This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.
1104_s_at
MEDLINE:
//Output
String id;
if(str.startsWith(prefix))
{
id = str.substring(prefix.length());
}
else
{
str = "";
}
str
prefix
id
//Output
ArrayList goIds = new ArrayList();
String[] ids = inputStr.split(" /// ");
for (int i = 0; i < ids.length; i++)
{
String[] moreIds = ids[i].split(" // ");
if(!goIds.contains(moreIds[0]))
{
String goId;
int x = moreIds[0].length();
if(x == 3)
{
goId = "GO:0000" + moreIds[0];
}
else if(x == 4)
{
goId = "GO:000" + moreIds[0];
}
else if(x == 5)
{
goId = "GO:00" + moreIds[0];
}
goIds.add(goId);
}
}
inputStr
goIds
//Output
ArrayList interproIds = new ArrayList();
String[] ids = inputStr.split(" /// ");
for (int i = 0; i < ids.length; i++)
{
String[] moreIds = ids[i].split(" // ");
if(!interproIds.contains(moreIds[0]))
{
interproIds.add(moreIds[0]);
}
}
inputStr
interproIds
\s///\s
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
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
destroySession
http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymapper?wsdl
getInterPro
http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymapper?wsdl
getRepresentativePublicId
http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymapper?wsdl
getSwissProt
http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymapper?wsdl
getGeneOntologyMolecularFunction
http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl
getDot
http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl
addTerm
http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymapper?wsdl
getEC
//Output
ArrayList ecNumbers = new ArrayList();
String[] ids = inputStr.split(" /// ");
for (int i = 0; i < ids.length; i++)
{
//Remove EC: prefix
String ecNumber = ids[i];
//ecNumber = ecNumber.substring(3);
ecNumber = ecNumber.toLowerCase();
if(!ecNumbers.contains(ecNumber))
{
ecNumbers.add(ecNumber);
}
}
inputStr
ecNumbers
http://soap.genome.jp/KEGG.wsdl
get_pathways_by_enzymes
For cross-referencing between databanks
EMBL
acc
MEDLINE
http://dbk-ed.mib.man.ac.uk:8080/axis/services/srs_links.ebi_srslinks
org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
http://soap.genome.jp/KEGG.wsdl
mark_pathway_by_objects
This call to a Blastn service at the DDBJ is to check that the target sequence of the probe set is specific to the gene whose mRNA expression that the probe sequences have been designed to measure.
blastn
ddbjhum
http://xml.nig.ac.jp/wsdl/Blast.wsdl
searchSimple
http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymapper?wsdl
getTargetSequence
The UniProt Knowledgebase is a central database of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
acc
http://dbk-ed.mib.man.ac.uk:8080/axis/services/srs_ebi_uniprotsequence.ebi_uniprot
MEDLINE is the NLM's premier bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences. MEDLINE contains bibliographic citations and author abstracts from more than 4,000 biomedical journals published in the United States and 70 other countries. The file contains over 12 million citations dating back to the mid-1960's. Coverage is worldwide, but most records are from English-language sources or have English abstracts.
all
http://dbk-ed.mib.man.ac.uk:8080/axis/services/srs_ebi_literature.ebi_medline2007
The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the Swiss-Prot Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva. Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available. The EBI network services include database searching and sequence similarity searching facilities.
acc
http://dbk-ed.mib.man.ac.uk:8080/axis/services/srs_ebi_dnasequence.ebi_embl
Calculates DNA RNA/DNA melting temperature
http://www.ebi.ac.uk/soaplab/services/nucleic_composition.dan
UniprotAndPDB
file:/D:/terrybiteImport/examples/examples/testworkflows/uniprotandPDBxml.xml
chemical/x-swissprot
chemical/x-embl-dl-nucleotide
text/xml
text/x-graphviz
application/octet-stream
image/png
chemical/x-pdb
Completed
addTermToViz
getDotFromViz
Scheduled
Running
Completed
getDotFromViz
destroyVizSession
Scheduled
Running