[Biopython] cannot find elink_090910.dtd

[Chris Fields]

On Dec 23, 2009, at 8:03 AM, Peter wrote:

> On Wed, Dec 23, 2009 at 1:29 PM, Silvio Tschapke
> <silvio.tschapke at googlemail.com> wrote:
>> 
>> I have copied the DTD file in
>> /usr/local/lib/python2.6/dist-packages/biopython-1.53-py2.6-linux-i686.egg/Bio/Entrez/DTDs/
>> now and it seems to work. Great! I have installed Biopython with
>> 
>> python setup.py build
>> python setup.py test
>> sudo python setup.py install
> 
> OK - good :)
> 
>> But will I have the same problems when I use eSearch, or eQuery and so
>> on? Because all of the DTD will not be up to date. So far I only
>> copied this DTD for eLink you posted.
> 
> I *hope* that this was the only DTD file we were missing. If
> not, please do let us know so we can fix this for other users.
> 
> In the short term, you would again need to download and fetch
> other missing DTD files in the same way. You can generally look
> at the start of the XML file to see where the DTD can be found, e.g.
> 
>>>> from Bio import Entrez
>>>> Entrez.email = "your.name.here at example.com"
>>>> print Entrez.elink(dbfrom="pubmed", id="12345678").read(300)
> <?xml version="1.0"?>
> <!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 10 August
> 2009//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_090910.dtd">
> <eLinkResult>
> ...
> 
> Thanks,
> 
> Peter

Just a quick question: is there any particular reason you need the DTDs?  The BioPerl eutils interface doesn't use them at all, primarily b/c they aren't required on our end.

chris