Unpronounceable bioinformatics database names

First a quick reminder that an acronym is something that is meant to be pronounced as an entire word (e.g. NATO, AIDS etc.). Sometimes these end up becoming regular, non-capitalized, words (e.g. radar, laser).

In contrast, an initialism is something where the component letters are read out individually (e.g. BBC, CPU). In bioinformatics, there are also names which are part acronym and part initialism (e.g.GWAS…which I have only every heard pronounced as gee-was).

Most initialisms that we use in everday life tend to be short (2–4 letters) because this makes them easier to read and to pronounce. As you move past 4 letters, you run the risk of making your initialism unprouncible and unmemorable.

So here are some recently published bioinformatics tools with names that are a bit cumbersome to repeat. For each one I include how someone might try to pronounce them. Try repeating these names quickly and for an added test, see how many of these names you can remember 5 minutes after you read this:

5 characters

• CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics: cee-car-eff-dee-bee? — this assumes that 'Ce' and 'Ca' are not treated separately as two letters…one could argue that if it is not clear how your bioinformatics tool name should be pronounced, then it does not have a good name.
• EHFPI: a database and analysis resource of essential host factors for pathogenic infection: ee-aitch-eff-pee-aye
• PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands: pee-ay-aye-dee-bee — this is a particularly bad choice of name as it will read to many as 'paid-bee'
• rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development: ar-ar-en-dee-bee (the first 3 characters are not easy to say quickly!)
• The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome: tee-tee-ess-em-aye

6 characters

• DBTMEE: a database of transcriptome in mouse early embryos: dee-bee-tee-em-ee-ee — I accept that maybe this one is just pronounced dee-bee-tee-me, but once again do you really want there to be uncertaintly as to how the name of your bioinformatics tool is read by others?
• euL1db: the European database of L1HS retrotransposon insertions in humans: ee-you-ell-one-dee-bee
• SASBDB, a repository for biological small-angle scattering data: ess-ay-ess-bee-dee-bee
• WDSPdb: a database for WD40-repeat proteins: dub-ball-you-dee-ess-pee-dee-bee

7 characters

• BCCTBbp: the Breast Cancer Campaign Tissue Bank bioinformatics portal: bee-cee-cee-tee-bee-bee-pee
• PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool: pee-eff-pee-slash-ee-ess-gee (only 6 characters if you omit the slash I guess)
• PHI-DAC: protein homology database through dihedral angle conservation: pee-aitch-aye-dash-dee-ay-cee (shorter if you omit dash and/or pronounce 'DAC' as a word)

And the winner goes to…

• BioVLAB-MMIA-NGS: microRNA–mRNA integrated analysis using high-throughput sequencing data: this is a 7-letter initialism that comes after a three syllable (non-standard) word, so to pronounce this you have to say bio-vee-lab-em-em-aye-ay-en-gee-ess!!!

Conclusions

If you want people to actually use your bioinformatics tools, then you should aim to give them names that are memorable and pronounceable.

More bioinformatics link rot: where is EUROCarbDB?

Update 2015-01-19 15.19: I contacted the corresponding author about this and now the EurocarbDB link in the original paper works.

First published online a few months ago in the journal Bioinformatics (September 12th, 2014):

• EUROCarbDB(CCRC): a EUROCarbDB node for storing glycomics standard data

The name of this resource is not the snappiest name out there. "Oh, you're interested in resources for glycomics, have you tried EuroCarbDB-open parentheses-cee-cee-ar-cee-close parentheses?", but leaving that aside the paper lists the following URLs as part of the abstract:

Availability and implementation: The installation with the glycan standards is available at http://glycomics.ccrc.uga.edu/eurocarb/. The source code of the project is available at https://code.google.com/p/ucdb/.

The first link says that the server is down. The parent page (http://glycomics.ccrc.uga.edu/ seems to make no mention at all of this resource (not that I can find anywhere). Following the second link in the abstract, I found the following text:

An incubator project for the future direction of the EUROCarbDB project. More to follow.... This new project is in it's infancy - please use the original EUROCarbDB site. A new project will be hosted at UniCarb-DB (http://www.unicarb-db.org to reflect the continued work of the developers

I followed the first of these links to the 'original' EUROCarbDB site. This Google Code page in turn told me that the online version of EuroCarbDB is hosted by the European Institute of Bioinformatics.

