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NCBI Gi to Kegg Pathway Images

Workflow Entry: NCBI Gi to Kegg Pathway Images

Created at: 12/01/12 @ 09:38:10 Last updated: 12/01/12 @ 15:04:00

Version 2 (latest) (of 2)

Version created on: 12/01/12 @ 15:00:21 by: Katy Wolstencroft | Revision comments Expand

Last edited on: 12/01/12 @ 15:03:58 by: Katy Wolstencroft

Title: NCBI Gi to Kegg Pathway Images

Type: Taverna 2

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Description

This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (1)

Name	Description
Gi_numbers	Accepts a list of genbank gene identifiers without the gi: prefix

Processors (15)

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

Beanshells (4)

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

Outputs (4)

Name	Description
gene_descriptions	Returns a list of gene descriptions from genbank
pathway_by_genes	Returns a list of KEGG pathway identifiers for all pathways the query gene is involved with
pathway_descriptions	Returns a list of KEGG pathway identifiers and descriptions for each pathway the query gene is involved with
color_pathway_by_objects_image	Returns a list of pathway diagrams, with the query genes highlighted

Datalinks (19)

Source	Sink
Gi_numbers	add_ncbi_to_string:input
bconv:return	extract_gene_ids:input
merge_pathways_2:concatenated	remove_nulls_2:input
merge_descriptions:concatenated	remove_Nulls:input
merge_pathways:concatenated	btit1:string
extract_gene_ids:output	btit:string
add_ncbi_to_string:output	bconv:string
split_by_regex:split	get_pathways_by_genes:genes_id_list
get_pathways_by_genes:return	merge_pathways:stringlist
merge_pathways:concatenated	Remove_duplicate_pathways:stringlist
regex:value	split_by_regex:regex
extract_gene_ids:output	split_by_regex:string
btit:return	merge_descriptions:stringlist
Remove_duplicate_pathways:strippedlist	merge_pathways_2:stringlist
split_by_regex:split	displayPathways:ID
remove_Nulls:output	gene_descriptions
remove_nulls_2:output	pathway_by_genes
btit1:return	pathway_descriptions
displayPathways:Get_Image_From_URL_image	color_pathway_by_objects_image

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Katy Wolstencroft

Information License

All versions of this Workflow are licensed under:

Information Credits (2)

(People/Groups)

Information Attributions (1)

(Workflows/Files)

NCBI Gi to Kegg Pathways

Information Tags (6)

Original Uploader tags

genbank
|
genes
|
gi
|
image
|
ncbi
|
pathways

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Information Featured In Packs (0)

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Information Ratings (0)

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Information Attributed By (0)

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None

Information Favourited By (0)

No one

Information Statistics

52 viewings

61 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - NCBI Gi to Kegg Pathway Images

Created on: Thursday 12 January 2012 @ 09:38:10 (GMT)

Created by: Katy Wolstencroft

Last edited on: Thursday 12 January 2012 @ 12:23:50 (GMT)

Last edited by: Katy Wolstencroft

Revision comments:

None

Latest Version:
[2] - NCBI Gi to Kegg Pathway Images

Created on: Thursday 12 January 2012 @ 15:00:21 (GMT)

Created by: Katy Wolstencroft

Last edited on: Thursday 12 January 2012 @ 15:03:58 (GMT)

Last edited by: Katy Wolstencroft

Revision comments:

None

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Taverna 2

Original Uploader

Katy Wolstencroft

NCBI Gi to Kegg Pathway Descriptions (v2)

Created: 12/01/12 @ 09:46:31 | Last updated: 12/01/12 @ 14:54:37

Credits: Katy Wolstencroft

Attributions: NCBI Gi to Kegg Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 6 times | Downloaded: 8 times

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