ProP 1.0.ws0Template service
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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
| Filename | Type | Compatibility | Author | Description |
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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.
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example.fsa (1.3 KB) |
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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.
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xml-compile.pl (1.9 KB) |
Perl |
NA |
Peter Fischer Hallin |
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)
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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.
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