discusses how

“Researchers report in the journal Analytical Chemistry that a new “sniff test” can measure degradation of old books and historical documents.”

The work they are doing actually seems quite interesting. But alas, the way they describe it does not. They refer to this method as “material degradomics“. I fortunately do not have access to the paper at home but a google search reveals some text from their paper

Through similarities with metabolomics,(15) we propose to define a new field of material degradomics (and related terms, Table 1).

I literally dread what is in table 1. For creating a new omics term that seems thoroughly unnecessary and distracting, I am giving Matija Strli and colleagues one of my coveted “Worst New Omics Word Awards.” Hat tip to PaulBo who posted a comment about this on my “Fermentome” award post.

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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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Worst new omics word award #5: fermentome

I do not have access to the article but the abstract is all I need to give out my fifth “Worst New Omics Word Award“

Fermentation of undigested foods in the colon by its resident bacteria affects not only colonic health (protection against inflammation and tumour formation) but also influences metabolic health. Studying fermentation directly is difficult for lack of access. We hypothesise that the anatomical structure of the colon is suited to act as a fermenting chamber with the gaseous molecules (VOCs) emitted having direct effects on the colonocytes as well as gut neural and metabolic effects. We refer to this complex system as the ‘fermentome’, and further hypothesise that alteration in the ‘fermentome’ through dietary modification will have a direct impact on colonic as well as metabolic health and disease. The VOCs emitted may play a role in bacterial chemical signalling within the colon but importantly could also function as a ‘gas’ biomarker. Measurement of such VOCs through non-invasive methods would have important application as a hypothesis-generating tool with subsequent clinical application.

From an article titled “Colonic fermentation – More than meets the nose” in Medical Hypotheses, Volume 73, Issue 5, Pages 753-756 by R.P. Arasaradnama, M.W. Pharaoh, G.J. Williams, C.U. Nwokolo, K.D. Bardhana, S. Kumar

Not really much to say other than, this one is a stinker.
Hat tip to @steinsky for tweeting to me about this.

——–
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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Worst new omics word award: Omnigenomics by (surprisingly) @Genomicron

Well, been taking a break from this award, as I am in over my head with teaching right now. But could not resist this one. Based on a tip from Marcio Pie in Brazil I checked out T. Ryan Gregory’s recent posting (Genomicron: Omnigenomics) on his normally excellent Genomicron Blog. And he has clearly been overcome with H1N1 fever or something like that, as he discusses in this new posting, his desire to coin a catchy new omics word to describe his work on comparisons of genome size across species.

And he has chosen, get ready

OMNIGENOMICS

Proposed neologism: “Omnigenomics”

Etymology: Latin “omnis” (all or everything) + genomics (study of genomes)

Sample usage: “What do you do?” / “Omnigenomics” / “What’s that?” / “I study the total amount of DNA in different species of animals, which includes genes and all the other sequences, most of which are non-coding and…”

All I can say, as I did in the comments on his blog, is

Nooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooo.

And for this full slide down the slippery slope of omics words, T. Ryan Gregory is the recipient of my fourth “Worst New Omics Word Award.” Check out previous winners:diseasome, ethomics, and Museomics. (I note if you look through Google results, domain names with omnigenomics in them have been registered previously and then allowed to expire. Those were good deaths. Hope the resurrection is short lived).


——–
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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Worst new omics word award: diseasome (thx @steinsky @noahwilliamgray @mocost )

And the winner of the “worst new omics word award” is “diseasome.”

Credit for pointing this one out goes to Noah Gray and MoCost on Twitter. See Mos first post here: Twitter / Mo: Diseasome project visualiz …

And some follow up:

Amazingly, I missed this when the New York Times used it in a headline: “Mapping the Human ‘Diseasome’ – Interactive Graphic – NYTimes.com” and in many other reports (see Google search here).

What does diseasome actually mean? I do not know. And it does seem really unnecessary to me. And since I got blasted (justifiably) a bit by one of the people I gave my previous award to here is a clarification. I am not commenting here on the science behind the “diseasome” work. Just the word. And the word, I do not like.

Previous awards I have given:

On Friendfeed:

http://friendfeed.com/treeoflife/fe60b5ea/worst-new-omics-word-award-diseasome-thx?embed=1

——–
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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Worst new omics word award: ethomics

Well, look at what I just saw on twitter:

tlemberger omics mania: ‘ethomics’ http://is.gd/wOcg – should be added to http://omics.org/ but perhaps also nominated for this http://is.gd/g2Bc

That is from Thomas Lemberger and so I followed the last link first, since I thought I might be to, well me. And indeed it was a link to my “Worst new omics word award” for museumomics.

And so then I went to the link on ethomics: High-throughput ethomics in large groups of : Drosophila : Abstract : Nature Methods.
And indeed they use “ethomics” – what is clearly a quite new omics word (only 62 google hits as of this PM). I confess, I stopped reading at the abstract because it was just too much:

We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.

For trying to extend omics to ethogram and beahvioral plots I am giving my second coveted “worst new omics word award” to Kristin Branson, Alice A Robie, John Bender, Pietro Perona & Michael H Dickinson. Here is a prediction – ethomics will not become widely used – not soon – not ever. Thanks for pointing this one out Thomas.

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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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Worst new omics award: ethomics

Oops – posted this to the wrong blogspot blog.  Please go to my Tree of Life blog to see this post here.  
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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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Worst New Omics Word Award: Museomics

OK.  So I coined my my omics word many years ago (phylogenomics).  Fine.  Sue me.  But the spread of omics words is getting really icky.  And a new one really seems lame.  The word is “museomics”which I saw for the first time in a press release today from Cold Spring Harbor Press about a paper in Genome Research. 

I mean, the study of the Tasmanian Tiger seems like it could be interesting (have not read the paper) and there is some really fun stuff happening these days using Roche/454 sequencing. 
But meseomics?  Not to disparage museums which are critical to all of biology in my opinion.  But to me the term in a way treats museums as simply a place we store organisms before we get DNA out of them.  For this, the team at Penn St. that led this project and apparently coined the term museomics (see here where they define the term) is getting my new “Worst New Omics Word Award.” 

In addition I am proposing my favorite new Omics words using their model:
  1. Roadkillomics (to go along with roadside field guides)
  2. Backyardomics (e.g., could be some sort of native plant thing)
  3. Hospitalomics (e.g., MRSA)
  4. Backoftheenvelopomics (for the anthrax case)
  5. Stuffinmypocketomics (hey, I have found some $&%$ stuff there)
  6. Restaurantomics (e.g., O157H7)
  7. Footballomics (there have been studies of MRSA transmission in games, why not omics)
  8. Slowfoodomics (genomics of things you get within 50 miles of your neighborhood)
  9. Ebayomics (genomics of things you get off Ebay)
  10. Stuffthecatdraggedinomics (my cats would like this)
  11. Wherethesundontshinomics (human microbiome?)
Any others suggestions?
——–
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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