Explain concept scores

Created: 2012-02-07 11:05:50 Last updated: 2014-07-14 09:41:34

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Explain concept scores of concept profiles (enrichment with concept set).

This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
matchConcept	Concept Profile list (by concept identifier). Examples 79822, 25362
maxNrResults	Maximum number of concepts to return.
queryConceptSet

Processors (7)

Name	Type	Description
return_ConceptContributionTable	xmlsplitter
ConceptContributionTable_ConceptContributionTable	xmlsplitter
explainScores	wsdl	Wsdl http://ws.biosemantics.org/ConceptRecognizerService?wsdl Wsdl Operation explainScores
explainScores_input	xmlsplitter
explainScores_output	xmlsplitter
explainScores_return	xmlsplitter
Beanshell	beanshell	Script ArrayList tmp = new ArrayList(inputList); tmp.add(item); outputList = tmp;

Beanshells (1)

Name	Description	Inputs	Outputs
Beanshell		inputList item	outputList

Outputs (4)

Name	Description
ConceptName
ConceptID
ConceptContribution
xml_table

Datalinks (13)

Source	Sink
explainScores_return:ConceptContributionTable	return_ConceptContributionTable:input
return_ConceptContributionTable:ConceptContributionTable	ConceptContributionTable_ConceptContributionTable:input
explainScores_input:output	explainScores:parameters
maxNrResults	explainScores_input:cutoffValue
Beanshell:outputList	explainScores_input:conceptCUIs
explainScores:parameters	explainScores_output:input
explainScores_output:return	explainScores_return:input
matchConcept	Beanshell:item
queryConceptSet	Beanshell:inputList
ConceptContributionTable_ConceptContributionTable:conceptName	ConceptName
ConceptContributionTable_ConceptContributionTable:conceptId	ConceptID
ConceptContributionTable_ConceptContributionTable:contribution	ConceptContribution
explainScores_return:ConceptContributionTable	xml_table

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Reinout van Schouwen

Information License

All versions of this Workflow are licensed under:

Information Version 4 (of 7)

Information Credits (1)

(People/Groups)

Reinout van Schouwen

Information Attributions (0)

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None

Information Tags (4)

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Information Shared with Groups (1)

BioSemantics

Information Featured In Packs (2)

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Information Attributed By (2)

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Information Favourited By (0)

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Information Statistics

4794 viewings

1755 downloads

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Citations (0)

None

Version History

In chronological order:

explainScores demo

Created by Reinout van Schouwen on Tuesday 07 February 2012 11:05:50 (UTC)

Last edited by Reinout van Schouwen on Wednesday 21 March 2012 14:21:27 (UTC)
ExplainScores demo

Created by Reinout van Schouwen on Wednesday 21 March 2012 15:02:25 (UTC)

Last edited by Reinout van Schouwen on Wednesday 21 March 2012 15:10:04 (UTC)

Revision comment:

Use the 'explainScoresAsString' operation instead, which takes a comma separated string as parameter.
Explain concept scores

Created by Kristina Hettne on Tuesday 26 June 2012 12:52:31 (UTC)

Revision comment:

This revision is fully annotated and explains concept matching scores between two concept profiles.
Explain concept scores

Created by Kristina Hettne on Wednesday 18 July 2012 13:57:19 (UTC)

Revision comment:

Added annotations.
Explain concept scores

Created by Kristina Hettne on Friday 14 September 2012 10:01:37 (UTC)
Explain concept scores

Created by Kristina Hettne on Tuesday 05 February 2013 21:19:44 (UTC)
Explain concept scores

Created by Kristina Hettne on Monday 14 July 2014 09:41:34 (UTC)

Revision comment:

Updated examples to the latest concept database version.

Reviews (1)

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Peter 't Hoen

Title: Title

Rating: not yet rated

Created: 2013-03-21 09:02:08 | Updated: 2013-03-21 09:02:08

Should this not be called "Explain concept match scores"

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Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Comments: Database: one of CAS, DRUG, etc. The supported databases are listed below (database, description, example). CAS, Chemical Abstracts Service registry number, 64-17-5. DRUG, Drug Bank, DB00316. AF, Affymetrix, 200007_at. CHEB, ChEBI, 16236. CHID, ChemIDplus, 0000050000. EG, Entrez-Gene, 3064. GO, Gene Ontol...