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: 2009-12-04 16:04:38 Last updated: 2010-11-30 12:18:53

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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

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Version 5 (latest) (of 5)

Information Credits (1)

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Paul Fisher

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Information Favourited By (4)

Information Statistics

14759 viewings

8979 downloads

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Version History

In chronological order:

Entrez Gene to KEGG Pathway

Created by Paul Fisher on Wednesday 03 October 2007 18:36:00 (UTC)
Entrez Gene to KEGG Pathway

Created by Paul Fisher on Wednesday 03 October 2007 18:36:00 (UTC)

Last edited by Paul Fisher on Tuesday 13 November 2007 16:16:10 (UTC)
Entrez Gene to KEGG Pathway

Created by Paul Fisher on Friday 27 February 2009 14:49:42 (UTC)

Revision comment:

Revision of the split_gene_ids service to reflect changes to the Kegg output
Entrez Gene to KEGG Pathway

Created by Paul Fisher on Friday 04 December 2009 16:04:38 (UTC)

Revision comment:

Updated inner nested workflow beanshell to reflect KEGG wsdl changes
Entrez Gene to KEGG Pathway

Created by Paul Fisher on Tuesday 30 November 2010 12:18:52 (UTC)

Revision comment:

Fixed bug with beanshell - changed ncbi-gi to ncbi-geneid

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Comments (3)

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Rexissimus

If you change

if (trimmedSplit.length == 2)

if (trimmedSplit.length == 3)

split_gene_ids

it will actually work

You can try 24605 as input

Maybe this is because of a change in the output of Kegg_gene_ids_all_species

Maybe

if (trimmedSplit.length >= 3)

is better since it would allow for future expansions

Otherwise good example of web service usage

/Tommy

Paul Fisher

Thank you for your feedback. It's much appreciated.

Paul

LissaCo...	Saturday 16 November 2013 06:39:14 (UTC)
	good example of web service usage.

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