Workflow Entry: Get KEGG gene descriptions and pathways

Created at: 30/04/10 @ 16:09:29      Last updated: 30/04/10 @ 16:12:02
Information Version 1 (of 1)

Version created on: 30/04/10 @ 16:09:29 by: Nadia Cerezo   |   Revision comments Expand

Last edited on: 30/04/10 @ 16:12:03 by: Nadia Cerezo

Title: Get KEGG gene descriptions and pathways

Type: Taverna 2


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Information Description

This workflow takes a list of KEGG gene identifiers and supplies descriptions associated to said genes + pathways including all genes and the descriptions associated to said pathways.

The list_to_string local beanshell scripts merely transform a given list into a string of unique not-null elements separated by new lines (for batch btit use).

Note that the input is a real taverna list : multiple values must be declared as multiple values instead of a single string value with distinct identifiers separated by new lines.

This workflow is a slight modification of one made by Paul Fisher called "Get Kegg Gene information".


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Information Workflow Components

Information Authors (2)
Information Titles (2)
Information Descriptions (4)
Inputs (1)
Processors (5)
Beanshells (2)
Outputs (2)
Datalinks (7)
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Information Workflow Type

Taverna 2

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Version History

Earliest Version:
[1] - Get KEGG gene descriptions and pathways

Created on: Friday 30 April 2010 @ 16:09:29 (GMT)

Created by: Nadia Cerezo

Last edited on: Friday 30 April 2010 @ 16:12:03 (GMT)

Last edited by: Nadia Cerezo

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This Workflow only has one version.



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Workflow Other workflows that use similar services (88)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.


Original Uploader

Workflow Pathways and Gene annotations forQTL region (v1)

Created: 20/01/12 @ 09:32:55 | Last updated: 20/01/12 @ 09:32:56

Credits: User Bonilla

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

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

Viewed: 14 times | Downloaded: 4 times

This Workflow has no tags!

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Original Uploader

Workflow Pathways and Gene annotations for RefSeq ids (v1)

Created: 15/11/10 @ 12:25:01 | Last updated: 15/11/10 @ 12:28:12

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to search for pathways in the KEGG pathway database.

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

Viewed: 62 times | Downloaded: 35 times

Tags (34):

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What is this?

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Non-Information Resource URI: http://www.myexperiment.org/workflows/1237


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