Molecular Interactions from IntAct PSICQUIC service (SOAP)

Created: 2011-05-17 07:09:30 Last updated: 2011-07-20 15:14:56

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Get molecular interaction data in psi-mitab25 format from IntAct through its PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:(KHDRBS1 OR HCK)". This workflow finds by itself how many queries needs to make (SOAP service limited to 200 binary interactions per call) to be able to return all the results in one file.

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Workflow Components

Authors (1)

Titles (2)

Descriptions (2)

Dependencies (0)

Inputs (1)

Name	Description
MIQL_query	MIQL query ... http://code.google.com/p/psicquic/wiki/MiqlReference MIQL query

Processors (17)

Name	Type	Description
getByQuery	wsdl	Wsdl http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/psicquic?wsdl Wsdl Operation getByQuery
getByQuery_input	xmlsplitter
getByQuery_output	xmlsplitter
getByQuery_infoRequest	xmlsplitter
mitab25	stringconstant	Value psi-mi/tab25
splitPsicquicQueries	beanshell	Script /* Constants / int count = Integer.parseInt(totalNumberOfInteractions); int queryRange = Integer.parseInt(blockSize); int queryStart = 0; / Changing values / int start = queryStart; int range = queryRange; int stop = queryStart + queryRange -1; / result container */ List firstResultList = new ArrayList(); int numOfQueries = (int) Math.ceil((double)count/(double)queryRange); for(int i=0; i= count){ range = count - start; stop = start + range -1; } firstResultList.add(start); }
getByQuery_2	wsdl	Wsdl http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/psicquic?wsdl Wsdl Operation getByQuery
getByQuery_2_input	xmlsplitter
getByQuery_2_output	xmlsplitter
2_infoRequest	xmlsplitter
count	stringconstant	Value count
2_queryResponse	xmlsplitter
queryResponse_resultInfo	xmlsplitter
getByQuery_queryResponse	xmlsplitter
queryResponse_resultSet	xmlsplitter
blockSize_value	stringconstant	Value 10
mergeMitab	beanshell	Script String mitab = ""; for(Object mitabPart:mitabList){ mitab += mitabPart; }

Beanshells (2)

Name	Description	Inputs	Outputs
splitPsicquicQueries		totalNumberOfInteractions blockSize	firstResultList
mergeMitab		mitabList	mitab

Outputs (1)

Name	Description
MITAB	Molecular interactions results in MITAB format ... http://code.google.com/p/psicquic/wiki/MITAB26Format MITAB25 ... http://code.google.com/p/psicquic/wiki/MITAB26Format MITAB

Datalinks (20)

Source	Sink
getByQuery_input:output	getByQuery:parameters
MIQL_query	getByQuery_input:query
getByQuery_infoRequest:output	getByQuery_input:infoRequest
getByQuery:parameters	getByQuery_output:input
mitab25:value	getByQuery_infoRequest:resultType
splitPsicquicQueries:firstResultList	getByQuery_infoRequest:firstResult
blockSize_value:value	getByQuery_infoRequest:blockSize
queryResponse_resultInfo:totalResults	splitPsicquicQueries:totalNumberOfInteractions
blockSize_value:value	splitPsicquicQueries:blockSize
getByQuery_2_input:output	getByQuery_2:parameters
2_infoRequest:output	getByQuery_2_input:infoRequest
MIQL_query	getByQuery_2_input:query
getByQuery_2:parameters	getByQuery_2_output:input
count:value	2_infoRequest:resultType
getByQuery_2_output:queryResponse	2_queryResponse:input
2_queryResponse:resultInfo	queryResponse_resultInfo:input
getByQuery_output:queryResponse	getByQuery_queryResponse:input
getByQuery_queryResponse:resultSet	queryResponse_resultSet:input
queryResponse_resultSet:mitab	mergeMitab:mitabList
mergeMitab:mitab	MITAB