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NCBI Gi to Kegg Pathways

Workflow Entry: NCBI Gi to Kegg Pathways

Created at: 08/06/09 @ 18:39:38 Last updated: 14/12/09 @ 11:51:20

Version 1 (of 1)

Version created on: 08/06/09 @ 18:39:38 by: Paul Fisher | Revision comments Expand

Last edited on: 14/12/09 @ 11:51:22 by: Paul Fisher

Title: NCBI Gi to Kegg Pathways

Type: Taverna 1

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Description

This workflow converts a list of NCBI gi numbers and converts them to a list of KEGG genes. Those KEGG gene ids are subsequently turned into KEGG pathway identifiers and descriptions. It also removes any null values from a list of strings.

Example input for this workflow is as follows (new line separated):
gi:215422388
gi:120407068

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Option 1:

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Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/786/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
Gi_numbers

Processors (14)

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

Beanshells (4)

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

Outputs (4)

Name	Description
gene_descriptions
pathway_by_genes
pathway_descriptions
Kegg_strings

Links (18)

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

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

(Workflows/Files)

None

Information Tags (6)

Original Uploader tags

bconv
|
gene
|
genes
|
ncbi
|
pathway
|
pathways

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Information Shared with Groups (0)

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Information Ratings (0)

Current:

0.0 / 5

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Information Attributed By (7)

(Workflows/Files)

Private item
geneID to KEGG Pathways
NCBI Gi to Kegg Pathway Descriptions
NCBI Gi to Kegg Pathway Images
Private item
NCBI Gi to Kegg Pathways
Compare genome, extract proteins which are drug targets, apply to KEGG pathway

Information Favourited By (1)

Ian Laycock

Information Statistics

1419 viewings

895 downloads

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Citations (0)

None

Version History

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

Created on: Monday 08 June 2009 @ 18:39:38 (GMT)

Created by: Paul Fisher

Last edited on: Monday 14 December 2009 @ 11:51:22 (GMT)

Last edited by: Paul Fisher

Revision comments:

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This Workflow only has one version.

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Other workflows that use similar services (91)

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

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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