Uses biomart over the current Ensembl human genome data set to extract all gene ontology terms allocated to genes on X and Y chromosomes. Shows the context of all those uniquely mapped to Y (so not mapped or implied by mappings to X) and colour codes as follows : <ol> <li>Terms shown in purple are those explicitly mapped to genes on the Y chromosome and neither explicitly nor implicitly mapped to any on X</li> <li>Terms in red are those implied by those in purple and not explicitly or implicity mapped to any genes in X</li> <li>Yellow terms are those explicitly mapped in X</li> <li>Green terms are those implied by terms mapped in both X and Y</li> </ol> List set1not2 = new ArrayList(); List set2not1 = new ArrayList(); List union = new ArrayList(); List intersection = new ArrayList(); Set set1set = new HashSet(); set1set.addAll(set1); Set set2set = new HashSet(); set2set.addAll(set2); Set unionSet = new HashSet(); for (Iterator i = set2set.iterator(); i.hasNext(); ) { Object item = i.next(); if (set1set.contains(item)) { intersection.add(item); } else { set2not1.add(item); } } for (Iterator i = set1set.iterator(); i.hasNext(); ) { Object item = i.next(); if (set2set.contains(item) == false) { set1not2.add(item); } } unionSet.addAll(set1set); unionSet.addAll(set2set); union.addAll(unionSet); set1 set2 union intersection set1not2 set2not1 crimson Set outputs = new HashSet(); for (Iterator i = in.iterator(); i.hasNext();) { outputs.add(i.next()); } out = new ArrayList(); out.addAll(outputs); in out http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl markTerm org.embl.ebi.escience.scuflworkers.java.EchoList org.embl.ebi.escience.scuflworkers.java.FailIfFalse Set outputs = new HashSet(); for (Iterator i = in.iterator(); i.hasNext();) { outputs.add(i.next()); } out = new ArrayList(); out.addAll(outputs); in out org.embl.ebi.escience.scuflworkers.java.FlattenList http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl createSession http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl getAncestors List set1not2 = new ArrayList(); List set2not1 = new ArrayList(); List union = new ArrayList(); List intersection = new ArrayList(); Set set1set = new HashSet(); set1set.addAll(set1); Set set2set = new HashSet(); set2set.addAll(set2); Set unionSet = new HashSet(); for (Iterator i = set2set.iterator(); i.hasNext(); ) { Object item = i.next(); if (set1set.contains(item)) { intersection.add(item); } else { set2not1.add(item); } } for (Iterator i = set1set.iterator(); i.hasNext(); ) { Object item = i.next(); if (set2set.contains(item) == false) { set1not2.add(item); } } unionSet.addAll(set1set); unionSet.addAll(set2set); union.addAll(unionSet); set1 set2 union intersection set1not2 set2not1 http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl getAncestors http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl destroySession org.embl.ebi.escience.scuflworkers.java.FailIfTrue purple http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl addTerm org.embl.ebi.escience.scuflworkers.java.EchoList http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl markTerm true Set outputs = new HashSet(); for (Iterator i = in.iterator(); i.hasNext();) { outputs.add(i.next()); } out = new ArrayList(); out.addAll(outputs); in out http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl markTerm gold http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl markTerm chartreuse3 http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl getDot Homo sapiens genes (NCBI36) Homo sapiens genes (NCBI36) text/x-graphviz Completed getDot destroySession Scheduled Running Completed addTerm showUniqueToY Scheduled Running Completed showUniqueToY showCommon Scheduled Running Completed Fail_if_true PassAllTerms Scheduled Running Completed Fail_if_false PassUniqueTerms Scheduled Running Completed showCommon showAnnotatedNonUnique Scheduled Running Completed showAnnotatedNonUnique getDot Scheduled Running Completed showCommon showAnnotatedUnique Scheduled Running Completed showAnnotatedUnique getDot Scheduled Running