This workflow uses one or more services that are deprecated as of 31st December 2012 (about 12 years ago), and may no longer function. Show details...

Pathways and Gene annotations forQTL region

Created: 2011-03-24 15:14:48 Last updated: 2011-03-24 15:37:48

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This workflow searches for genes found from a set of differentially expressed probestes, in Human, Homo sapiens. The workflow requires an input human affymetrix probeset identifiers. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database.

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Authors (1)

Titles (1)

Descriptions (2)

Dependencies (0)

Inputs (1)

Name	Description
probeset_list

Processors (40)

Name	Type	Description
regex_2	stringconstant	Value \n
merge_kegg_references	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
split_for_duplicate_pathways	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
merge_uniprot_ids	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
REMOVE_NULLS_2	beanshell	Script 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"); }
merge_entrez_genes	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
split_gene_ids	beanshell	Script 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"); }
merge_genes_and_pathways_3	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
remove_uniprot_duplicates	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
merge_pathway_list_1	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
remove_Nulls	beanshell	Script 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"); }
merge_gene_desc	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
merge_genes_and_pathways	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
binfo	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation binfo
remove_pathway_nulls_2	beanshell	Script 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"); }
kegg_pathway_release	stringconstant	Value kegg pathway
merge_pathway_list_2	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
concat_kegg_genes	localworker	Script output = string1 + string2;
remove_pathway_nulls	beanshell	Script 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"); }
add_uniprot_to_string	beanshell	Script 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"); }
create_report	beanshell	Script result = ensemblGene_Id + "," + entrezGeneId + "," + externalGeneId + "," + chromoName + "," + geneStart + "," + geneEnd + "," + ensemblTranscriptId + "," + uniprotAcc;
pathway_descriptions	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation btit
Kegg_gene_ids	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation bconv
add_ncbi_to_string	beanshell	Script 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"); }
merge_patwhay_ids	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
merge_pathway_desc	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
remove_duplicate_kegg_genes	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
remove_duplicate_ids	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
gene_descriptions	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation btit
split_for_duplicates	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
remove_pathway_duplicates	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
merge_reports	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
remove_entrez_duplicates	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
merge_genes_and_pathways_2	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
remove_nulls_3	beanshell	Script 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"); }
Kegg_gene_ids_2	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation bconv
Get_pathways	workflow
flatten_pathway_files	soaplab	Endpoint http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.flatten_pathway_files
hsapiens_gene_ensembl_2	biomart
split_probesets	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }

Beanshells (11)

Name	Inputs	Outputs
REMOVE_NULLS_2	input	output
split_gene_ids	input	output
remove_Nulls	input	output
remove_pathway_nulls_2	input	output
remove_pathway_nulls	input	output
add_uniprot_to_string	input	output
create_report	ensemblGene_Id entrezGeneId externalGeneId chromoName geneStart geneEnd ensemblTranscriptId uniprotAcc	result
add_ncbi_to_string	input	output
remove_nulls_3	input	output
concat_gene_pathway_ids	pathway_ids gene_id	output
concat_ids	input	output

Outputs (8)

Name	Description
merged_pathways
gene_descriptions
pathway_descriptions
kegg_pathway_release
report
kegg_external_gene_reference
pathway_ids
genes_pathways

Datalinks (59)

