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Get KEGG gene descriptions and pathways

Created: 2010-04-30 16:09:29 Last updated: 2010-04-30 16:12:02

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This workflow takes a list of KEGG gene identifiers and supplies descriptions associated to said genes + pathways including all genes and the descriptions associated to said pathways.

The list_to_string local beanshell scripts merely transform a given list into a string of unique not-null elements separated by new lines (for batch btit use).

Note that the input is a real taverna list : multiple values must be declared as multiple values instead of a single string value with distinct identifiers separated by new lines.

This workflow is a slight modification of one made by Paul Fisher called "Get Kegg Gene information".

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Descriptions (4)

This workflow gets takes a list of KEGG gene identifiers and supplies descriptions associated to said genes + pathways including all genes and the descriptions associated to said pathways. The list_to_string local beanshell scripts merely transform a given list into a string of unique not-null elements separated by new lines (for batch btit use). Note that the input is a real taverna list : multiple values must be declared as multiple values instead of a single string value with distinct identifiers separated by new lines. This workflow is a slight modification of one made by Paul Fisher called "Get Kegg Gene information".

This workflow gets takes a list (depth=1) of KEGG gene identifiers and supplies descriptions associated to said genes + pathways including all genes and the descriptions associated to said pathways. The list_to_string local beanshell scripts merely transform a given list into a string of unique not-null elements separated by new lines (for batch btit use). This workflow is a slight modification of one made by Paul Fisher called "Get Kegg Gene information".

Dependencies (0)

Inputs (1)

Name	Description
kegg_gene_id_list	List of gene identifiers (from KEGG database).

Processors (5)

Name	Type	Description
btit	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation btit
get_pathways_by_genes	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_pathways_by_genes
list_to_string	beanshell	Script StringBuffer sb = new StringBuffer(); Iterator i = list.iterator(); List strippedList = new ArrayList(); strippedList.add(""); while (i.hasNext()) { String item = i.next().toString(); if (!strippedList.contains(item)) { strippedList.add(item); sb.append(item); if (i.hasNext()) { sb.append("\n"); } } } string = sb.toString();
btit_2	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation btit
list_to_string_2	beanshell	Script StringBuffer sb = new StringBuffer(); Iterator i = list.iterator(); List strippedList = new ArrayList(); strippedList.add(""); while (i.hasNext()) { String item = i.next().toString(); if (!strippedList.contains(item)) { strippedList.add(item); sb.append(item); if (i.hasNext()) { sb.append("\n"); } } } string = sb.toString();

Beanshells (2)

Name	Description	Inputs	Outputs
list_to_string		list	string
list_to_string_2		list	string

Outputs (2)

Name	Description
gene_descriptions	Gene identifiers and the corresponding definitions (from KEGG database). Gene identifiers and the corresponding descriptions (from KEGG database). Note : each line is a different couple gene id: description
pathway_descriptions	Pathway identifiers and the corresponding descriptions (from KEGG database). Note : each line is a different couple pathway id: description

Datalinks (7)

Source	Sink
list_to_string:string	btit:string
kegg_gene_id_list	get_pathways_by_genes:genes_id_list
kegg_gene_id_list	list_to_string:list
list_to_string_2:string	btit_2:string
get_pathways_by_genes:return	list_to_string_2:list
btit:return	gene_descriptions
btit_2:return	pathway_descriptions

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Information Workflow Type

Taverna 2

Information Uploader

Nadia Cerezo

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Information Version 1 (of 1)

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Information Attributions (1)

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Get Kegg Gene information

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Information Statistics

3331 viewings

1753 downloads

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Get KEGG gene descriptions and pathways

Created by Nadia Cerezo on Friday 30 April 2010 16:09:29 (UTC)

Last edited by Nadia Cerezo on Friday 30 April 2010 16:12:03 (UTC)

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Get KEGG gene descriptions and pathways

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