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Get pathways by external reference

Workflow Entry: Get pathways by external reference

Created at: 13/01/10 @ 12:21:59

Version 3 (latest) (of 3)

Version created on: 13/01/10 @ 12:21:59 by: Thomaskelder | Revision comments Expand

Title: Get pathways by external reference

Type: Taverna 1

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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.

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http://www.myexperiment.org/workflows/391/download?version=3
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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
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.
findPathwaysByXref	arbitrarywsdl	See the Service entry for this web service.
findPathwaysByXrefInput	local

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	getId:xml-text
findPathwaysByXref:parameters	getNames:xml-text
findPathwaysByXref:parameters	getSpecies:xml-text
findPathwaysByXrefInput:output	findPathwaysByXref:parameters
identifier	findPathwaysByXrefInput:ids
system_code	findPathwaysByXrefInput:codes
getId:nodelist	pathway_ids
getNames:nodelist	pathway_names
getSpecies:nodelist	pathway_species

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Thomask...

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Thomaskelder

Information Attributions (0)

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None

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Information Tags (5)

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Information Shared with Groups (0)

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Information Featured In Packs (1)

WikiPathways workflows

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Information Favourited By (0)

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Information Statistics

723 viewings

999 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - Get pathways by external reference

Created on: Tuesday 16 September 2008 @ 11:18:51 (GMT)

Created by: Thomaskelder

Last edited on: Tuesday 16 September 2008 @ 11:35:40 (GMT)

Last edited by: Thomaskelder

Revision comments:

None

Previous Versions:
[2] - Get pathways by external reference

Created on: Friday 14 November 2008 @ 14:21:46 (GMT)

Created by: Thomaskelder

Revision comments:

Updated workflow to stable identifiers on WikiPathways

Latest Version:
[3] - Get pathways by external reference

Created on: Wednesday 13 January 2010 @ 12:21:59 (GMT)

Created by: Thomaskelder

Revision comments:

Adapted workflow to modified signature of findPathwaysByXref function.

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Other workflows that use similar services (2)

Taverna 1

Original Uploader

Thomask...

Write pathway to disk (v2)

Created: 14/11/08 @ 14:21:12 | Last updated: 14/11/08 @ 14:21:13

Credits: Thomaskelder

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Downloads and writes a pathway from WikiPathways to a local disk in the given file type.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 101 times | Downloaded: 34 times

Tags (5):

View

Download (v2)

Taverna 2

Original Uploader

Thomask...

Download pathways for external references list (Taverna 2) (v1)

Created: 03/02/09 @ 12:46:13

Credits: Thomaskelder

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 108 times | Downloaded: 51 times

Tags (5):