get human and mouse phenotypes for a gene

Created: 2011-05-20 15:18:50 Last updated: 2012-03-29 09:01:06

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This workflow gets phenotype annotations associated with human genes and the mouse orthologs from human (GWAS Central) and mouse (EuroPhenome and MGI) databases.

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Authors (1)

Titles (4)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
humanGeneSymbolList
europhenomeSignificance
gwascentralAssociationThreshold

Processors (4)

Name	Type	Description
Merge_String_List_to_a_String	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
Split_string_into_string_list_by_regular_expression	localworker	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]); } }
Mus	workflow
Homo	workflow

Beanshells (0)

Outputs (3)

Name	Description
humanPhenotype_gwascentral
mousePhenotype_mgi
mousePhenotype_europhenome

Datalinks (9)

Source	Sink
Homo:gwascentralPhenotype	Merge_String_List_to_a_String:stringlist
humanGeneSymbolList	Split_string_into_string_list_by_regular_expression:string
europhenomeSignificance	Mus:europhenomeSignificance
Split_string_into_string_list_by_regular_expression:split	Mus:humanGeneSymbol
Split_string_into_string_list_by_regular_expression:split	Homo:humanGeneSymbol
gwascentralAssociationThreshold	Homo:gwascentralAssociationThreshold
Merge_String_List_to_a_String:concatenated	humanPhenotype_gwascentral
Mus:mgiMp	mousePhenotype_mgi
Mus:europhenomeMp	mousePhenotype_europhenome

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Information Workflow Type

Taverna 2

Information Uploader

Tim Beck

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

Information Credits (1)

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Tim Beck

Information Attributions (0)

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Information Statistics

3876 viewings

1307 downloads

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Version History

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Get Human and Mouse Phenotypes for a Gene

Created by Tim Beck on Friday 20 May 2011 15:18:50 (UTC)

Last edited by Tim Beck on Friday 20 May 2011 15:47:36 (UTC)
get human and mouse phenotypes for a gene

Created by Tim Beck on Thursday 29 March 2012 09:01:05 (UTC)

Revision comment:

Incorporates changes to the GWAS Central REST services and now uses the dedicated EuroPhenome BioMart.

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get human and mouse phenotypes for a gene

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Other workflows that use similar services (2)