The Functional Units:Abstractions for Web Service Annotation

Paolo Missier Katy Wolstencroft Franck Tanoh Peter Li

Sean Bechhofer Khalid Belhajjame Steve Pettifer Carole Goble

School of Computer Science, University of Manchester (UK)

SWF 2010

Functional Unit (FU)

• Service description abstraction • Services as functional tasks• Independent from technology used • FU within the boundary of a service

SOAPSOAP RESTREST DASDAS OTHERSOTHERSSERV

ICE FUNCTIONAL UNIT

Motivations

• Useful for tools and resources integration• Automated Life Science applications and workflow

systems (Taverna, Kepler, Trident, KNIME…)• Estimates 3500+ public web services

1-Web Services in the Life Sciences

2-Web Services issues

• Not properly documented• Poorly annotated • Distributed• Hard to find • Hard to get how they work

<wsdl:message name="getGlimmersResponse"> <wsdl:part name="getGlimmersReturn"

type="xsd:string"/> </wsdl:message> <wsdl:message name="aboutServiceRequest"/> <wsdl:message name="getGlimmersRequest"> <wsdl:part name="in0" type="xsd:string"/> <wsdl:part name="in1" type="xsd:string"/> <wsdl:part name="in2" type="xsd:string"/> <wsdl:part name="in3" type="xsd:string"/> <wsdl:part name="in4" type="xsd:string"/> <wsdl:part name="in5" type="xsd:string"/> <wsdl:part name="in6" type="xsd:string"/> <wsdl:part name="in7" type="xsd:int"/> <wsdl:part name="in8" type="xsd:string"/>

Motivations

e.g. a WSDL document

3-Existing annotation frameworks

• SAWSDL (Semantic Annotations for WSDL)

• WSMO (Web Service Modeling Ontology)

• OWL-S • Feta

Motivations

• Annotation at the interface level • Tied to the service technology • Difficult for user to understand • Wrong level of abstraction

Motivations

4-Shortcoming Existing frameworks

The BioCatalogue

http://www.biocatalogue.org/

The BioCatalogue

• A means to pool metadata about services• A means to discover and reuse services• A means to curate services• A platform for service monitoring and analytics• A generic service annotation model for community

annotation

Truth about web services

Different types and different behaviors: • Each operation performs a single domain

related task e.g. KEGG web service

• A single operation performs several domain related tasks => Polymorphic services e.g. searchSimple operation from BLAST web service by DDBJ

• Multiple operation of the same service combined in a manner to perform a single domain related task => operation patterns e.g. InterProScan web service by EBI

FU by example

• 1- One operation, one FU 1 Operation performs 1 domain related task

• KEGG • SABIO-RK• BioMoby • Etc…

Inputs

Outputs

Data resources

FU aligned with service operation

query database program

searchSimple

FU by example

• 2-One operation multiple FUse.g. SearchSimple from blast web service by DDBJ

PD: protein sequence databaseND: nucleotide sequence database

proteinBlast

blastp proteinPD

nucleotideBlast

blastn nucleotide ND

proteinNucleotideBlast

tblastn nucleotideND

nucleotideProteinBlast

blastx protein PD

nucleotideBlastFrameTranslation

tblastx nucleotide ND

5 FU for searchSimple

FU by example

• Multiple operation, one FU• Operations orchestration or pattern based• Asynchronous service• Server like services (e.g soaplab)

Inputs

Outputs

Data resources

Protein Motifs analysis

Protein sequence

Protein Motifs

Inte

rPro

Scan

FUNCTIONAL UNIT

SOAPrunInterProScan CheckStatus Get_XML_Result

FU for InterProScan

FU by example

• Composite FUs Task A + Task B = Task C2 or more Functional Units when combined can produceanother Functional Unit

Inputs

Outputs

Data resources

Composite of the service properties • Input • Task• Output • Underlying data resources

FU defined

Inputs

Outputs

Data resources

Specifying the FU

We used: • An OWL-based semantic annotation• The myGrid ontology for core annotation

vocabulary

Specifying the FU by example

• Describing a KEGG operation (getEnzymeByGene) as FU

Specifying the FU by example

• Describing a pattern based service (e.g. interProScan) as FU

FU usefulness

• Identify domain relevant operations from a given service

• Same level of abstraction as the user • Enhance service discovery • Conceal service technology • Workflow composition

Cost of identifying the FU

• Yet another ‘thing’ to annotate • triple the curation effort • Rely on the curators to identify the FUs• Domain knowledge required

To reduce the cost • Use existing pool of workflows available at myExperiment

http://www.myexperiment.org/

•Use existing tool such as QuASAR

•Encourage Web Service providers

Summary

• Abstraction handle the diversity of service type (SOAP, REST) and behaviors

• Concrete example of how to use the service• Enhance web service annotation • Enhance web service discovery • Development of FU by the BioCatalogue team

ongoing

Acknowledgments

• Jiten Bhagat, Mannie Tagarira, Sergejs AleksejevsSchool of Computer Science, University of Manchester (UK)

• Eric Nzuobontane, Thomas Laurent, Rodrigo LopezEMBL European Bioinformatics Institute, Cambridge (UK)

• Jerzy OrlowskiLaboratory of Bioinformatics and Protein Engineering,International Institute of Molecular and Cell Biology in Warsaw,Poland