SNPs to Concept Set through Concept Profile Matching v2

Created: 2012-06-26 10:27:33 Last updated: 2013-02-05 20:49:12

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Purpose: Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (7)

Name	Description
Max_no_of_results	The top matches from the concept profile matching procedure.
SNP_ID	ID for the SNP (dbSNP format (http://www.ncbi.nlm.nih.gov/snp)).
EntrezGene_database_type_ID	The ID for the EntrezGene database (Erasmus MC ontology format).
Max_no_of_results_to_explain	Maximum number of top contributing concepts (concepts that contribute most to the matching score between two concept profiles).
Max_no_of_supporting_documents	Max number of supporting documents to return.
Concept_set_ID	The ID of the predefined Concept Set to match with.
Max_no_of_co_occurring_documents	Max number of supporting documents to return.

Processors (9)

Name	Type	Description
Match_concept_profiles	workflow	Purpose of component in workflow: The purpose of this component (nested workflow) in this workflow is to match the concept profiles of genes identified by proximity to SNPs, to the profiles of Gene Ontology (GO) concepts (from the GO process branch). The assumption is that the genetic variation close to these genes indicate genetic variation that is potentially causative for the phenotype under study. Results: The results of this component are biological processes (GO concepts) associated with genes close to input SNPs, ranked in the order of the match score between the input concepts. The results suggest which biological processes are associated with the putative genetic causes as indicated by the identified genes associated with the identified SNPs.
SNP_ID2EntrezGene_ID	workflow	Purpose of component in workflow: This component maps a SNP ID to EntrezGene IDs.
Explain_concept_scores	workflow	Purpose of component in workflow: This component retieves the concepts contributing most to the match perfomed in the Match_concept_profiles component.
Supporting_Documents_EntrezGeneIDs	workflow	Purpose of component in workflow: This component (nested workflow) finds supporting documents for the association between the explaining concepts and the concepts representing the input Entrez Gene IDs.
Supporting_Documents_Matched_Concepts	workflow	Purpose of component in workflow: This component (nested workflow) finds the documents that support the suggested association between input concept IDs and associated Concept IDs
EntrezGeneID_to_ConceptID	workflow	Purpose of component in workflow: The purpose of this component (nested workflow) here is to map Gene Ontology and entrez gene identifiers (the external database identifiers) to the concept identifier used in the Erasmus MC ontology, developed by the BioSemantics Group in Rotterdam. The ontology can be seen as a concept database compiled from various common thesauri and ontologies.
Get_Concept_IDs	workflow	Purpose of component in workflow: This component retieves the concept IDs within a concept set.
Get_concept_information	workflow	Purpose of component in workflow: To retrieve the name of the concept from the ontology.l
Co_occurring_documents_matched_concepts	workflow	Purpose of component in workflow: This component retieves the co-occuring documents for the query concept and the matched concept.

Beanshells (1)

Name	Description	Inputs	Outputs
Beanshell		inputList item	outputList

Outputs (12)

Name	Description
Match_conceptCUI	Matching Concept Identifiers
Similarity_score_between_query_and_match_conceptCUI	Similarity Score Query and Match Concept IDs
Top_contributing_conceptCUI_beween_query_and_match_conceptCUIs	Top contributing Concept ID between Query and Matching Concept IDs
Top_contributing_conceptnames_between_query_and_match_conceptCUIs	Top Contributing Concept Name Query and Explaining Concept IDs
Supporting_document_IDs_between_query_conceptCUI_and_explained_conceptCUI	Supporting PubMed Document IDs Query and explaining Concept IDs
Supporting_document_titles_between_query_conceptCUI_and_explained_conceptCUI	Supporting Document Title Query and Explaining Concept IDs
Query_conceptCUI	Query Concept Identifiers
Supporting_document_IDs_between_match_conceptCUI_and_explained_conceptCUI	Supporting PubMed Document ID Match and explained Concept IDs
Supporting_document_titles_between_match_conceptCUI_and_explained_conceptCUI	Supporting Document Title Match and Explained Concept IDs
Match_conceptName
Co_occurring_document_IDs_between_query_conceptCUI_and_matched_conceptCUI	The IDs for the documents where the query and match concepts co-occur.
Co_occurring_document_titles_between_query_conceptCUI_and_matched_conceptCUI	The titels for the documents where the query and match concepts co-occur.

Datalinks (32)

