REACH - Registration, Evaluation, Authorisation and Restriction of Chemicals

REACH - Registration, Evaluation, Authorisation and Restriction of Chemicals is a fine example of acronym contrivance (although lacking the panache of a good pre hoc concoction). Not got the right words for something catchy? Just ignore the inconvenient word!

“[REACH] streamlines and improves the former legislative framework on chemicals of the European Union (EU). The main aims of REACH are to ensure a high level of protection of human health and the environment from the risks that can be posed by chemicals, the promotion of alternative test methods, the free circulation of substances on the internal market and enhancing competitiveness and innovation.”

I guess you can’t blame them for trying to make it more interesting.

MAGIC - the Meta-Analyses of Glucose and Insulin-related traits Consortium

The final human genetics consortium (for now) is MAGIC - the Meta-Analyses of Glucose and Insulin-related traits Consortium, another co-author of the DIAGRAM consortium. This is probably the most contrived of the lot, in that it failed to use all its words but did include “Consortium”. At the same time, being part of MAGIC has a certain appeal above CHARGE, DIAGRAM or GIANT.

“MAGIC (the Meta-Analyses of Glucose and Insulin-related traits Consortium) represents a collaborative effort to combine data from multiple GWAS to identify additional loci that impact on glycemic and metabolic traits.

MAGIC investigators have initially studied fasting glucose, fasting insulin, 2h glucose and HBA1c, as well as performed meta-analysis of more sophisticated measures of insulin secretion and sensitivity. Through these efforts, dozens of loci influencing these traits have been idenified, a subset of which also influence risk of type 2 diabetes.”

There is a certain degree of magic involved in a good genome-wide association study (GWAS) but I still rate this one ad hoc.

If contrived consortium acronyms are your thing, you can probably do a lot worse than sign up to the Table of Contents alerts for the journal Nature Genetics.

PEPPER - Protein complex Expansion using Protein-Protein intERactions

Another offering from the ever-fruitful world of bioinformatics today - with a fruit, fittingly enough.

PEPPER - Protein complex Expansion using Protein-Protein intERactions - pulls out all the stops when it comes to contriving a functional word, skipping words and using internal letters.

For the curious, PEPPER is available from the Cytoscape App Store and is:

“designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. Pepper identifies connected subgraph by using multi-objective optimization involving two functions: (i) the coverage, a solution must contain as many proteins from the seed as possible, (ii) the density, the proteins of a solution must be as connected as possible, using only interactions from a proteome-wide interaction network.”

Despite its use of “seed lists”, I don’t think there is a direct connection with peppers, so PEPPER is being classified as an ad hoc intranym.

I’m not sure if there’s a bigger version of the logo available but if you look carefully, you can see the little chilli peppers.

Winterhalter C et al. (2014) PEPPER: cytoscape app for protein complex expansion using protein-protein interaction networks. Bioinformatics. Aug 18. pii: btu517. [Epub ahead of print]

MFSPSSMpred - Masked, Filtered and Smoothed Position-Specific Scoring Matrix-based predictor

Today’s post is a bit odd, as it is an anti-ORCA acronym. There is a reason why contrived acronyms exist, and I think that MFSPSSMpred is a prime example. The acronym itself is almost informative, although it fails to identify what it is trying to predict. (Short molecular recognition features in this case.) Still, imagine yourself in a lab meeting, trying to tell your supervisor which prediction tool you were using from memory!

MFSPSSMpred does have one thing going for it, though, and that’s Google-friendliness. Providing you spell it right, that is!

P.S. Whilst Googling MFSPSSMpred, I discovered that OCTAGON-winning Keith Bradnam got there first and MFSPSSMpred is a JABBA Award winner!

MODULUS - Methods Of Determining and Understanding Light elements from Unequivocal Stable isotope compositions

Another one from Rosetta, MODULUS - Methods Of Determining and Understanding Light elements from Unequivocal Stable isotope compositions - is described in Cosmos as part of the PTOLEMY instrumentation "to understand the geochemistry of light elements, such as hydrogen, carbon, nitrogen and oxygen".

That’s a lot of words and definitely an ORCA level of commitment to contrive a word out of it, even if they were not able to use them all!

ADAN - prediction of protein-protein interAction of moDular domAiNs

The ADAN Database - prediction of protein-protein interAction of moDular domAiNs - breaks the rules, really, as it is not technically an acronym. To be honest, I am not really sure what it is but it seemed so contrived that it warranted an ORCA entry. To add to the confusion, I do not know what “Adan” (the word rather than the database) is nor its relevance to protein-protein interactions, which is one of my own research areas.

As the database seems to be hosted by Universidad Miguel Hernández in Spain, the only thing I can think is that it is a backronym homage to Spanish footballer, Antonio Adán!

h/t: Nico.

ACHOO - Autosomal dominant Compelling Helio-Ophthalmic Outburst

ACHOO - Autosomal dominant Compelling Helio-Ophthalmic Outburst - syndrome is another name for Photic sneeze reflex. This is the condition that affects around a fifth to a third of the population in which stimuli such as bright lights trigger uncontrolled sneezing. (Also known as “sun sneezing”.)

According to the source from which I discovered ACHOO, the ABC Science Weekly Update, it is “a funny acronym invented by doctors to help them remember the essentials of the photic sneeze reflex!” Personally, I think that “Photic sneeze reflex” is clearer than “Autosomal dominant Compelling Helio-Ophthalmic Outburst”! I suspect they were just having a bit of fun but, either way, it gets the coveted pre hoc status for such a well-aligned (if somewhat over contrived) acronym. (It’s just a shame about the “dominant” bit, which, ironically is probably the most likely bit to be forgotten!)

ASSET - Accelerated Segment Switch in Exons to alter Targeting

See the entry for RAVER. These guys had clearly tried so hard to contrive an acronym that was a dictionary word (surely it should really be ASSEAT?) that I thought they deserved their own entry.

ASSET - Accelerated Segment Switch in Exons to alter Targeting:

Doley R, Mackessy SP & Kini RM (2009).Role of accelerated segment switch in exons to alter targeting (ASSET) in the molecular evolution of snake venom proteins. BMC Evol Biol. 9:146.