Forum: The Organisation Of Really Contrived Acronyms (Orca)
4
gravatar for Niallhaslam
4.1 years ago by
Niallhaslam2.3k
Dublin
Niallhaslam2.3k wrote:

Really glad to see that The Organisation of Really Contrived Acronyms (ORCA) has been reactivated. Thought that a few people in here might like to contribute. Bioinformatic tools seem to be particularly guilty of this, I've been guilty of a few myself.

So what are some of biostars' readers favourites.

forum • 4.1k views
ADD COMMENTlink modified 4.1 years ago by Jeremy Leipzig17k • written 4.1 years ago by Niallhaslam2.3k
1

Is Biostar itself an acronym? :-)

ADD REPLYlink written 4.1 years ago by Giovanni M Dall'Olio25k

Much like the ensEMBL/Ensembl thing, this is actually the first time that I have realised that it is "Biostar" and not "BioStars". (I thought it was "BIOinformatics STARS" - for aren't we all? :op )

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Cabbagesofdoom110
1

indeed, there is an inconsistency there - the original name was Biostar but when it came to domain names only biostars.org was available. All things considered Biostars would probably be more appropriate of a name - we're just waiting for a cease-and-desist order from the motherboard maker as motivation to change the name

ADD REPLYlink written 4.1 years ago by Istvan Albert ♦♦ 73k

but it's still www.biostars.com .....

ADD REPLYlink written 4.1 years ago by Daniel3.5k
1

Isn't the American Association Against Acronym Abuse (AAAAA) taking care of this?

ADD REPLYlink written 4.1 years ago by Christian2.5k
1

How about: "biology inspired objectives imparting frequently obtuse random mathematical algorithms that irritate computer scientists"

ADD REPLYlink written 4.1 years ago by Alastair Kerr5.2k

"...INstigating frequently obtuse..." ? (Or where you going for ImpartiNg, which is cheating! :op)

ADD REPLYlink written 4.1 years ago by Cabbagesofdoom110

I was cheating but I do prefer INstigating :->

ADD REPLYlink written 4.1 years ago by Alastair Kerr5.2k
1

Linking to a related post CRAC: funny and/or weird names for bioinformatics tools

ADD REPLYlink written 4.1 years ago by Istvan Albert ♦♦ 73k

Worse as it confuses the name CRAC, which it is also the name for a DNA-RNA hybrid technique

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Alastair Kerr5.2k

Given the contrived nature of some acronyms, and the pedant nature of ORCA, perhaps it should be re-branded as the Organisation of Really Contrived Abbreviations (ORCA).

ADD REPLYlink written 4.1 years ago by Hamish2.9k

I don't follow. ORCA is not particularly pedantic and, even if it were, "Acronym" seems wholly appropriate given its definition. If it were pendantic in nature, the big thing to change would be "Organisation"...

ADD REPLYlink written 4.1 years ago by Cabbagesofdoom110

Now I get to put my pedant hat on :-)

Acronym refers to the use of initial letters (commonly on the first, but sometime more) of the words in the phrase being abbreviated. In many of the more fun examples of abbreviations that appear to be acronyms, a mixture of letters appearing in the phrase is used, not just those from the start of the words. A common example would be XML (eXtendable Mark-up Language), which would not count as a acronym due to the use of 'X' instead of 'E'.

ADD REPLYlink written 4.1 years ago by Hamish2.9k

OK. But what has this do to with ORCA? (XML is not in ORCA) Is it the "of" that is the issue? Or are you suggesting that it should become "Abbrevations" to let things like XML into the fold?

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Cabbagesofdoom110

well it ought to be Abbreviation rather then Acronym - otherwise it would fall under the Department of the Redundancy Reduction Department.

ADD REPLYlink written 4.1 years ago by Istvan Albert ♦♦ 73k
1

Hmmm. If I wasn't too lazy to change the logo then I would probably change it. As it is, ORCA is not pedantic and will accept Abbreviations if they are sufficiently worthy/contrived!

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Cabbagesofdoom110
7
gravatar for Istvan Albert
4.1 years ago by
Istvan Albert ♦♦ 73k
University Park, USA
Istvan Albert ♦♦ 73k wrote:

BioStar - BIOinformatic Special Tactics And Rescue

Also another relevant post: CRAC: funny and/or weird names for bioinformatics tools

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Istvan Albert ♦♦ 73k
5
gravatar for Emily_Ensembl
4.1 years ago by
Emily_Ensembl13k
EMBL-EBI
Emily_Ensembl13k wrote:

We often get asked what Ensembl is an acronym for. But it isn't an acronym at all. We use the word "ensemble", to mean bringing together because we bring together data, and we incorporate the EMBL from the European Molecular Biology Lab (who pay about 2/3 of Ensembl employees' wages) and that's it, ENS doesn't stand for anything. It's really a play on words that incorporates somebody else's acronym.

Maybe we should just make something stupid up for the ENS:

Ensembl of Nucleotide Sequences from the European Molecular Biology Lab

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Emily_Ensembl13k
2

It would appear that I have lost the ability to type the word "ensemble" with the "e" on the end.

ADD REPLYlink written 4.1 years ago by Emily_Ensembl13k
1

Bonus of not adding the e back is that you get a recursive acronym a la GNU.

