Introduction to CeBiTec webservices

Abstract: Welcome to the CeBiTec webservice manual. This document contains all information needed to access the webservices provided by the CoryneRegNet, EMMA and GenDB projects. The locations of the respective wsdl files are given for automatic configuration of webservice APIs. They should work with any programming language. Any further information such as the proxy adresses are contained in the respective wsdl files and are therefore automatically set.

All methods are described with their parameters and yield values. Examples are given, made using NuSOAP for PHP.

CoryneRegNet

WSDL location:	https://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/v4/CoryneRegNet/soap/soap_server_wsdl.php?wsdl
Methods:	getTfGeneIDs() Gets the gene IDs corresponding to the given transcription factor. Input: xsd:string -- Transcription factor Output: tns:ArrayOfGeneID -- Gene IDs getOrganisms() Gets the organism names matching the given search term. Input: xsd:string -- The search term Output: tns:ArrayOfOrganismNameIDStruct -- Gene IDs getGeneID() Gets the unique IDs for the given genes Input: tns:ArrayOfGeneID -- An array of genes Output: tns:ArrayOfInputUniqueGeneIDStruct -- An array of pairs of input genes and their unique ID. regulates() Gets outgoing regulations of the given genes Input: tns:ArrayOfGeneID -- An array of genes Output: tns:ArrayOfRegStruct -- An array of hashes of regulation data. isRegulatedBy() Gets incoming regulations of the given genes Input: tns:ArrayOfGeneID -- An array of genes Output: tns:ArrayOfRegStruct -- An array of hashes of regulation data. getOperonByGeneID() Gets the operons that control the given genes. Input: tns:ArrayOfGeneID -- An array of genes Output: tns:ArrayOfGeneIDOperonStruct -- An array of hashes data on the operons.
Example implemetation:	<?php require_once('nusoap/lib/nusoap.php'); $urlwsdl = "https://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/v3.1/CoryneRegNet/soap/soap_server_wsdl.php?wsdl"; $client = new soapclient($urlwsdl, true); $err = $client->getError(); if ($err) { echo '<h2>Constructor error</h2><pre>' . $err . '</pre>'; } $proxy = $client->getProxy(); echo '<h2><code>getTfGeneIDs()</code></h2>'; echo '<b>Input: </b> <code>"NC_000913"</code>'; $result = $proxy->getTfGeneIDs("NC_000913"); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>getOrganisms()</code></h2>'; echo '<b>Input: </b> <code>"oli"</code>'; $result = $proxy->getOrganisms("oli"); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>getGeneID()</code></h2>'; echo '<b>Input: </b> <code>["cg0012","cg0444"]</code>'; $result = $proxy->getGeneID(array("cg0012","cg0444")); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>regulates()</code></h2>'; echo '<b>Input: </b> <code>["cg0012","cg0444"]</code>'; $result = $proxy->regulates(array("cg0012","cg0444")); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>isRegulatedBy()</code></h2>'; echo '<b>Input: </b> <code>["cg0012","cg0444"]</code>'; $result = $proxy->isRegulatedBy(array("cg0012","cg0444")); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>getOperonByGeneID()</code></h2>'; echo '<b>Input: </b> <code>["cg21103"]</code>'; $result = $proxy->getOperonByGeneID(array("cg2103")); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } ?>
Example results:	getTfGeneIDs() ============== Input: "NC_000913" Result: ------- Array ( [0] => b0020 [1] => b1334 . . . [143] => b4241 ) getOrganisms() ============== Input: "oli" Result: ------- Array ( [0] => Array ( [organismID] => NC_000913 [organismName] => Escherichia coli K12 ) ) getGeneID() ========== Input: ["cg0012","cg0444"] Result: ------- Array ( [0] => Array ( [inputGeneID] => cg0012 [uniqueGeneID] => cg0012 ) [1] => Array ( [inputGeneID] => cg0444 [uniqueGeneID] => cg0444 ) ) regulates() =========== Input: ["cg0012","cg0444"] Result: ------- Array ( [0] => Array ( [geneID] => cg0444 [regulations] => Array ( [0] => Array ( [geneID] => cg0052 [regType] => - [evidence] => predicted [pubmed] => 15090522 ) [1] => Array ( [geneID] => cg0053 [regType] => - [evidence] => predicted [pubmed] => 15090522 ) . . . [44] => Array ( [geneID] => cg4001 [regType] => - [evidence] => predicted [pubmed] => ) ) ) [1] => Array ( [geneID] => cg0012 [regulations] => Array ( [0] => Array ( [geneID] => cg1147 [regType] => + [evidence] => experimental [pubmed] => 16194234 ) [1] => Array ( [geneID] => cg1151 [regType] => + [evidence] => experimental [pubmed] => 16194234 ) . . . [8] => Array ( [geneID] => cg1380 [regType] => + [evidence] => experimental [pubmed] => 16194234 ) ) ) ) isRegulatedBy() Input: ["cg0012","cg0444"] Result: ------- Array ( [0] => Array ( [geneID] => cg0444 [regulations] => Array ( [0] => Array ( [geneID] => cg0444 [regType] => - [evidence] => experimental [pubmed] => 15090522;17114251 ) [1] => Array ( [geneID] => cg2831 [regType] => + [evidence] => experimental [pubmed] => 17114251 ) ) ) [1] => Array ( [geneID] => cg0012 [regulations] => Array ( [0] => Array ( [geneID] => cg3253 [regType] => - [evidence] => predicted [pubmed] => 15853877 ) ) ) ) getOperonByGeneID() =================== Input: ["cg21103"] Result: ------- Array ( [0] => Array ( [geneID] => cg2103 [operon] => Array ( [operonID] => OP_cg2103 [firstGeneID] => cg2103 [genes] => Array ( [0] => cg2103 [1] => cg2104 ) ) ) )

