Annotate a gene list with disease concepts

Created: 2013-02-06 20:02:24

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Purpose:

Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match.

Author comments:

The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.

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http://www.myexperiment.org/workflows/3397/download?version=1
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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (5)

Name	Description
Entrez_gene_DB_ID	The ID for the EntrezGene database (Erasmus MC ontology format).
Entrez_gene_IDs	Genes to be annotated (Entrez gene format, see http://www.ncbi.nlm.nih.gov/gene)
Disease_or_syndrome_concept_set	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 corresponds to the concept set "Disease or Syndrome".
Match_concept_cutoff	Max number of concepts to return from the concept profile matching procedure.
Explained_concepts_cutoff	Max number of explanatory concepts to return for a concept profile match.

Processors (8)

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 to the profiles of disease concepts (from the Disease or Syndrome branch). Results: The results of this component are diseases associated with genes, ranked in the order of the match score between the input concepts. The results suggest which diseases are associated with the difference in gene expression in the underlying experiment.
DatabaseID_to_ConceptID	workflow	Purpose of component in workflow: The purpose of this component (nested workflow) here is to map 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.
Split_string_into_string_list_by_regular_expression	localworker	This local service prepares the list of genes for fast processing: make comma-separated list. 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]); } }
Text_constant	stringconstant	The constant that is used by the local service, in this case ",". Value \n
Get_concept_name	workflow	Purpose of component in workflow: To retrieve the name of the concept from the ontology.
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();
Text_constant_2	stringconstant	The constant that is used by the local service, in this case ",". Value ,
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.

Beanshells (1)

Name	Description	Inputs	Outputs
makeCommaSeparatedString	This script concatenates the two input concept id strings and adds a comma in between.	item1 item2	output

Outputs (6)

Name	Description
Matched_disease_names	Names for the concepts from the concept profile match.
Summed_Similarity_score	Concept match similarity score from the matching procedure.
Explained_concept_name	The concept names of the explanatory concepts.
Explained_concept_ID	The concept IDs of the explanatory concepts.
Match_concept_ID	IDs for the concepts from the concept profile match.
Query_concept_ID	IDs for the concepts from the concept profile query.

Datalinks (19)

Source	Sink
Match_concept_cutoff	Match_concept_profiles:Cutoff
Disease_or_syndrome_concept_set	Match_concept_profiles:Match_concept_set
Merge_String_List_to_a_String:concatenated	Match_concept_profiles:Query_concept_ID
Entrez_gene_DB_ID	DatabaseID_to_ConceptID:DatabaseID
Split_string_into_string_list_by_regular_expression:split	DatabaseID_to_ConceptID:IDvalue
Text_constant:value	Split_string_into_string_list_by_regular_expression:regex
Entrez_gene_IDs	Split_string_into_string_list_by_regular_expression:string
Match_concept_profiles:Match_concept_ID	Get_concept_name:Concept_ID
Text_constant_2:value	Merge_String_List_to_a_String:seperator
DatabaseID_to_ConceptID:Concept_IDs	Merge_String_List_to_a_String:stringlist
Match_concept_profiles:Query_concept_ID	Explain_concept_scores:C_ConceptID
Explained_concepts_cutoff	Explain_concept_scores:cutoff
Match_concept_profiles:Match_concept_ID	Explain_concept_scores:A_ConceptID
Get_concept_name:Concept_name	Matched_disease_names
Match_concept_profiles:Similarity_score	Summed_Similarity_score
Explain_concept_scores:B_ConceptName	Explained_concept_name
Explain_concept_scores:B_ConceptID	Explained_concept_ID
Match_concept_profiles:Match_concept_ID	Match_concept_ID
Match_concept_profiles:Query_concept_ID	Query_concept_ID