This workflow takes in a search term and a database (e.g. snp, gene, protein) in which to perfom the search over. The result is an xml file containing summary information about the search term
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl
run_eSearch
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
String temp = xml;
String id_xml = "<Id>";
List info = new ArrayList();
List image = new ArrayList();
List db = new ArrayList();
List id = new ArrayList();
String url_image = "http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?t=l&cid=";
String url_info = "http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=";
String[] split = temp.split(id_xml);
String temp2 = "";
// start at index 1 because of xml fragment at position 0 caused by split
for(int k = 1; k < split.length; k++) {
temp2 = split[k].split("</Id>")[0];
info.add(url_info + temp2);
image.add(url_image + temp2);
db.add(db_search);
id.add(temp2);
}
xml
db_search
image
info
db
id
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl
run_eSummary
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
pccompound