Workflow Entry: Get pathways by external reference

Created at: 16/09/08 @ 11:18:51 Last updated: 14/11/08 @ 14:21:46

Version 2 (latest) (of 2)

Version created on: 14/11/08 @ 14:21:46 by: Thomaskelder | Revision comments Expand

Title: Get pathways by external reference

Type: Taverna 1

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

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.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

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/391/download?version=2
[ More Info Expand ]

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

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)

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