Question: Is There An Easy And Automated Way To Resolve Gene Names Into A Consistent Naming System?
1
gravatar for KCC
7.4 years ago by
KCC4.0k
Cambridge, MA
KCC4.0k wrote:

Suppose I have several lists of genes in a text file, from different papers and different years. The gene names come from different naming systems.

How would you go about translating them all into ensembl gene names?

gene • 1.8k views
ADD COMMENTlink modified 7.4 years ago by Damian Kao15k • written 7.4 years ago by KCC4.0k
4
gravatar for girlwithglasses
7.4 years ago by
Oakland, CA
girlwithglasses280 wrote:

ID / gene name mapping is a problem that will be keeping bioinformaticists employed for the next few centuries. AFAIK there are no "easy" ways to convert the names given in various publications to the names used by Ensembl, unfortunately, but you could try some of the tools listed here: ID mapping tools.

ADD COMMENTlink written 7.4 years ago by girlwithglasses280
2
gravatar for Istvan Albert
7.4 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

Short answer: there probably isn't.

For a possible strategy see the most viewed Biostar question (with 18K views): Gene ID conversion tool

ADD COMMENTlink written 7.4 years ago by Istvan Albert ♦♦ 84k
0
gravatar for Damian Kao
7.4 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

Some kind of a mass literature data-mining operation could make it more amenable by linking terms and phrases together. Maybe some of those cool IBM Watson natural language parsing algorithms can help in this.

ADD COMMENTlink written 7.4 years ago by Damian Kao15k
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