[Biopython-dev] Bio.WWW; database access

Michiel De Hoon mdehoon at c2b2.columbia.edu
Wed Nov 14 02:16:06 UTC 2007

> However, what about the fact that some online resources (e.g. GenBank) 
> will return several sorts of data (e.g. journal references and 
> sequences) and/or in a range of file formats (e.g. GenBank, Fasta, XML, 
> ...).  In this situation, having the online interface separate from the 
> format parsers makes some sense.

I agree. My suggestion would be

1) Split Bio.WWW.ExPASy (access to Swissprot, Prodoc, Prosite) between
Bio.SwissProt, Bio.Prosite, and Bio.Prodoc as appropriate 
2) Put Bio.WWW.InterPro in Bio.InterPro
3) Put Bio.WWW.SCOP in Bio.SCOP
4) NCBI Entrez is a special case since it contains many different sorts of
data. Bio.GenBank doesn't seem to be the best place for it, as NCBI Entrez is
much more than GenBank. I would therefore suggest to move Bio.WWW.NCBI to
Bio.Entrez (currently an empty module in Biopython), and merge this code with
the database access code in Bio.GenBank and Bio.EUtils.


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032
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