EMMA

WSDL location:	https://www.cebitec.uni-bielefeld.de/groups/brf/software/emma/web_service_emma.wsdl
Methods:	fetchAllProjects() Gets all available EMMA projects. Input: --none-- Output: tns:ArrayOfString -- The projects fetchAllExperiments() Gets all experminents in the given project. Input: xsd:string -- The project Output: tns:ArrayOfString -- The experiments fetchAllExperimentalFactorsByExperiment() Gets all factors associated with the given experiment in the given project. Input: xsd:string -- The project xsd:string -- The experiment Output: tns:ArrayOfString -- The factors fetchAllExperimentalFactorValuesByFactorAndExperiment() Gets all factor values for given project, experiment and factor. Input: xsd:string -- The project xsd:string -- The experiment xsd:string -- The factor Output: tns:ArrayOfString -- The factor values fetchAllReporterByName() Gets the valid reporter names for the given gene. Input: xsd:string -- The project xsd:string -- The experiment xsd:string -- The gene name Output: tns:ArrayOfString -- The valid reporter names fetchLatestSignificantMeanM1WithBestQuality ¬ ByExperimentAndReporterAndFactorAndFactorValue() Gets the latest significant mean expression value of best quality for the given project, experiment, reporter, factor, and factor value. Input: xsd:string -- The project xsd:string -- The experiment xsd:string -- The reporter xsd:string -- The factor xsd:string -- The factor value Output: xsd:double -- The M-value
Example implemetation:	<?php require_once('nusoap/lib/nusoap.php'); $urlwsdl = "https://www.cebitec.uni-bielefeld.de/groups/brf/software/emma/web_service_emma.wsdl"; $client = new soapclient($urlwsdl, true); $err = $client->getError(); if ($err) { echo '<h2>Constructor error</h2><pre>' . $err . '</pre>'; $version = phpversion(); echo 'This Server runs PHP version', $version; } $proxy = $client->getProxy(); echo '<h2><code>fetchAllProjects()</code></h2>'; echo '<b>Input: </b> void'; // <code>"cg0012"</code>'; $result = $proxy->fetchAllProjects(); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>fetchAllExperiments()</code></h2>'; echo '<b>Input: </b> <code>"EMMA2:Coryne"</code>'; $result = $proxy->fetchAllExperiments("EMMA2:Coryne"); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>fetchAllExperimentalFactorsByExperiment()</code></h2>'; echo '<b>Input: </b> <code>"EMMA2:Coryne","Heat Shock"</code>'; $result = $proxy->fetchAllExperimentalFactorsByExperiment("EMMA2:Coryne","Heat Shock"); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>fetchAllExperimentalFactorValuesByFactorAndExperiment()</code></h2>'; echo '<b>Input: </b> <code>"EMMA2:Coryne","Heat Shock","Strains"</code>'; $result = $proxy->fetchAllExperimentalFactorValuesByFactorAndExperiment("EMMA2:Coryne","Heat Shock","Strains"); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>fetchAllReporterByName()</code></h2>'; echo '<b>Input: </b> <code>"EMMA2:Coryne","Heat Shock","R:ORF.3301_2"</code>'; $result = $proxy->fetchAllReporterByName("EMMA2:Coryne","Heat Shock","R:ORF.3301_2"); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>fetchLatestSignificantMeanM1WithBestQualityByExperimentAndReporterAndFactorAndFactorValue()</code></h2>'; echo '<b>Input: </b> <code>"EMMA2:Coryne","Heat Shock","R:ORF.3301_2","Strains","WT"</code>'; $result = $proxy->fetchLatestSignificantMeanM1WithBestQualityByExperimentAndReporterAndFactorAndFactorValue('EMMA2:Coryne','Heat Shock','R:ORF.3301_2','Strains','WT'); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } ?>
Example result:	fetchAllProjects() ================== Input: void Result: ------- Array ( [0] => mage_test [1] => mage_test_alu [2] => EMMA2:coryne [3] => EMMA2.Coryne-Center ) fetchAllExperiments() ===================== Input: "EMMA2:Coryne" Result: ------- Array ( [0] => Heat Shock ) fetchAllExperimentalFactorsByExperiment() ========================================= Input: "EMMA2:Coryne","Heat Shock" Result: ------- Array ( [0] => Array ( [0] => Strains [1] => Temperature ) ) fetchAllExperimentalFactorValuesByFactorAndExperiment() ======================================================= Input: "EMMA2:Coryne","Heat Shock","Strains" Result: ------- Array ( [0] => WT [1] => Delta hspR (cg3097) [2] => Delta hrcA (cg2516) ) fetchAllReporterByName() ======================== Input: "EMMA2:Coryne","Heat Shock","R:ORF.3301_2" Result: ------- Sorry, but no reporter 'R:ORF.3301_2' is contained in a data-set. fetchLatestSignificantMeanM1WithBestQualityByExperimentAndReporterAndFactorAndFactorValue() =========================================================================================== Input: "EMMA2:Coryne","Heat Shock","R:ORF.3301_2","Strains","WT" Result: ------- -0.24257469371488

