Saturday, 31 August 2013

FACE - Free-Air CO2 Enrichment

Free-Air CO2 Enrichment (FACE) is not the most contrived acronym in the world but it’s worth a quick mention because (1) I am involved in a project looking at the effects of elevated CO2 and (2) it is one of those acronyms that, whilst hard to Google without extra keywords, gives lots of opportunities for punny titles. (And who doesn’t love a punny title now and again.) Indeed, one such punny title was the inspiration of today’s post, an ecology Editor’s Choice article in Science: “About FACE” (Sugden AM, 2013. Science 341: 938).

As faces do emit CO2 and, by doing so, enrich the free-air CO2, I’m rating FACE as post hoc. (Although I don’t think that’s what they had in mind!)

Thursday, 29 August 2013

ORCAE - Online Resource for Community Annotation of Eukaryotes

Another contribution from top ORCA spotter, Bethan, and another animal-themed genome resource. This one was too good to ignore: ORCAE - Online Resource for Community Annotation of Eukaryotes:

ORCAE is an online genome annotation resource offering users the necessary tools and information to validate and correct gene annotations. The system is build on the wiki philosophy, all modifications to a certain gene are stored and can be found back in the annotation history of that gene. To be able to modify genes however you will need to have a user account. Anonymous users can browse the public genomes but don’t have editing rights.

Sterck L, Billiau K, Abeel T, Rouzé P & Van de Peer Y (2012). ORCAE: online resource for community annotation of eukaryotes. Nat. Methods 9:1041.

Wednesday, 28 August 2013

BADGER - British Aristocrats Disregard Government Expert's Research

The last acronym, whilst badgery, did not really capture the right tone so I opted to create my own:

BADGER - British Aristocrats Disregard Government Expert’s Research.

Like the badger cull, it’s not pretty but (unlike the cull) it makes the point, I think.

A close second was: BADGER - British Aristocrats Defy Gathered Evidence and Research. Feel free to submit your own in the comments.

BADGER - Bay Area Digital GEo-Resource

To highlight the plight of the British badger, I wanted a BADGER acronym today. The best I have found (thanks to Acronyms List) is BADGER - Bay Area Digital GEo-Resource:

The Bay Area Digital GeoResource (BADGER) Project is a three year project to develop a non-profit community service that offers on-line access to San Francisco Bay Area geographic data. This resource will provide an easy and efficient method of accessing information developed from satellite and aerial imagery, maps, and databases to industry, government agencies and the general public.

BADGER is a collaboration between Lockheed-Martin and two more acronyms: National Aeronautics and Space Administration (NASA) Ames Research Center and the Bay Area Shared Information Consortium (BASIC). BASIC itself is worthy of ORCA, I think.

One of their other acronyms is not so impressive:

The user is asked to identify the site by street address or assessor’s parcel number. The application code then locates the site and displays the parcel boundary on a digital orthophotoquad (DOQQ).

I am not sure where the second Q comes from!

Monday, 26 August 2013

JABBA - Just Another Bogus Bioinformatics Acronym

As already noted in the recent Biostars post, my own field of bioinformatics is particularly bad (or good, depending on your point of view,) at spawning contrived acronyms. Sometimes this works. Sometimes it doesn’t. Sometimes, you get the feeling that people are trying a little too hard.

Keith Bradnam has a long and illustrious career in bioinformatics - I first met him when I was a PhD student in Nottingham in the late ’90s, where he was probably the number one local bioinformatics guru. As a result, he has seen more that his fair share of acronym atrocities committed in the name of science. This has resulted in his creation of the Just Another Bogus Bioinformatics Acronym (JABBA) Award.

I won’t reveal the winner of the inaugural JABBA award here - you’ll have to read Keith’s post, linked above, to find out - but ORCA is sufficiently impressed with Keith’s commitment to using acronyms to fight acronyms, that he is being awarded the inaugural Outstanding Contribution To Acronym Generation Or Notoriety (OCTAGON) award. Congratulations, Keith!

