[Biopython-dev] Bio.Entrez & Bio.EUtils

Michiel de Hoon mjldehoon at yahoo.com
Sat May 24 14:26:27 UTC 2008

Dear all,

I have essentially completed the parser in Bio.Entrez. AFAICT, it works with all kinds of XML files returned by NCBI's Entrez Utilities, except for the Pubmed Central database (Pubmed itself is fine). I am using this module a lot for my own work, so it has received quite a lot of testing. As a case in point, there are 40 unit tests for the Bio.Entrez parser. These, by the way, can show you some examples of how to use this module. The documentation is now also updated.

This module may at some point replace Bio.EUtils, so if you are using this module you might want to try Bio.Entrez to see if it covers everything Bio.EUtils covers.


Peter <biopython at maubp.freeserve.co.uk> wrote:Bio.Entrez (Michiel). I see you've been very busy with the new
simplified XML parsers (see bug 2488).  This looks like a big
improvement on the rather repetitive coding needed in the first draft.
 Are you still actively making further refinements?  How many Entrez
XML file formats are still needed?


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