,
,
org.embl.ebi.escience.scuflworkers.java.FlattenList
org.embl.ebi.escience.scuflworkers.java.FlattenList
org.embl.ebi.escience.scuflworkers.java.FlattenList
org.embl.ebi.escience.scuflworkers.java.FlattenList
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
org.embl.ebi.escience.scuflworkers.java.StringListMerge
\n
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
Homo sapiens genes (NCBI36)
GO_information = gene_id + "," + go + "," + go_des + "," + evi
gene_id
go
go_des
evi
GO_information
ENSG00000117242
ENSG00000158828
ENSG00000117242
,
\n
,
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
org.embl.ebi.escience.scuflworkers.java.StringListMerge
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
Homo sapiens genes (NCBI36)
ensemblInfo = geneEnsembl_id + "," + entrezGeneID + "," + gene_name + "," + gene_des + "," + gene_chr + "," + gene_start + "," + gene_stop + "," + gene_stand + "," + band
geneEnsembl_id
gene_des
gene_chr
gene_start
gene_stop
gene_stand
gene_name
entrezGeneID
band
ensemblInfo
ENSG00000117242
ENSG00000117242
ENSG00000158828
ENSG00000158828
\n
,
,
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
org.embl.ebi.escience.scuflworkers.java.StringListMerge
Homo sapiens SNPs (dbSNP127;ENSEMBL;TSC1;HGVbase15)
hsapien = snpID + "," + ensemblID + "," + chr_name + "," + chrom_start + "," + allele + "," + chrom_stand + "," + ensembl_type + "," + validated + "," + peptide_shift
snpID
chr_name
ensemblID
chrom_start
allele
chrom_stand
ensembl_type
validated
peptide_shift
hsapien
rs1043502
rs10799658
hsa:
http://www.genome.jp
,
\n
org.embl.ebi.escience.scuflworkers.java.StringConcat
org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
org.embl.ebi.escience.scuflworkers.java.StringListMerge
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
trim1 = in.trim();
out = trim1.replace("path:hsa","");
in
out
url = "kegg/pathway/hsa/hsa" + id + ".gif";
id
url
// Create the list
List list = new LinkedList(); // Doubly-linked list
list = new ArrayList(); // List implemented as growable array
// Append an element to the list
list.add(word);
output = list;
word
output
id_result = result.replace("path",id + "-path");
id
result
id_result
http://soap.genome.jp/KEGG.wsdl
btit
http://soap.genome.jp/KEGG.wsdl
get_pathways_by_genes
24
7167
png/*
Input as the entrez gene ID from NCBI and the out put is the OMIM ID and the OMIM description
org.embl.ebi.escience.scuflworkers.java.StringSetDifference
String tmp = new String(in);
x = in.indexOf("OMIM NO");
y = in.indexOf("TITLE");
out = in.substring(x+8,y-x);
in
out
length = in.length();
if (length > 2 ){
out = in ;
} else {
}
in
out
org.embl.ebi.escience.scuflworkers.java.FlattenList
out = entrezid + "," + omimid
entrezid
omimid
out
gene
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
\n
/*[local-name(.)='eFetchResult'] /*[local-name(.)='Entrezgene-Set'] /*[local-name(.)='Entrezgene'] /*[local-name(.)='Entrezgene_unique-keys'] /*[local-name(.)='Dbtag'] /*[local-name(.)='Dbtag_tag'] /*[local-name(.)='Object-id'] /*[local-name(.)='Object-id_id']
get Info
http://xml.nig.ac.jp/wsdl/OMIM.wsdl
get
net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl
run_eFetch
Input example:
24
7167
1650
65018
get_motifs_by_gene(string:genes_id, string:db)
Search motifs in the specified gene. The value of 'db' can be 'pfam' for Pfam, 'pspt' for PROSITE pattern, 'pspf' for PROSITE profile or 'all' for all the above.
Return value:
ArrayOfMotifResult
Example:
# Returns the all pfam motifs in the E. coli gene 'b0002'
get_motifs_by_gene('eco:b0002', 'pfam')
all
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
http://soap.genome.jp/KEGG.wsdl
get_motifs_by_gene
\n
org.embl.ebi.escience.scuflworkers.java.StringConcat
hsa:
// Input คือ Unique_Entrez_ID ex. hsa:24
//เอา output ทุกตัวจาก XML ยกเว้น evalue
motif_info = motif_id +", " + definition + ", "+ genes_id + ", " + start_position + ", " + end_position + ", " + score;
motif_id
definition
genes_id
start_position
end_position
score
motif_info
org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
Entrez gene ID ex.
24
7167
24
7167
1650
65018
rs1043502
rs10799658