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. //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 //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 org.embl.ebi.escience.scuflworkers.java.WebImageFetcher net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker 35048_at \s/PDB:/\s org.embl.ebi.escience.scuflworkers.java.SplitByRegex \s///\s org.embl.ebi.escience.scuflworkers.java.SplitByRegex MEDLINE: //Output String id; if(str.startsWith(prefix)) { id = str.substring(prefix.length()); } else { str = ""; } str prefix id Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB &compression=None http://www.rcsb.org/pdb/cgi/export.cgi/1CRN.pdb?format=PDB&pdbId= org.embl.ebi.escience.scuflworkers.java.WebPageFetcher org.embl.ebi.escience.scuflworkers.java.StringConcat org.embl.ebi.escience.scuflworkers.java.StringConcat PDB identifier such as '1crn' chemical/x-pdb Given a list of Gene IDs this workflow will query against the Ensembl human genome data to fetch the genomic region for each gene, extend that region by 1000bp in each direction and use this set of ranges, one per gene, to build a query against dbSNP to return the SNP identifier and location information (chromosome name, strand and position) Given a list of Gene IDs this workflow will query against the Ensembl human genome data to fetch the genomic region for each gene, extend that region by 1000bp in each direction and use this set of ranges, one per gene, to build a query against dbSNP to return the SNP identifier and location information (chromosome name, strand and position) org.embl.ebi.escience.scuflworkers.java.EchoList Homo sapiens SNPs (dbSNP 126; HGVbase 15; TSC 1; affy GeneChip Mapping Array) Homo sapiens genes (NCBI36) result = chrom + "," + strand + "," + chromStart + "," + codingSNP + "," + snpID; strand chromStart chrom snpID codingSNP result text/plain List of Ensemble gene identifiers for human. http://www.mygrid.org.uk/ontology#gene_id http://www.mygrid.org.uk/ontology#gene_id For cross-referencing between databanks SPTREMBL AllText PDB http://phoebus.cs.man.ac.uk:1977/axis/services/linking.srslinks 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://soap.genome.jp/KEGG.wsdl get_pathways_by_enzymes http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl destroySession http://www.ebi.ac.uk/collab/mygrid/service1/goviz/GoViz.jws?wsdl createSession http://soap.genome.jp/KEGG.wsdl mark_pathway_by_objects Calculates DNA RNA/DNA melting temperature http://www.ebi.ac.uk/soaplab/services/nucleic_composition.dan Execute Blast blastp PDB http://xml.nig.ac.jp/wsdl/Blast.wsdl searchSimple 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 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 http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymapper?wsdl getRepresentativePublicId For cross-referencing between databanks EMBL acc MEDLINE http://dbk-ed.mib.man.ac.uk:8080/axis/services/srs_links.ebi_srslinks http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymapper?wsdl getEnsembl 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 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 http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymapper?wsdl getGeneOntologyMolecularFunction 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 getInterPro http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymapper?wsdl getEC Execute Blast with parameter blastp PDB -m 8 http://xml.nig.ac.jp/wsdl/Blast.wsdl searchParam chemical/x-swissprot chemical/x-embl-dl-nucleotide text/xml text/x-graphviz application/octet-stream image/png Completed addTermToViz getDotFromViz Scheduled Running Completed getDotFromViz destroyVizSession Scheduled Running