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...

Gi_to_pathway.xml

Created: 2008-07-12 09:20:04 Last updated: 2008-07-12 20:07:57

Download Workflow

No description has been set

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/262/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (0)

Processors (7)

Name	Type	Description
GETPATHWAYS	arbitrarywsdl
GETIMAGE	local
KEGGBASEURL	stringconstant
add_ncbi_string	beanshell
Kegg_id_conv	arbitrarywsdl
parse_result	beanshell
Gi_number	stringconstant

Beanshells (2)

Name	Description	Inputs	Outputs
add_ncbi_string		input	output
parse_result		input	abbr ids

Outputs (3)

Name	Description
KEGG_pathways
kegg_protein_id
pathway_id

Links (10)

Source	Sink
GETIMAGE:image	KEGG_pathways
GETPATHWAYS:return	GETIMAGE:url
GETPATHWAYS:return	pathway_id
Gi_number:value	add_ncbi_string:input
KEGGBASEURL:value	GETIMAGE:base
Kegg_id_conv:return	parse_result:input
parse_result:abbr	GETPATHWAYS:abbr
parse_result:ids	GETPATHWAYS:oids
Kegg_id_conv:return	kegg_protein_id
add_ncbi_string:output	Kegg_id_conv:string

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Antoon Goderis

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

(Workflows/Files)

None

Information Tags (1)

Uploader tags

benchmarks

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (1)

Paul Fisher workflows for benchmarks PR and CA2

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (1)

Ian Laycock

Information Statistics

2146 viewings

1961 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Gi_to_pathway.xml

Created by Antoon Goderis on Saturday 12 July 2008 09:20:04 (UTC)

Last edited by Antoon Goderis on Saturday 12 July 2008 20:07:57 (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 (94)

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