Annotate gene list with top ranking concepts

None

/ns2:mapDatabaseIDListToConceptIDsResponse/return/DatabaseIDConceptSetList/DatabaseIDConceptSetTuple/ConceptSet
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();

/ns2:getSimilarConceptProfilesPredefinedResponse/return/MatchConceptProfileList/MatchConceptProfile
/ns2:getSimilarConceptProfilesPredefinedResponse/return/SummedSimilarityScoreList/SummedSimilarityScore
/ns2:getConceptProfileResponse/return/name
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);
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();

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();

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();

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".

Name	Type	Description
mapDatabaseIDListToConceptIDs_input	xmlsplitter
XPath_Service	xpath	Xpath Expression /ns2:mapDatabaseIDListToConceptIDsResponse/return/DatabaseIDConceptSetList/DatabaseIDConceptSetTuple/ConceptSet
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_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);
Merge_String_List_to_a_String_2	localworker	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();
Merge_String_List_to_a_String_3	localworker	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();
Merge_String_List_to_a_String_4	localworker	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();
mapDatabaseIDListToConceptIDs_2	wsdl	get the concept profile identifiers Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation mapDatabaseIDListToConceptIDs
getSimilarConceptProfilesPredefined_2	wsdl	perform concept profile matching between the gene list and the prefefined concept set. Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation getSimilarConceptProfilesPredefined
getConceptProfile_2	wsdl	get human readable names for the results by mapping the concept profile identifiers back to the database Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation getConceptProfile

Name	Description
score
processes
concept_ids

Source	Sink
gene_IDs	mapDatabaseIDListToConceptIDs_input:databaseIDs
database_name	mapDatabaseIDListToConceptIDs_input:databaseName
mapDatabaseIDListToConceptIDs_2:parameters	XPath_Service:xml_text
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_2:parameters	get_concept_ids:xml_text
getSimilarConceptProfilesPredefined_2:parameters	get_scores:xml_text
get_concept_ids:nodelist	getConceptProfile_input:conceptId
getConceptProfile_2:parameters	get_bps:xml_text
get_bps:nodelist	Flatten_List:inputlist
Flatten_List:outputlist	Merge_String_List_to_a_String_2:stringlist
get_concept_ids:nodelist	Merge_String_List_to_a_String_3:stringlist
get_scores:nodelist	Merge_String_List_to_a_String_4:stringlist
mapDatabaseIDListToConceptIDs_input:output	mapDatabaseIDListToConceptIDs_2:parameters
getSimilarConceptProfilesPredefined_input:output	getSimilarConceptProfilesPredefined_2:parameters
getConceptProfile_input:output	getConceptProfile_2:parameters
Merge_String_List_to_a_String_4:concatenated	score
Merge_String_List_to_a_String_2:concatenated	processes
Merge_String_List_to_a_String_3:concatenated	concept_ids

Annotate gene list with top ranking concepts

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