8
$\begingroup$

I've struggled in the past with designing data(bases) around gene-identifiers that evolve over time. For example, UniProt and Ensembl change their identifiers for certain proteins/genes and the IDs go stale after a while (years). HGNC seems possibly better for this? What I'd like is to have a single unique identifier for each human gene that will remain stable for many years. I know genes get re-classified occasionally, but you shouldn't end-up with a new identifier for the same locus.

Suggestions?

Thanks

$\endgroup$
1
  • $\begingroup$ We use HGNC. But there's certainly no guarantee the symbol will stay the same for years. $\endgroup$ Jan 17, 2017 at 19:19

1 Answer 1

1
$\begingroup$

Maintaining IDs consistency is a common problem. I've never seen any reasonable solutions for it and don't believe that there are any. However, there are a few shortcuts.

  1. You can create an extra table with aliases for later renamings and refer them to original ids. Pros - it is flexible. Cons - maintaining is exhausting and you need to figure a way to explain to users why they input one id and receive other.
  2. The solution is pretty obvious - if you'd like to have "a single unique identifier for each human gene that will remain stable for many years" you can just take a snapshot of current state of any database you like and don't touch it for many years. You can release version-specific releases of your database and specify versions of reference database you use. E.g. "Glioblastoma_drug_perturbation_2016_(GRCh38_ENS87)".
$\endgroup$

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .