[Biopython] cannot find elink_090910.dtd

[Peter]

On Wed, Dec 23, 2009 at 10:57 AM, 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

Hi Silvio,

Yep, I don't have that file either, it looks like we missed it :(
The NCBI website don't make it easy to find (as far as I could
tell, none of the DTD pages list this file). However, the XML
tells us where to try:
http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/eLink_090910.dtd

I've added this to our repository, and it will be in the next release.

You'll need to download that DTD file. How did you install Biopython?
It looks like the file would need to go inside the egg - so it might
be easier to (re)install from source with this extra file in the source
code subdirectory Bio/Entrez/DTDs. Or start by grabbing the latest
Biopython code from git. Does that make sense?

However, even with the DTD file, I'm getting "Error 111
(Connection refused)" for your example. Maybe the NCBI are
doing some maintenance work at the moment?

Merry Christmas,

Peter