[Biopython-dev] Online access, Bio.PubMed & Bio.GenBank vs Bio.Entrez

[Peter]

In August 2008 Peter wrote:
> This is a slightly long email covering what to do with the online code
> in Bio.PubMed and Bio.GenBank, and how to make Bio.Entrez easier to
> use.  All these modules are essentially wrapping access to the NCBI
> Entrez database via the Entrez Programming Utilities (EUtils).
> http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

One problem I raised in August with the online parts of Bio.PubMed
and Bio.GenBank was they didn't provide a way to supply the user's
email address.  An email address can now be specified via Bio.Entrez
BEFORE calling the Bio.PubMed or Bio.GenBank online functions,
however this is non-obvious.

However, we still have the inherent problem that these simple
functions do not allow use of the NCBI's history feature.  (Of course,
for some situations this is never going to apply and therefore isn't
a problem).

> In addition to encouraging the use of Bio.Entrez by documenting it
> prominently in the tutorial, we could go further and deprecate the
> "user friendly" Bio.PubMed and Bio.GenBank wrapper functions.
> What do people think of this?  Deprecating the Dictionary classes in
> particular could be a good idea as they use the old fashioned parser
> objects.

In the release notes for Biopython 1.48, I wrote:
>> Bio.PubMed and the online code in Bio.GenBank are now considered
>> obsolete, and we intend to deprecate them after the next release.
>> For accessing PubMed and GenBank, please use Bio.Entrez instead.

Are we agreed on deprecating (some or all of) these bits for Biopython
1.49?  I'm happy to put the question to the main mailing list first.

Peter