Explain score between two concepts

Created: 2015-04-03 20:49:40

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Purpose of workflow: This workflow takes two ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group). The example values for this workflow are tailored to describe the relationship between two entrez gene ids. The user can change that by using other ids and a database identifier for the db (in our case is EG for entrez gene ids).

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
geneidA	entrez gene id for geneA
geneidB	entrez gene id for geneB
db	database identifier for mapping the appropriate ids to our concept profile database. in our case is EG for entrez gene ids

Processors (20)

Name	Type	Description
explainScoresStringInput	wsdl	This Web service takes the two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned by the Web service. The concept contribution is also reported by the Web service. The concept contribution is the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group). Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation explainScoresStringInput
explainScoresStringInput_input	xmlsplitter
makeCommaSeparatedString	beanshell	This script concatenates the two input concept id strings and adds a comma in between. Script String tmp = item1+","+item2; output = tmp;
Text_constant	stringconstant	Value 100
XPath_Service_explain_concept	xpath	Xpath Expression /ns2:explainScoresStringInputResponse/return/ConceptContributionTable/conceptContributions/conceptName
XPath_Service_score	xpath	Xpath Expression /ns2:explainScoresStringInputResponse/return/ConceptContributionTable/conceptContributions/contribution
mapDatabaseIDToConceptIDs	wsdl	web service that maps the entrez gene identifier to our concept profile database Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation mapDatabaseIDToConceptIDs
mapDatabaseIDToConceptIDs_2	wsdl	web service that maps the entrez gene identifier to our concept profile database Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation mapDatabaseIDToConceptIDs
mapDatabaseIDToConceptIDs_input	xmlsplitter
mapDatabaseIDToConceptIDs_2_input	xmlsplitter
XPath_Service	xpath	Xpath Expression /ns2:mapDatabaseIDToConceptIDsResponse/return/conceptIDsAsString
XPath_Service_2	xpath	Xpath Expression /ns2:mapDatabaseIDToConceptIDsResponse/return/conceptIDsAsString
getConceptProfile	wsdl	get human readable names for the results by mapping the concept profile identifiers back to the database Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation getConceptProfile
getConceptProfile_input	xmlsplitter
getConceptProfile_2	wsdl	get human readable names for the results by mapping the concept profile identifiers back to the database Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation getConceptProfile
getConceptProfile_2_input	xmlsplitter
XPath_Service_3	xpath	Xpath Expression /ns2:getConceptProfileResponse/return/name
XPath_Service_3_2	xpath	Xpath Expression /ns2:getConceptProfileResponse/return/name
Merge_String_List_to_a_String_2	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();
Merge_String_List_to_a_String_2_2	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();

Beanshells (1)

Name	Description	Inputs	Outputs
makeCommaSeparatedString	This script concatenates the two input concept id strings and adds a comma in between.	item1 item2	output

Outputs (4)

Name	Description
contribution_score	the score of its contributing concept is listed here.
contribution_concept	in this output the concepts that contribute to the association are enlisted
geneA	human readable form of geneidA
geneB	human readable form of geneidB

Datalinks (27)

Source	Sink
explainScoresStringInput_input:output	explainScoresStringInput:parameters
makeCommaSeparatedString:output	explainScoresStringInput_input:conceptCUIsAsString
Text_constant:value	explainScoresStringInput_input:cutoffValue
XPath_Service:nodelist	makeCommaSeparatedString:item1
XPath_Service_2:nodelist	makeCommaSeparatedString:item2
explainScoresStringInput:parameters	XPath_Service_explain_concept:xml_text
explainScoresStringInput:parameters	XPath_Service_score:xml_text
mapDatabaseIDToConceptIDs_input:output	mapDatabaseIDToConceptIDs:parameters
mapDatabaseIDToConceptIDs_2_input:output	mapDatabaseIDToConceptIDs_2:parameters
geneidB	mapDatabaseIDToConceptIDs_input:ID
db	mapDatabaseIDToConceptIDs_input:database
geneidA	mapDatabaseIDToConceptIDs_2_input:ID
db	mapDatabaseIDToConceptIDs_2_input:database
mapDatabaseIDToConceptIDs_2:parameters	XPath_Service:xml_text
mapDatabaseIDToConceptIDs:parameters	XPath_Service_2:xml_text
getConceptProfile_input:output	getConceptProfile:parameters
XPath_Service:nodelist	getConceptProfile_input:conceptId
getConceptProfile_2_input:output	getConceptProfile_2:parameters
XPath_Service_2:nodelist	getConceptProfile_2_input:conceptId
getConceptProfile:parameters	XPath_Service_3:xml_text
getConceptProfile_2:parameters	XPath_Service_3_2:xml_text
XPath_Service_explain_concept:nodelist	Merge_String_List_to_a_String_2:stringlist
XPath_Service_score:nodelist	Merge_String_List_to_a_String_2_2:stringlist
Merge_String_List_to_a_String_2_2:concatenated	contribution_score
Merge_String_List_to_a_String_2:concatenated	contribution_concept
XPath_Service_3:nodelist	geneA
XPath_Service_3_2:nodelist	geneB

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Eleni

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Information Statistics

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1062 downloads

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Explain score between two concepts

Created by Eleni on Friday 03 April 2015 20:49:37 (UTC)

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DatabaseID to ConceptID (7)

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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...

Created: 2012-06-25 | Last updated: 2014-07-14

Credits: Marco Roos Martijn Schuemie Reinout van Schouwen BioSemantics

Taverna 2

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Explain concept scores (7)

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Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the pe...

Created: 2012-02-07 | Last updated: 2014-07-14

Credits: Reinout van Schouwen

Explain score between two concepts

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