[Biopython-dev] PubMed E-Utility 2010 DTD changes

Peter biopython at maubp.freeserve.co.uk
Mon Nov 23 21:49:31 UTC 2009

Hi all,

See below - it look like there are two new DTD files to add to Bio.Entrez


---------- Forwarded message ----------
From:  <utilities-announce at ncbi.nlm.nih.gov>
Date: Mon, Nov 23, 2009 at 8:35 PM
Subject: [Utilities-announce] PubMed E-Utility 2010 DTD changes
To: utilities-announce at ncbi.nlm.nih.gov

PubMed E-Utility Users,

We anticipate switching to the updated PubMed 2010 DTDs on December 14,

2010 DTDs are available from the Entrez DTD page:

The DTD changes for the 2010 production year, as noted in the Revision
Notes section near the top of each DTD, include:

NLM MedlineCitationSet DTD used for MEDLINE/PubMed XML data files:

1.  The CommentsCorrections group of elements was reorganized. Through
the 2009 data year, the publications cited in CommentsCorrections were
defined as elements. For the 2010 DTD, they are defined as valid values
to the RefType attribute, and a new attribute value, Cites, was created.
Cites will contain PMIDs and source data for items in the bibliography
or list of references at the end of an article that is deposited in
PubMed Central (PMC). There is no RefType attribute corresponding to
Cites for PMIDs and source data of articles in which a paper is cited.

In the implementation for 2010, RefType = "Cites" will contain only
PMIDs and source data for citations where an actual PMID for the cited
article exists in the NLM Data Creation and Maintenance System (DCMS).
It is therefore possible for a citation to be present in the article's
list of references and yet the PMID is not included in the Cites list
because it is not present in the NLM DCMS. Cites will be present in the
baseline files; however, the subsequent update frequency of Cites lists
is not yet determined. Again, all Cites data for this initial
implementation are coming from articles in PMC.

2. NameID element was added to Author and Investigator elements. NameID
is a possibly multiply-occurring, optional element permissible within
the Author (personal and collective) and Investigator elements. It is
intended as a unique identifier associated with the name. The value in
the NameID attribute Source designates the organizational authority that
established the unique identifier. There is no target date for
implementation of this field; it is a placeholder for now.

Additional information is available from the Announcements to NLM Data
2010 DTD and XML Changes; File Distribution Schedule Changes:

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