This workflow uses one or more services that are deprecated as of 31st December 2012 (almost 12 years ago), and may no longer function. Show details...

casimir_paper

Created: 2008-01-22 16:22:26 Last updated: 2008-05-30 14:40:41

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This workflow first of all recovers Ensembl Gene IDs, Embl IDs and genomic coordinates from a BioMart mouse genome query.

The Embl IDs are converted into KEGG Gene IDs and subsequent KEGG Pathway IDs using KEGG webservices. URLs to the pathways diagrams at KEGG are also recovered as well as a merged output of the ensembl gene ID, embl ID and KEGG pathway ID.

The other branch of the workflow recovers SNPs for the genes and SNP variations per mouse mouse strain using a MOLGENIS variant wrapper around the Mouse Phenome Database (MPD). See http://www.myexperiment.org/files/31 for the MOLGENIS DSL definition of MPD used to generate the services used in this workflow

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Workflow Components

Inputs (0)

Processors (6)

Name	Type	Description
mmusculus_gene_ensembl	biomart	Mus musculus genes (NCBIM37)
mouse_embl_ids	biomart	Mus musculus genes (NCBIM37)
MergeShell	beanshell
Nested_Workflow	workflow
Flatten_list	local
Merge_string_list_to_string	local

Beanshells (2)

Name	Description	Inputs	Outputs
SplitBean		input	output
MergeShell		ensemblGeneID emblID keggGeneID	mergedOutput

Outputs (2)

Name	Description
a
d

Links (9)

Source	Sink
Flatten_list:outputlist	d
MergeShell:mergedOutput	Flatten_list:inputlist
Merge_string_list_to_string:concatenated	MergeShell:keggGeneID
Nested_Workflow:c	Merge_string_list_to_string:stringlist
mouse_embl_ids:mmusculus_gene_ensembl.ensembl_gene_id	MergeShell:ensemblGeneID
Nested_Workflow:a	a
mmusculus_gene_ensembl:mmusculus_gene_ensembl.ensembl_gene_id	mouse_embl_ids:mmusculus_gene_ensembl.ensembl_gene_id_filter
mouse_embl_ids:mmusculus_gene_ensembl.embl	MergeShell:emblID
mouse_embl_ids:mmusculus_gene_ensembl.embl	Nested_Workflow:string2

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Taverna 1

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Damian

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Damian

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casimir

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6557 viewings

2223 downloads

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Case example for CASIMIR paper on solutions to databse interoperability

Created by Damian on Tuesday 22 January 2008 16:22:26 (UTC)

Last edited by Damian on Tuesday 22 April 2008 11:21:21 (UTC)
casimir_paper

Created by Damian on Tuesday 22 January 2008 16:22:26 (UTC)

Last edited by Damian on Friday 30 May 2008 14:40:41 (UTC)

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Morris Swertz	Monday 21 April 2008 14:10:58 (UTC)
	See http://www.myexperiment.org/files/31 for MOLGENIS definition of mouse phenome database.

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