Following the link for the online version of EUROCarbDB takes me to what seems to be a closed down site at the EBI titled 'What happened to the EuroCarbDB website?' which has this to say:

The pilot project ended in 2009 but efforts to obtain renewed funding have unfortunately not been successful. The EuroCarbDB website was hosted by the Protein Data Bank in Europe at EMBL-EBI but has now been discontinued

So that's all very helpful then.

Are there too many biological databases?

The annual 'Database' issue of Nucleic Acids Research (N.A.R.) was recently published. It contains a mammoth set of 172 papers that describe 56 new biological databases as well as updates to 115 others. I've already briefly commented on one of these papers, and expect that I'll be nominating several others for JABBA awards.

In this post I just wanted to comment on the the seemingly inexorable growth of these computational resources. There are databases for just about everything these days. Different species, different diseases, different types of sequence, different biological mechanisms…every possible biological topic has a relevant database, and sometimes they have several.

It is increasinly hard to even stay on top of just how many databases are out there. Wikipedia has a listing of biological databases as well as a category for biological databases, but both of these barely scratch the surface of what is out there.

So maybe one might turn to 'DBD': a Database of Biological Datsbases or even MetaBase which also describes itself as a 'Database of Biological Databases' (please don't start thinking about creating 'DBDBBDB': A Database of Databases of Biological Databases!).

However, the home pages of these two sites were last updated in 2008 and 2011 respectively, perfectly reflecting one of the problems in the world of biological databases…they often don't get removed when they go out of date. In a past life, I was a developer of several databases at something called UK CropNet. Curation of these databases, particularly the Arabidopis Genome Resource, effectively stopped when I left the job in 2001 but the databases were only taken offline in 2013!!!

So old, out-of-date, databases are part of the problem, but the other issue is that there seems to be some independent databases that — in an ideal world — should really be merged with similar databases. E.g. there is a database called BeetleBase that describes its remit as follows:

BeetleBase is a comprehensive sequence database and important community resource for Tribolium genetics, genomics and developmental biology.

This database has been around since at least 2007 though I'm not entirely sure if it is still being actively developed. However, I was still surprised to see this paper as part of the N.A.R. Database issue:

• iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum

iBeetle-Base has been seemingly developed from a separate group of people from BeetleBase. Is it helpful to the wider community to have two databases like this, with confusingly similar names? It's possible that iBeetle-Base people tried reaching out to the BeetleBase folks to include their data in the pre-existing database, but were rebuffed or found out that BeetleBase is no longer a going concern. Who knows, but it just seems a shame to have so much genomics information for a species split across multiple databases.

I'm not sure what could, or should, be done to tackle these issues. Should we discourage new databases if there are already existing resources that cover much of the subject matter? Should we require the people who run databases to 'wind up' the resources in a better way when funding runs out (i.e. retire databases or make it abundantly clear that a resource is no longer being updated)? Is it even possible to set some minimum standards for database usage that must be met in order for subsequent 'update papers' to get published (i.e. 'X' DB accesses per month)?

diArk – the database for eukaryotic genome and transcriptome assemblies in 2014 →

A new paper in Nucleic Acids Research describes a database that I was not aware of. The abstract features an eye-catching, not to mention ambitious, claim (the emphasis is mine):

The database…has been developed with the aim to provide access to all available assembled genomes and transcriptomes.

The diArk database currently features data on 2,771 species. There are many options to filter your search queries including filtering by 'sequencing type' and by the status of completion. So when I search for 'completed' genome sequencing projects, it reports that there 3,626 projects corresponding to 1,848 species. The FAQ has this to say regarding 'completeness':

The term completeness is intended to describe the coverage of the genome and the chance to find all homologs of the gene of interest.

I was a bit put off by the interface to this database. As far as I can tell, diArk is mostly containing links to other resources (rather than hosting any sequence information). There are lots of very small icons everywhere which are hard to understand (unless you mouse over each icon). When I went to the page for Caenorhabditis elegans, I was struck by the confusing nature of just posting links to every C. elegans resource on the web. There are 12 'Project' links listed. Which one gives you access to the latest version of the genome sequence?

diArk summary of Caenorhabditis elegans data

As a final comment, I noticed that the latest entry on the diArk news page is from September 2011 which is a bit worrying (nothing newsworthy has happened in the last 3 years?).