Question: Options For Automatically Retrieving Entrez Gene Names From Id?
0
gravatar for Matt LaFave
6.0 years ago by
Matt LaFave280
San Diego, CA
Matt LaFave280 wrote:

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.

perl bioperl entrez • 2.4k views
ADD COMMENTlink modified 6.0 years ago by Neilfws48k • written 6.0 years ago by Matt LaFave280

What species are you are you referring to?

ADD REPLYlink written 6.0 years ago by Bert Overduin3.6k

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.

ADD REPLYlink written 6.0 years ago by Matt LaFave280
1
gravatar for Neilfws
6.0 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

You can use the TogoWS REST service. For example:

http://togows.dbcls.jp/entry/gene/566758/official_symbol
# returns "brca2"
ADD COMMENTlink written 6.0 years ago by Neilfws48k
0
gravatar for Bert Overduin
6.0 years ago by
Bert Overduin3.6k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.6k wrote:

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.

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Bert Overduin3.6k
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