SNP_ID2EntrezGene_ID

Created: 2012-06-26 09:50:25 Last updated: 2013-03-11 13:56:56

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Maps a SNP, or a list of SNPs, to EntrezGene ID(s).

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
SNP_ID	Use (a list of) Database of Single Nucleotide Polymorphisms (dbSNP) IDs as input, separated by the newline character (\n).

Processors (4)

Name	Type	Description
hsapiens_snp	biomart
hsapiens_gene_ensembl	biomart
Split_string_into_string_list_by_regular_expression	localworker	Splits the list of dbSNP IDs on newline (\n). Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
regex_value	stringconstant	The regular expression value to be used for the split. Value \n

Beanshells (0)

Outputs (1)

Name	Description
EG_ID_list	A list of EntrezGene IDs.

Datalinks (7)

Source	Sink
Split_string_into_string_list_by_regular_expression:split	hsapiens_snp:hsapiens_snp.snp_filter_filter
hsapiens_snp:hsapiens_snp.chr_name	hsapiens_gene_ensembl:hsapiens_gene_ensembl.chromosome_name_filter
hsapiens_snp:hsapiens_snp.chrom_start	hsapiens_gene_ensembl:hsapiens_gene_ensembl.end_filter
hsapiens_snp:hsapiens_snp.chrom_start	hsapiens_gene_ensembl:hsapiens_gene_ensembl.start_filter
regex_value:value	Split_string_into_string_list_by_regular_expression:regex
SNP_ID	Split_string_into_string_list_by_regular_expression:string
hsapiens_gene_ensembl:hsapiens_gene_ensembl.entrezgene	EG_ID_list

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Kristina Hettne

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 4)

Information Credits (2)

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Information Attributions (0)

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None

Information Tags (3)

Uploader tags

ensembl
|
gene
|
snp

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Information Shared with Groups (3)

Information Featured In Packs (1)

Functional annotation of SNPs using next-generation text mining

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Information Attributed By (1)

(Workflows/Files)

SNPs to Concept Set through Concept Profile Matching v2

Information Favourited By (0)

No one

Information Statistics

3282 viewings

1320 downloads

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Citations (0)

None

Version History

In chronological order:

SNP_ID2EntrezGene_ID

Created by Kristina Hettne on Tuesday 26 June 2012 09:50:25 (UTC)
SNP_ID2EntrezGene_ID

Created by Kristina Hettne on Wednesday 18 July 2012 13:59:03 (UTC)

Revision comment:

Added annotations. New design by Harish Dharuri.
SNP_ID2EntrezGene_ID

Created by Kristina Hettne on Friday 20 July 2012 08:23:46 (UTC)

Revision comment:

Changed the default width parameter to 300 kb and added annotations.
SNP_ID2EntrezGene_ID

Created by Kristina Hettne on Friday 14 September 2012 10:05:55 (UTC)

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Comments (1)

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Magnus Palmblad	Monday 11 March 2013 13:57:43 (UTC)
	Works great and is well documented. Perhaps the output could also include a list with the gene names?

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