Wrapping third-party analytical

services for caBIG

Taverna-caBIG project

Stian Soiland-ReyesAlexandra Nenadic

University of Manchester, UK

http://www.mygrid.org.uk/dev/wiki/display/caGrid

September 2009

Agenda

• Project overview

• Primary goals

• Service selection

• Why these services?

• Why wrapping?

• Wrapping benefits?

• How we did it

• How does it work

• Architecture

• UML models

• Example client and outputs

• Project info

Project overview

• Taverna-caBIG cooperation on several levels:

1. caGrid-enabling third party analytical services

2. Taverna Workbench enhancements for:

• Semantic search of caBIG services

• Invocation of caBIG services from Taverna workflows

• Support for secure caBIG services (interacting with GAARDS infrastructure prior to service invocation)

• This presentation addresses caGrid-enablement of third party analytical services (wrapping + achieving silver level of compatibility)

Primary goals

• Identify two publicly available analytical

services currently accessible through

Taverna

• Wrap, i.e. caGrid-enable, the services:

• Design the wrapper services in UML and

semantically describe/annotate them

using caBIG’s tooling (EA + SIW)

• Wrap/implement and deploy them as

standard caBIG services on caGrid

(Introduce)

Analytical service selection

• Services have been selected in collaboration with caBIG Workflow Working Group, lead by Juli Klemm

• Winners:

• NCBI BLAST service hosted by EBI (European Bioinformatics Institute)

• Protein and nucleotide sequence similarity search service

• InterProScan service hosted by EBI

• Scans a range of protein signatures in InterPro warehouse against a protein sequence

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.

NCBI BLAST service

• A popular sequence similarity search tool using local sequence alignment

• Supports sequences of proteins, DNA, RNA

• Searches sequences in a whole range of databases:

• UNIPROT, NCBI, EMBL, etc.

• SOAP web service hosted by EMBL-EBI

InterProScan service

• InterPro warehouse integrates various databases of protein domains and functional sites

• Searches the InterPro warehouse using protein signature recognition methods, e.g. blastprodom, gene3d, hmmpfam, hmmsmart, scanregexp, profilescan..

• SOAP web service hosted by EMBL-EBI

Why wrapping the services?

• Original services use various data formats for inputs/outputs (although xml)

• Does not conform to the caBIG compatibility rules

• Output format was not even compatible with input format

• The requirement for the wrapped service:

• Translate the input data from caBIG-compatible xml to xml format understood by analytical services

• Convert the received results back to a format understood by caBIG clients

NCBI BLAST Output (Untranslated)<?xml version="1.0"?><EBIApplicationResult xmlns="http://www.ebi.ac.uk/schema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ebi.ac.uk/schema/ApplicationResult.xsd"><Header>...</Header><SequenceSimilaritySearchResult> <hits total="1"> <hit number="1" database="uniprot" id="WAP_RAT" ac="P01174" length="137"description="Whey acidic protein OS=Rattus norvegicus GN=Wap PE=1 SV=2"> <alignments total="1"> <alignment number="1"> <score>763</score> <bits>298</bits> <expectation>8e-80</expectation> <identity>100</identity> <positives>100</positives> <querySeq start="1" end="137">MRCSISLVLGLLALEVALARNLQEHVFNSVQSMCSDDSFSEDTECINCQTNEECAQNDMCCPSSCGRSCKTPVNIEVQKAGRCPWNPIQMIAAGPCPKDNPCSIDSDCSGTMKCCKNGCIMSCMDPEPKSPTVISFQ</querySeq> <pattern>MRCSISLVLGLLALEVALARNLQEHVFNSVQSMCSDDSFSEDTECINCQTNEECAQNDMCCPSSCGRSCKTPVNIEVQKAGRCPWNPIQMIAAGPCPKDNPCSIDSDCSGTMKCCKNGCIMSCMDPEPKSPTVISFQ</pattern> <matchSeq start="1" end="137">MRCSISLVLGLLALEVALARNLQEHVFNSVQSMCSDDSFSEDTECINCQTNEECAQNDMCCPSSCGRSCKTPVNIEVQKAGRCPWNPIQMIAAGPCPKDNPCSIDSDCSGTMKCCKNGCIMSCMDPEPKSPTVISFQ</matchSeq> </alignment> </alignments> </hit></hits></SequenceSimilaritySearchResult></EBIApplicationResult>

InterProScan Output (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>

Motivational workflow

This Taverna workflow uses both Blast and InterProScan which can be replaced with wrapped versions of the services

Nested workflow that internally invokes InterProScan and checks job status before fetching results

Nested workflow that internally invokes NCBI BLAST and checks job status before fetching results

Web Service that looks up protein sequences in a database. Will be replaced with the caBIG service caBIO.

