GetWikiPWByENS

Created: 2015-10-02 09:36:00 Last updated: 2015-10-12 12:41:56

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This workflow uses the WikiPathways Webservice/API to query for pathways containing a specific ENSEMBL identifier. The mapping service behind WikiPathways takes care of the identifier mapping, making sure that all relevant results are found even if they were originally reported using a different identifier scheme.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
ens_id	ENSEMBL identifer

Processors (5)

Name	Type	Description
findPathwaysByENSXref	rest	The WikiPathways Webservice/API is queried for pathways with a specific ENSEMBL identifier.
Parse_pathway_URIs	xpath	The unique resource identifiers are parsed from the WikiPathways XML file output. Xpath Expression /ns1:findPathwaysByXrefResponse/ns1:result/ns2:url
Split_string_into_string_list_by_regular_expression	localworker	If an input file is used, this service will split the file on the newline character, making sure that the file is parsed correctly. 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 character to split the input string (or text in file) on. Currently newline character (\n). Value \n
Parse_species	xpath	The species are parsed from the WikiPathways XML file output. Xpath Expression /ns1:findPathwaysByXrefResponse/ns1:result/ns2:species

Beanshells (0)

Outputs (3)

Name	Description
pathway_URI_list	Pathway unique resource identifer, usually a resovable link.
ens_id	ENSEMBL identifer
species_list	The species for which the pathway is annotated.

Datalinks (8)

Source	Sink
Split_string_into_string_list_by_regular_expression:split	findPathwaysByENSXref:
findPathwaysByENSXref:responseBody	Parse_pathway_URIs:xml_text
regex_value:value	Split_string_into_string_list_by_regular_expression:regex
ens_id	Split_string_into_string_list_by_regular_expression:string
findPathwaysByENSXref:responseBody	Parse_species:xml_text
Parse_pathway_URIs:nodelist	pathway_URI_list
Split_string_into_string_list_by_regular_expression:split	ens_id
Parse_species:nodelist	species_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 2)

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Information Tags (4)

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Information Shared with Groups (1)

BioSemantics

Information Featured In Packs (2)

Pathway analysis with WikiPathways
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Information Statistics

1998 viewings

1062 downloads

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Citations (0)

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Version History

In chronological order:

GetWikiPWByENS

Created by Kristina Hettne on Friday 02 October 2015 09:35:59 (UTC)
GetWikiPWByENS

Created by Kristina Hettne on Monday 12 October 2015 12:41:56 (UTC)

Revision comment:

Changes to make the workflow more compatible for running with the Taverna command line tool from within the R environment.