Workflow Entry: omim and pathways

Created at: 03/03/09 @ 13:17:27 Last updated: 02/11/09 @ 10:13:38

Version 2 (latest) (of 2)

Version created on: 03/03/09 @ 13:17:27 by: Katy Wolstencroft | Revision comments Expand

Last edited on: 02/11/09 @ 10:13:39 by: Katy Wolstencroft

Title: omim and pathways

Type: Taverna 1

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Description

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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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/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	See the Service entry for this web service.
KeggGenestoPathways	workflow
OMIM	arbitrarywsdl	get Keyword See the Service entry for this web service.

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