ADD REPLYlink written 4.1 years ago by Niallhaslam2.3k

When and why did the name change from ensEMBL to Ensembl? Or has it always Ensembl and I was just deluded for many years?

ADD REPLYlink written 4.1 years ago by Alastair Kerr5.2k

Well hitting the Internet Archive and the literature finds it has been Ensembl since at least 2000:

However like you I remember the name being represented as "ensEMBL" back then. It could be this was an affectation of those who knew the origin of the name and wanted to make the relationship between Ensembl and EMBL-Bank more obvious to the community.

ADD REPLYlink written 4.1 years ago by Hamish2.9k

We still use it in our old file systems though, eg our API.

ADD REPLYlink written 4.1 years ago by Emily_Ensembl13k

I have a hazy memory of ensEMBL being written on the entry page of the web site

ADD REPLYlink written 4.1 years ago by Alastair Kerr5.2k

I got it in my head that it was ensEMBL and it has taken many years to shift. (I think a lot of comments in my code still have it as ensEMBL.)

ADD REPLYlink written 4.1 years ago by Cabbagesofdoom110

Please note that Emily_Ensembl is using "EMBL" to mean the EMBL-Bank nucleotide sequence database (part of the European Nucleotide Archive (ENA), which is a member of the International Nucleotide Sequence Database Collaboration). Which was originally established at the European Molecular Biology Laboratory (EMBL) back in the early 1980s.

ADD REPLYlink written 4.1 years ago by Hamish2.9k
4
gravatar for Cabbagesofdoom
4.1 years ago by
Southampton
Cabbagesofdoom110 wrote:

My favourite at the time (2004) was PORNSTAR, which might have even been written PORN*. I can't remember what it did and I am too scared to do a search for it... at work, at least.

The one that instigated the revival was emailed to me by a colleague: the feline genome web browser, Genome Annotation Resource FIELDs (GARFIELD).

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Cabbagesofdoom110
1

Now I want there to be a canine database called Odie :-)

ADD REPLYlink written 4.1 years ago by Hamish2.9k
1

Online Dog In Ensembl? (http://www.ensembl.org/Canis_familiaris/Info/Index)

ADD REPLYlink written 4.1 years ago by Cabbagesofdoom110
4
gravatar for lzwright
4.1 years ago by
lzwright150
NYC
lzwright150 wrote:

My current favorite is UPARSE

Did you mean: PARSE

Search Results have head up arse - Idioms and phrases - The Free Dictionary idioms.thefreedictionary.com/have+head+up+arse‎ Definition of have head up arse in the Idioms Dictionary. have head up arse phrase. What does have head up arse expression mean? Definitions by the largest ...

UPARSE OTU clustering - Drive5.com www.drive5.com/uparse/‎ UPARSE is a new OTU clustering method to be published soon in Nature Methods. Benchmark results show that UPARSE produces much more accurate OTUs, .

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by lzwright150

True story:

UPARSE

ADD REPLYlink written 4.1 years ago by Istvan Albert ♦♦ 73k
3
gravatar for Hamish
4.1 years ago by
Hamish2.9k
UK
Hamish2.9k wrote:

Some that come to mind:

  • DARNED: DAtabase of RNa EDiting
  • PSICQUIC: Protemics Standard Initiative Common QUery InterfaCe
  • STRING: Search Tool for Recurring Instances of Neighbouring Genes
  • EMBOSS has many examples of fun program names...
    • acdc: ACD file checker
    • syco: synonymous codon usage
    • tfm: the "fine" manual

I have to admit to liking DoriC (Database of oriC regions), although I can't help but wonder which Doric was the inspiration.

Keith Bradnam has recently commented on the apparent acronym used for BeAtMuSiC, quite how that name relates to the full name of "prediction of Binding Affinity Changes upon MutationS" is a mystery.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Hamish2.9k

I always think of chocolate milk when I see "PSICQUIC"

ADD REPLYlink written 4.1 years ago by sarahhunter590
2
gravatar for Emily_Ensembl
4.1 years ago by
Emily_Ensembl13k
EMBL-EBI
Emily_Ensembl13k wrote:

ENCODE (ENCyclopaedia Of Dna Elements) is fairly contrived.

ADD COMMENTlink written 4.1 years ago by Emily_Ensembl13k
2
gravatar for sarahhunter
4.1 years ago by
sarahhunter590
Cambridge, UK
sarahhunter590 wrote:

We were specifically instructed to create a resource that did what it said on the tin (or rather we were told that the name on the tin should clearly indicate what the resource did!)

Hence, EBI metagenomics was called what it is, rather than one of it's original proposed names (e.g. GAIA - metaGenome Analysis, Interpretation and Archiving) :-)

ADD COMMENTlink written 4.1 years ago by sarahhunter590
1
gravatar for Jeremy Leipzig
4.1 years ago by
Philadelphia, PA
Jeremy Leipzig17k wrote:

In 2005 I wrote a web application called InSiPiD: Integration Site Pipeline and Database:

http://www.bushmanlab.org/tutorials/insipid

ADD COMMENTlink written 4.1 years ago by Jeremy Leipzig17k
0
gravatar for Fred
4.1 years ago by
Fred650
Paris, France
Fred650 wrote:

I Just found this one: PARSEC: PAtteRn SEarch and Contextualization

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Fred650
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