NSF asks for comments on "genomes-phenomes" program; here’s a comment – phenome is a silly #badomics term

Hmm.  Just got this in the emails.

BIO seeks community input on Genomes-Phenomes research frontiersJohn Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes.  The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry.The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO’s future research investments and activities relevant to understanding genomes-phenomes relationships.To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link:Sign-up.  Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding.  Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki.Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to bio-gen-phen@nsf.gov.

Nice that they are seeking input. But really – does NSF have to adopt “phenome” as a term? How exactly is this different from “phenotype”? This seems to be a case of exactly what I was criticizing in my Badomics article in Gigascience and in all my posts here (eg bad omics words of the day, Worst New Omics Word Award, badomics, etc). Blech. Genomics is really interesting. I have worked on it for many years. But there is no need to contaminate the literature by using new, uninformative, oversold terms like “phenome”.

Bad Ome-like word of the week: symbiome

Well I got pointed to this paper: Transgenerational Transmission of the Glossina pallidipes Hytrosavirus Depends on the Presence of a Functional Symbiome

And as many might guess – the word “symbiome” did not sit well with me.  Alas, they don’t define it in the paper.  So I can’t really quibble with their definition.  But I did find some other stuff out there that, well, at least helps see how other people are using the word:

I can’t really tell from most of these if “symbiome” can be a useful term or not sometimes.  Certainly the iPhylo example above has potential.  But in general, the word seems awkward at best.  Now – as far as I can tell, nobody is using it in the context of “genomics” so this does not fit in with my “badomics” obsession.  But it still does not make me feel warm and fuzzy so I am going to give it a pseudo-award – the Bad Ome-like word award.

Badomics word of the year? Nutrimetabonomics

So I guess a thank you is owed to Joseph McPhee for this tweet:

The link in the tweet is to this paper.

Nutrimetabonomics: Applications for Nutritional Sciences, with Specific Reference to Gut Microbial Interactions – Annual Review of Food Science and Technology, 4(1):

Wow. Nutrimetabonomics.  In a paper.  And amazingly they had a conference on this too. 11th-13th April 2012- First Nutrimetabonomics Workshop to consider …  I do not even know what to say.  This is NOT a good omics word.  It is definitely a bad bad bad omics word.  A very bad one (note – the field might be interesting .. the word however is bad).

For more on #Badomics words see

#Badomics word of the day, week and month: the morphome

Well, I have been avoiding the badomics meme for a little bit but cannot help getting back into it for this one.  From this paper: BMC Biology | Full text | The songbird syrinx morphome: a three-dimensional, high-resolution, interactive morphological map of the zebra finch vocal organ.  Yes, that is right – rolls right off the tongue – the songbird syrinx morphome.

The key sentence assigning guilt for this

“Here we present an annotated high-resolution three-dimensional (3D) morphological dataset, which we have dubbed a morphome,”

Note – I love the move for more high throughput, digital morphological data.  It rocks.  It will make for some interesting science.  It however, does not deserve it’s own ome word.

For more on this meme see All my writings on badomics words.

H/T David Coil …

A badomics word for good purposes: new paper on the "ridiculome"

Quick post here.  There is a new paper in BMC Biology which uses a bad omics word in the paper and in the title: BMC Biology | Full text | Logic modeling and the ridiculome under the rug.  Fortunately they are using the term to poke a bit of fun at people who think genomics will solve all of their research problems.

Yes Virginia, even the cervix has a #microbiome ……….. or does it?

Just read over the following paper: PLoS ONE: The Cervical Microbiome over 7 Years and a Comparison of Methodologies for Its Characterization

It is interesting and has lots of tidbits worth looking at in more detail including

  • An analysis of methods for classifying sequence reads as to which organism they likely come from
  • comparison of amplification and sequencing methods
  • long time period covered in the sampling
  • and much more
But what struck me more than anything is that, well, they referred to the microbial community that they were sampling as the “cervical microbiome.”  And though what they discuss here is fascinating in many ways, I am beginning to wonder if every site on the human body (or sites on other organisms) should have its own microbiome.    Or, another way of looking at this is – where do we draw the line between niches?  Is there a eyebrow microbiome?  A left elbow microbiome?  A testicle microbiome?  Certainly, I view the microbes that live in and on people as part of an ecosystem.  But I think just as biomes in the world around us should be defined by – well – something bigger than just GPS coordinates – so too microbiomes should probably be a bit bigger than just the microbes found in a particular body site.  Starting to wonder if we are going to see a proliferation of microbiomes just as we have seen a proliferation of OMIC words.  Ooh — this could give me something new to give an award for.  

