Prioritize gene list

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

/ns2:getSimilarConceptProfilesResponse/MatchingResult/SimilarityScoreLists/ScoreList/QueryScoreTupleList/score
/ns2:getSimilarConceptProfilesResponse/MatchingResult/MatchConceptProfileList/MatchConceptProfile
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:getSimilarConceptProfilesResponse/MatchingResult/MatchConceptProfileList/MatchConceptProfile
/ns2:getConceptProfileResponse/return/name
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();

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);

Name	Description
gene_IDs	a comma separated gene list to prioritized
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
concept_id	id of the concept to match the gene list against, entrez gene ids in the case where database_name = EG In our case we use the entrez gene identifier to match our gene list against the huntingtin protein

Name	Type	Description
mapDatabaseIDListToConceptIDs_input	xmlsplitter
XPath_Service	xpath	Xpath Expression /ns2:mapDatabaseIDListToConceptIDsResponse/return/DatabaseIDConceptSetList/DatabaseIDConceptSetTuple/ConceptSet
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 ,
mapDatabaseIDListToConceptIDs_2	wsdl	get the concept profile identifiers Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation mapDatabaseIDListToConceptIDs
mapDatabaseIDListToConceptIDs_2_2	wsdl	get the concept profile identifiers Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation mapDatabaseIDListToConceptIDs
mapDatabaseIDListToConceptIDs_2_2_input	xmlsplitter
XPath_Service_2	xpath	Xpath Expression /ns2:mapDatabaseIDListToConceptIDsResponse/return/DatabaseIDConceptSetList/DatabaseIDConceptSetTuple/ConceptSet/conceptIDsAsString
Merge_String_List_to_a_String_5	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();
getSimilarConceptProfiles	wsdl	perform concept profile matching between the gene list and the concept, to prioritize the gene list Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation getSimilarConceptProfiles
getSimilarConceptProfiles_input	xmlsplitter
Merge_String_List_to_a_String_2_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();
Text_constant	stringconstant	Value 10000000
XPath_Service_3	xpath	Xpath Expression /ns2:getSimilarConceptProfilesResponse/MatchingResult/SimilarityScoreLists/ScoreList/QueryScoreTupleList/score
XPath_Service_3_2	xpath	Xpath Expression /ns2:getSimilarConceptProfilesResponse/MatchingResult/MatchConceptProfileList/MatchConceptProfile
Merge_String_List_to_a_String_2_2_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();
XPath_Service_3_3	xpath	Xpath Expression /ns2:getSimilarConceptProfilesResponse/MatchingResult/MatchConceptProfileList/MatchConceptProfile
getConceptProfile	wsdl	obtain human readable names for the results Wsdl http://ws.biosemantics.org/ConceptProfileMiningService?wsdl Wsdl Operation getConceptProfile
getConceptProfile_input	xmlsplitter
XPath_Service_4	xpath	Xpath Expression /ns2:getConceptProfileResponse/return/name
Merge_String_List_to_a_String_2_2_2_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();
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);

Name	Description
individ_scores	the individual score for each association: geneA - concept
concept_ids
concept_name	human readable names of the results

Source	Sink
gene_IDs	mapDatabaseIDListToConceptIDs_input:databaseIDs
database_name	mapDatabaseIDListToConceptIDs_input:databaseName
mapDatabaseIDListToConceptIDs_2:parameters	XPath_Service:xml_text
XPath_Service:nodelist	Merge_String_List_to_a_String:stringlist
separator:value	Merge_String_List_to_a_String:seperator
mapDatabaseIDListToConceptIDs_input:output	mapDatabaseIDListToConceptIDs_2:parameters
mapDatabaseIDListToConceptIDs_2_2_input:output	mapDatabaseIDListToConceptIDs_2_2:parameters
concept_id	mapDatabaseIDListToConceptIDs_2_2_input:databaseIDs
database_name	mapDatabaseIDListToConceptIDs_2_2_input:databaseName
mapDatabaseIDListToConceptIDs_2_2:parameters	XPath_Service_2:xml_text
XPath_Service_2:nodelist	Merge_String_List_to_a_String_5:stringlist
separator:value	Merge_String_List_to_a_String_5:seperator
getSimilarConceptProfiles_input:output	getSimilarConceptProfiles:parameters
Merge_String_List_to_a_String:concatenated	getSimilarConceptProfiles_input:matchConceptProfileList
Merge_String_List_to_a_String_5:concatenated	getSimilarConceptProfiles_input:queryConceptProfileList
Text_constant:value	getSimilarConceptProfiles_input:cutoffValue
XPath_Service_3:nodelist	Merge_String_List_to_a_String_2_2:stringlist
getSimilarConceptProfiles:parameters	XPath_Service_3:xml_text
getSimilarConceptProfiles:parameters	XPath_Service_3_2:xml_text
XPath_Service_3_2:nodelist	Merge_String_List_to_a_String_2_2_2:stringlist
getSimilarConceptProfiles:parameters	XPath_Service_3_3:xml_text
getConceptProfile_input:output	getConceptProfile:parameters
XPath_Service_3_3:nodelist	getConceptProfile_input:conceptId
getConceptProfile:parameters	XPath_Service_4:xml_text
Flatten_List:outputlist	Merge_String_List_to_a_String_2_2_2_2:stringlist
XPath_Service_4:nodelist	Flatten_List:inputlist
Merge_String_List_to_a_String_2_2:concatenated	individ_scores
Merge_String_List_to_a_String_2_2_2:concatenated	concept_ids
Merge_String_List_to_a_String_2_2_2_2:concatenated	concept_name

Prioritize gene list

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