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

Entrez Gene to KEGG Pathway

Created: 2014-01-30 14:03:39

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This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

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Workflow Components

Inputs (1)

Name	Description
gene

Processors (7)

Name	Type	Description
mergePathways_2	local
merge_pathways	local
split_gene_ids	beanshell
Add_ncbi_to_string	workflow
get_pathways_by_genes	arbitrarywsdl
lister	arbitrarywsdl
Kegg_gene_ids_all_species	arbitrarywsdl

Beanshells (2)

Name	Description	Inputs	Outputs
add_ncbi_to_string		input	output
split_gene_ids		input	output

Outputs (1)

Name	Description
merged_kegg_pathways

Links (8)

Source	Sink
Add_ncbi_to_string:Kegg_strings	Kegg_gene_ids_all_species:string
Kegg_gene_ids_all_species:return	split_gene_ids:input
gene	Add_ncbi_to_string:Gi_numbers
get_pathways_by_genes:return	merge_pathways:stringlist
lister:listerReturn	get_pathways_by_genes:genes_id_list
merge_pathways:concatenated	mergePathways_2:stringlist
split_gene_ids:output	lister:file
mergePathways_2:concatenated	merged_kegg_pathways

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Information Workflow Type

Taverna 1

Information Uploader

Alice Heliou

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Information Version 1 (of 1)

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Alice Heliou

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Information Statistics

1000 viewings

917 downloads

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Version History

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Entrez Gene to KEGG Pathway

Created by Alice Heliou on Thursday 30 January 2014 14:03:38 (UTC)

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