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Pathways and Gene annotations for RefSeq ids

Created: 2010-11-15 12:25:01 Last updated: 2010-11-15 12:28:12

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This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to search for pathways in the KEGG pathway database.

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Inputs (1)

Name	Description
ref_seq_dna_ids

Processors (40)

Name	Type	Description
kegg_pathway_release	stringconstant	Value kegg pathway
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"); }
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"); }
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"); }
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"); }
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"); }
create_report	beanshell	Script result = ensemblGene_Id + "," + entrezGeneId + "," + externalGeneId + "," + chromoName + "," + geneStart + "," + geneEnd + "," + ensemblTranscriptId + "," + uniprotAcc + "," + Affy_Mouse430_2;
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"); }
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_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); } }
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_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();
pathway_descriptions	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation btit
binfo	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation binfo
Kegg_gene_ids_2	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation bconv
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();
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();
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();
regex_2	stringconstant	Value \n
Kegg_gene_ids	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation bconv
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]); } }
gene_descriptions	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation btit
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();
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_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();
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_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); } }
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();
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); } }
concat_kegg_genes	localworker	Script output = string1 + string2;
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();
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();
mmusculus_gene_ensembl	biomart
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_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();
Get_pathways	workflow
flatten_pathway_files	soaplab	Endpoint http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.flatten_pathway_files
Split_string_into_string_list_by_regular_expression	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
split_gene_ids	input	output
remove_pathway_nulls_2	input	output
remove_Nulls	input	output
remove_pathway_nulls	input	output
add_uniprot_to_string	input	output
remove_nulls_3	input	output
create_report	ensemblGene_Id entrezGeneId externalGeneId chromoName geneStart geneEnd ensemblTranscriptId uniprotAcc Affy_Mouse430_2	result
REMOVE_NULLS_2	input	output
add_ncbi_to_string	input	output
concat_ids	input	output
concat_gene_pathway_ids	pathway_ids gene_id	output

Outputs (8)

Name	Description
merged_pathways
gene_descriptions
pathway_descriptions
kegg_pathway_release
report
kegg_external_gene_reference
pathway_ids
genes_pathways

Datalinks (60)

Source	Sink
concat_kegg_genes:output	split_gene_ids:input
merge_patwhay_ids:concatenated	remove_pathway_nulls_2:input
merge_entrez_genes:concatenated	remove_Nulls:input
merge_pathway_desc:concatenated	remove_pathway_nulls:input
REMOVE_NULLS_2:output	add_uniprot_to_string:input
merge_gene_desc:concatenated	remove_nulls_3:input
mmusculus_gene_ensembl:mmusculus_gene_ensembl.external_gene_id	create_report:externalGeneId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.ensembl_gene_id	create_report:ensemblGene_Id
mmusculus_gene_ensembl:mmusculus_gene_ensembl.ensembl_transcript_id	create_report:ensemblTranscriptId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.end_position	create_report:geneEnd
mmusculus_gene_ensembl:mmusculus_gene_ensembl.uniprot_swissprot_accession	create_report:uniprotAcc
mmusculus_gene_ensembl:mmusculus_gene_ensembl.entrezgene	create_report:entrezGeneId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.start_position	create_report:geneStart
mmusculus_gene_ensembl:mmusculus_gene_ensembl.affy_mouse430_2	create_report:Affy_Mouse430_2
mmusculus_gene_ensembl:mmusculus_gene_ensembl.chromosome_name	create_report:chromoName
merge_uniprot_ids:concatenated	REMOVE_NULLS_2:input
split_for_duplicates:split	remove_duplicate_kegg_genes:stringlist
mmusculus_gene_ensembl:mmusculus_gene_ensembl.uniprot_swissprot_accession	remove_uniprot_duplicates:stringlist
mmusculus_gene_ensembl:mmusculus_gene_ensembl.entrezgene	remove_entrez_duplicates:stringlist
remove_uniprot_duplicates:strippedlist	merge_uniprot_ids:stringlist
remove_duplicate_ids:strippedlist	pathway_descriptions:string
kegg_pathway_release:value	binfo:db
add_ncbi_to_string:output	Kegg_gene_ids_2:string
remove_pathway_duplicates:strippedlist	merge_pathway_desc:stringlist
merge_genes_and_pathways_2:concatenated	merge_genes_and_pathways_3:stringlist
merge_pathway_list_1:concatenated	merge_pathway_list_2:stringlist
add_uniprot_to_string:output	Kegg_gene_ids:string
regex_2:value	split_for_duplicate_pathways:regex
merge_pathway_list_2:concatenated	split_for_duplicate_pathways:string
remove_duplicate_kegg_genes:strippedlist	gene_descriptions:string
merge_genes_and_pathways:concatenated	merge_genes_and_pathways_2:stringlist
remove_duplicate_ids:strippedlist	merge_patwhay_ids:stringlist
concat_kegg_genes:output	merge_kegg_references:stringlist
Get_pathways:pathway_ids	merge_pathway_list_1:stringlist
split_for_duplicate_pathways:split	remove_duplicate_ids:stringlist
Get_pathways:pathway_genes	merge_genes_and_pathways:stringlist
regex_2:value	split_for_duplicates:regex
split_gene_ids:output	split_for_duplicates:string
pathway_descriptions:return	remove_pathway_duplicates:stringlist
Kegg_gene_ids_2:return	concat_kegg_genes:string2
Kegg_gene_ids:return	concat_kegg_genes:string1
remove_entrez_duplicates:strippedlist	merge_entrez_genes:stringlist
gene_descriptions:return	merge_gene_desc:stringlist
Split_string_into_string_list_by_regular_expression:split	mmusculus_gene_ensembl:mmusculus_gene_ensembl.refseq_dna_filter
remove_Nulls:output	add_ncbi_to_string:input
create_report:result	merge_reports:stringlist
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
regex_2:value	Split_string_into_string_list_by_regular_expression:regex
ref_seq_dna_ids	Split_string_into_string_list_by_regular_expression:string
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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Pathways and Gene annotations for RefSeq ids

Created by Paul Fisher on Monday 15 November 2010 12:25:01 (UTC)

Last edited by Paul Fisher on Monday 15 November 2010 12:28:12 (UTC)

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Pathways and Gene annotations for RefSeq ids

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