[Biopython-dev] [Bug 2393] Bio.GenBank.NCBIDictionary fails with release 1.44

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Nov 13 09:24:31 UTC 2007


------- Comment #7 from biopython-bugzilla at maubp.freeserve.co.uk  2007-11-13 04:24 EST -------
Michiel has moved this discussion to the developers' mailing list.

> I'd be happy to use the code from Bio.WWW.NCBI, but I don't think that
> Bio.WWW is a good location for an EntrezDictionary class. As a case in point,
> I didn't know that Bio.WWW contains code to access NCBI Entrez, and I
> couldn't guess it from its name.

I correctly guessed from the name Bio.WWW.NCBI that it was an API for the
NCBI's online tools (but I tend to refer to the NCBI rather than Entrez in

> With a module like Bio.GenBank, it is clear from its name what it is about.

Yes, it does mean both the file format and the online database.

> Furthermore, the different submodules Bio.WWW.ExPASy, Bio.WWW.InterPro,
> Bio.WWW.NCBI, and Bio.WWW.SCOP don't seem to have much in common.

Apart from all being interfaces to online/web databases? Well no, but if this
was followed more strictly it would make the top level module list much

> I think that the existing modules Bio.SwissProt, Bio.Prosite, Bio.InterPro,
> Bio.SCOP, containing the respective parsers, are more logical places to keep
> the database access code.

Maybe.  I agree we should rationalise things, and getting rid of Bio.WWW might
be the most straight forward simplification - see mailing list.

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