Match concept profiles

Created: 2011-12-02 09:07:34 Last updated: 2014-07-14 13:31:23

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The workflow can be used to match a set of concept profiles with another set of concept profiles. The result is a list of concepts ordered by their match to the query concept profiles.

The workflow matches two sets of concept profiles. At the time of writing the concepts are derived from human, rat, and mouse terminologies, ontologies, and database identifiers. The profiles are lists of concepts ranked by their association with the identifying concept, as determined by co-location statistics computed from MedLine (up until 2009 at the time of writing).

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
Cutoff	The number of resulting matched concepts that will be shown.
MatchConceptSet	The ConceptSet that is to be matched. For example a list consisting of concept ids: 3088049, 3088115, 3089563, 3090191, 3092619, 3094840, 3098813, 3103320, 3103643, 3108241, 3109737
QueryConceptSet	The ConceptSet (a list of concept identifiers) to be queried. For example: 4275360

Processors (7)

Name	Type	Description
getSimilarConceptProfiles	wsdl	Wsdl http://ws.biosemantics.org/ConceptRecognizerService?wsdl Wsdl Operation getSimilarConceptProfiles
getSimilarConceptProfiles_input	xmlsplitter
getSimilarConceptProfiles_output	xmlsplitter
getSimilarConceptProfiles_MatchingResult	xmlsplitter
Filter_ConceptID	localworker	Script import java.util.regex.*; filteredlist = new ArrayList(); Pattern thePat = Pattern.compile(regex); int theGroup = Integer.parseInt(group); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); Matcher matcher = thePat.matcher(item); if (matcher.find()) { filteredlist.add(matcher.group(theGroup)); } }
regex_value	stringconstant	Value
group_value	stringconstant	Value 1

Beanshells (0)

Outputs (4)

Name	Description
MatchResultList
SimilarityScore
SummedSimilarityScore
MatchConceptID

Datalinks (13)

Source	Sink
getSimilarConceptProfiles_input:output	getSimilarConceptProfiles:parameters
Cutoff	getSimilarConceptProfiles_input:cutoffValue
QueryConceptSet	getSimilarConceptProfiles_input:queryConceptProfileList
MatchConceptSet	getSimilarConceptProfiles_input:matchConceptProfileList
getSimilarConceptProfiles:parameters	getSimilarConceptProfiles_output:input
getSimilarConceptProfiles_output:MatchingResult	getSimilarConceptProfiles_MatchingResult:input
regex_value:value	Filter_ConceptID:regex
group_value:value	Filter_ConceptID:group
getSimilarConceptProfiles_MatchingResult:MatchConceptProfileList	Filter_ConceptID:stringlist
getSimilarConceptProfiles_MatchingResult:MatchConceptProfileList	MatchResultList
getSimilarConceptProfiles_MatchingResult:SimilarityScoreLists	SimilarityScore
getSimilarConceptProfiles_MatchingResult:SummedSimilarityScoreList	SummedSimilarityScore
Filter_ConceptID:filteredlist	MatchConceptID

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Marco Roos

Information License

All versions of this Workflow are licensed under:

Information Version 2 (of 6)

Information Credits (4)

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Information Tags (14)

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Information Shared with Groups (1)

BioSemantics

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Information Attributed By (3)

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Information Statistics

4251 viewings

1624 downloads

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Citations (0)

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Version History

In chronological order:

Match concept profiles

Created by Marco Roos on Friday 02 December 2011 09:07:34 (UTC)
Match concept profiles

Created by Kristina Hettne on Tuesday 26 June 2012 12:59:33 (UTC)

Revision comment:

Minor modifications.
Match concept profiles

Created by Kristina Hettne on Wednesday 18 July 2012 13:56:02 (UTC)

Revision comment:

Added annotations.
Match concept profiles

Created by Kristina Hettne on Friday 14 September 2012 09:57:48 (UTC)
Match concept profiles

Created by Kristina Hettne on Tuesday 05 February 2013 21:09:50 (UTC)
Match concept profiles

Created by Kristina Hettne on Monday 14 July 2014 13:31:23 (UTC)

Revision comment:

Edited examples to reflect latest concept database update. Added extra output port for the individual similarity 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...

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

Credits: Marco Roos Martijn Schuemie Reinout van Schouwen BioSemantics

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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

Match concept profiles

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