Wrapping analytical

services for caBIG

Taverna-caGrid technical review

meetingStian Soiland-Reyes, myGridUniversity of Manchester, UK

2009-01-23http://www.mygrid.org.uk/dev/wiki/display/caGrid

Agenda

• Project overview• Primary goals• Service

selection• Services

identified• Architecture• Service outputs

• Service outputs• UML model• Template workflow• Work so far• Implementation

plan

Project overview

• Taverna caGrid cooperation•Taverna workbench enhancements

for caGrid•Grid-enabling analytical services•caGrid security support for Taverna

• This presentation deals with the analytical services

Primary goals

• Identify two publicly available analytical web services currently accessible through Taverna

• caGrid-enable the services; semantically described using caBIG’s infrastructure

• Demonstrate building of workflows combining the new services with existing caBIG services

Service selection

• Selected services in collaboration with the caGrid Workflow working group, lead by Juli

• Winners:•NCBI Blast hosted by EBI•InterProScan hosted by EBI

Why these services?

• Freely available• Highly reliable, hosted by EBI• Widely used by the scientific

community• Can be combined with existing caBIG

tools in biologically meaningful workflows•caBIO, GridPIR, etc.

Services identified

• NCBI Blast•A popular similarity search tool using

local sequence alignment•Supports sequences of proteins, DNA,

RNA•Searches sequences in a whole range

of databases•SWISSPROT, UNIPROT, NCBI, EMBL, etc.

•SOAP web service hosted by EMBL-EBI

Services identified

• InterProScan•Integrates various databases of

protein domains and functional sites

•Searches using protein signature recognition methods

•SOAP web service hosted by EMBL-EBI

Architecture

Architecture as pseudo codeclass CaGridClient: def main(): endpointReference = wrappedService.invoke(inputs) endpointReference.subscribe() def resourcePropertyChanged(): outputs = endpointReference.getResourceProperty() print "Result", outputs class WrappedService: def invoke(inputs): convertedInputs = dataConverter.convertFromCaGrid(inputs) jobId = serviceInvoker.invoke(convertedInputs) endpointReference = new EndpointReference(jobId) return endpointReference

def outputReturned(jobId, outputs): convertedOutputs = dataConverter.convertToCaGrid(outputs) endpointReference.setResourceProperty(convertedOutputs) class ServiceInvoker: def invoke(convertedInputs): jobId = originalService.invoke(convertedInputs) return jobId

Output InterProScan (Untranslated)<EBIInterProScanResults xmlns="http://www.ebi.ac.uk/schema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ebi.ac.uk/schema/InterProScanResult.xsd"> <Header>..</Header><interpro_matches> <protein id="uniprot|P01174|WAP_RAT" length="137" crc64="1C2E8ADA9FD97949" > <interpro id="IPR008197" name="Whey acidic protein, 4-disulphide core" type="Domain" parent_id="IPR015874"> <child_list><rel_ref ipr_ref="IPR008198"/></child_list> <contains><rel_ref ipr_ref="IPR002098"/></contains> <classification id="GO:0030414" class_type="GO"> <category>Molecular Function</category> <description>protease inhibitor activity</description> </classification> <match id="G3DSA:4.10.75.10" name="Whey_acidic_protein_4-diS_core" dbname="GENE3D"> <location start="77" end="128" score="9.899996308397199E-5" status="T" evidence="Gene3D" /> </match> <match id="PF00095" name="WAP" dbname="PFAM"> <location start="30" end="72" score="6.30000254573025E-5" status="T" evidence="HMMPfam" /> <location start="79" end="126" score="1.59999889349247E-14" status="T" evidence="HMMPfam" /> </match> </interpro> <interpro id="IPR008198" name="Proteinase inhibitor I17" type="Domain" parent_id="IPR008197"> ...</interpro> </protein></interpro_matches></EBIInterProScanResults>

Output InterProScan (Untranslated)<EBIInterProScanResults xmlns="http://www.ebi.ac.uk/schema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ebi.ac.uk/schema/InterProScanResult.xsd"> <Header>..</Header><interpro_matches> <protein id="uniprot|P01174|WAP_RAT" length="137" crc64="1C2E8ADA9FD97949" > <interpro id="IPR008197" name="Whey acidic protein, 4-disulphide core" type="Domain" parent_id="IPR015874"> <child_list><rel_ref ipr_ref="IPR008198"/></child_list> <contains><rel_ref ipr_ref="IPR002098"/></contains> <classification id="GO:0030414" class_type="GO"> <category>Molecular Function</category> <description>protease inhibitor activity</description> </classification> <match id="G3DSA:4.10.75.10" name="Whey_acidic_protein_4-diS_core" dbname="GENE3D"> <location start="77" end="128" score="9.899996308397199E-5" status="T" evidence="Gene3D" /> </match> <match id="PF00095" name="WAP" dbname="PFAM"> <location start="30" end="72" score="6.30000254573025E-5" status="T" evidence="HMMPfam" /> <location start="79" end="126" score="1.59999889349247E-14" status="T" evidence="HMMPfam" /> </match> </interpro> <interpro id="IPR008198" name="Proteinase inhibitor I17" type="Domain" parent_id="IPR008197"> ...</interpro> </protein></interpro_matches></EBIInterProScanResults>

UML model: wrapped InterproScan

UML model: wrapped NCBIBlast

Template workflow

http://www.myexperiment.org/workflows/230

EBI_dbfetch_fetchBatch will be replaced with the caBIG service caBIO

This workflow uses both NCBIBlast and InterproScan which will be replaced with the wrapped services

Work so far• Identified services and example workflow • Described services (Deliverable 3.2)• Modelled service inputs and outputs in UML

according to caGrid guidelines• Still a few tweaks needed for WS-

Resource usage• Architecture and implementation plan for

wrapping services (Deliverable 3.3)• JavaDoc needs updating for WS-Resource

Implementation plan• Generate Common Data Elements for inputs

and outputs and verify Silver compatability• Generate semantically annotated XMIs• Submit Silver compatability review package

• Implement and deploy wrapped services• Using Introduce and possibly gRavi• Implement, test , deploy• We’ll start with this before submitting CDEs

• Build caGrid-based workflow using services

Any questions..?