Match gene lists based on information in literature

Created: 2012-04-17 08:55:46 Last updated: 2012-04-25 07:54:26

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[THIS WORKFLOW IS IN BETA STAGE]

This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes.

Example to explain (by analogy):

When a group of informaticians is matched against biology, the informaticians working in biology may be ranked on top, while the most enriched concept among such an informatician and biology may be 'bioinformatics'.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (4)

Name	Description
matchEntrezGenes_CSV	List of Entrez Gene identifiers (number only) separated by comma's (nothing else), e.g. 3065,2146 for HDAC1,EZH2. The service is currently limited to rat, human, and mouse.
queryEntrezGenes_CSV	Entrez gene list to match the gene list against, e.g. 3064 for HTT
maxMatchesToReport	Maximum number of concepts to report after matching the concept lists.
maxNrToExplain	Maximum number of concepts to explain.

Processors (17)

Name	Type	Description
Explain_concept_scores	workflow
Match_concept_profiles	workflow
SplitCSV2	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]); } }
regex_value	stringconstant	Value ,
mapConceptIdToDatabases	wsdl	Wsdl http://ws.biosemantics.org/ConceptRecognizerService?wsdl Wsdl Operation mapConceptIdToDatabases
mapConceptIdToDatabases_input	xmlsplitter
mapConceptIdToDatabases_output	xmlsplitter
mapConceptIdToDatabases_return	xmlsplitter
DatabaseID_to_ConceptID	workflow
DatabaseID_value	stringconstant	Value EG
DatabaseID_to_ConceptID_2	workflow
SplitCSV1	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]); } }
return_databaseIdList	xmlsplitter
databaseIdList_databaseIdList	xmlsplitter
Concatenate_two_strings	localworker	Script output = string1 + string2 + string3;
colon	stringconstant	Value :
parseURL	localworker	Script String ueurl = new String(); ueurl=URLEncoder.encode(url); output_text = "\"" + ueurl +"\""; output_html = ""+ ueurl + "";

Beanshells (1)

Name	Description	Inputs	Outputs
Beanshell		inputList item	outputList

Outputs (5)

Name	Description
TopMatchingConcepts	Matching concepts ordered by matching score. The number of concepts is determined by the given maximum number of matching concepts (maxMatchesToReport).
TopContributingConcepts	Ordered list of concepts that may explain the matching score for a concept-concept association. The reported number of concepts is limited by the given maximum (maxNrToExplain).
SummedSimilarityScore
CommonIDTopConcepts	Common identifier for matching concepts (identifier by which the concept is also referred to by)
TopMatchingConcepts_href

Datalinks (29)

Source	Sink
maxNrToExplain	Explain_concept_scores:maxNrResults
Match_concept_profiles:MatchConceptID	Explain_concept_scores:matchConcept
DatabaseID_to_ConceptID:concepts	Explain_concept_scores:queryConceptSet
maxMatchesToReport	Match_concept_profiles:Cutoff
DatabaseID_to_ConceptID_2:concepts	Match_concept_profiles:MatchConceptSet
DatabaseID_to_ConceptID:concepts	Match_concept_profiles:QueryConceptSet
matchEntrezGenes_CSV	SplitCSV2:string
regex_value:value	SplitCSV2:regex
mapConceptIdToDatabases_input:output	mapConceptIdToDatabases:parameters
Match_concept_profiles:MatchResultList	mapConceptIdToDatabases_input:conceptId
mapConceptIdToDatabases:parameters	mapConceptIdToDatabases_output:input
mapConceptIdToDatabases_output:return	mapConceptIdToDatabases_return:input
DatabaseID_value:value	DatabaseID_to_ConceptID:DatabaseID
SplitCSV1:split	DatabaseID_to_ConceptID:IDvalue
DatabaseID_value:value	DatabaseID_to_ConceptID_2:DatabaseID
SplitCSV2:split	DatabaseID_to_ConceptID_2:IDvalue
queryEntrezGenes_CSV	SplitCSV1:string
regex_value:value	SplitCSV1:regex
mapConceptIdToDatabases_return:databaseIdList	return_databaseIdList:input
return_databaseIdList:databaseIdList	databaseIdList_databaseIdList:input
colon:value	Concatenate_two_strings:string2
databaseIdList_databaseIdList:database	Concatenate_two_strings:string1
databaseIdList_databaseIdList:ID	Concatenate_two_strings:string3
Match_concept_profiles:MatchResultList	parseURL:url
parseURL:output_text	TopMatchingConcepts
Explain_concept_scores:ConceptName	TopContributingConcepts
Match_concept_profiles:SummedSimilarityScore	SummedSimilarityScore
Concatenate_two_strings:output	CommonIDTopConcepts
parseURL:output_html	TopMatchingConcepts_href

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Marco Roos

Information License

All versions of this Workflow are licensed under:

Information Version 5 (of 7)

Information Credits (5)

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Information Attributions (2)

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Information Tags (11)

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Information Attributed By (1)

(Workflows/Files)

SNPs to Concept Set through Concept Profile Matching v2

Information Favourited By (1)

Reinout van Schouwen

Information Statistics

4704 viewings

1790 downloads

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Citations (0)

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Version History

In chronological order:

Match potentially related concepts and explain

Created by Marco Roos on Tuesday 17 April 2012 08:55:46 (UTC)

Last edited by Marco Roos on Tuesday 17 April 2012 08:58:20 (UTC)
Match potentially related concepts and explain

Created by Marco Roos on Tuesday 17 April 2012 10:46:51 (UTC)

Last edited by Marco Roos on Tuesday 17 April 2012 10:47:30 (UTC)
[untitled]

Created by Marco Roos on Wednesday 25 April 2012 00:29:15 (UTC)

Revision comment:

This version matches two gene lists.
Match gene lists based on information in literature

Created by Marco Roos on Wednesday 25 April 2012 00:31:22 (UTC)

Revision comment:

Updated annotations.
Match gene lists based on information in literature

Created by Marco Roos on Wednesday 25 April 2012 07:36:47 (UTC)

Revision comment:

Added hyperlink output and changed URL output of concept ID.
Match gene lists based on information in literature

Created by Marco Roos on Wednesday 25 April 2012 07:41:54 (UTC)

Revision comment:

Changed output in attemtp to have sensible output with t2web.
Match gene lists based on information in literature

Created by Marco Roos on Wednesday 25 April 2012 07:54:24 (UTC)

Revision comment:

Changed output for t2web.