Using CQL to query protein sequence data

Created: 2009-05-07 14:28:59

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To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR

Adapted from http://www.myexperiment.org/workflows/600

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Titles (2)

Descriptions (4)

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Processors (13)

Name	Type	Description
Extract_SwissProtID_to_GridPIR_query	beanshell	Script String id = ""; int n1 = input.indexOf("SWISS-PROT:"); int n2 = input.indexOf('\|', n1); id = input.substring(n1+11, n2); String output = " ";
Extract_protSequence_to_caBIO_query	beanshell	Script String id = ""; int n1 = input.indexOf("protSequence=\""); int n2 = input.indexOf('"', n1+14); id = input.substring(n1+14, n2); String output = " ";
caBIO_input_query	xmlsplitter
GridPIR_query_input	xmlsplitter
CPAS_query_output	xmlsplitter
caBIO_input	xmlsplitter
GridPIR_input	xmlsplitter
CPAS_input	xmlsplitter
CPAS_query_input	xmlsplitter
CPAS_query	wsdl	Wsdl http://cpas.nci.nih.gov:8080/wsrf/services/cagrid/CpasSvc?wsdl Wsdl Operation query
GridPIR_query	wsdl	Wsdl http://141.161.25.20:8080/wsrf/services/cagrid/GridPIR?wsdl Wsdl Operation query
caBIO_query	wsdl	Wsdl http://cabiogrid32.nci.nih.gov:80/wsrf/services/cagrid/CaBIO32GridSvc?wsdl Wsdl Operation query
CPAS_query_P999999	stringconstant	Value

Beanshells (2)

Name	Description	Inputs	Outputs
Extract_SwissProtID_to_GridPIR_query		input	output
Extract_protSequence_to_caBIO_query		input	output

Outputs (3)

Name	Description
CPAS_result
GridPIR_result
caBIO_result

Datalinks (15)

Source	Sink
CPAS_query_output:CQLQueryResultCollection	Extract_SwissProtID_to_GridPIR_query:input
CPAS_query_output:CQLQueryResultCollection	Extract_protSequence_to_caBIO_query:input
Extract_protSequence_to_caBIO_query:output	caBIO_input_query:CQLQuery
Extract_SwissProtID_to_GridPIR_query:output	GridPIR_query_input:CQLQuery
CPAS_query:parameters	CPAS_query_output:input
caBIO_input_query:output	caBIO_input:cqlQuery
GridPIR_query_input:output	GridPIR_input:cqlQuery
CPAS_query_input:output	CPAS_input:cqlQuery
CPAS_query_P999999:value	CPAS_query_input:CQLQuery
CPAS_input:output	CPAS_query:parameters
GridPIR_input:output	GridPIR_query:parameters
caBIO_input:output	caBIO_query:parameters
CPAS_query:parameters	CPAS_result
GridPIR_query:parameters	GridPIR_result
caBIO_query:parameters	caBIO_result

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Information Workflow Type

Taverna 2

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Stian Soiland-Reyes

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Stian Soiland-Reyes

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Using CQL to query protein sequence data

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Using CQL to query protein sequence data

Created by Stian Soiland-Reyes on Thursday 07 May 2009 14:29:01 (UTC)

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Taverna 1

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Wei Tan

Using CQL to query protein sequence data (1)

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To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR. Scientific value To query protein sequence information out of 3 caGrid data services: caBIO, CPAS and GridPIR. To analyze a protein sequence from different data sources. Steps Querying CPAS and get the id, name, value of the sequence. Querying caBIO and GridPIR using the id or name obtained from CPAS.

Created: 2008-12-05 | Last updated: 2009-07-14

Credits: Wei Tan

Using CQL to query protein sequence data

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