Text Mining: Extracting Some Genes And Some Variations From An Article.
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10.4 years ago

Hi all,

I've got a large article containing many sentences like the following one: (that is to say, it contains a Gene and some variations )

In the above-mentioned study by Roden & al. , mutations in SCN2B were identified in 2 unrelated individuals with atrial fibrillation. The mutations (c.82C>T resulting in p.R28W, and c.83G>A resulting in p.R28Q) were located in the amino terminus of the β2-subunit,

I'm would like to extract a table with the gene identifiers and the mutations in the proteins. I'm about starting collecting those data by hand :-( , do you know any tool that could help me ?

Thanks !

text identifiers extraction variant • 2.0k views
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not sure but at least forgene symbols, can't you get that from genecard ?!

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10.4 years ago

Have you tried the systems reviewed here: http://www.biomedcentral.com/1471-2105/10/S8/S1/table/T1

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Thanks Casey , That's interesting, I'll try tomorrow.

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10.4 years ago

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Hopefully it will give you some clue or some inspiration.

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10.4 years ago
Javier • 0

Maybe it's a little bit old, but the following paper includes relevant information about the issue. Good luck,

http://genomebiology.com/2005/6/7/224

Javier.

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10.4 years ago
Rama ▴ 40

HI,

You can use Reflect to extract gene identifiers. Some journals already highlight the gene names using Reflect. http://reflect.ws/ R

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