PICR - Protein Identifier Cross-Reference Service

    <project name="PICR client" default="client" basedir=".">

        <path id="jaxws.classpath">
            <pathelement location="${java.home}/../lib/tools.jar"/>
            <fileset dir="${javaws.home.lib}">
                <include name="*.jar"/>
                <exclude name="j2ee.jar"/>
            </fileset>
        </path>

        <taskdef name="wsimport" classname="com.sun.tools.ws.ant.WsImport">
            <classpath refid="jaxws.classpath"/>
        </taskdef>

        <target name="client">
            <wsimport
                    debug="true"
                    verbose="true"
                    keep="true"
                    extension="false"
                    destdir="${build}"
                    sourcedestdir="${src}"
                    package="uk.ac.ebi.picr"
                    wsdl="http://www.ebi.ac.uk/Tools/picr/service?wsdl">
            </wsimport>
        </target>

    </project>

import uk.ac.ebi.picr.*;

[...]

AccessionMapperService service = new AccessionMapperService();
AccessionMapperInterface port;
port = service.getAccessionMapperPort();

//the accession you wish to map
String queryID = "P29375";

//the version of the accession
//can be null or a number
String queryIdVersion = null;

//a list of all databases to map to
List<String> searchDB = new ArrayList<String>();
searchDB.add("SWISSPROT");
searchDB.add("TREMBL");

//the NEWT taxonomy ID to limit the mappings to
//can be null or a number. Do not specify 0 for null.
String taxonID = "9606";     //H. Sapiens

//true to return only active mappings
//false to return all mappings, including inactive ones
boolean activeOnly = true;

List<UPEntry> uPEntries = port.getUPIForAccession(queryID, queryIdVersion, searchDB, taxonID, activeOnly);

//there might be multiple UPEntries as the submitted accession
//might be associated with more than one sequence
for (UPEntry uPEntry : uPEntries) {

    //the identical cross-references contain all mappings
    //that fit the search parameters and match with 100%
    //sequence identity to the submitted accession
    if (uPEntry.getIdenticalCrossReferences() != null) {
         for (CrossReference iRef : uPEntry.getIdenticalCrossReferences()) {
             String matchAcc = iRef.getAccession();
             String matchDB = iRef.getDatabaseName();
             Integer taxID = Integer.parseInt(iRef.getTaxonId());
             // do something with them ...
         }
     }

    //the logical cross-references contain all mappings
    //that fit the search parameters and come from the UniprotKB
    //They are not guaranteed to have 100% sequence identity
    if (uPEntry.getLogicalCrossReferences() != null) {
         for (CrossReference iRef : uPEntry.getLogicalCrossReferences()) {
             String matchAcc = iRef.getAccession();
             String matchDB = iRef.getDatabaseName();
             Integer taxID = Integer.parseInt(iRef.getTaxonId());
             // do something with them ...
         }
     }
}