When your tools are broken, just change the data

Update August 7 2020
The gene symbol renaming is now official. Here’s the publication (not open access, should be), coverage at The Verge and more coverage at The Register. The latter with quotes from me.

It’s been 3 years since we last visited that old favourite recurring topic, data corruption by Excel. Specifically, the unwanted auto-conversion of identifiers that look like dates, e.g. SEPT1, to – well, dates.

Here’s a new twist – well, a two year-old twist in fact, as I don’t keep up to date with this field any longer:

Yes, in 2017 the HGNC decided that the solution to this long-standing issue is to rename the offending genes to prevent the auto-conversion. I’m yet to determine whether anything more came of the proposal.

It is I suppose a practical suggestion that will work. The newsletter states that:

Our initial consultation with the research community publishing on these genes had very mixed results

I bet it did. However, given that ongoing consultation with the research community about the inappropriate use of software has had essentially no results in 15+ years, perhaps it is the most effective solution to the problem.

What’s in a (gene) name?

I’ve posted before on standard names (or lack thereof) for genes and proteins and in particular, the whacky names of which biologists are so fond. Hopefully they now realise that in the age of bioinformatics – where we have to find stuff easily – descriptions such as ken and barbie, scott of the antarctic or glass-bottom boat are, um, unhelpful to say the least.

So hot on the heels of my “man, you can publish anything in bioinformatics these days” post comes:

Seringhaus, M. et al. (2008).
Uncovering trends in gene naming.
Genome Biology 9:401 Abstract | DOI 10.1186/gb-2008-9-1-401

We take stock of current genetic nomenclature and attempt to organize strange and notable gene names. We categorize, for instance, those that involve a naming system transferred from another context (for example, Pavlov’s dogs). We hope this analysis provides clues to better steer gene naming in the future.

It’s actually a fun and informative read.

See also: FlyNome, Clever Drosophila gene names and Sonic Hedgehog Sounded Funny, at First. From the latter source: “It’s a cute name when you have stupid flies and you call it a ‘turnip,’ ” Dr. Doe said. “When it’s linked to development in humans, it’s not so cute any more.”