Explain concept scores

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

Download Workflow

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 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).

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/2725/download?version=7
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
C_ConceptID	The concept id of the C concept.
cutoff	Maximum number of explanatory concepts to return.
A_ConceptID	The concept id of the A concept.

Processors (7)

Name	Type	Description
explainScoresStringInput	wsdl	This Web service 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 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
explainScoresStringInput_output	xmlsplitter
explainScoresStringInput_return	xmlsplitter
return_ConceptContributionTable_2	xmlsplitter
2_ConceptContributionTable	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;

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 (3)

Name	Description
B_ConceptName	The concept name of the explanatory B concept.
B_ConceptID	The concept ID of the explanatory B concept.
B_ConceptContribution	The contribution score, that 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).

Datalinks (12)

Source	Sink
explainScoresStringInput_input:output	explainScoresStringInput:parameters
cutoff	explainScoresStringInput_input:cutoffValue
makeCommaSeparatedString:output	explainScoresStringInput_input:conceptCUIsAsString
explainScoresStringInput:parameters	explainScoresStringInput_output:input
explainScoresStringInput_output:return	explainScoresStringInput_return:input
explainScoresStringInput_return:ConceptContributionTable	return_ConceptContributionTable_2:input
return_ConceptContributionTable_2:ConceptContributionTable	2_ConceptContributionTable:input
C_ConceptID	makeCommaSeparatedString:item2
A_ConceptID	makeCommaSeparatedString:item1
2_ConceptContributionTable:conceptName	B_ConceptName
2_ConceptContributionTable:conceptId	B_ConceptID
2_ConceptContributionTable:contribution	B_ConceptContribution

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Reinout van Schouwen

Information License

All versions of this Workflow are licensed under:

Information Version 7 (latest) (of 7)

Information Credits (1)

(People/Groups)

Reinout van Schouwen

Information Attributions (0)

(Workflows/Files)

None

Information Tags (4)

Uploader tags

Log in to add Tags

Information Shared with Groups (1)

BioSemantics

Information Featured In Packs (2)

Log in to add to one of your Packs

Information Attributed By (2)

(Workflows/Files)

Information Favourited By (0)

No one

Information Statistics

4817 viewings

1765 downloads

[ see breakdown ]

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)

Write your own Review

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"

[ more ]

View

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (18)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 2

Uploader

Marco Roos

DatabaseID to ConceptID (7)

Download

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...