[Biopython-dev] [BioPython] PubMed find_related

[Peter]

On Sat, Nov 29, 2008 at 5:22 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>
> The problem this user encountered was that the DeprecationWarning in
> PubMed.find_related function contained very little information and did
> not mention that Entrez.elink is the appropriate function to use:
>
> "Find related articles in PubMed, returns an ID list (DEPRECATED).
> Please use Bio.Entrez instead as described in the Biopython Tutorial."

We could make the deprecation warnings from Bio.PubMed (and the online
bits of Bio.GenBank) a little more explicit about which bits of
Bio.Entrez to use.  I made a start on updating Bio/PubMed.py on my
work computer on Friday, so I'll try to remember to finish this off on
Monday.

> and in addition that currently the description of Bio.Entrez.elink in the
> tutorial is almost empty. Instead of adding a function to Bio.Entrez
> that helps this particular user, we should improve our documentation
> to enable all users to use Bio.Entrez appropriately.

The tutorial update for elink looks good (see below).

> The set of helper functions to Bio.Entrez that we could write is
> virtually endless; we should not go down that path.

I take your point - there are lots of possible helper functions we
could consider.  As long as we cover the typical use cases in the
tutorial that should be enough.

On Sat, Nov 29, 2008 at 7:04 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> I've expanded your example a bit and added it to the documentation of Entrez.elink. Thanks!
>
> --Michiel.

That looks good - and tries to explain the nested result structure too.

Peter