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The Functional Units presented by Franck Tanoh at IEEE 2010 Fourth International Workshop on Scientific Workflows (SWF 2010)
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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