[Biopython-dev] Bio.Entrez / next Biopython release.

[Michiel de Hoon]

Hi everybody,

As discussed previously, I created a module Bio.Entrez for interacting with NCBI's Entrez databases (GenBank, PubMed, and many others). This is essentially Bio.WWW.NCBI renamed to Bio.Entrez; Bio.WWW.NCBI still exists in the same location but is deprecated. In the process, I updated this module to include all of NCBI Entrez Programming Utilities, and deprecated those that have been superseded at NCBI. The code is now in CVS as Bio/Entrez.py. In hindsight, it would probably have been a better idea to use Bio/Entrez/__init__.py in case we want to expand Bio.Entrez, but anyway this can be rectified before creating the next Biopython release.

I also wrote some documentation for Bio.Entrez. You can have a preview at http://biopython.org/DIST/docs/tutorial/Tutorial-proposal.html; Chapter 6 describes Bio.Entrez, and gives a good overview of the current status of this module.

The module Bio.Entrez was created in response to Bug #2393:
http://bugzilla.open-bio.org/show_bug.cgi?id=2393
Using Bio.Entrez, we can fix this bug easily, and then create a new release. This is one thing to consider though:
Like Bio.WWW.NCBI, Bio.Entrez provides access to NCBI's Entrez databases but does not provide parsers for the output generated by NCBI (note: some file formats generated by NCBI Entrez' sequence databases can be parsed by Bio.SeqIO). Our options are then:
1) Keep Bio.Entrez as a module only to access NCBI Entrez, but not to parse the results.
2) Add parsers to Bio.Entrez.
3) Make a new Biopython release now, and potentially add parsers later.

Suggestions, preferences, comments, anybody?

--Michiel.

       
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