Source	Sink
concat_kegg_genes:output	merge_kegg_references:stringlist
regex_2:value	split_for_duplicate_pathways:regex
merge_pathway_list_2:concatenated	split_for_duplicate_pathways:string
remove_uniprot_duplicates:strippedlist	merge_uniprot_ids:stringlist
merge_uniprot_ids:concatenated	REMOVE_NULLS_2:input
remove_entrez_duplicates:strippedlist	merge_entrez_genes:stringlist
concat_kegg_genes:output	split_gene_ids:input
merge_genes_and_pathways_2:concatenated	merge_genes_and_pathways_3:stringlist
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.uniprot_swissprot_accession	remove_uniprot_duplicates:stringlist
Get_pathways:pathway_ids	merge_pathway_list_1:stringlist
merge_entrez_genes:concatenated	remove_Nulls:input
gene_descriptions:return	merge_gene_desc:stringlist
Get_pathways:pathway_genes	merge_genes_and_pathways:stringlist
kegg_pathway_release:value	binfo:db
merge_patwhay_ids:concatenated	remove_pathway_nulls_2:input
merge_pathway_list_1:concatenated	merge_pathway_list_2:stringlist
Kegg_gene_ids:return	concat_kegg_genes:string1
Kegg_gene_ids_2:return	concat_kegg_genes:string2
merge_pathway_desc:concatenated	remove_pathway_nulls:input
REMOVE_NULLS_2:output	add_uniprot_to_string:input
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.entrezgene	create_report:entrezGeneId
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.external_gene_id	create_report:externalGeneId
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.start_position	create_report:geneStart
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.uniprot_swissprot_accession	create_report:uniprotAcc
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.ensembl_transcript_id	create_report:ensemblTranscriptId
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.ensembl_gene_id	create_report:ensemblGene_Id
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.chromosome_name	create_report:chromoName
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.end_position	create_report:geneEnd
remove_duplicate_ids:strippedlist	pathway_descriptions:string
add_uniprot_to_string:output	Kegg_gene_ids:string
remove_Nulls:output	add_ncbi_to_string:input
remove_duplicate_ids:strippedlist	merge_patwhay_ids:stringlist
remove_pathway_duplicates:strippedlist	merge_pathway_desc:stringlist
split_for_duplicates:split	remove_duplicate_kegg_genes:stringlist
split_for_duplicate_pathways:split	remove_duplicate_ids:stringlist
remove_duplicate_kegg_genes:strippedlist	gene_descriptions:string
regex_2:value	split_for_duplicates:regex
split_gene_ids:output	split_for_duplicates:string
pathway_descriptions:return	remove_pathway_duplicates:stringlist
create_report:result	merge_reports:stringlist
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.entrezgene	remove_entrez_duplicates:stringlist
merge_genes_and_pathways:concatenated	merge_genes_and_pathways_2:stringlist
merge_gene_desc:concatenated	remove_nulls_3:input
add_ncbi_to_string:output	Kegg_gene_ids_2:string
remove_duplicate_kegg_genes:strippedlist	Get_pathways:gene_ids
remove_pathway_nulls:output	flatten_pathway_files:pathway_descriptions_direct_data
remove_nulls_3:output	flatten_pathway_files:gene_descriptions_direct_data
merge_genes_and_pathways_3:concatenated	flatten_pathway_files:merged_pathways_direct_data
split_probesets:split	hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.ensembl_gene_id_filter
probeset_list	split_probesets:string
regex_2:value	split_probesets:regex
merge_genes_and_pathways_3:concatenated	merged_pathways
remove_nulls_3:output	gene_descriptions
remove_pathway_nulls:output	pathway_descriptions
binfo:return	kegg_pathway_release
merge_reports:concatenated	report
merge_kegg_references:concatenated	kegg_external_gene_reference
remove_pathway_nulls_2:output	pathway_ids
flatten_pathway_files:output	genes_pathways

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Taverna 2

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Paul Fisher

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Paul Fisher

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1590 downloads

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Pathways and Gene annotations forQTL region

Created by Paul Fisher on Thursday 24 March 2011 15:14:48 (UTC)

Last edited by Paul Fisher on Thursday 24 March 2011 15:37:48 (UTC)

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Taverna 2

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Paul Fisher

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway data...

Created: 2011-01-21 | Last updated: 2011-01-21

Credits: Paul Fisher

Taverna 2

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Paul Fisher

Pathways and Gene annotations for QTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in rice, Oryza sativa. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniGene identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway d...

Created: 2011-05-27 | Last updated: 2011-05-27

Credits: Paul Fisher

Pathways and Gene annotations forQTL region

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