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NCBI Gi to Kegg Pathways

Workflow Entry: NCBI Gi to Kegg Pathways

Created at: 19/03/10 @ 13:47:39 Last updated: 19/03/10 @ 13:52:45

Version 1 (of 1)

Version created on: 19/03/10 @ 13:47:39 by: Ian Laycock | Revision comments Expand

Last edited on: 19/03/10 @ 13:52:46 by: Ian Laycock

Title: NCBI Gi to Kegg Pathways

Type: Taverna 2

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Description

User inputs background and foreground colour to be used to highlight proteins in KEGG pathway image. User provides NCBI GI numbers. Worflow calculates KEGG ID and pathway ID and sends value to colour service, which adds colour to that KEGG id on pathway image. Also outputs kegg description, pathway description and url of image.

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Workflow Components

Authors (2)

Titles (1)

Descriptions (2)

Inputs (3)

Name	Description
Gi_numbers	imports gi numbers to be used by the workflow to create the pathways
fg_color	colours used for the foreground colouring of the pathways
bg_color	colours used for the background colouring of the pathways

Processors (18)

Name	Type	Description
merge_pathways	localworker
merge_pathways_2	localworker
merge_descriptions	localworker
Remove_duplicate_pathways	localworker
get_pathways_by_genes	wsdl	See the Service entry for this web service.
btit	wsdl	See the Service entry for this web service.
btit1	wsdl	See the Service entry for this web service.
bconv	wsdl	See the Service entry for this web service.
remove_Nulls	beanshell
extract_gene_ids	beanshell
remove_nulls_2	beanshell
add_ncbi_to_string	beanshell
Get_image_from_URL	localworker
color_pathway_by_objects_2	wsdl	See the Service entry for this web service.
split_by_regex_2	localworker
regex_2	stringconstant
split_by_regex	localworker
regex	stringconstant

Beanshells (4)

Name	Inputs	Outputs
remove_Nulls	input	output
extract_gene_ids	input	output
remove_nulls_2	input	output
add_ncbi_to_string	input	output

Outputs (6)

Name	Description
KEGGID	kegg ids
pathway_by_genes	pathway ids
pathway_descriptions	pathway ids and corresponding pathways descriptions
kegg_descriptions	Kegg Ids and corresponding Kegg descriptions
URL	corresponding url to the pathway id
image	corresponding image to the pathway id

Datalinks (27)

Source	Sink
get_pathways_by_genes:return	merge_pathways:stringlist
Remove_duplicate_pathways:strippedlist	merge_pathways_2:stringlist
btit:return	merge_descriptions:stringlist
merge_pathways:concatenated	Remove_duplicate_pathways:stringlist
split_by_regex:split	get_pathways_by_genes:genes_id_list
extract_gene_ids:output	btit:string
merge_pathways:concatenated	btit1:string
add_ncbi_to_string:output	bconv:string
merge_descriptions:concatenated	remove_Nulls:input
bconv:return	extract_gene_ids:input
merge_pathways_2:concatenated	remove_nulls_2:input
Gi_numbers	add_ncbi_to_string:input
color_pathway_by_objects_2:return	Get_image_from_URL:url
fg_color	color_pathway_by_objects_2:fg_color_list
bg_color	color_pathway_by_objects_2:bg_color_list
split_by_regex_2:split	color_pathway_by_objects_2:pathway_id
split_by_regex:split	color_pathway_by_objects_2:object_id_list
regex_2:value	split_by_regex_2:regex
remove_nulls_2:output	split_by_regex_2:string
regex:value	split_by_regex:regex
extract_gene_ids:output	split_by_regex:string
extract_gene_ids:output	KEGGID
remove_nulls_2:output	pathway_by_genes
btit1:return	pathway_descriptions
remove_Nulls:output	kegg_descriptions
color_pathway_by_objects_2:return	URL
Get_image_from_URL:image	image

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Ian Laycock

Information License

All versions of this Workflow are licensed under:

Information Credits (2)

(People/Groups)

Information Attributions (2)

(Workflows/Files)

Information Tags (5)

Original Uploader tags

bconv
|
color
|
kegg
|
ncbi
|
pathway

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Information Attributed By (1)

(Workflows/Files)

FINAL VERSION

Information Favourited By (0)

No one

Information Statistics

1000 viewings

537 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - NCBI Gi to Kegg Pathways

Created on: Friday 19 March 2010 @ 13:47:39 (GMT)

Created by: Ian Laycock

Last edited on: Friday 19 March 2010 @ 13:52:46 (GMT)

Last edited by: Ian Laycock

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