[Bioperl-l] EUtilities interface

Sendu Bala bix at sendu.me.uk
Wed Jun 21 14:23:28 EDT 2006


Chris Fields wrote:
> I'm working on a new eutilities interface which I hope to commit by late
> summer.  It's basically a rewrite of WebDBSeqI/NCBIHelper.  I set up a
> generic web database interface, which I call Bio::DB::WebDBI, and the
> EUtilities interface, Bio::DB::EUtilitiesI.  The idea is that you can query
> NCBI for any information available via Entrez Utilities (i.e. taxonomy,
> pubmed, sequences, dbSNP, Gene, etc); you're not limited to sequence-only
> info like Bio::DB::WebDBSeqI.  
> 
> My only concern is confusion over names, particularly WebDBI vs. WebDBSeqI.
> Does anyone think this will be an issue?

Well, I don't. Sounds good to me. What's the intended relationship 
between WebDBI and EUtilitiesI? Would your work end up in the removal of 
direct XML parsing from Bio::DB::Taxonomy::entrez? Or would it just 
convert the code that gets the XML to a one line statement or so?


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