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NCBI Gi to Kegg Pathways

Created: 2009-06-08 18:39:38 Last updated: 2009-12-14 11:51:20

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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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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
get_pathways_by_genes	arbitrarywsdl
btit	arbitrarywsdl
remove_nulls_2	beanshell
remove_Nulls	beanshell
add_ncbi_to_string	beanshell
extract_gene_ids	beanshell
bconv	arbitrarywsdl

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 Uploader

Paul Fisher

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)

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None

Information Tags (6)

Uploader tags

bconv
|
gene
|
genes
|
ncbi
|
pathway
|
pathways

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Information Attributed By (9)

(Workflows/Files)

Item doesn't exist anymore
UnigeneID to KEGG Pathways
Private item
Private item
UnigeneID to KEGG Pathways
NCBI Gi to Kegg Pathway Descriptions
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

3155 viewings

2060 downloads

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Citations (0)

None

Version History

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NCBI Gi to Kegg Pathways

Created by Paul Fisher on Monday 08 June 2009 18:39:38 (UTC)

Last edited by Paul Fisher on Monday 14 December 2009 11:51:22 (UTC)

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