This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database. kegg pathway \n mus_musculus org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.SplitByRegex org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringConcat String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\n"); } input output org.embl.ebi.escience.scuflworkers.java.StringListMerge String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); nonEmpty.add(trimmed); } String output = ""; for (int i = 0; i < nonEmpty.size(); i++) { output = output + "ncbi-geneid:" + (String) (nonEmpty.elementAt(i) + "\n"); } input output org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\n"); } input output org.embl.ebi.escience.scuflworkers.java.StringListMerge String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\n"); } input output String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); nonEmpty.add(trimmed); } String output = ""; for (int i = 0; i < nonEmpty.size(); i++) { output = output + "uniprot:" + (String) (nonEmpty.elementAt(i) + "\n"); } input output result = ensemblGene_Id + "," + entrezGeneId + "," + externalGeneId + "," + chromoName + "," + geneStart + "," + geneEnd + "," + ensemblTranscriptId + "," + uniprotAcc + "," + Affy_Mouse430_2; ensemblGene_Id entrezGeneId externalGeneId chromoName geneStart geneEnd ensemblTranscriptId uniprotAcc Affy_Mouse430_2 result String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\n"); } input output String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\n"); } input output String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); String[] trimmedSplit = trimmed.split("\t"); if (trimmedSplit.length > 2) { nonEmpty.add(trimmedSplit[1].trim()); } } String output = ""; for (int i = 0; i < nonEmpty.size(); i++) { output = output + (String) (nonEmpty.elementAt(i) + "\n"); } input output Mus musculus genes (NCBIM36) http://soap.genome.jp/KEGG.wsdl bconv http://soap.genome.jp/KEGG.wsdl bconv http://soap.genome.jp/KEGG.wsdl binfo http://soap.genome.jp/KEGG.wsdl btit Mus musculus genes (NCBIM36) This workflow removes any null values from a list of strings This workflow removes any null values from a list of strings \n String pathway_id_input = pathway_ids.trim(); String gene_id_input = gene_id.trim(); String output = ""; output = gene_id_input + "\t" + pathway_id_input; pathway_ids gene_id output org.embl.ebi.escience.scuflworkers.java.StringListMerge http://soap.genome.jp/KEGG.wsdl btit org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.SplitByRegex String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\t"); } input output org.embl.ebi.escience.scuflworkers.java.StringListMerge http://soap.genome.jp/KEGG.wsdl get_pathways_by_genes http://phoebus.cs.man.ac.uk:8081/axis/EnsemblListner.jws?wsdl lister Retrieves the current databases from ENSEMBL for a species http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.getcurrentdatabase