[Biopython-dev] Namespace for online resources?

[Peter Cock]

On Fri, Feb 1, 2013 at 1:54 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Hi Lenna,
>
>> Regarding point (2), is your primary concern namespace clutter or
>> importing efficiency?
>
> Regarding point (2), my primary concern is that a Bio.WWW module would
> group together modules that don't have much in common with each other. I
> agree to your point that the category of internet access is more fundamental
> than the category of parsers. But still, which modules should then go into a
> Bio.WWW module? Any module whose sole purpose is to use the internet (that
> would exclude Bio.Entrez)? Any module whose main purpose is to use the
> internet? This would be unclear; for example, Bio.Entrez may or may not fall
> in that category, depending on how you use the module. Any module whose
> functionality includes internet access? Then if one day we add access to the
> JASPAR database over the internet to Bio.Motif, it would have to move to
> Bio.WWW.
>
> Currently most modules are organized by theme (Bio.Seq, Bio.Motif,
> Bio.Cluster, Bio.Phylo, Bio.Entrez, etc.). For each theme, we have one
> module, one chapter in the documentation, one test of unit tests, one set of
> doctests, which I think is a huge advantage both in terms of clarity and in
> terms of user experience.

Also with the theme approach, most (if not all) the themes are likely to
have some online resources (databases or remote APIs). On those
grounds it makes sense to keep online motif functionality (like weblogo)
under Bio.Motif, and so on.

People leaning for a Bio.WWW grouping: Bow, Lenna, Kevin
(which could be a big disruption with lots of code relocation)

People leaning against a Bio.WWW grouping: Michiel, Peter (me)
(which would also be the status quo, so no disruption).

In the specific case of Kevin's TAIR code for fetch Arabidopsis sequences,
Bio.TAIR (lower case?) is consistent with current usage. Somewhere under
Bio.Seq* also seems sensible to me, as I wrote at the start of this thread.

Regards,

Peter