Month: March 2010

Bad omics word of the day: nutriome

And the winner is …
From the abstract “strategies to determine dietary reference values of single micronutrients and micronutrient combinations (nutriomes)”

As with my last Bad Omics word, I have no real clue what that means. But it seems this author has been using the term for a while.

Some other papers have defined it more concisely such as “Nutriomic analysis is a postgenomic-based study of nutritious components (nutriome).”

Yuck yuck and double yuck is what I say.


Hat tip to @nutrigenomics and @larry_parnell and @eurogene for pointing this one out. 
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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: transactome

Hat tip again to Rami Aziz for pointing this out on twitter
From the abstract: “The definition of transcriptional networks through measurements of changes in gene expression profiles and mapping of transcription factor binding sites is limited by the moderate overlap between binding and gene expression changes and the inability to directly measure global nuclear transcription (coined “transactome”).”

I have no real clue what that means.

I confess, going to skip this paper.  So I will not figure out if there is some clearer meaning. But here’s a guess – the word is unnecessary.

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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: N-terminome

Yes indeed. Someone has used N-terminome.

Nature Protocols: System-Wide Proteomic Identification of Protease Cleavage Products by Terminal Amine Isotopic Labeling of Substrates

From the introduction:
“The sequence and nature of all the protein amino-termini (N-termini) within the proteome (the N-terminome) provides valuable functional annotation, since translation start sites, N-terminal isoforms, modifications and truncations determine the cellular localization, activity and fate of most proteins”
Prediction: will not get widespread use.
But they will get an award today: the Bad Omics Word of the Day.

Hat tip to @mglo for this one.
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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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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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Wildhorse Ag Buffer and Burrowing Owls

Just thought I would post some pics here from a walk on the Ag Buffer trail behind WildHorse gold course. Lots of burrowing owls out there these days.

http://picasaweb.google.com/s/c/bin/slideshow.swf

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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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