Filter concepts with profiles

Created: 2012-09-14 10:14:12 Last updated: 2014-07-14 10:12:32

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This workflow removes concepts that have no concept profile in the concept profile database, since only concepts with a concept profile can be used for concept profile matching.

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Titles (1)

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Inputs (1)

Name	Description
Concept_ID	The input concept ID (Erasmus MC ontology format).

Processors (6)

Name	Type	Description
filterConceptsWithProfile	wsdl	This Web service takes a (list of) concepts as input and returns the concept IDs of the concepts in the list that have a concept profile. Wsdl http://ws.biosemantics.org/ConceptRecognizerService?wsdl Wsdl Operation filterConceptsWithProfile
filterConceptsWithProfile_output	xmlsplitter
filterConceptsWithProfile_return	xmlsplitter
filterConceptsWithProfile_input	xmlsplitter
Filter_List_of_Strings_by_regex	localworker	This service filters the list at every occurrence of the specified regular expression. The regular expression provided in this case is an empty string: ^\S+$ Script filteredlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (item.matches(regex)) { filteredlist.add(item); } }
regex_value	stringconstant	The regular expression to be used for filtering. In this case: ^\S+$ Value ^\S+$

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Outputs (1)

Name	Description
Concepts_with_profiles	Concept IDs (Erasmus MC ontology format) with profiles.

Datalinks (7)

Source	Sink
filterConceptsWithProfile_input:output	filterConceptsWithProfile:parameters
filterConceptsWithProfile:parameters	filterConceptsWithProfile_output:input
filterConceptsWithProfile_output:return	filterConceptsWithProfile_return:input
Concept_ID	filterConceptsWithProfile_input:conceptSet
regex_value:value	Filter_List_of_Strings_by_regex:regex
filterConceptsWithProfile_return:conceptIDsAsString	Filter_List_of_Strings_by_regex:stringlist
Filter_List_of_Strings_by_regex:filteredlist	Concepts_with_profiles

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Information Workflow Type

Taverna 2

Information Uploader

Kristina Hettne

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Information Version 3 (of 4)

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Information Statistics

2978 viewings

1349 downloads

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Version History

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Filter concepts with profiles

Created by Kristina Hettne on Friday 14 September 2012 10:14:12 (UTC)

Last edited by Kristina Hettne on Friday 14 September 2012 10:18:40 (UTC)
Filter concepts with profiles

Created by Kristina Hettne on Friday 14 September 2012 13:37:07 (UTC)
Filter concepts with profiles

Created by Kristina Hettne on Tuesday 05 February 2013 20:27:00 (UTC)

Last edited by Kristina Hettne on Tuesday 05 February 2013 20:28:57 (UTC)
Filter concepts with profiles

Created by Kristina Hettne on Monday 14 July 2014 10:12:32 (UTC)

Revision comment:

Updates examples to reflect the latest concept database update.

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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...

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Filter concepts with profiles

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