Get pathways by external reference

Created: 2010-01-13 12:21:59

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Finds pathways on WikiPathways by an external gene/protein/metabolite reference. See http://www.pathvisio.org/Help_1.1#Supported_database_systems for a list of supported database systems.

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Workflow Components

Inputs (2)

Name	Description
identifier	The identifier of the external reference (e.g. P48039).
system_code	The code of the external database to use. Use an empty string if you don't want to restrict the database system.

Processors (5)

Name	Type	Description
getId	local
getNames	local	XPath query to extract the names list from the xml response.
getSpecies	local	XPath query to extract the species list from the xml response.
findPathwaysByXrefInput	local
findPathwaysByXref	arbitrarywsdl

Beanshells (0)

Outputs (3)

Name	Description
pathway_names	A list with the names of the pathways that were found.
pathway_species	A list with the species of the pathways that were found.
pathway_ids

Links (9)

Source	Sink
findPathwaysByXref:parameters	getNames:xml-text
findPathwaysByXref:parameters	getSpecies:xml-text
findPathwaysByXrefInput:output	findPathwaysByXref:parameters
identifier	findPathwaysByXrefInput:id
system_code	findPathwaysByXrefInput:code
findPathwaysByXref:parameters	getId:xml-text
getId:nodelist	pathway_ids
getNames:nodelist	pathway_names
getSpecies:nodelist	pathway_species

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Information Workflow Type

Taverna 1

Information Uploader

Thomask...

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Information Version 2 (of 3)

Information Credits (1)

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Thomaskelder

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Information Statistics

3081 viewings

2416 downloads

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Version History

In chronological order:

Get pathways by external reference

Created by Thomaskelder on Tuesday 16 September 2008 11:18:51 (UTC)

Last edited by Thomaskelder on Tuesday 16 September 2008 11:35:40 (UTC)
Get pathways by external reference

Created by Thomaskelder on Friday 14 November 2008 14:21:46 (UTC)

Revision comment:

Updated workflow to stable identifiers on WikiPathways
Get pathways by external reference

Created by Thomaskelder on Wednesday 13 January 2010 12:21:59 (UTC)

Revision comment:

Adapted workflow to modified signature of findPathwaysByXref function.

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