Question

Is There An Easy And Automated Way To Resolve Gene Names Into A Consistent Naming System?

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11.2 years ago

KCC ★ 4.1k

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 • 2.5k views

ADD COMMENT • link updated 11.2 years ago by Damian Kao 16k • written 11.2 years ago by KCC ★ 4.1k

score 4 · Answer 1 · 2013-02-15

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11.2 years ago

girlwithglasses ▴ 280

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 COMMENT • link 11.2 years ago by girlwithglasses ▴ 280

score 2 · Answer 2 · 2013-02-15

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11.2 years ago

Istvan Albert 100k

Short answer: there probably isn't.

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

ADD COMMENT • link 11.2 years ago by Istvan Albert 100k

score 0 · Answer 3 · 2013-02-15

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11.2 years ago

Damian Kao 16k

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 COMMENT • link 11.2 years ago by Damian Kao 16k