Shim that splits a stringinto a list of Fasta strings

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

Benefits of wrapped services

• Making analytical services from other service providers available to caBIG users

• Wrapped services are caBIG Silver Level compatible:

• Ensures shared meaning and interoperability between these and other caBIG services

• Data can be exchanged and understood between services

How we wrapped the services (1)

• Making the services ‘silver’ encompassed:

1. Modelled data in UML using Enterprise Architect (EA)

2. Exported model to XMI from EA

3. Using the SIW tool, the XMI file has been semantically annotated using caBIG’s vocabularies/ontologies

4. Common Data Elements (CDEs) have been generated for services inputs/outputs, reviewed by the curation team and loaded into caDSR production database

5. Annotated XMI loaded back to the EA to update UML

How we wrapped the services (2)

6. From the EA, the UML model was exported to a set of xsd files

7. The xsd files have been imported into the Introduce tool, which was used to generate the skeleton APIs of the wrapped services

8. Axis 2 was used to invoke the original InterPro and NCBI BLAST services from the wrapper services

9. The wrapped services are asynchronous; job status and results are available as WSRF resource properties and can be subscribed to using WS-Notifications. There is also a synchronous version where polling is done from the client side.

How it works

• Client: using client library, calls wrapped WSRF web service

• Service: convert input to original format, submit converted input to original service, return a Job Resource that references the jobID

• Client: Subscribe to notifications from job resource

• Job Monitor (server): For all jobs, check status using jobID, notify client on completion

• Client library: Request output data

• Job Resource: Convert data from original format,Return converted data to client

Architecture of wrapped services

UML model of wrapped NCBI BLAST

UML model of wrapped InterProScan

Reused several data elements

•Green classes in diagram reused from IRWG

•Sequence, NucleicAcidSequence

•DatabaseCrossReference

•GeneGenomicIdentifier et al.

•Red UML classes in diagram reused from PIR

•ProteinSequence

•Partial reuse of attributes in ProteinDomainLocation

Example client NCBI Blast

NCBIBlastClient client = new NCBIBlastClient(url);NCBIBlastInput input = new NCBIBlastInput();ProteinSequenceRepresentation sequenceRepresentation = new ProteinSequenceRepresentation();ProteinGenomicIdentifier proteinId = new ProteinGenomicIdentifier();proteinId.setDataSourceName("uniprot");proteinId.setCrossReferenceId("wap_rat");sequenceRepresentation.setProteinId(proteinId);input.setSequenceRepresentation(sequenceRepresentation);NCBIBlastInputParameters params = new NCBIBlastInputParameters();params.setEmail("mannen@soiland-reyes.com");params.setQueryDatabase(new MolecularSequenceDatabase("", "uniprot"));params.setBlastProgram(BLASTProgram.BLASTP);input.setNcbiBLASTInputParameters(params);NCBIBlastClientUtils clientUtils = new NCBIBlastClientUtils(client);NCBIBlastOutput ncbiBlastOut = clientUtils.ncbiBlastSync(input, TIMEOUT_SECONDS * 1000);SequenceSimilarity[] similarities = ncbiBlastOut.getSequenceSimilarities();for (SequenceSimilarity similarity : similarities) { for (Alignment align : similarity.getAlignments()) { SequenceFragment querySequenceFragment = align.getQuerySequenceFragment(); System.out.print("Q: " + querySequenceFragment.getSequence().getValue()); (..)

data

id

Example SOAP input NCBI Blast

<service:NcbiBlastRequest xmlns:service="http://www.mygrid.org.uk/2009/cagrid/servicewrapper/service/NCBIBlast" xmlns="gme://Taverna-caGrid.caBIG/1.0/uk.org.mygrid.cagrid.domain.ncbiblast" xmlns:irwg="http://www.mygrid.org.uk/2009/cagrid/servicewrapper/imported/IRWG" xmlns:common="gme://Taverna-caGrid.caBIG/1.0/uk.org.mygrid.cagrid.domain.common" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <service:nCBIBlastInput> <NCBIBlastInput> <ncbiBLASTInputParameters> <blastProgram>BLASTP</blastProgram> <email>mannen@soiland-reyes.com</email> <queryDatabase> <common:name>uniprot</common:name> <common:description /> </queryDatabase> </ncbiBLASTInputParameters> <sequenceRepresentation xsi:type="irwg:ProteinSequenceRepresentation"> <irwg:proteinId> <irwg:crossReferenceId>wap_rat</irwg:crossReferenceId> <irwg:dataSourceName>uniprot</irwg:dataSourceName> </irwg:proteinId> </sequenceRepresentation> </NCBIBlastInput> </service:nCBIBlastInput></service:NcbiBlastRequest>