OMG – Without a doubt the worst omics word ever – The Sexome

I really have nothing to say here.  I just got pointed to a new paper by Thiago Venancio.  The paper is – I kid you not: Understanding the Sexome: Measuring and Reporting Sex Differences in Gene Systems.  I don’t have access to the paper but here is the abstract which is all you need

The current male bias in biomedical research should be eliminated. The large sex differences in incidence and progression of diseases mean that sex-biased factors are an untapped source of factors that protect from disease. Greater understanding will come from intensified study of the “sexome,” which is the sum of sex-biased effects on gene networks and cell systems. The global search for sites and mechanisms of sex-specific regulation in diverse tissues will provide unanticipated insights into physiological regulation and targets for novel therapies.

That is without a doubt the worst omics word I have ever seen.  All my previous posts about bad omics words pale in comparison (though I encourage you to read them: Worst New Omics Word Award and bad omics word of the day).

Worst new omics word award: circomics – running circles around my head

Wow – this is really not a good “omics” word.  Check out this paper title and it’s abstract Circular DNA genomics (circomics) exemplified for g… [Virology. 2012] – PubMed – NCBI

Circomics was coined to describe the combination of rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) and pyro-sequencing to investigate the genome structures of small circular DNAs. A batch procedure is described using 61 plant samples from Asia, South America and Central America which revealed 83 contig sequences of geminiviral DNA components and 4 contig sequences of DNA satellites. The usefulness of this approach is validated for the Brazilian begomoviruses, and the sequence fidelity is determined by comparing the results with those of conventional cloning and sequencing of Bolivian begomoviruses reported recently. Therefore, circomics has been proven to be a major step forward to economize costs and labor and to characterize reliably geminiviral genomes in their population structure of the quasi species.

This definitely fits the category of a “bad omics” word which I have history of complaining about but had been ignoring for a bit.  But I am back.  I am giving “Circomics” a “Worst New Omics Word Award” here because, well, it seems completely unnecessary and distracting.

Hat tip to AJ Cann for pointing this one out on Google Plus.

#badomics word for the week: nascentome

Here is a #badomics word to ponder – the nascentome

From this paper PLoS ONE: Nascentome Analysis Uncovers Futile Protein Synthesis in Escherichia coli

It was called to my attention via twitter:

 ayrrisBIO – Appistry 

Awe MT  But it’s so new. Give nascentome a chance. RT  word: The ‘nascentome’:
 Aaron Best 

But it’s so fresh and new. Give nascentome a chance. RT word: The ‘nascentome’: 
 Malcolm M. Campbell 

Worthy candidate for  word of the year: ‘nascentome’. Blech.  via 

 word: The ‘nascentome’:  

It is a really bad omits word.  So we are giving it an award.  Not sure which one yet.  But one of these:

Why #badomics words can also be very good: a case in study with museomics #JGIUM

Well, my snarky blog style with some of my awards comes with some risks. Today I experienced one of them. Stephan Schuster gave me some serious major grief over a post I wrote a few years ago. In the post I gave him an award for “Worst new omics word” for the word museomics. I gave this award because, well, I don’t like the word. I stand by my complaints about the word. But Stephan did highlight ( in his comments to me in the back of the room at the JGI User Meeting) that the word has been remarkably useful at getting money and attention for museum based genomics studies.

So I guess here is the dilemma. I realize new omics words can get attention. Omics is after all very hot still. But I write about #badomics words both because I think it is fun and also because I think people are careless with the language much of the time. Many omics words are really awful with no benefits. But some, fit my criteria as being badomics words, but can have positive benefits. To the public, the word museomics probably conjures up exactly what museum people want – the image of cutting edge science. Though I love museums, to some the conjure up images of dust and cobwebs and crotchety old scientists wandering around the halls in the dark. So the term museomics may indeed turn this on it’s head. This term even to me conjures up images of museums doing cool things. So alas, I guess this is a mea culpable of sorts. I still think the word itself is not great. After all, if you think about it, all it really means is doing genomics with museum specimens. But clearly Stephan has a good point … Getting attention to science is a good thing. So I guess badomics words can be used for good.

I am still going to snark about badomics words. But I will try to make more mention of the potential value they have in spreading science and omics to the masses ….

– Posted using BlogPress from my iPad

UPDATE 5/13/2013
What a wimp out.  Museomics is such a bad bad bad omics word.