[Bioperl-l] NCBI Genbank ID to TaxonID via Bioperl?

[Jason Stajich]

cool - i don't remember that being part of the eutils interface  
before - I'll see about adding it to the Bio::DB::Taxonomy module now.

-jason
On Jun 22, 2005, at 2:46 AM, Rob Edwards wrote:

> Possibly the easiest way to do this is using the eutils facilities.
>
> e.g.
>
> This url will retrieve the tax id for gi 1234
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi? 
> dbfrom=nucleotide&db=taxonomy&id=1234
>
> will return:
> <eLinkResult>
> <LinkSet>
>     <DbFrom>nucleotide</DbFrom>
>     <IdList>
>         <Id>1234</Id>
>     </IdList>
>     <LinkSetDb>
>         <DbTo>taxonomy</DbTo>
>         <LinkName>nucleotide_taxonomy</LinkName>
>         <Link>
>             <Id>9940</Id>
>         </Link>
>     </LinkSetDb>
> </LinkSet>
> </eLinkResult>
>
> Rob
>
>
> On Jun 21, 2005, at 6:27 AM, Michael Spitzer wrote:
>
>
>> Dear All,
>>
>> For a list of approx. 20 GI numbers (NCBI GenBank IDs) I need the  
>> taxon ID as given in the corresponding full GenBank record. Which  
>> is the easiest way to accomplish this task automatically? Does  
>> Bioperl help? Can one access this function via the NCBI website  
>> (possibly, using Bioperl)? Or, does one have to download the whole  
>> GenBank database?
>>
>> All I could find out is that there is a function 'gi2taxid' in the  
>> NCBI toolkit, but I have no experience with using the toolkit, and  
>> I hope that there is an easier 'Bioperl' way to solve the problem  
>> - could BIO::DB::NCBIHelper be the way to go? Any help or hints  
>> are greatly appreciated!
>>
>> Kind regards,
>>
>> Michael Spitzer
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>>
>>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/