data

reused

id

Example client output NCBI BlastRunning NCBI Blast client

uk.org.mygrid.cagrid.servicewrapper.service.ncbiblast.example. ExampleNCBIBlastClient -url <service url> -- Using default service at http://cagrid.taverna.org.uk:8080/wsrf/services/cagrid/NCBIBlastCalling NCBI Blast synchronously (Set -DGLOBUS_LOCATION=/Users/bob/cagrid/ws-core-4.0.3 to do asynchronous client calls)Found 50 similaritiesSimilarity in uniprot:WAP_RAT (sequence length:137) 1 alignments Alignment score=763.0 bits=298.0 eValue=1.0E-79 Q: MRCSISLVLGLLALEVALARNLQEHVFNSVQSMCSDDSFSEDTECINCQTNEECAQNDMCCPSSCGRSCKTPVNIEVQKAGRCPWNPIQMIA AGPCPKDNPCSIDSDCSGTMKCCKNGCIMSCMDPEPKSPTVISFQ 1-137 P: MRCSISLVLGLLALEVALARNLQEHVFNSVQSMCSDDSFSEDTECINCQTNEECAQNDMCCPSSCGRSCKTPVNIEVQKAGRCPWNPIQMIA AGPCPKDNPCSIDSDCSGTMKCCKNGCIMSCMDPEPKSPTVISFQ M: MRCSISLVLGLLALEVALARNLQEHVFNSVQSMCSDDSFSEDTECINCQTNEECAQNDMCCPSSCGRSCKTPVNIEVQKAGRCPWNPIQMIA AGPCPKDNPCSIDSDCSGTMKCCKNGCIMSCMDPEPKSPTVISFQ 1-137Similarity in uniprot:Q3UQ94_MOUSE (sequence length:140) 1 alignments Alignment score=465.0 bits=183.0 eValue=4.0E-45 Q: MRCSISLVLGLLALEVALARNLQEHVFNSVQSMCSDDSFSEDTECINCQTNEECAQNDMCCPSSCGRSCKTPVNIEVQKAGRCPWNPIQMIA A-GPCPKDNPCSIDSDCSGTMKCCKNGCIMSCMDPEPKSPTVI 1-134 P: MRC ISLVLGLLALEVALA+NL+E VFNSVQSM S E TECI CQTNEECAQN MCCP SCGR+ KTPVNI V KAG CPWN +QMI+ + GPCP CS D +CSG MKCC C+M+C P P+ ++I M: MRCLISLVLGLLALEVALAQNLEEQVFNSVQSMFPKASPIEGTECIICQTNEECAQNAMCCPGSCGRTRKTPVNIGVPKAGFCPWNLLQMIS STGPCPMKIECSSDRECSGNMKCCNVDCVMTCTPPVPEVWSII 1-134

data id

Example SOAP output NCBI Blast<NCBIBlastOutput xmlns:xsd="http://www.w3.org/2001/XMLSchema" ...>

<sequenceSimilarities> <accessionNumber>P01174</accessionNumber> <description>Whey acidic protein OS=Rattus norvegicus GN=Wap PE=1 SV=2</description> <sequenceLength>137</sequenceLength> <sequenceId> <irwg:crossReferenceId>WAP_RAT</irwg:crossReferenceId> <irwg:dataSourceName>uniprot</irwg:dataSourceName> </sequenceId> <alignments> <bits>298.0</bits> <eValue>1.0E-79</eValue> <identity>100</identity> <positives>100</positives> <score>763.0</score> <sequenceSimilarityPattern>MRCSISLVLGLLALEVAL..ISFQ</sequenceSimilarityPattern> <matchSequenceFragment> <end>137</end> <start>1</start> <sequence> <irwg:value>MRCSISLVLGLLALEVAL..ISFQ</irwg:value> <irwg:valueInFastaFormat xsi:nil="true" /> </sequence> </matchSequenceFragment> <querySequenceFragment> <end>137</end> <start>1</start> <sequence> <irwg:value>MRCSISLVLGLLALEVAL..ISFQ</irwg:value> <irwg:valueInFastaFormat xsi:nil="true" /> </sequence> </querySequenceFragment> </alignments> </sequenceSimilarities> datareuse

did

Project info

•On gForge: https://gforge.nci.nih.gov/projects/taverna-cagrid/

•On myGrid wiki: http://www.mygrid.org.uk/dev/wiki/display/caGrid/Home

•Source and documentation available via Subversion: https://gforge.nci.nih.gov/svnroot/taverna-cagrid/