[BioPython] biopython soap?

[Giovanni Marco Dall'Olio]

On Fri, Feb 20, 2009 at 4:18 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> 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?

No particular reason :)
Just curious about trying soap.


>> 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.

Thanks.. I am using it already.
Yes, I was referring to dbSNP on ncbi.


> 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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