[Biopython] Access Entrez gene DB using rettype 'gb'

[Peter]

On Wed, Dec 8, 2010 at 1:12 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> David;
>
>> Thanks, Brad and Peter, for your solutions. I'm going to use a modified
>> version of Brad's Internet-based script to work with my genes of
>> interest. I'll keep your solution in mind, Peter, in case I need to use
>> the script offline in the future.
>
> Glad that those worked out for you.
>
>> One question that this has prompted (for me) is: Why not extend
>> BioPython to support queries that NCBI does not, itself, support? I am a
>> newcomer, but it seems like the Entrez model is simply a wrapper for the
>> NCBI interfaces and protocols. But there is potential for more.
>>
>> Is there any interest in boosting the Entrez model to support common
>> tasks like bacterial gene lookups?
>
> That sounds great. Biopython is completely open source and we
> welcome contributions of general purpose, tested code. Support for
> different tasks exists because generous folks had a need for that
> functionality and coded it in a reusable way.
>
> Entrez gene XML support would be a fairly big task, since there is
> quite a bit in there that might be of interest to different users,
> but definitely welcome.

What's wrong with the current Entrez XML parser for the gene
database? Is this one of the corner cases where the NCBI are
not currently returning "proper" XML with a DTD?

> Another useful contribution would be a Cookbook entry describing the
> problem and solution. Since these are examples, they can be more
> specific than a library but also provide useful direction and help
> for others with similar needs:
>
> http://biopython.org/wiki/Category:Cookbook

Absolutely - if you can work out some standard useful combinations
of the Entrez tools as cookbook form, they may form the basis of a
potential higher level interface on top of the core Entrez API  (I think
Michael has commented on this before).

Peter