[Biopython] [eFetch] doesn't work with NLMcatalog

[Lenna Peterson]

I emailed NCBI. I'll post on both the mailing list and the github issue
when/if I hear back.

Cheers,

Lenna

On Mon, Dec 7, 2015 at 4:32 PM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> On Mon, Dec 7, 2015 at 7:32 PM, Lenna Peterson <arklenna at gmail.com> wrote:
> > The problem is that the DOCTYPE is missing from the XML file.
> >
> > For example, a nucleotide XML file begins like this:
> >
> > <?xml version="1.0"?>
> >  <!DOCTYPE GBSet PUBLIC "-//NCBI//NCBI GBSeq/EN"
> > "http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd">
> >  <GBSet>
> >
> > As far as I can tell, this is the appropriate DTD:
> > http://www.nlm.nih.gov/databases/dtd/nlmcatalogrecordset_150101.dtd
> >
> > However, because the DTD is not specified in the file, the parser does
> not
> > know where to find it.
> >
> > Cheers,
> >
> > Lenna
> >
>
> This looks like https://github.com/biopython/biopython/issues/354
> again - could someone write to the NCBI again since this doesn't seem
> to have been fixed yet on their side?
>
> Peter
>
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