[BioPython] biopython soap?

[Brad Chapman]

Giovanni;
I did quite a bit of work with SOAP/WebServices at my old job, and
generally working with it from python is a pain. As you mention,
suds is actively developed and has a nice interface but in my
experience it will choke on a lot of WSDLs. ZSI works stably for
many cases, but the interface and usage is a bit messy.

If your goal is to access dbSNP, using the Entrez EUtils REST
interfaces Biopython already wraps should definitely be preferred; I
am in agreement with Peter's comments.

If your goal is to play with SOAP in a biological context, one good
target is the PubChem interface
(http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap_help.html) which
I don't believe has corresponding REST access. If you go this
route, I did some initial work with ZSI and could share my code with
you.

Brad


> 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
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