[Biopython-dev] [BioPython] PubMed find_related

[Michiel de Hoon]

> The deeply nested nature of the XML results do suggest that
> a helper function in Bio.Entrez would be useful here.  Maybe
> something like:
> 
> def find_related(dbfrom, id) :
>     #Returns a list of dictionaries containing Score and ID
>     # matched
>     result = read(elink(dbfrom=dbfrom, id=id))
>     return result[0]["LinkSetDb"][0]['Link']
> 
> It might make more sense to return just a list of ID
> strings, but the score may be interesting.
>

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."

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

--Michiel.