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geneId_to_pathway.xml

Workflow Entry: geneId_to_pathway.xml

Created at: 12/07/08 @ 09:16:00 Last updated: 12/07/08 @ 11:48:03

Version 1 (of 1)

Version created on: 12/07/08 @ 09:16:00 by: Antoon Goderis | Revision comments Expand

Last edited on: 12/07/08 @ 11:48:03 by: Antoon Goderis

Title: geneId_to_pathway.xml

Type: Taverna 1

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Workflow Components

Inputs (1)

Name	Description
gene

Processors (7)

Name	Type	Description
merge_pathways	local
mergePathways_2	local
lister	arbitrarywsdl
split_gene_ids	beanshell
get_pathways_by_genes	arbitrarywsdl	See the Service entry for this web service.
Kegg_gene_ids_all_species	arbitrarywsdl	See the Service entry for this web service.
Add_ncbi_to_string	workflow

Beanshells (2)

Name	Description	Inputs	Outputs
add_ncbi_to_string		input	output
split_gene_ids		input	output

Outputs (1)

Name	Description
merged_kegg_pathways

Links (8)

Source	Sink
Add_ncbi_to_string:Kegg_strings	Kegg_gene_ids_all_species:string
Kegg_gene_ids_all_species:return	split_gene_ids:input
gene	Add_ncbi_to_string:Gi_numbers
get_pathways_by_genes:return	merge_pathways:stringlist
lister:listerReturn	get_pathways_by_genes:genes_id_list
merge_pathways:concatenated	mergePathways_2:stringlist
mergePathways_2:concatenated	merged_kegg_pathways
split_gene_ids:output	lister:file

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Antoon Goderis

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

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None

Information Tags (1)

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benchmarks

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Information Featured In Packs (1)

Paul Fisher workflows for benchmarks PR and CA2

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Information Statistics

245 viewings

650 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - geneId_to_pathway.xml

Created on: Saturday 12 July 2008 @ 09:16:00 (GMT)

Created by: Antoon Goderis

Last edited on: Saturday 12 July 2008 @ 11:48:03 (GMT)

Last edited by: Antoon Goderis

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Other workflows that use similar services (96)

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

Taverna 1

Original Uploader

Paul Fisher

Arabidopsis thaliana Microarray Analysis (v1)

Created: 08/07/09 @ 16:28:34

Credits: Paul Fisher

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

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