Sunday, 25 August 2013

GARFIELD - Genome Annotation Resource FIELDs (a cat genome browser)

This seemed like an appropriate “Caturday” post. GARFIELD is short for Genome Annotation Resource FIELDs and is a real pre hoc contrived acronym, for this is a cat genome browser. It’s a shame that there is nothing inherently feline about the expanded name, which suggests that sacrifices were made in pursuit of the desired acronym, but it’s still a worthy effort.

As well as its clear ORCA credentials, GARFIELD has a special place in ORCA as it was an email about it from a friend and collaborator that first brought the idea of resuscitating ORCA to mind. Thanks, Bethan!

Pontius JU & O’Brien SJ (2007), Genome Annotation Resource Fields—GARFIELD: A Genome Browser for Felis catus. J Hered 98 (5): 386-389.

Saturday, 24 August 2013

BIOSTAR - BIOinformatic Special Tactics And Rescue

Thanks to official Friend of ORCA™, Niall, ORCA has hit the Biostar forum. Quite a few of the suggested acronyms in the thread are already queued up for (re)posting but check out Niall's post for an earlier look at some of the riches the field of bioinformatics provides in terms of contrived acronyms - good and bad!

Biostar administrator Istvan Albert contributed one for Biostar itself: BIOinformatic Special Tactics And Rescue. I don't think Biostar is actually an acronym in reality. (Although I always thought it was BioStars and was short for Bioinformatics Stars!) This might constitute a new class of acronym - one that is made up after the word has already been in existence for a while. Inverted post hoc, maybe.

I am guessing that Istvan was inspired by SWAT - Special Weapons And Tactics - a classic that probably deserves a place in ORCA itself. I reckon SWAT is also post hoc - they go and swat the bad guys but it's a tenuous link at best.

PS. If you like this sort of thing, you should also check out another Biostars forum post, CRAC: funny and/or weird names for bioinformatics tools.

Friday, 23 August 2013

ORCA - the Organisation of Really Contrived Acronyms

The obvious, though possibly not best, acronym to kick things off is ORCA itself:

The Organisation of Really Contrived Acronyms.
orca noun any of various whales, esp. the killer whale.

organisation noun
a group of people formed into a society, union, or especially business.

really adv.
very; genuinely

contrived adj.
forced or artificial.

acronym noun
a word made from the first letters or syllables of other words.

ORCA was founded in 2004 by Rich Edwards, then a postdoctoral researcher in the lab of Prof Denis Shields at the Royal College of Surgeons in Ireland. I’m not sure now where these definitions come from (possibly OED online) but I have decided to stick with the original 2004 definitions. The term “Organisation” is a bit of a stretch but then these are contrived acronyms.

ORCA is an ad hoc acronym - until we discover that cetaceans are prolific abbreviators, at least. (Who knows what those clicks and whistles mean‽)

Thursday, 22 August 2013

Resurrecting the beast

ORCA, the Organisation for Really Contrived Acronyms, has been dormant for many years. ORCA was created as a fun little side-project when I was a postdoc at the Royal College of Surgeons in Ireland and was in the middle of a particularly productive spell of contrived acronym names for bioinformatics programs - many of them mine!

In the years since it has dwindled and ultimately disappeared when the old server hosting it perished. Recently, however, an acronym emailed to me by a friend reminded me of the old project and I did a little Google search for “organisation of really contrived acronyms”. The old site, long gone, was not found but there were three hits. One was a Facebook competition post by the Canadian Museum of Nature from March 2009:

Trivia Game—Whales Tohorā
What do the Oral Cancer Awareness Foundation, Ireland’s Organisation of Really Contrived Acronyms, and the Ontario Region Ceramic Association have in common?

This game is inspired by
Whales Tohorā
at the Canadian Museum of Nature
March 2 – September 3, 2012

For some reason, this inspired me to resurrect the old beast! Acronyms to follow…