Ensembl_genes_to_swiss_id.xml

Created: 2008-07-12 10:16:31 Last updated: 2008-07-12 10:16:48

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Workflow Components

Inputs (1)

Name	Description
genes_in_region

Processors (10)

Name	Type	Description
getGeneInfo	arbitrarywsdl
comma2	stringconstant
parse_swiss	beanshell
spit_by_regex2	local
lister	arbitrarywsdl
regex2	stringconstant
FindNameList	seqhound	Given a list of ID from PDB, SwissProt, or PIR sequence identifiers, retrieves a list of gi's. Note that EMBL shares accession numbers with GenBank. EMBL GenInfo identifiers may be returned using these accessions; for example SHoundFindAcc(X13776) will return GI 45269. EMBL also has its own identifiers (which the NCBI and SeqHound refer to as 'name'). So the same GI may be returned by SHoundFindName("PAAMIR").
comma_separated2	local
parsing_options	stringconstant
parse_ddbj_gene_info	soaplabwsdl	extract information from geneGeneInfo processor at http://xml.nig.ac.jp/wsdl/Ensembl.wsdl

Beanshells (1)

Name	Description	Inputs	Outputs
parse_swiss		input	output

Outputs (5)

Name	Description
genes_in_qtl
gene_info
parsed_data
Swiss_List_to_Gi_list
swiss_ids

Links (14)

Source	Sink
comma2:value	comma_separated2:seperator
comma_separated2:concatenated	FindNameList:nameList
genes_in_region	lister:file
getGeneInfo:Result	parse_ddbj_gene_info:file_direct_data
lister:listerReturn	getGeneInfo:geneId
parse_ddbj_gene_info:output	parse_swiss:input
parse_swiss:output	spit_by_regex2:string
parsing_options:value	parse_ddbj_gene_info:options
FindNameList:result	Swiss_List_to_Gi_list
getGeneInfo:Result	gene_info
parse_ddbj_gene_info:output	parsed_data
parse_swiss:output	swiss_ids
regex2:value	spit_by_regex2:regex
spit_by_regex2:split	comma_separated2:stringlist

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Information Workflow Type

Taverna 1

Information Uploader

Antoon Goderis

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Paul Fisher

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benchmarks

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Paul Fisher workflows for benchmarks PR and CA2

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Information Statistics

1958 viewings

1893 downloads

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Version History

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Ensembl_genes_to_swiss_id.xml

Created by Antoon Goderis on Saturday 12 July 2008 10:16:31 (UTC)

Last edited by Antoon Goderis on Saturday 12 July 2008 10:16:48 (UTC)