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hERG 1.0c.ws0

Prediction of cardiotoxicity of drugs


WSDL hERG/hERG_1_0c_ws0.wsdl
Schema definitions ../common/ws_common_1_0c.xsd
ws_herg_1_0c_ws0.xsd

We recommend that the first time users should load the WSDL file above to SoapUI and investigate the Web Service operations in that environment. SoapUI is a desktop application for inspecting, invoking, developing and functional/load/compliance testing of Web Services over HTTP. It can be downloaded free of charge from http://www.soapui.org/.

Examples of client side scripts using the service

FilenameTypeCompatibilityAuthorDescription
test_herg.pl (2.6 KB) Perl 1.0c ws0 Edita Bartaseviciute
This script runs the hERG 1.0c.ws0 Web Service. It requires no input; to be used for testing in the EMBRACE WS Registry.
example.smi (269 B)
herg.pl (2.9 KB) Perl 1.0c ws0 Edita Bartaseviciute
This script runs the hERG 1.0c.ws0 Web Service. It reads a SMI file from STDIN and produces the predictions in a simple text table.
xml-compile.pl (1.9 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)

Usage

# download the required scripts
wget http://www.cbs.dtu.dk/ws/hERG/examples/xml-compile.pl
wget http://www.cbs.dtu.dk/ws/hERG/examples/herg.pl

perl herg.pl [-s] < example.smi 

Documentation

      INTRODUCTION

      This Web Service implements hERG 1.0. It predicts cardiotoxicity of drug
      molecules. The method is described in detail in the following article:

      hERG Classification Model Based on a Combination of Support Vector Machine
      Method and GRIND Descriptors.
      Li Q, Joergensen FS, Oprea T, Brunak S, Taboureau O.
      Mol Pharm: 4;5:117-127, 2008.

      Alongside this Web Service the hERG method is also implemented as
      a traditional paste-and-click WWW server at:

          http://www.cbs.dtu.dk/services/hERG-1.0/

      The traditional server offers extended functionality and comprehensive
      documentation. It is suitable for close investigation of few molecules;
      this service is recommended for high throughput projects.

      TECHNICAL NOTE

      The main output data type 'anndata' is reused from biological sequence
      analysis where it normally contains protein or nucleotide sequences annotations.
      This Web Service, however, is about molecules, not sequences. Therefore,
      the names of the tags e.g. 'sequence' might seem misleading. We have
      chosen to reuse some data types anyway as they have proved very versatile.

      WEB SERVICE OPERATION

      This Web Service is fully asynchronous; the usage is split into the
      following three operations:

      1. runService    

         Input:  The following parameters and data:

                 * sort             sort the output by predicted cardiotoxicity
                                    (no value, just presence/absence);
                                    
                 * moleculedata     mulitple elements of type 'molecule':
                   * molecule         answers to one molecule:
                     * id               unique identifier for the molecule
                     * comment          optional comment (ignored by this service)
                     * smiles           molecule description string in SMI format

         Output: Unique job identifier

      2. pollQueue

         Input:  Unique job identifier

         Output: 'jobstatus' - the status of the job
                 Possible values are QUEUED, ACTIVE, FINISHED, WAITING,
                 REJECTED, UNKNOWN JOBID or QUEUE DOWN

      3. fetchResult

         Input:  Unique job identifier of a FINISHED job

         Output: * 'annsource'
                     'method'              name of the method, here always 'hERG';
                     'version'             version of the method: here always 1.0c;

                   'ann'                   annotations - one element per input molecule
                     'sequence'              standard sequence object (reused for molecules)
                       'id'                  molecule identifier
                     'annrecords/annrecord'
                       'feature'             feature name, here always 'hERG';
                       'global'              always present, indicates the whole molecule 
                       'score'
                         'key'                 here always: main
                         'value'               score value
                       'comment'             answer: high, low or '-'
      CONTACT

      Questions concerning the scientific aspects of the hERG method should
      go to Olivier Taboureau, otab@cbs.dtu.dk; technical questions concerning
      the Web Service should go to Edita Bartaseviciute, edita@cbs.dtu.dk or
      Kristoffer Rapacki, rapacki@cbs.dtu.dk.