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NCBI Gi to Kegg Pathway Descriptions

Workflow Entry: NCBI Gi to Kegg Pathway Descriptions

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

Version 2 (latest) (of 2)

Version created on: 12/01/12 @ 14:54:36 by: Katy Wolstencroft | Revision comments Expand

Title: NCBI Gi to Kegg Pathway Descriptions

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 (14)

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

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 (3)

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

Datalinks (17)

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
remove_Nulls:output	gene_descriptions
remove_nulls_2:output	pathway_by_genes
btit1:return	pathway_descriptions

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Katy Wolstencroft

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Katy Wolstencroft

Information Attributions (1)

(Workflows/Files)

NCBI Gi to Kegg Pathways

Information Tags (8)

Original Uploader tags

bconv
|
genbank
|
gene
|
genes
|
gi
|
ncbi
|
pathway
|
pathways

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Information Ratings (0)

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Information Attributed By (0)

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Information Favourited By (0)

No one

Information Statistics

42 viewings

70 downloads

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Citations (0)

None

Version History

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

Created on: Thursday 12 January 2012 @ 09:46:31 (GMT)

Created by: Katy Wolstencroft

Revision comments:

None

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

Created on: Thursday 12 January 2012 @ 14:54:36 (GMT)

Created by: Katy Wolstencroft

Revision comments:

None

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