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Workflow Entry: Entrez Gene to KEGG Pathway

Created at: 04/12/09 @ 16:04:38      Last updated: 30/11/10 @ 12:18:53
Information Version 5 (latest) (of 5)
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Version created on: 30/11/10 @ 12:18:52 by: Paul Fisher   |   Revision comment Expand

Title: Entrez Gene to KEGG Pathway

Type: Taverna 1


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Information 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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Inputs (1)
Processors (7)
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Outputs (1)
Links (8)
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Information Workflow Type

Taverna 1

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Comments Comments (3)

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  • Thursday 21 February 2008 @ 23:54:21 (UTC)

    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

     

  • Wednesday 02 December 2009 @ 16:59:46 (UTC)

    Thank you for your feedback. It's much appreciated.

    Paul

  • Saturday 16 November 2013 @ 06:39:14 (UTC)

    good example of web service usage.




Workflow Other workflows that use similar services (98)

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


Original Uploader

Workflow qtl_pathway_3.xml (1)

Created: 12/07/08 @ 09:10:15 | Last updated: 12/07/08 @ 11:44:53

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Viewed: 51 times | Downloaded: 52 times

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (1)

Created: 27/05/11 @ 11:06:11 | Last updated: 27/05/11 @ 11:06:52

Credits: User Paul Fisher

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 rice, Oryza sativa. 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 UniGene 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 d...

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

Viewed: 73 times | Downloaded: 29 times

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Non-Information Resource URI: http://www.myexperiment.org/workflows/15


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