Tag: bad omics word of the day

#Badomics word of the day (or even month): Culturomics

Omics omics omics. The suffix is everywhere. And this paper has one of the worst ones I have seen in a while: Quantitative Analysis of Culture Using Millions of Digitized Books. paper came out right when I started winter vacation, which is why I am getting to it now …
In this paper, which is pretty cool, the authors make use of digitized books to track and study cultural trends. The data is f#*$#$ impressive. The results are very very interesting. The press coverage was very positive. The word, however, was and is awful. Did they really really have to call it culturomics, thereby contaminating their fascinating work with all the baggage of genomics? Really? Really? For that you get a Bad Omics Word of the Day Award.
Anyway – here are some links to coverage of the culturomics work, which as I said, is quite impressive. Just wish they had come up with their own non omicy word:
Hat tips to many people including Morgan Langille, Elizabeth Pringle, Michael Dunn, Nick Matzke, Mihai Pip and Sergios-Orestis Kolokotronis for calling my attention to culturomics.
——–
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.

——–

Another good paper, but bad omics word of the day: uniqueome

Wow. This is bad. Really not much to say here other than to point you to a new paper by Koehler et al in Bioinformatics:

The Uniqueome: A mappability resource for short-tag sequencing — Bioinformatics

Paper seems useful. The word. It is simply awful. And the winner of today’s “Bad omics word of the day“.  Hat tips to @leomrtns and @neilfws 

From “The Uniqueome: A mappability resource for short-tag sequencing
Ryan Koehler, Hadar Issac , Nicole Cloonan,*, and Sean M. Grimmond.” Bioinformatics (2010) doi: 10.1093/bioinformatics 

——–
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.

——–

Good paper but bad omics word of the day: drugome

Already tweeted about this but felt it had to be given more prominent status. There is a new, interesting paper in PLoS Computation Biology: The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications
But that word – drugome. Here is their definition

The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’

I really do not think they need to make that into a “ome” word. Mind you, the study is cool and useful. But that word. It is not very good. And thus they are winners of my “Bad omics word of the day” award.

Figure 2. A protein-drug interaction network to illustrate similarities between the binding sites of M.tb proteins (blue), and binding sites containing approved drugs (red). From Kinnings SL, Xie L, Fung KH, Jackson RM, Xie L, et al. (2010) The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications. PLoS Comput Biol 6(11): e1000976. doi:10.1371/journal.pcbi.1000976 

Hat tip to @7T1 and @dgaston83 and @toranaga for pointing this one out.
——–
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.

——–

Bad omics word of the day: waveomics

Let’s just cut to the chase.  The Bad Omics Word of the Day is Waveomics.  Suggested to me by SeaSaver.

On the one hand, I really like that people in biology related fields are putting out preprints in places like Nature Precedings.  On the other hand, this one is a bit painful from the omics terminology point of view: Waveomics: bringing experimental data to online collaboration : Nature Precedings
Well, the term is really just, well, awful.  Here is a key phrase about it:

A Robot is introduced here, waveomics, which provides the first example of allowing experimental data from multiple sources to be queried and shared in the Google Wave environment.

The concept is not so bad in principle – the author Neil Swainston (who has done some cool things – check out his blog and his slideshare presentations and his Academia.Edu page for some detail) was trying to design tools for streaming genomics data in Google Wave.  So this is not a critique of Neil or his work, just of the word waveomics.

Thankfully, in many ways, Google Wave is going extinct.  I guess we should wave good bye to waveomics too. 

——–
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.

——–

Bad omics word of the day: adversomics h/t @jennifergardy @mentalindigest

Well, I guess the bad omics blogger in me is back. The bad omics word of the day today is adversomics. First pointed out to me by Jim C at from MentalIndigestion and now reintroduced to me by Jennifer Gardy.
This one is so awful I had to write it up. The first I know of it is here in an article by Gregory Poland et al. entitled “Adversomics: The Emerging Field of Vaccine Adverse Event Immunogenetics”. And now in a new article by the same authors: Application of pharmacogenomics to vaccines where they say

Another area of importance is genetically determined vaccine-associated adverse events, which we have called ‘adversomics’

I note this is the same group that brought us a previous bad omics word of the day winner in “vaccinomics“. So they are double winners. Hooray for them.
——–
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.

——–

Bad omics word of the day: Bibliome

(Note – this was supposed to be published tomorrow but clicked the wrong button – so we will have two today – yay)

And here is a doozy.  The bad omics word of the day is … Bibliome. See for example, the source of all knowledge (Wikipedia): Bibliome – Wikipedia, the free encyclopedia Which also refers to some other related omics words the literaturome and the textome.  Now, every one at once, 1,2, 3, groan.

Back to the bibliome which is described in Wikipedia as follows:

“The bibliome is the totality of biological text corpus. This term was coined around 2000 in EBI (European Bioinformatics Institute) to denote the importance of biological text information. 

The first uses seem to be in and around 2001. See this article from Nature Reviews Genetics in 2001 Mining the bibliome.  And another one with a very similar title in EMBO in 2002: Mining the Bibliome (with some other words in the title).  And another one in Pharmacogenomics entitled Mining the bibliome. 

And though I would have thought and hoped that it would not get used much it has shown up here and there for a while (see for example Ten thousand views of bioinformatics: a bibliome perspective.). 

So here is a question – what exactly is “the totality of biological text corpus”?  And does this thing, whatever it is, need an omics word?

Hat tip to @rdmpage and others for pointing this one out.

——–
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.

——–

Bad omics word of the day: epitehliome epitheliome

The Bad Omics Word of the Day: Epitheliome. Not really much to say. See for example:

The epitheliome: agent-based modelling of the social behaviour of cells. [Biosystems. 2004 Aug-Oct] – PubMed result

Hat tip to Steve Koch on Friendfeed for 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.

——–

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. 
——–
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.

——–

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.

——–
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.

——–

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.
——–
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.

——–