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Get Kegg Gene information

Workflow Entry: Get Kegg Gene information

Created at: 26/01/09 @ 18:06:12 Last updated: 14/12/09 @ 12:05:21

Version 2 (latest) (of 2)

Version created on: 26/01/09 @ 18:06:12 by: Paul Fisher | Revision comments Expand

Last edited on: 14/12/09 @ 12:05:23 by: Paul Fisher

Title: Get Kegg Gene information

Type: Taverna 1

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Description

This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.

Example input for this workflow is given below (new line separated):

mmu:13163

hsa:1616

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Run

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Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/611/download?version=2
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
kegg_gene_id_list

Processors (11)

Name	Type	Description
btit	arbitrarywsdl	See the Service entry for this web service.
get_pathways_by_genes	arbitrarywsdl	See the Service entry for this web service.
regex	stringconstant
Remove_duplicate_pathways	local
merge_descriptions	local
merge_pathways	local
split_by_regex	local
merge_pathways_2	local
remove_nulls_2	beanshell
remove_Nulls	beanshell
btit1	arbitrarywsdl	See the Service entry for this web service.

Beanshells (2)

Name	Description	Inputs	Outputs
remove_nulls_2		input	output
remove_Nulls		input	output

Outputs (3)

Name	Description
gene_descriptions
pathway_by_genes
pathway_descriptions

Links (14)

Source	Sink
Remove_duplicate_pathways:strippedlist	merge_pathways_2:stringlist
btit1:return	pathway_descriptions
btit:return	merge_descriptions:stringlist
get_pathways_by_genes:return	merge_pathways:stringlist
kegg_gene_id_list	btit:string
kegg_gene_id_list	split_by_regex:string
merge_descriptions:concatenated	remove_Nulls:input
merge_pathways:concatenated	Remove_duplicate_pathways:stringlist
merge_pathways:concatenated	btit1:string
merge_pathways_2:concatenated	remove_nulls_2:input
regex:value	split_by_regex:regex
split_by_regex:split	get_pathways_by_genes:genes_id_list
remove_Nulls:output	gene_descriptions
remove_nulls_2:output	pathway_by_genes

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

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None

Information Tags (6)

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Information Shared with Groups (2)

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Information Ratings (1)

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5.0 / 5

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Information Attributed By (3)

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Information Favourited By (3)

Information Statistics

1187 viewings

1350 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - Get Kegg Gene information

Created on: Monday 05 January 2009 @ 13:20:34 (GMT)

Created by: Paul Fisher

Revision comments:

None

Latest Version:
[2] - Get Kegg Gene information

Created on: Monday 26 January 2009 @ 18:06:12 (GMT)

Created by: Paul Fisher

Last edited on: Monday 14 December 2009 @ 12:05:23 (GMT)

Last edited by: Paul Fisher

Revision comments:

None

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Comments (1)

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Franck Tanoh	Wednesday 28 January 2009 @ 11:40:50 (GMT)
	you can use this kegg id : "path:hsa05216" to test this workflow

Other workflows that use similar services (91)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 2

Original Uploader

Katy Wolstencroft

NCBI Gi to Kegg Pathway Descriptions (v2)

Created: 12/01/12 @ 09:46:31 | Last updated: 12/01/12 @ 14:54:37

Credits: Katy Wolstencroft

Attributions: NCBI Gi to Kegg Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 6 times | Downloaded: 8 times

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