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Kegg pathway diagrams

Workflow Entry: Kegg pathway diagrams

Created at: 13/03/10 @ 08:17:39

Version 1 (of 1)

Version created on: 13/03/10 @ 08:17:40 by: Jannetta | Revision comments Expand

Title: Kegg pathway diagrams

Type: Taverna 2

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Description

Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.

for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures

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http://www.myexperiment.org/workflows/1118/download?version=1
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Workflow Components

Authors (1)

Titles (1)

Descriptions (2)

Inputs (2)

Name	Description
gene_ids	A list of KEGG gene ids
Species	The three letter species code used by KEGG The three letter species code KEGG

Processors (4)

Name	Type	Description
get_pathways_by_genes	wsdl	See the Service entry for this web service.
mark_pathway_by_objects	wsdl	See the Service entry for this web service.
Get_Image_From_URL	localworker
Workflow89	workflow

Beanshells (0)

Outputs (6)

Name	Description
attachmentlist
KeggPathwayIDs	A list of the pathways found.
attachmentlist2
KeggImage	A list of pathway images in png format. If no pathway is found in which all the specified genes are involved, the list will be empty.
keggimageurl	The URLs of the images produced for the KeggImage output The URLs of the images produced for the KeggImage output.
keggGeneNames	A list of the gene ids, that was given as input with the species code concatenated.

Datalinks (12)

Source	Sink
Workflow89:string	get_pathways_by_genes:genes_id_list
get_pathways_by_genes:return	mark_pathway_by_objects:object_id_list
get_pathways_by_genes:return	mark_pathway_by_objects:pathway_id
mark_pathway_by_objects:return	Get_Image_From_URL:url
Species	Workflow89:part1
gene_ids	Workflow89:part2
get_pathways_by_genes:attachmentList	attachmentlist
get_pathways_by_genes:return	KeggPathwayIDs
mark_pathway_by_objects:attachmentList	attachmentlist2
Get_Image_From_URL:image	KeggImage
mark_pathway_by_objects:return	keggimageurl
Workflow89:string	keggGeneNames

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Jannetta

Information License

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Information Credits (1)

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Jannetta

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Information Tags (3)

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Information Statistics

355 viewings

431 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - Kegg pathway diagrams

Created on: Saturday 13 March 2010 @ 08:17:40 (GMT)

Created by: Jannetta

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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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