[Biopython-dev] Re: Re: Bio.PubMed find_related additional keyword options

[Michael Hoffman]

On Thu, 22 May 2003, Andrew Dalke wrote:

> Michael Hoffman:
>  > Naaah, I'll just use EUtils instead... Thanks for the pointer.
> 
> Let me know of what improvements are needed for a final release.

Some suggestions:

1) Print debug info (DUMP_URL etc.) to stderr, not stdout. I can supply
a patch if you want.

2) Include the pubmed DTD and necessary includes with the EUtils
distribution.

3) Use Bio.WWW.RequestLimiter. I'll volunteering a patch.

4) Documentation. ;-) I unfortunately can't afford to pay for this,
but if the README explained briefly what each of the modules did and
said that the bulk of the documentation was in their docstrings, that
would be a great start.

> > However, it is useful to have the ResultsParser from
> > Bio.PubMed.find_related exposed since that functionality is not yet in
> > EUtils.
> 
> Like that one, thanks!

I can supply a quick patch to BioPython to do this. Jeff?

> (There are a few other things, like I learned today that EUtils now
> has its own machine name - that was announced on NCBI's EUtils
> mailing list.  These need to be changed in the EUtils code ...
> Someone want to pay for that?  :)

I'd like to but can't, but I will do it for free if you want. :-)
-- 
Michael Hoffman <grouse at alumni.utexas.net>
The University of Texas at Austin