Greg Landrum wrote:
Hi Markus,
I did a bit of exploring of the Pubchem Power User Gateway this
morning and discovered that they have a SOAP interface:
http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap_help.html
They even include a bit of help and some examples for using that
interface from Python:
http://pubchem.ncbi.nlm.nih.gov/pug_soap/examples/python_zsi/python_zsi.html
This provides a pretty straightforward way of interacting with the PUG
from Python.
I made some minor modifications to one of the sample scripts provided
in order to come up with the attached script. It shows how to convert
a list of pubchem CIDs into an RDKit SDMolSupplier. You will need to
have ZSI installed and to run wsdl2py as indicated on the above page.
This is, perhaps, a place to start.
-greg
Hi Greg, hi Noel,
first of all, thank you for the support so far. However I did not get to
the point, where I can understand all that
XML/PUG/SOAP/wsdl - stuff. I got the CIDsToSupplier function running
quite well, but I can not get the idea behind those
web-services. Pretty new to me :-). Right now I tried hard to do the
following task:
for a given Mol:
-do a similarity search by PUG
(that's pretty well described by SimilaritySearch.py)
-retrieve the list of CIDs of similar Mols
(I think I got the Idea from Greg's script)
-look If there are assays providing bioactivity data for any of these CIDs
(I know, that I can query this info by the following url from eLink:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pccompound&db=pcassay&id=<CID
here>)
-get some assay info and IC50s ... (that should be possible by
'GetAssayColumnDescriptions' an then getting the columns of interest)
I'm not quite sure, if that would be a task for Noel's cinfony, or if
things like that can be coded rather easily, with some more experience
(especially about the XML based eUtils). The BioPython.Entrez Module
doesn't seem to suit my needs, too. I'll keep tryin' :-)
By the way: See you in Goslar,
Markus
