[BioPython] Deprecating Bio.EUtils in favour of Bio.Entrez?

Peter biopython at maubp.freeserve.co.uk
Wed Aug 13 21:26:52 UTC 2008


Hello to all the NCBI fans...

As you may know, the NCBI Entrez database has some "Entrez Programming
Utilities" also known as EUtils,
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

As of Biopython 1.45, the module Bio.Entrez (originally Bio.WWW.NCBI)
supported all the EUtils functions, and as of Biopython 1.46 could
parse the NCBI XML output too.  This code is well documented with a
whole Bio.Entrez chapter in the tutorial, which means we are now in a
position to retire the older unmaintained Bio.EUtils module.

We'd like to propose the deprecation of Bio.EUtils in the next release
of Biopython, in favour of Bio.Entrez.

If anyone is currently using Bio.EUtils, then we'd like to hear from
you.  It should be possible to offer advice on migrating the code to
Bio.Entrez, or we can reconsider deprecating Bio.EUtils if there is
some major functionality that would be lost, or users that would be
inconvenienced by its premature retirement.

Thank you,

Peter



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