Filter concepts with profiles

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

Download Workflow

Purpose: Filter a list of concept id(s) by returning only those with a concept profile in the database.

Preview

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/3178/download?version=4
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

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

Processors (8)

Name	Type	Description
filterConceptsWithProfile	wsdl	This Web service operation takes a (list of) concepts as input and returns the concept IDs of those with a profile. Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?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+$
Split_string_into_string_list_by_regular_expression	localworker	Split on newline (\n) character. 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_1	stringconstant	Split on newline (\n) character. Value \n

Beanshells (0)

Outputs (1)

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

Datalinks (9)

Source	Sink
filterConceptsWithProfile_input:output	filterConceptsWithProfile:parameters
filterConceptsWithProfile:parameters	filterConceptsWithProfile_output:input
filterConceptsWithProfile_output:return	filterConceptsWithProfile_return:input
Split_string_into_string_list_by_regular_expression:split	filterConceptsWithProfile_input:conceptSet
regex_value:value	Filter_List_of_Strings_by_regex:regex
filterConceptsWithProfile_return:conceptIDsAsString	Filter_List_of_Strings_by_regex:stringlist
Concept_ID	Split_string_into_string_list_by_regular_expression:string
regex_value_1:value	Split_string_into_string_list_by_regular_expression:regex
Filter_List_of_Strings_by_regex:filteredlist	Concepts_with_profiles

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Kristina Hettne

Information License

All versions of this Workflow are licensed under:

Information Version 4 (latest) (of 4)

Information Credits (4)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (6)

Uploader tags

Log in to add Tags

Information Shared with Groups (3)

Information Featured In Packs (2)

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

2970 viewings

1346 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

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.

Reviews (0)

No reviews yet

Be the first to review!

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...

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

Credits: Marco Roos Martijn Schuemie Reinout van Schouwen BioSemantics

Taverna 2

Uploader

Reinout van Schouwen

Explain concept scores (7)

Download

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

Filter concepts with profiles

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Wsdl

Wsdl Operation

Script

Value

Script

Value

Reviews (0)

Comments (0)

Other workflows that use similar services (18)