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InviteWorkflow Entry: Entrez Gene to KEGG Pathway
| Citations (0) | Version History | Reviews (0) | Comments (2) |
 Version 5 (latest)
(of 5)
|
Version created on:
30/11/10 @ 12:18:52
by:
Paul Fisher
|
Revision comments 
Title: Entrez Gene to KEGG Pathway
Type: Taverna 1
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Description
This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.
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http://www.myexperiment.org/workflows/15/download?version=5
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Earliest Version:
[1] - Entrez Gene to KEGG Pathway
Previous Versions:
[2] - Entrez Gene to KEGG Pathway
[4] - Entrez Gene to KEGG Pathway
Latest Version:
[5] - Entrez Gene to KEGG Pathway
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Other workflows that use similar services
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Original Uploader |
Created: 08/07/09 @ 16:28:34
Credits:
License: Creative Commons Attribution-No Derivative Works 3.0 Unported License
This workflow searches for genes which are found to be differentially expressed in a microarray study using Arabidopsis thaliana. The workflow requires an input of a list of differentially expressed AffyMetrix Probeset identifiers. Data is then extracted from BioMart to annotate each of the genes. The 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 pathway database.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 145 times | Downloaded: 30 times Tags (19): |
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Original Uploader |
Created: 12/07/08 @ 09:15:13 | Last updated: 12/07/08 @ 20:20:52
Credits:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 73 times | Downloaded: 37 times Tags (1): |
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Linked Data
Non-Information Resource URI: http://www.myexperiment.org/workflows/15
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Copyright © 2007 - 2011 The University of Manchester and University of Southampton
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If you change
if (trimmedSplit.length == 2)
to
if (trimmedSplit.length == 3)
in
split_gene_ids
it will actually work
You can try 24605 as input
Maybe this is because of a change in the output of Kegg_gene_ids_all_species
Maybe
if (trimmedSplit.length >= 3)
is better since it would allow for future expansions
Otherwise good example of web service usage
/Tommy
Thank you for your feedback. It's much appreciated.
Paul