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
\n
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
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.SplitByRegex
kegg pathway
mus_musculus
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
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
,
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++)
{
String trimmed = split[i].trim();
nonEmpty.add(trimmed);
}
String output = "";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + "Affy:Mouse430_2:" + (String) (nonEmpty.elementAt(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
result = ensemblGeneId + "," + entrezGeneId + "," + externalGeneId + "," + chromoName + "," + geneStart + "," + geneEnd + "," + ensemblTranscriptId + "," + uniprotAcc + "," + affy_Mouse430_2 + "," + affy_Mouse430a_2;
ensemblGeneId
entrezGeneId
externalGeneId
chromoName
geneStart
geneEnd
ensemblTranscriptId
uniprotAcc
affy_Mouse430_2
affy_Mouse430a_2
result
org.embl.ebi.escience.scuflworkers.java.StringListMerge
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
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.StringListMerge
Mus musculus genes (NCBIM36)
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#ensembl_genes_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#gene_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#Entrez_Gene_ID
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#Affymetrix_probe_set_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#Affymetrix_probe_set_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#UniProt_accession
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#end
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#start
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#chromosome
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#ensembl_gene_record_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#ensembl_transcript_record_id
"/></rdf:Description>
RMA Normalised
The mouse microarray experiment
Mus musculus genes (NCBIM36)
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#ensembl_genes_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#chromosome
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#start
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#end
"/></rdf:Description>
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
org.embl.ebi.escience.scuflworkers.java.StringListMerge
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
org.embl.ebi.escience.scuflworkers.java.StringListMerge
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
org.embl.ebi.escience.scuflworkers.java.StringConcat
org.embl.ebi.escience.scuflworkers.java.StringListMerge
http://soap.genome.jp/KEGG.wsdl
btit
http://soap.genome.jp/KEGG.wsdl
bconv
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#UniProt_accession
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#KEGG_genes_id
"/></rdf:Description>
The query function
http://dbkcodon.ch.umist.ac.uk/test/maxdBrowse/sequences/geneHunter8/wsdl.xml
query
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#Affymetrix_probe_set_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#gene_expression_report
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#microarray_database
"/></rdf:Description>
http://soap.genome.jp/KEGG.wsdl
bconv
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#UniProt_accession
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#KEGG_genes_id
"/></rdf:Description>
http://soap.genome.jp/KEGG.wsdl
binfo
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#KEGG_pathway_database
"/></rdf:Description>
17
29000000
32500000
0,1,2,3
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
http://phoebus.cs.man.ac.uk:8081/axis/EnsemblListner.jws?wsdl
lister
http://soap.genome.jp/KEGG.wsdl
get_pathways_by_genes
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#KEGG_genes_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#pathway_record_id
"/></rdf:Description>
http://soap.genome.jp/KEGG.wsdl
btit
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#pathway_record_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#pathway_description
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#KEGG_genes_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#pathway_record_id
"/></rdf:Description>
org.embl.ebi.escience.scuflworkers.java.StringListMerge
org.embl.ebi.escience.scuflworkers.java.StringConcat
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
org.embl.ebi.escience.scuflworkers.java.StringListMerge
\n
org.embl.ebi.escience.scuflworkers.java.StringListMerge
http://phoebus.cs.man.ac.uk:8081/axis/EnsemblListner.jws?wsdl
lister
http://soap.genome.jp/KEGG.wsdl
get_pathways_by_genes
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#KEGG_genes_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#pathway_record_id
"/></rdf:Description>
http://soap.genome.jp/KEGG.wsdl
btit
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#pathway_record_id
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#pathway_description
"/></rdf:Description>
Retrieves the current databases from ENSEMBL for a species
http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.getcurrentdatabase
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#species
"/></rdf:Description>
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="
"><rdf:type rdf:resource="
ontology#Ensembl
"/></rdf:Description>