This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user 2005 500 /*[local-name(.)='eSearchResult']/*[local-name(.)='IdList']/*[local-name(.)='Id'] pubmed 2008 String[] split = abstracts.split("\n"); String phenotype_term = phenotype.trim(); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); // String mytext = split[i].substring(split[i].indexOf(0), split[i].indexOf(" AND ")); nonEmpty.add(trimmed); } String output = ">> " + phenotype_term + "\n"; for (int i = 0; i < nonEmpty.size(); i++) { output = output + (String) (nonEmpty.elementAt(i) + "\n"); } phenotype abstracts 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 org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge String id = id.trim(); String abstract_text = abstract_text.trim(); String dates_text = dates.trim(); String output = ""; output = id + "\t" + dates_text + "\t" + abstract_text; id abstract_text dates output file:/Users/sowen/tmp/pauls_workflow-inner.xml http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl run_eSearch