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ProP 1.0.ws0

Template service


WSDL ProP/ProP_1_0_ws0.wsdl
Schema definitions http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd
http://www.cbs.dtu.dk/ws/ProP/ws_prop_1_0_ws0.xsd
http://bioxsd.org/BioXSD-0.4.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
prop.pl (3.5 KB) Perl 1.0 ws0 Edita Bartaseviciute
This script runs the ProP 1.0.ws0 Web Service. It reads FASTA file from STDIN and produces predictions in a simple table.
example.fsa (1.3 KB)
test_prop.pl (4.9 KB) Perl 1.0 ws0 Edita Bartaseviciute
This script runs the ProP 1.0.ws0 Web Service. It requires no input; to be used for testing in the EMBRACE WS Registry.
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/ProP/examples/xml-compile.pl
wget http://www.cbs.dtu.dk/ws/ProP/examples/prop.pl

perl prop.pl < example.fsa 

Documentation

      INTRODUCTION

      This Web Service implements ProP v. 1.0.ws0. It predicts arginine and lysine propeptide cleavage sites in 
      eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default.
      The method is described in detail in the following article:
      
      Prediction of proprotein convertase cleavage sites.
      Peter Duckert, Soren Brunak and Nikolaj Blom.
      Protein Engineering, Design and Selection: 17: 107-112, 2004. 
      
      Alongside this Web Service the ProP method is also implemented as
      a traditional paste-and-click WWW server at:
      
            http://www.cbs.dtu.dk/services/ProP/
      
      The traditional server offers extended functionality and comprehensive 
      documentation. It is suitable for close investigation of few proteins; 
      this service is recommended for high throughput projects.


      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
                 
                 *  'sequenceRecord'          answers to one sequence:
                      * 'sequence'              protein sequence. The sequence must be written 
                                                using the one letter amino acid code in capital letters:
                                                `ACDEFGHIKLMNPQRSTVWY'.Other letters will be converted 
                                                to `X' and treated as unknown amino acids. Other symbols, 
                                                such as whitespace and numbers, will be ignored;
                      * 'customNote'            optional comment;
                      * 'formalReference' 
                          * 'accession'           unique identifier for the sequence.
         
         
         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: *  'annotatedSequence'        annotations - one element per input sequence;
                      *  'sequenceRecord'        answers to one sequence:
                          *  'sequence'            protein sequence given as an input;
                          *  'formalReference'
                              * 'accession'          unique identifier for the input sequence;
                                  
                      * 'annotation'
                          *  'feature'
                              *  'name'              feature name, here always 'ProP';
                          *  'occurence'           occurence of a feature in a sequence;
                              *  'position'          always present, indicates the position for each
                                                     arginine (R) and lysine (K) residue in the sequence;
                                  *  'point'           residues number;
                              *  'evidence'
                                  *  'predicted'
                                      *  'methodId'      id composed of today's day, name and version of the method.
                                                         Example: 6-4-2010ProP-1.0ws0;
                                      *  'score'
                                          *  'type'         score type name, here always 'main', indicating the main prediction score;
                                          *  'value'        prediction score value. If the score is >0.5 the residue is predicted 
                                                            to be followed by a propeptide cleavage site; the higher the score the more 
                                                            confident the prediction; 
                                      *  'verdict'        contains 'Present' if the residue is predicted to be followed by a propeptide 
                                                          cleavage site, and 'Impossible' if the residue is not predicted to be followed 
                                                          by a propeptide cleavage site.
        
      
      
      Please note, that input and output data types of the ProP v. 1.0.ws0 Web Service 
      are defined by the external canonical BioXSD XML-Schema.
      
      CONTACT

      Technical questions concerning the Web Service 
      should go to Edita Bartaseviciute,edita@cbs.dtu.dk 
      or Kristoffer Rapacki, rapacki@cbs.dtu.dk.