NCBI Gi to Kegg Pathway Descriptions

Created: 2012-01-12 09:46:31 Last updated: 2013-01-30 13:36:27

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This workflow accepts a list of NCBI gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

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http://www.myexperiment.org/workflows/2659/download?version=5
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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
genes	Accepts a list of NCBI Gene Identifiers

Processors (17)

Name	Type	Description
regex	stringconstant	Value \n
split_by_regex	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]); } }
Split_gene_list	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]); } }
regex_value	stringconstant	Value \n
bconvREST	rest
target_value	stringconstant	Value mmu
ExtractGeneName	localworker	Script import java.util.regex.*; filteredlist = new ArrayList(); Pattern thePat = Pattern.compile(regex); int theGroup = Integer.parseInt(group); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); Matcher matcher = thePat.matcher(item); if (matcher.find()) { filteredlist.add(matcher.group(theGroup)); } }
group_value	stringconstant	Value 0
regex_value_2	stringconstant	Value mmu:[0-9]{4,}
btit_REST	rest
getPathwaybyGene	rest
ExtractPathwayName	localworker	Script import java.util.regex.*; filteredlist = new ArrayList(); Pattern thePat = Pattern.compile(regex); int theGroup = Integer.parseInt(group); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); Matcher matcher = thePat.matcher(item); if (matcher.find()) { filteredlist.add(matcher.group(theGroup)); } }
group_value_1	stringconstant	Value 0
regex_value_3	stringconstant	Value path:[0-9a-z]{5,}
pathwayEntry	rest
pathwayImage	rest
add_ncbi_to_string	beanshell	Script String[] split; Vector nonEmpty = new Vector(); if(input.indexOf("__cr____cn__") != -1) { split = input.split("__cr____cn__"); } else if(input.indexOf(",") != -1) { split = input.split(","); } else { split = input.split("\n"); } 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-gi:" + (String) (nonEmpty.elementAt(i) + "\n"); }

Beanshells (1)

Name	Description	Inputs	Outputs
add_ncbi_to_string		input	output

Outputs (5)

Name	Description
kegg_mouseID	Produces a mapping of NCBI and KEGG gene identifiers
gene_description	produces a list of gene descriptions and their KEGG Gene IDs
pathDescRest	Retrieves the pathway entry from the KEGG database
pathwayID	Produces a list of pathway IDs for each gene ID
PathwayImage	Retrieves the pathway image from the KEGG database

Datalinks (22)

Source	Sink
regex:value	split_by_regex:regex
ExtractGeneName:filteredlist	split_by_regex:string
regex_value:value	Split_gene_list:regex
add_ncbi_to_string:output	Split_gene_list:string
Split_gene_list:split	bconvREST:source
target_value:value	bconvREST:target
bconvREST:responseBody	ExtractGeneName:stringlist
group_value:value	ExtractGeneName:group
regex_value_2:value	ExtractGeneName:regex
ExtractGeneName:filteredlist	btit_REST:geneID
split_by_regex:split	getPathwaybyGene:geneID
group_value_1:value	ExtractPathwayName:group
regex_value_3:value	ExtractPathwayName:regex
getPathwaybyGene:responseBody	ExtractPathwayName:stringlist
ExtractPathwayName:filteredlist	pathwayEntry:pathID
ExtractPathwayName:filteredlist	pathwayImage:pathID
genes	add_ncbi_to_string:input
bconvREST:responseBody	kegg_mouseID
btit_REST:responseBody	gene_description
pathwayEntry:responseBody	pathDescRest
getPathwaybyGene:responseBody	pathwayID
pathwayImage:responseBody	PathwayImage