{"id":657,"date":"2008-07-02T23:32:15","date_gmt":"2008-07-02T23:32:15","guid":{"rendered":"http:\/\/occamstypewriter.org\/mindthegap\/2008\/07\/02\/in_which_i_crave_some_nomenclatural_consistency\/"},"modified":"2008-07-02T23:32:15","modified_gmt":"2008-07-02T23:32:15","slug":"in_which_i_crave_some_nomenclatural_consistency","status":"publish","type":"post","link":"https:\/\/occamstypewriter.org\/mindthegap\/2008\/07\/02\/in_which_i_crave_some_nomenclatural_consistency\/","title":{"rendered":"In which I crave some nomenclatural consistency"},"content":{"rendered":"

I was chatting with Richard<\/a> the other day about his pet protein ZRANB2. Something about the name rang a bell, and sure enough I found that one of its orthologues was present in my own cell morphology screen. I was interested to see that we called the same gene ZNF265 instead, so Richard tootled around and discovered that this gene’s ‘official’ symbol was ZNF265 according to OMIM<\/a>, but ZRANB2 according to NCBI Entrez<\/a> and HGNC<\/a>.<\/p>\n

\n\"\"<\/p>\n

\nSweeter than pancakes<\/strong> iHOP is one of several useful genomics resources<\/p>\n

\nMost genes have a bewildering array of synonyms, of course, but in this day and age, you would hope that the genomics community would have settled on one unique one. In short, Richard and I shouldn’t have had to stop to disambiguate before delving into the really interesting questions, and this was the third such hitch I’d experienced in the past month. I’ve been using the superlative iHOP<\/a> (Information Hyperlinked over Proteins) as my one-stop genomics shop (a site which, incidentally, falls firmly into the ZNF265 camp), so I emailed the person in charge, Robert Hoffman, to see if he could shed any light.<\/p>\n

\nRobert, who turns out to be a lovely chap, told me that the HGNC is the ultimate authority; they curate and publish the latest names, and other organizations pick them up. “Of course,” he pointed out, “this does not mean that other people will understand you better if you use the official HGNC name, because many continue using the names the are used to.” So why didn’t iHOP call Richard’s gene by the HGNC appellation, ZRANB2? He confessed that this information is updated on iHOP only twice a year because it takes a long time for people to take up the trend, and meanwhile the NCBI ID number is more critical. NCBI, he notes, is quicker to respond to any changes in HGNC nomenclature.<\/p>\n

\nSo, I’ve duly bookmarked the HGNC website, but I still think there is a big problem out there. If any of you are in the gene discovery business, you’ll know that when you start getting interested in a new gene, it’s a nightmare to find a consensus nucleotide sequence in GenBank<\/a>. I am not wholly innocent in this entire affair, as I single-handedly deposited about sixty different sequences for the feline leukemia virus envelope gene into GenBank during grad school, a veritable menagerie of subtle and esoteric polymorphisms. If you want to find out the common or garden FeLV env sequence in this mess, good luck to you. Associated with each gene name are not just polymorphic sequences, but truncations, splice variants, fusion proteins and the like. The FeLV community recognizes at least two ‘type species’ of the virus \u2013 FeLV-A\/Glasgow and FeLV-61E \u2013 but this information is not, as far as I can see, linked to any of the GenBank entries. And it’s the same story for any gene you look up \u2013 which of the hundreds of entries, or sometimes thousands, is the ‘right’ one?<\/p>\n

\nAnd the next step is even more disheartening. Looking up your new gene of interest in PubMed is not an easy way to grasp a coherent idea of what’s been published in the literature. Abstracts are littered with synonyms (and some pairs of different genes have the same synonym), but there is no unique gene identifier, as far as I can see, associated with the abstracts. I have no doubt that text miners are hard at work at this problem, but I haven’t seen anything helpful recently. And when you start being interested in homologues in other species, things start to get even murkier.<\/p>\n

\nI realize that my gripes are probably na\u00efve and possibly reflect ignorance of the state of play, but I suspect I am not alone. Maybe a good first step would be for journals to enforce the use of the NCBI ID number (or some other approved unique identifier) in all abstracts that mention a gene name, and for PubMed to add them retrospectively to their older abstracts.<\/p>\n","protected":false},"excerpt":{"rendered":"

I was chatting with Richard the other day about his pet protein ZRANB2. Something about the name rang a bell, and sure enough I found that one of its orthologues was present in my own cell morphology screen. I was … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-657","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts\/657","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/comments?post=657"}],"version-history":[{"count":0,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts\/657\/revisions"}],"wp:attachment":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/media?parent=657"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/categories?post=657"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/tags?post=657"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}