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

[Peter]

> You can do a linked search/retrieve using Bio.Entrez as documented in
> our tutorial for an esearch/efetch example using nucleotide sequences.
> This is currently done as the last example in the chapter, so I'm
> considering making this topic a little more high profile (and moving
> it before the examples).

I've make this example into a full section, and linked to it more
prominently in the earlier sections.

> In addition to encouraging the use of Bio.Entrez by documenting it
> prominently in the tutorial,

The tutorial in CVS has been updated to cover using PubMed with
Bio.Entrez, and now doesn't mention the search or download functions
in Bio.PubMed or Bio.GenBank.

> ... 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.

Bio.Entrez in CVS will now issue a warning if an email address has not
been supplied, in order to encourage user compliance with the NCBI
guidelines.  Does anyone think this is too harsh?  There is a small
risk this will encourage people to use a dummy email address just to
silence the warning...

Also, as a side effect of this change, the wrapper functions in
Bio.PubMed and Bio.GenBank will now trigger this new warning (unless
an email address has been setup in Entrez), e.g.

>>> from Bio import Entrez, PubMed
>>> Entrez.email = "A.N.Other at example.com"
>>> from Bio import PubMed
>>> pubmed_id_list = PubMed.search_for("orchids")
>>> print pubmed_id_list
['18701671', '18687799', '18627489', '18627452', '18586527', ...., '17751120']
>>> print len(pubmed_id_list)
226

Peter