Duplicate names in bioinformatics: #10 MAGMA

I've written about this problem enough times now, that I thought I'd promote it to its own series. Check out the previous posts that deal with this subject.

Compare and contrast:

• 2002: MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition
• 2007: MAGMA: analysis of two-channel microarrays made easy
• 2007: MAGMA: An Algorithm for Mining Multi-level Patterns in Genomic Data
• 2008: MAGMA (molecular animation, graphics and modeling application framework)
• 2015: MAGMA: Generalized Gene-Set Analysis of GWAS Data

More duplicate names for bioinformatics software: a tale of two HIPPIES

Image from Flickr user ochre_jelly

Thanks to Sara Gosline (@sargoshoe) for bringing this to my attention. Compare and contrast the following:

• HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores
• HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements

The former tool, published in 2012 in PLOS ONE, takes its name from 'Human Integrated Protein-Protein Interaction rEference' (it was doing so well until it reached the last letter). The latter tool ('High-throughput Identification Pipeline for Promoter Interacting Enhancer elements') was published in 2014 in the journal Bioinformatics.

Leaving aside the issue of whether these names are worthy of a JABBA award, the issue here is that we have yet another duplicate set of software names for two different bioinformatics tools. The authors of the 2nd paper could, and should, have checked for 'prior art'.

If you are planning to develop a new bioinformatics tool and have thought of a possible name, please take the time to do the following:

1. Visit http://google.com (or your preferred web search engine of choice)
2. In the search box type the proposed name of your tool followed by a space
3. Then add the word 'bioinformatics'
4. Click search
5. That's it

24 carat JABBA awards

Here is a new paper published in the journal PLOSBuzzFeed…sorry, I mean PLOS Computational Biology:

• A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome

It's a good job that they mention the name of the algorithm ninety-one times in the paper, otherwise you might forget just how bogus the name is. At least DIAMOnD has that lower-case 'n' which means that no-one will confuse it with:

• Fast and sensitive protein alignment using DIAMOND

This second DIAMOND paper dates all the way back to November 2014. Where does this DIAMOND get its name?

Double Index AlignMent Of Next-generation sequencing Data

This DIAMOND gets a bonus point for having a website link in the paper which doesn't seem to work.

So DIAMOnD and DIAMOND are both the latest recipients of JABBA awards for giving us Just Another Bogus Bioinformatics Acronym.

Bogus bioinformatics acronyms…there's a lot of them about

Time for some new JABBA awards to recognize the ongoing series of crimes perpetrated in the name of bioinformatics. Two new examples this week…

Exhibit A (h/t @attilacsordas): from arxiv.org we have…

• CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

CoMEt derives from 'Combinations of Mutually Exclusive Alterations'. Of course the best way of making it easy for people to find your bioinformatics tool is to give it an identical name as an existing tool which does something completely different. So don't be surprised if you search for the web for 'CoMEt' only to find a bioinformatics tool called 'CoMet' from 2011 (note the lower-case 'e'!). CoMet is a web server for comparative functional profiling of metagenomes.

Exhibit B: from the journal Bioinformatics — the leading provider of bogus bioinformatics acronyms since 1998 — we have…

• MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis

MUSCLE is derived from 'Multi-platform Unbiased optimization of Spectrometry via Closed-Loop Experimentation'. Multi-platform you say? What platforms would those be? From the paper:

MUSCLE is a stand-alone desktop application and has been tested on Windows XP, 7 and 8

What, no love for Windows Vista?

Of course, it should be obvious to anyone that this bioinformatics tool called MUSCLE should in no way be confused with the other (pre-existing) bioinformatics tool called MUSCLE.