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omim and pathways

Created: 2009-03-03 13:17:27 Last updated: 2009-11-02 10:13:38

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This workflow searches OMIM for entries associated with a particular disease in OMIM, returns the IDs and maps them to Kegg Gene IDs. For each gene, it then gets the description and any corresponding pathways those genes are involved with

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http://www.myexperiment.org/workflows/688/download?version=2
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Workflow Components

Inputs (0)

Processors (8)

Name	Type	Description
Remove_duplicate_strings	local
Filter_KeggGenes	local
Filter_list_of_strings_extracting_match_to_a_regex	local
Split_string_into_string_list_by_regular_expression	local
Concatenate_two_strings	local
bconv	arbitrarywsdl
KeggGenestoPathways	workflow
OMIM	arbitrarywsdl	get Keyword

Beanshells (2)

Name	Description	Inputs	Outputs
remove_Nulls		input	output
remove_nulls_2		input	output

Outputs (4)

Name	Description
KeggGenes
geneDescriptions
pathways
pathwayDescriptions

Links (11)

Source	Sink
Concatenate_two_strings:output	bconv:string
Filter_KeggGenes:filteredlist	KeggGenestoPathways:kegg_gene_id_list
Filter_list_of_strings_extracting_match_to_a_regex:filteredlist	Concatenate_two_strings:string2
KeggGenestoPathways:gene_descriptions	geneDescriptions
KeggGenestoPathways:pathway_by_genes	pathways
KeggGenestoPathways:pathway_descriptions	pathwayDescriptions
OMIM:Result	Split_string_into_string_list_by_regular_expression:string
Remove_duplicate_strings:strippedlist	Filter_KeggGenes:stringlist
Split_string_into_string_list_by_regular_expression:split	Filter_list_of_strings_extracting_match_to_a_regex:stringlist
bconv:return	KeggGenes
bconv:return	Remove_duplicate_strings:stringlist

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Katy Wolstencroft

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

Information Credits (2)

(People/Groups)

Information Attributions (1)

(Workflows/Files)

Get Kegg Gene information

Information Tags (9)

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Information Shared with Groups (1)

Tutorial

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Information Favourited By (0)

No one

Information Statistics

2641 viewings

2101 downloads

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Citations (0)

None

Version History

In chronological order:

GenesandPAthways_diseaseAssociations

Created by Katy Wolstencroft on Friday 27 February 2009 16:28:47 (UTC)

Last edited by Katy Wolstencroft on Friday 27 February 2009 16:31:41 (UTC)
omim and pathways

Created by Katy Wolstencroft on Tuesday 03 March 2009 13:17:27 (UTC)

Last edited by Katy Wolstencroft on Monday 02 November 2009 10:13:39 (UTC)

Revision comment:

This is the same workflow displaying an expanded view of the nested workflow