[Biopython] cannot find elink_090910.dtd

[Peter]

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