[BioPython] Bio.Medline parser

[Peter]

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