This workflow uses one or more services that are deprecated as of 31st December 2012 (almost 12 years ago), and may no longer function. Show details...

Gene to Pathways

Created: 2012-07-09 18:27:21 Last updated: 2012-07-10 08:02:44

Download Workflow

This is a Taverna workflow that given a gene ID fetches the corespondondings pathways. To do so, the workflow make use of two KEGG web services.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/3001/download?version=1
[ More Info Expand ]

Workflow Components

Authors (0)

Titles (0)

Descriptions (0)

Dependencies (0)

Inputs (0)

Processors (3)

Name	Type	Description
get_enzymes_by_gene	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_enzymes_by_gene
get_pathways_by_enzymes	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_pathways_by_enzymes
Gene_Value_Constant	stringconstant	Value eco:b0002

Beanshells (0)

Outputs (1)

Name	Description
Pathways

Datalinks (3)

Source	Sink
Gene_Value_Constant:value	get_enzymes_by_gene:genes_id
get_enzymes_by_gene:return	get_pathways_by_enzymes:enzyme_id_list
get_pathways_by_enzymes:return	Pathways

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Khalid Belhajjame

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Khalid Belhajjame

Information Attributions (0)

(Workflows/Files)

None

Information Tags (0)

None

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (1)

Gene_To_Pathway using Taverna and Vistrails

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

824 viewings

715 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Gene to Pathways

Created by Khalid Belhajjame on Monday 09 July 2012 18:27:21 (UTC)

Last edited by Khalid Belhajjame on Tuesday 10 July 2012 08:02:43 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (93)

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

Taverna 2

Uploader

Alibukhari

NCBI Gi to Kegg Pathways (1)

Download

"This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings."This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.

Created: 2011-03-28 | Last updated: 2011-03-28

Credits: Alibukhari

Taverna 1

Uploader

Paul Fisher

Cow-Human Ortholog Pathways and Gene annot... (2)

Download

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the cow, Bos taurus. 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. As the Cow genome is currently unfinished, the workflow subsequently maps the cow ensembl gene ids to human orthologues. Entrez and UniProt identifiers are then identified...

Created: 2007-10-03 | Last updated: 2009-12-03

Gene to Pathways

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Value

Reviews (0)

Comments (0)

Other workflows that use similar services (93)