[Biopython] Bio.Entrez/Medline DTD problems - missing DTD nlmmedlinecitationset_100301.dtd

[Guy Eakin]

 I am learning biopython and seem to be having trouble parsing efetch
generated xml.

Maybe I am confused here, but I can't for the life of me Get my xml to parse
correctly, and it seems to be coming up with a missing dtd error using both
Medline.parse and Entrez.parse. (traceback for medline below below)

 nlmmedlinecitationset_100301.
dtd and pubmed_100301.dtd seem to be missing from my biopython
installation, and unavailable from the following NCBI sites:

http://www.ncbi.nlm.nih.gov/dtd/ or
http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/

My apologies if this is user error; i do not see reference to this DTD issue
in the archives so am posting the incident. Is this just bad luck during my
learning curve, or am I missing something conceptual here?

 Thanks,

Guy



Traceback (most recent call last):

 File
"C:\Python26\Lib\site-packages\pythonwin\pywin\framework\scriptutils.py",
line 312, in RunScript

   exec codeObject in __main__.__dict__

 File "C:\ieye\ieye\citations\pubmed_search_fxn.py", line 36, in <module>

   parsed_results = Entrez.read(fetch_handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\__init__.py", line 262, in
read

   record = handler.read(handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 108, in
read

   self.parser.ParseFile(handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 381, in
externalEntityRefHandler

   parser.ParseFile(handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 377, in
externalEntityRefHandler

   raise RuntimeError(message)

RuntimeError: Unable to load DTD file nlmmedlinecitationset_100301.dtd.