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

[Rob Edwards]

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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