Options For Automatically Retrieving Entrez Gene Names From Id?

Question

[Matt LaFave]

This is somewhat related to my Bioperl Bio::Db::Entrezgene No Longer Works. I've been using the BioPerl module Bio::DB::EntrezGene to automate my conversion of EntrezGene IDs (as retrieved from BioMart) to Entrez gene names. However, that module no longer seems to work. I'd still like to have a automated way of retrieving Entrez gene names, so I was wondering if anyone here had any suggestions as to how to go about it. For example, are there other (still-functional) BioPerl modules that can retrieve the gene name, given the EntrezGene ID? It doesn't have to be in BioPerl (although something in Perl would be nice); really, I'd just like to avoid having to pull down gene entries manually at Batch Entrez.

[Bert Overduin]

What species are you are you referring to?

[Matt LaFave]

Most of the time, the gene names I need to fetch are for zebrafish, but I've also needed to do it for humans and mice.

Answer 1

[Neilfws]

You can use the TogoWS REST service. For example:

http://togows.dbcls.jp/entry/gene/566758/official_symbol
# returns "brca2"

Answer 2

[Bert Overduin]

As I expect that the Entrez gene name is basically the same as the gene name used in Ensembl, you could use the Ensembl REST API for this. The nice thing is that you can incorporate the REST requests in scripts written in any language, or use them directly from the command line.

For example the REST request

http://beta.rest.ensembl.org/xrefs/name/zebrafish/566758?external_db=EntrezGene&content-type=application/json

returns

[{"display_id":"brca2","primary_id":"566758","version":"0","description":"breast cancer 2, early onset","dbname":"EntrezGene","synonyms":["fancd1"],"info_type":"DEPENDENT","info_text":"","db_display_name":"EntrezGene"}]

where brca2 is the gene name.

Hope this helps.