[Bioperl-l] Getting gene symbol and gene descriptions

Chris Mungall cjm at berkeleybop.org
Mon Oct 27 20:44:24 EDT 2008


You could do a SQL query for these on the GO database:

http://berkeleynop.org/goose

On Oct 27, 2008, at 5:08 PM, John O. Woods wrote:

> Hi folks,
>
> I have lists of protein-coding genes in fruit fly (by FlyBase id),  
> and in
> arabidopsis thaliana (by TAIR locus ID: AT...). I need to get the gene
> symbol name and gene description for each of these.
>
> I tried using GenPept::get_Stream_by_id, but I can't figure out how to
> extract the symbol or description that way.
>
> I've also tried BioMart, but that doesn't seem to have data for  
> Arabidopsis
> (and it's timing out for fruit fly for some reason).
>
> There's also a flat file on TAIR's website, but it looks to be out  
> of date.
> I'd much prefer to get the symbols that are considered "primary" in  
> GenPept.
>
>
> I was also wondering: I know FlyBase allows anonymous access to its  
> Chado
> DB. Is this possible with TAIR? They seem to ignore my emails,  
> sadly--or
> perhaps I'm sending them to the wrong place.
>
> Cheers,
> John Woods
> UT Austin
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