Annotate gene list with top ranking concepts

Created: 2013-12-03 17:46:25 Last updated: 2015-04-03 20:48:10

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This workflow annotates a comma separated gene list with a predefined
concept set as for example Biological processes or Disease/syndrome. To obtain the particular id for each concept set (e.g. "5" for Biological processes), the workflow listPredefinedConceptSets needs to run first.
The workflow is using the anni web services and is implemented using the Xpath query from Taverna.

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Authors (1)

Titles (1)

Descriptions (1)

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Inputs (4)

Name	Description
gene_IDs	a comma separated gene list to be annotated
database_name	The ID for the database that will be used to match the gene list and obtain their concept ids. Here we used entrez gene ids, and therefor db_name = EG
cutoff	max number of the matching concepts to be retrieved
predefined_conceptset_id	ID of the predefined concept set to match with. These IDs can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID (5) corresponds to the concept set "Biological Processes".

Processors (13)

Name	Type	Description
mapDatabaseIDListToConceptIDs	wsdl	Wsdl http://sequenomics.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation mapDatabaseIDListToConceptIDs
mapDatabaseIDListToConceptIDs_input	xmlsplitter
XPath_Service	xpath	Xpath Expression /ns2:mapDatabaseIDListToConceptIDsResponse/return/DatabaseIDConceptSetList/DatabaseIDConceptSetTuple/ConceptSet
getSimilarConceptProfilesPredefined	wsdl	Wsdl http://sequenomics.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation getSimilarConceptProfilesPredefined
getSimilarConceptProfilesPredefined_input	xmlsplitter
Merge_String_List_to_a_String	localworker	This local service prepares the list of concepts for fast processing: make comma-separated list. Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
separator	stringconstant	Value ,
get_concept_ids	xpath	Xpath Expression /ns2:getSimilarConceptProfilesPredefinedResponse/return/MatchConceptProfileList/MatchConceptProfile
get_scores	xpath	Xpath Expression /ns2:getSimilarConceptProfilesPredefinedResponse/return/SummedSimilarityScoreList/SummedSimilarityScore
getConceptProfile	wsdl	Wsdl http://sequenomics.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation getConceptProfile
getConceptProfile_input	xmlsplitter
get_bps	xpath	Xpath Expression /ns2:getConceptProfileResponse/return/name
Flatten_List	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);

Beanshells (0)

Outputs (2)

Name	Description
score
processes

Datalinks (18)

Source	Sink
mapDatabaseIDListToConceptIDs_input:output	mapDatabaseIDListToConceptIDs:parameters
gene_IDs	mapDatabaseIDListToConceptIDs_input:databaseIDs
database_name	mapDatabaseIDListToConceptIDs_input:databaseName
mapDatabaseIDListToConceptIDs:parameters	XPath_Service:xml_text
getSimilarConceptProfilesPredefined_input:output	getSimilarConceptProfilesPredefined:parameters
Merge_String_List_to_a_String:concatenated	getSimilarConceptProfilesPredefined_input:queryConceptProfileList
cutoff	getSimilarConceptProfilesPredefined_input:cutoffValue
predefined_conceptset_id	getSimilarConceptProfilesPredefined_input:conceptSetId
XPath_Service:nodelist	Merge_String_List_to_a_String:stringlist
separator:value	Merge_String_List_to_a_String:seperator
getSimilarConceptProfilesPredefined:parameters	get_concept_ids:xml_text
getSimilarConceptProfilesPredefined:parameters	get_scores:xml_text
getConceptProfile_input:output	getConceptProfile:parameters
get_concept_ids:nodelist	getConceptProfile_input:conceptId
getConceptProfile:parameters	get_bps:xml_text
get_bps:nodelist	Flatten_List:inputlist
get_scores:nodelist	score
Flatten_List:outputlist	processes

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Eleni

Information License

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Information Version 1 (earliest) (of 4)

Information Credits (1)

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Eleni

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Information Statistics

3056 viewings

1425 downloads

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Version History

In chronological order:

Annotate gene list with top ranking concepts + explain concept associations (Xpath implementation)

Created by Eleni on Tuesday 03 December 2013 17:46:22 (UTC)
Annotate gene list with top ranking concepts

Created by Eleni on Tuesday 18 February 2014 11:04:15 (UTC)

Revision comment:

additional output : concept ids
output in one file per output (previous version exported a list of items for each output)
Annotate gene list with top ranking concepts

Created by Eleni on Thursday 02 April 2015 12:05:22 (UTC)

Revision comment:

updated workflow with newer db version
Annotate gene list with top ranking concepts

Created by Eleni on Friday 03 April 2015 20:48:10 (UTC)

Revision comment:

workflow with improved annotation and new database

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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

Annotate gene list with top ranking concepts

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Workflow Components

Wsdl

Wsdl Operation

Xpath Expression

Wsdl

Wsdl Operation

Script

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Xpath Expression

Xpath Expression

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Xpath Expression

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