Get concept information

Created: 2012-07-06 14:20:40 Last updated: 2014-07-14 11:18:46

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The workflow takes a (list of) concept ID(s) as input and returns the profile, ID, definition and name of the concept.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

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Inputs (1)

Name	Description
Concept_ID	Concept ID of the concept to retrieve name and definition for.

Processors (6)

Name	Type	Description
getConceptProfile	wsdl	This Web service returns the concept profile for a given concept ID. Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation getConceptProfile
getConceptProfile_input	xmlsplitter
getConceptProfile_output	xmlsplitter
getConceptProfile_return	xmlsplitter
Split_string_into_string_list_by_regular_expression	localworker	Split list on newline character (\n). 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	Split on newline character (\n). Value \n

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Outputs (4)

Name	Description
Concept_ID	The concept ID.
Concept_definition	The definition of the concept.
Concept_name	The name of the concept.
ConceptVector	The concept profile in XML.

Datalinks (10)

Source	Sink
getConceptProfile_input:output	getConceptProfile:parameters
Split_string_into_string_list_by_regular_expression:split	getConceptProfile_input:conceptId
getConceptProfile:parameters	getConceptProfile_output:input
getConceptProfile_output:return	getConceptProfile_return:input
regex_value:value	Split_string_into_string_list_by_regular_expression:regex
Concept_ID	Split_string_into_string_list_by_regular_expression:string
getConceptProfile_return:conceptId	Concept_ID
getConceptProfile_return:definition	Concept_definition
getConceptProfile_return:name	Concept_name
getConceptProfile_return:ConceptVector	ConceptVector

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Kristina Hettne

Information License

All versions of this Workflow are licensed under:

Information Version 5 (latest) (of 5)

Information Credits (5)

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Information Tags (3)

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Information Attributed By (1)

(Workflows/Files)

Match concept to HPO profiles

Information Favourited By (0)

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Information Statistics

3662 viewings

1463 downloads

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Citations (0)

None

Version History

In chronological order:

Get concept information

Created by Kristina Hettne on Friday 06 July 2012 14:20:40 (UTC)
Get concept information

Created by Kristina Hettne on Wednesday 18 July 2012 13:55:32 (UTC)

Revision comment:

Added annotations.
Get concept information

Created by Kristina Hettne on Friday 14 September 2012 09:56:11 (UTC)
Get concept information

Created by Kristina Hettne on Tuesday 05 February 2013 20:44:31 (UTC)
Get concept information

Created by Kristina Hettne on Monday 14 July 2014 11:18:46 (UTC)

Revision comment:

Edited examples to reflect latest concept database update. Workflow now also return the profile in XML in order to avoid memory issues when splitting the list.

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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

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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

Get concept information

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Other workflows that use similar services (18)