[BioPython] biopython soap?

[Peter]

On Fri, Feb 20, 2009 at 2:47 PM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:
> Does biopython use any SOAP service?
> In that case, which library is used?

The deprecated and removed Bio.biblio used an old version of the EBI
SOAP API.  This used "import SOAP" internally.  I don't recall any
other SOAP code in Biopython.

> I would like to write a script to interrogate the NCBI dbSNP database,
> using the soap protocol and these wdsl:
> - http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html

Why do you specifically want to use their SOAP interface?

> Does biopython provide tools to interrogate the ncbi database directly
> from within a script? And how is it implemented?

Biopython's Bio.Entrez module allows you to use the NCBI Entrez
E-Utils databases (but this is not using SOAP), and this is pretty
well documented in our tutorial for the more mainstream databases.
>From using the Entrez einfo command, they do offer access to the "snp"
database which I assume is dbSNP.

See: http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp
"dbSNP is now incorporated into NCBI's Entrez system and can be
queried using the same approach as the other Entrez databases such as
PubMed and GenBank."

So if I was you, I'd just try Bio.Entrez instead of messing about with SOAP.

Peter