[Biopython] cannot find elink_090910.dtd

[Konrad Koehler]

Hi  Silvio,

This appears to be a temporary glitch with the Entrez database and not biopython.  For example, the following link should display the abstract, but current does not:

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=14630660&dopt=Abstract

A lot of other things in Entrez appear to be broken. For example internal links to RefSeq records from EntrezGene do not currently work.  For example, the RefSeq link from here:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2645

to here:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2645

doesn't work either.

Hopefully the problems in the Entrez database will be sorted out shortly.  Cheers,

Konrad

On Wednesday, December 23, 2009, at 11:57AM, "Silvio Tschapke" <silvio.tschapke at googlemail.com> wrote:
>Hi all,
>
>I am using ubuntu 9.10, python 2.6 and biopython 1.53
>But while running these two lines of code
>
>pmid = "14630660"
>results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid)
>
>I get the following error message posted at the bottom.
>So I searched at the proposed websites and in the web for
>"elink_090910.dtd" without success.
>I only found the files for elink_020511.dtd and something for 2010. But
>nothing related to elink_090910.dtd.
>Could you please help me how I can solve this problem?
>
>Cheers and merry christmas,
>Silvio
>
>
>Traceback (most recent call last):
>  File "/home/silvio/programming/python/first steps/biopythonTutorial.py",
>line 17, in <module>
>    results = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid))
>  File
>"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/__init__.py",
>line 258, in read
>    record = handler.read(handle)
>  File
>"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/Parser.py",
>line 108, in read
>    self.parser.ParseFile(handle)
>  File
>"/usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/Parser.py",
>line 377, in externalEntityRefHandler
>    raise RuntimeError(message)
>RuntimeError: Unable to load DTD file eLink_090910.dtd.
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