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Retrieve Pathways and Compound information from KEGG

Workflow Entry: Retrieve Pathways and Compound information from KEGG

Created at: 30/03/09 @ 09:22:36 Last updated: 30/03/09 @ 09:39:23

Version 1 (of 1)

Version created on: 30/03/09 @ 09:22:36 by: Michael Gerlich | Revision comments Expand

Last edited on: 30/03/09 @ 09:39:24 by: Michael Gerlich

Title: Retrieve Pathways and Compound information from KEGG

Type: Taverna 1

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Description

Given a KEGG compound identifier (e.g. cpd:C00905), this workflow queries KEGG DB for pathways and compound information for each of these compounds. As the KEGG pathway service tries to find pathways which contain all input compounds, the input list is split up to circumvent this behaviour and to search for only one compound in a pathway at a time. Compounds identified in pathways are marked as red in the resulting pathway image.

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Workflow Components

Inputs (1)

Name	Description
bget_in

Processors (9)

Name	Type	Description
bget	arbitrarywsdl	See the Service entry for this web service.
get_pathways_by_compounds	arbitrarywsdl	See the Service entry for this web service.
Convert_list_of_KeggIDs_into_1element_list_of_lists	local
Flatten_list	local
Flatten_list1	local
Remove_duplicate_strings	local
Split_string_into_string_list_by_regular_expression	local
mark_pathway_by_objects	arbitrarywsdl	See the Service entry for this web service.
Get_image_from_URL	local

Beanshells (0)

Outputs (2)

Name	Description
KEGG_bget
KEGG_pathways

Links (12)

Source	Sink
bget_in	Convert_list_of_KeggIDs_into_1element_list_of_lists:string
bget_in	bget:string
Convert_list_of_KeggIDs_into_1element_list_of_lists:split	Flatten_list1:inputlist
Convert_list_of_KeggIDs_into_1element_list_of_lists:split	get_pathways_by_compounds:compound_id_list
Flatten_list1:outputlist	mark_pathway_by_objects:object_id_list
Flatten_list:outputlist	Remove_duplicate_strings:stringlist
Get_image_from_URL:image	KEGG_pathways
Remove_duplicate_strings:strippedlist	Split_string_into_string_list_by_regular_expression:string
Split_string_into_string_list_by_regular_expression:split	mark_pathway_by_objects:pathway_id
mark_pathway_by_objects:return	Get_image_from_URL:url
bget:return	KEGG_bget
get_pathways_by_compounds:return	Flatten_list:inputlist

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Michael Gerlich

Information License

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Information Credits (1)

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Michael Gerlich

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Information Favourited By (1)

Ian Laycock

Information Statistics

445 viewings

591 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - Retrieve Pathways and Compound information from KEGG

Created on: Monday 30 March 2009 @ 09:22:36 (GMT)

Created by: Michael Gerlich

Last edited on: Monday 30 March 2009 @ 09:39:24 (GMT)

Last edited by: Michael Gerlich

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