Source	Sink
Max_no_of_results	Match_concept_profiles:Cutoff
EntrezGeneID_to_ConceptID:concepts	Match_concept_profiles:QueryConceptSet
Get_Concept_IDs:Concept_ID_set	Match_concept_profiles:MatchConceptSet
SNP_ID	SNP_ID2EntrezGene_ID:SNP_ID
Max_no_of_results_to_explain	Explain_concept_scores:maxNrResults
EntrezGeneID_to_ConceptID:concepts	Explain_concept_scores:matchConcept
Match_concept_profiles:MatchConceptID	Explain_concept_scores:queryConceptSet
Explain_concept_scores:ConceptID	Supporting_Documents_EntrezGeneIDs:associatedConceptCUI
Max_no_of_supporting_documents	Supporting_Documents_EntrezGeneIDs:MaxNoOfSupportingDocs
EntrezGeneID_to_ConceptID:concepts	Supporting_Documents_EntrezGeneIDs:conceptCUI
Match_concept_profiles:MatchConceptID	Supporting_Documents_Matched_Concepts:conceptCUI
Explain_concept_scores:ConceptID	Supporting_Documents_Matched_Concepts:associatedConceptCUI
Max_no_of_supporting_documents	Supporting_Documents_Matched_Concepts:MaxNoOfSupportingDocs
EntrezGene_database_type_ID	EntrezGeneID_to_ConceptID:DatabaseID
SNP_ID2EntrezGene_ID:EG_ID_list	EntrezGeneID_to_ConceptID:IDvalue
Concept_set_ID	Get_Concept_IDs:Concept_set_ID
Match_concept_profiles:MatchConceptID	Get_concept_information:Concept_ID
EntrezGeneID_to_ConceptID:concepts	Co_occurring_documents_matched_concepts:ConceptID_1
Match_concept_profiles:MatchConceptID	Co_occurring_documents_matched_concepts:ConceptID_2
Max_no_of_co_occurring_documents	Co_occurring_documents_matched_concepts:Cutoff_value
Match_concept_profiles:MatchConceptID	Match_conceptCUI
Match_concept_profiles:SummedSimilarityScore	Similarity_score_between_query_and_match_conceptCUI
Explain_concept_scores:ConceptID	Top_contributing_conceptCUI_beween_query_and_match_conceptCUIs
Explain_concept_scores:ConceptName	Top_contributing_conceptnames_between_query_and_match_conceptCUIs
Supporting_Documents_EntrezGeneIDs:DocumentID	Supporting_document_IDs_between_query_conceptCUI_and_explained_conceptCUI
Supporting_Documents_EntrezGeneIDs:DocumentTitle	Supporting_document_titles_between_query_conceptCUI_and_explained_conceptCUI
EntrezGeneID_to_ConceptID:concepts	Query_conceptCUI
Supporting_Documents_Matched_Concepts:DocumentID	Supporting_document_IDs_between_match_conceptCUI_and_explained_conceptCUI
Supporting_Documents_Matched_Concepts:DocumentTitle	Supporting_document_titles_between_match_conceptCUI_and_explained_conceptCUI
Get_concept_information:Concept_name	Match_conceptName
Co_occurring_documents_matched_concepts:Document_ID	Co_occurring_document_IDs_between_query_conceptCUI_and_matched_conceptCUI
Co_occurring_documents_matched_concepts:Document_title	Co_occurring_document_titles_between_query_conceptCUI_and_matched_conceptCUI

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Kristina Hettne

Information License

All versions of this Workflow are licensed under:

Information Version 3 (of 6)

Information Credits (7)

(People/Groups)

Information Attributions (8)

(Workflows/Files)

Find Supporting Documents
SNP_ID2EntrezGene_ID
DatabaseID to ConceptID
Match gene lists based on information in literature
Private item
Private item
Match concept profiles
Explain concept scores

Information Tags (19)

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Information Shared with Groups (3)

Information Featured In Packs (1)

Functional annotation of SNPs using next-generation text mining

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Information Attributed By (1)

(Workflows/Files)

Annotate a gene list with disease concepts

Information Favourited By (1)

Marco Roos

Information Statistics

4599 viewings

1685 downloads

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Citations (0)

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Version History

In chronological order:

SNPs to GO through Concept Profile Matching

Created by Kristina Hettne on Tuesday 26 June 2012 10:27:33 (UTC)
SNPs to GO through Concept Profile Matching

Created by Kristina Hettne on Friday 06 July 2012 14:12:55 (UTC)

Last edited by Kristina Hettne on Friday 06 July 2012 14:14:38 (UTC)

Revision comment:

The workflow now accepts a concept set ID number as input. The GO Biological Process concept set ID is used as an example. The workflow now includes two new nested components: Get_concept_IDs and Get_concept_information.
Functional SNP annotation through next-generation text mining

Created by Kristina Hettne on Wednesday 11 July 2012 15:25:14 (UTC)

Last edited by Kristina Hettne on Wednesday 18 July 2012 10:27:47 (UTC)

Revision comment:

The workflow now includes a component to find co-occurring documents between two concepts. It also reflects recent changes to the web service interface surrounding the naming of the concept set parameter.
Functional SNP annotation through next-generation text mining

Created by Kristina Hettne on Wednesday 18 July 2012 14:01:16 (UTC)

Last edited by Kristina Hettne on Wednesday 18 July 2012 14:02:45 (UTC)

Revision comment:

Added annotations. Replaced the nested components with the newer versions.
SNPs to Concept Set through Concept Profile Matching

Created by Kristina Hettne on Friday 14 September 2012 10:10:23 (UTC)
SNPs to Concept Set through Concept Profile Matching v2

Created by Kristina Hettne on Tuesday 05 February 2013 20:49:12 (UTC)

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Comments (1)

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Magnus Palmblad	Monday 11 March 2013 14:02:52 (UTC)
	Very nice workflow, but the output URLs (http://rdf.biosemantics.org/owl/...) do not work anymore. Perhaps you could update the workflow? (Då kan jag definitivt ge det en femma i betyg...).

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