myExperiment.org - Workflows - keggID to Kegg pathways with BioMoby services (Franck Tanoh) [Taverna 1 Workflow]

Workflow Entry: keggID to Kegg pathways with BioMoby services

Created at: 03/10/07 @ 18:36:22 Last updated: 05/03/08 @ 13:59:56

Version 3 (latest) (of 3)

Version created on: 03/10/07 @ 18:36:22 by: Franck Tanoh | Revision comments Expand

Last edited on: 05/03/08 @ 13:59:55 by: Franck Tanoh

Title: keggID to Kegg pathways with BioMoby services

Type: Taverna 1

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Keggid_to_kegg_pathways_with_biomoby_services_13382_3

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Description

This workflow retrieves KEGG pathway id and image given a KEGG gene id. e.g hsa:6402 or eco:b0002

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Option 1:

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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/38/download?version=3
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Workflow Components

Inputs (1)

Name	Description
KEGG_pathway_ID

Processors (6)

Name	Type	Description
getKeggPathwaysByKeggID	biomobywsdl	This service, given a KEGG identifier, attempts to retrieve KEGG pathways that that contain this ID. For example, passing in: hsa:6402 results in the following pathway returned: hsa04514.
Object	biomobyobject	an object
getKeggPathwayAsGif	biomobywsdl	This service, given a KEGG pathway, returns a Gif image of the pathway if it exists. For example, the <Object, KEGG_PATHWAY, 'hsa00053') returns a diagram of the pathway 'ASCORBATE AND ALDRATE METABOLISM'.
Parse_Moby_Data_Object	biomobyparser	Processor to parse the datatype Object
Parse_Moby_Data_b64_encoded_gif	biomobyparser	Processor to parse the datatype b64_encoded_gif
Decode_base64_to_byte	local

Outputs (2)

Name	Description
pathwayId
pathwayImage

Links (8)

Sink	Source
Object:id	KEGG_pathway_ID
getKeggPathwaysByKeggID:Object(keggID)	Object:mobyData
Decode_base64_to_byte:base64	Parse_Moby_Data_b64_encoded_gif:image_'content'
pathwayImage	Decode_base64_to_byte:bytes
pathwayId	Parse_Moby_Data_Object:id
Parse_Moby_Data_b64_encoded_gif:mobyData('b64_encoded_gif')	getKeggPathwayAsGif:b64_encoded_gif(image)
Parse_Moby_Data_Object:mobyData('Object')	getKeggPathwaysByKeggID:Object(Collection - 'pathways' As Simples)
getKeggPathwayAsGif:Object(pathway)	getKeggPathwaysByKeggID:Object(Collection - 'pathways' As Simples)