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 (4)

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

Beanshells (0)

Outputs (2)

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.

Links (7)

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

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Taverna 1

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Thomask...

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Information Version 1 (earliest) (of 3)

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Thomaskelder

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Information Statistics

3202 viewings

2570 downloads

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Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Created: 2009-02-03

Credits: Thomaskelder