When scripts fail, check databases

January 19, 2008 — nsaunders

Note to self: how many biological databases provide their release notes as an RSS feed?

One of my database mining scripts failed today; on reading the SwissProt What’s New page, I discovered why:

Changes concerning keywords (KW line)
Modified keywords:
    * Phosphorylation -> Phosphoprotein

More notes:

  • Is keyword a good way to mine SwissProt records?
  • The MOD_RES line changed recently too; clearly these changes can happen anytime, anywhere in a record
  • SwissProt PTMs also have AC and ID; to be incorporated in all records eventually?
Posted in bioinformatics, computing, perl, research diary, web resources.

3 Responses to “When scripts fail, check databases”

  1. Dan Says:
    January 21, 2008 at 10:50 pm

    For all upcoming UniProtKB changes please see http://www.expasy.org/sprot/relnotes/sp_soon.html

    Hope that helps!

  2. Elisabeth Gasteiger Says:
    January 22, 2008 at 7:06 pm

    The new UniProt web site will also provide news feeds:
    http://beta.uniprot.org/help/changes

  3. nsaunders Says:
    January 22, 2008 at 7:10 pm

    Good to know! Thanks Elisabeth.

Leave a Reply

« Researcher ID

Web trends in science: javascript »