[Biopython-dev] [Biopython - Bug #3422] (New) Missing

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Fri Mar 8 16:49:48 UTC 2013

Issue #3422 has been reported by Jared Sampson.

Bug #3422: Missing 

Author: Jared Sampson
Status: New
Priority: Normal
Target version: 
URL: http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/bookdoc_130101.dtd

When using Entrez.efetch to retrieve an XML file, I get the following warning about a missing DTD: bookdoc_130101.dtd


/path/to/my/virtualenv/lib/python2.7/site-packages/Bio/Entrez/Parser.py:522: UserWarning: Unable to load DTD file bookdoc_130101.dtd.

Bio.Entrez uses NCBI's DTD files to parse XML files returned by NCBI Entrez.
Though most of NCBI's DTD files are included in the Biopython distribution,
sometimes you may find that a particular DTD file is missing. While we can
access the DTD file through the internet, the parser is much faster if the
required DTD files are available locally.

For this purpose, please download bookdoc_130101.dtd from


and save it either in directory


or in directory


in order for Bio.Entrez to find it.

Alternatively, you can save bookdoc_130101.dtd in the directory
Bio/Entrez/DTDs in the Biopython distribution, and reinstall Biopython.

Please also inform the Biopython developers about this missing DTD, by
reporting a bug on http://bugzilla.open-bio.org/ or sign up to our mailing
list and emailing us, so that we can include it with the next release of

Proceeding to access the DTD file through the internet...



Also, the bugzilla.open-bio.org URL mentioned comes up empty.

Jared Sampson

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