[BioPython] Bio.Medline parser

[Michiel de Hoon]

Done -- see CVS.

--Michiel.


--- On Fri, 8/8/08, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [BioPython] Bio.Medline parser
> To: mjldehoon at yahoo.com
> Cc: biopython at biopython.org
> Date: Friday, August 8, 2008, 1:32 PM
> On Fri, Aug 8, 2008 at 3:14 PM, Michiel de Hoon wrote:
> >
> >> Maybe it would make sense just to describe
> >> the keys in the docstring, and that would be
> enough.
> >
> > OK I'll go with just the docstring for now. If
> users ask for it, we can add a more
> > descriptive function later.
> >
> >> Maybe we can just deprecate Bio.Medline (i.e. the
> >> plain text parser) in favour of Bio.Entrez (and
> its XML parser)?
> >
> > Usually I am in favor of deprecating modules if their
> usefulness is not clear. In
> > this case, however, Medline is a major database, the
> Medline record format is
> > readily available from NCBI, it is human readable
> (more or less) and computer
> > readable, the resulting Bio.Medline.Record may be
> easier to deal with than the
> > record created from XML by Bio.Entrez, and the parser
> is straightforward but
> > not entirely trivial. Being able to parse such a file
> is something I'd expect from
> > Biopython.
> 
> That sounds sensible.  Maybe we should have an example in
> the Tutorial
> of using Bio.Entrez to download some data in the plain text
> MedLine
> format, and parsing it with Bio.MedLine?  And perhaps also
> an
> equivalent using the XML Medline format parsed using
> Bio.Entrez?
> 
> Peter