GenDB

WSDL location:	https://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb-2.2/web_service_gendb.wsdl
Methods:	getRegionsForPathways() Gets the regions associated with the given pathways Input: xsd:string -- The username xsd:string -- The password xsd:string -- The project tns:ArrayOfString -- The pathways Output: apachens:Map -- A map of pathway names referring to arrays of region names getPathwaysForRegions() Gets the pathways associated with the given regions. Input: xsd:string -- The username xsd:string -- The password xsd:string -- The project tns:ArrayOfString -- The regions Output: tns:ArrayOfPathwayStruct -- A 2-dimensional array of structures containing a key, an EC number and an array of pathway parameters getAnnotationData() Gets the annotations for the given region Input: xsd:string -- The username xsd:string -- The password xsd:string -- The project xsd:string -- The region Output: apachens:Map -- A Map of regions referring to their annotations getRegionData() Gets all data on the given region. Input: xsd:string -- The username xsd:string -- The password xsd:string -- The project xsd:string -- The region Output: apachens:Map -- A Map of regions referring to their data set resolveRegions() Gets the valid name of a given region alias. Input: xsd:string -- The username xsd:string -- The password xsd:string -- The project xsd:string -- The alias of the region Output: tns:ArrayOfString -- The valid region names
Example implemetation in PERL:	#!/usr/bin/env perl use strict; use Carp; use Getopt::Std; use Term::ReadKey; use IO::Handle; use SOAP::Lite; use Data::Dumper; sub usage { print "\ntest_gendb_webservice_wsdl.pl - test the getAnnotationData webservice\n\n"; print "usage: test_gendb_webservice_wsdl -u <user> -p <project> -r <region_name>\n\n"; } our($opt_p, $opt_r, $opt_u); getopts('p:r:u:'); unless ($opt_p) { usage; print "\nNo project name given\n!"; exit 1; } unless ($opt_u) { usage; print "\nNo user name given\n!"; exit 1; } unless ($opt_r) { usage; print "\nNo region name given\n!"; exit 1; } print STDOUT "Enter your database password: "; ReadMode('noecho'); my $password = ReadLine(0); chomp $password; print STDOUT "\n"; ReadMode('normal'); print "Calling GenDB web service: getAnnotationData!\n\n"; my $result = SOAP::Lite ->service(' https://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb-2.2/web_service_gendb.wsdl') ->getAnnotationData($opt_u, $password, $opt_p, $opt_r); print &Dumper($result);
Example implemetation in PHP:	<?php require_once('nusoap/lib/nusoap.php'); $urlwsdl = "https://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb-2.2/web_service_gendb.wsdl"; $client = new soapclient($urlwsdl, true); $err = $client->getError(); if ($err) { echo '<h2>Constructor error</h2><pre>' . $err . '</pre>'; $version = phpversion(); echo 'This Server runs PHP version ', $version; } $proxy = $client->getProxy(); echo '<h2><code>getRegionsForPathways()</code></h2>'; echo '<b>Input: </b> <code>"user","pwd","GenDB_CoryneCenter",["cg0446"]</code>'; $result = $proxy->getRegionsForPathways("user","pwd","GenDB_CoryneCenter",array("cg0446")); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>getPathwaysForRegions()</code></h2>'; echo '<b>Input: </b> <code>"user","pwd","GenDB_CoryneCenter",["cg0446"]</code>'; $result = $proxy->getPathwaysForRegions("user","pwd","GenDB_CoryneCenter",array("cg0446")); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>getAnnotationData()</code></h2>'; echo '<b>Input: </b> <code>"user","pwd","GenDB_CoryneCenter","cg0444"</code>'; $result = $proxy->getAnnotationData("user","pwd","GenDB_CoryneCenter","cg0444"); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>getRegionData()</code></h2>'; echo '<b>Input: </b> <code>"user","pwd","GenDB_CoryneCenter","cg0444""</code>'; $result = $proxy->getRegionData("user","pwd","GenDB_CoryneCenter","cg0444"); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } echo '<h2><code>resolveRegions()</code></h2>'; echo '<b>Input: </b> <code>"user","pwd","GenDB_CoryneCenter","YP_224669.1"</code>'; $result = $proxy->resolveRegions("user","pwd","GenDB_CoryneCenter","YP_224669.1"); if ($proxy->fault) { // all right? echo '<h3>Fault</h3><pre>'; print_r($result); echo '</pre>'; } else { $err = $proxy->getError(); if ($err) { echo '<h3>Error</h3><pre>' . $err . '</pre>'; } else { echo '<h3>Result</h3><pre>'; print_r($result); echo '</pre>'; } } ?>
Example results:	getRegionsForPathways() ======================= Input: "user","pwd","GenDB_CoryneCenter",["cg0446"] Result: ------- Array ( [632] => Array ( [0] => 632 [1] => Benzoate degradation via CoA ligation [2] => Array ( [cg0446] => 1.3.99.1 ) ) [650] => Array ( [0] => 650 [1] => Butanoate metabolism [2] => Array ( [cg0446] => 1.3.99.1 ) ) [720] => Array ( [0] => 720 [1] => Reductive carboxylate cycle (CO2 fixation) [2] => Array ( [cg0446] => 1.3.99.1 ) ) [190] => Array ( [0] => 190 [1] => Oxidative phosphorylation [2] => Array ( [cg0446] => 1.3.99.1 ) ) [20] => Array ( [0] => 20 [1] => Citrate cycle (TCA cycle) [2] => Array ( [cg0446] => 1.3.99.1 ) ) ) getPathwaysForRegions() ======================= Input: "user","pwd","GenDB_CoryneCenter",["cg0446"] Result: ------- Array ( [0] => Array ( [0] => cg0446 [1] => 1.3.99.1 [2] => Array ( [0] => Array ( [0] => 720 [1] => Reductive carboxylate cycle (CO2 fixation) ) [1] => Array ( [0] => 632 [1] => Benzoate degradation via CoA ligation ) [2] => Array ( [0] => 20 [1] => Citrate cycle (TCA cycle) ) [3] => Array ( [0] => 650 [1] => Butanoate metabolism ) [4] => Array ( [0] => 190 [1] => Oxidative phosphorylation ) ) ) ) getAnnotationData() =================== Input: "user","pwd","GenDB_CoryneCenter","cg0444" Result: ------- Array ( [Gene Name] => [Gene Product] => transcriptional regulator, MerR family [COG Link] => http://www.ncbi.nlm.nih.gov/COG/old/palox.cgi?seq=COG0000 [GO Numbers] => Array ( ) [Function] => [Confidence] => [Comment] => [Date] => Wed Jan 10 10:39:24 2007 [Evidence] => not experimental [COG Funccat] => [Annotator] => EMBL+GenBank importer [COG Number] => COG0000 [Description] => [EC Number] => ) getRegionData() =============== Input: "user","pwd","GenDB_CoryneCenter","cg0444" Result: ------- Array ( [IEP] => 6.303 [TMH] => 0 [#AA] => 474 [Start] => 392208 [HTH_Motif] => 1 [Molweight] => 53864.672 [Aliases] => YP_224669.1 [Associated] => - [%GC] => 61.754 [%AC] => 57.895 [Status function] => annotated [Frame] => -1 [Signal_Peptide] => 0 [Starting 8] => atgggaaa [Length] => 1425 [Start/Stop Codon] => atg / taa [Ending 8] => cgccgtac [Status region] => status 3 [Stop] => 390784 [Name] => cg0444 ) resolveRegions() ================ Input: "user","pwd","GenDB_CoryneCenter","YP_224669.1" Result: ------- Array ( [0] => cg0444 )