Workflow Entry: BioMart_hsapiens_gene_ensembl_variation_Noom_Edit_09_12_2551

Created at: 17/12/08 @ 09:08:50 Last updated: 26/12/08 @ 07:51:00

Version 1 (of 1)

Version created on: 17/12/08 @ 09:08:50 by: Kasikrit | Revision comments Expand

Last edited on: 26/12/08 @ 07:51:03 by: Kasikrit

Title: BioMart_hsapiens_gene_ensembl_variation_Noom_Edit_09_12_2551

Type: Taverna 1

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Description

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Workflow Components

Inputs (1)

Name	Description
rsID	rs1043502 rs10799658

Processors (14)

Name	Type	Description
REG_Split_by_C	stringconstant
REG_Merge_by_C	stringconstant
Flatten_Entrez_ID	local
Flatten_list	local
Split_EnsemblID	local
Remove_dup_ID	local
Flatten_Ensembl_report	local
Merge_EnsemblID	local
Nested_GO_Update	workflow
Nested_hsapiens_snp	workflow
Nested_EnsemblGeneInformation	workflow
Nested_Pathway	workflow
Nested_OMIM	workflow	Input as the entrez gene ID from NCBI and the out put is the OMIM ID and the OMIM description
Nested_Motif	workflow

Beanshells (11)

Name	Inputs	Outputs
Make_GO_Report	Bio_ID Bio_Type Ensembl_ID	report
Merge_infomation	snpID chr_name ensemblID chrom_start allele chrom_stand ensembl_type validated peptide_shift	hsapien
Make_hsapiens_report	geneEnsembl_id gene_des gene_chr gene_start gene_stop gene_stand gene_name entrezGeneID band	ensemblInfo
concat_id_with_URL	id	url
Lister	word	output
trim_replace	in	out
prepare_id_result	id result	id_result
substring	in	out
remove_null	in	out
Beanshell_scripting_host	entrezid omimid	out
Create_Motif_Information	motif_id definition genes_id start_position end_position score	motif_info

Outputs (10)

Name	Description
Gene_Information
SNP_Information
Unique_Ensembl_ID
Unique_Entrez_ID
Pathway_Image
Pathways
Pathways_Description
GO_Information_Update
OMIM_Phenotype
Mofit_Information

Links (24)

Source	Sink
Flatten_Entrez_ID:outputlist	Nested_Motif:Entrez_GeneID
Flatten_Entrez_ID:outputlist	Nested_Pathway:Gene_Id
Flatten_list:outputlist	Merge_EnsemblID:stringlist
Merge_EnsemblID:concatenated	Split_EnsemblID:string
Nested_EnsemblGeneInformation:EnsemblGene_Information	Flatten_Ensembl_report:inputlist
Nested_EnsemblGeneInformation:Unique_EntrezID	Nested_OMIM:entrezID
Nested_Motif:Motif_Information	Mofit_Information
Nested_Pathway:Pathway_Image	Pathway_Image
Nested_Pathway:Pathways	Pathways
Nested_hsapiens_snp:SNP_Information	SNP_Information
Nested_hsapiens_snp:ensemblID	Flatten_list:inputlist
REG_Merge_by_C:value	Merge_EnsemblID:seperator
REG_Split_by_C:value	Split_EnsemblID:regex
Remove_dup_ID:strippedlist	Nested_EnsemblGeneInformation:ensembleID
rsID	Nested_hsapiens_snp:rsID_in
Remove_dup_ID:strippedlist	Nested_GO_Update:ensemblID
Flatten_Ensembl_report:outputlist	Gene_Information
Flatten_Entrez_ID:outputlist	Unique_Entrez_ID
Nested_EnsemblGeneInformation:Unique_EntrezID	Flatten_Entrez_ID:inputlist
Remove_dup_ID:strippedlist	Unique_Ensembl_ID
Split_EnsemblID:split	Remove_dup_ID:stringlist
Nested_GO_Update:GO_Information	GO_Information_Update
Nested_OMIM:OMIM_Phenotype	OMIM_Phenotype
Nested_Pathway:ID_with_PathwayDescriptions	Pathways_Description