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The Functional Units

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

  1. 1. 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
  2. 2. Functional Unit (FU) <ul><li>Service description abstraction </li></ul><ul><li>Services as functional tasks </li></ul><ul><li>Independent from technology used </li></ul><ul><li>FU within the boundary of a service </li></ul>SOAP REST DAS OTHERS SERVICE FUNCTIONAL UNIT
  3. 3. Motivations <ul><li>Useful for tools and resources integration </li></ul><ul><li>Automated Life Science applications and workflow systems (Taverna, Kepler, Trident, KNIME …) </li></ul><ul><li>Estimates 3500+ public web services </li></ul>1-Web Services in the Life Sciences
  4. 4. 2-Web Services issues <ul><li>Not properly documented </li></ul><ul><li>Poorly annotated </li></ul><ul><li>Distributed </li></ul><ul><li>Hard to find </li></ul><ul><li>Hard to get how they work </li></ul><wsdl:message name=&quot;getGlimmersResponse&quot;> <wsdl:part name=&quot; getGlimmers Return&quot; type=&quot;xsd:string&quot;/> </wsdl:message> <wsdl:message name=&quot;aboutServiceRequest&quot;/> <wsdl:message name=&quot;getGlimmersRequest&quot;> <wsdl:part name=&quot;in0&quot; type=&quot;xsd:string&quot;/> <wsdl:part name= &quot;in1&quot; type=&quot;xsd:string&quot;/> <wsdl:part name=&quot; in2 &quot; type=&quot;xsd:string&quot;/> <wsdl:part name=&quot; in3 &quot; type=&quot;xsd:string&quot;/> <wsdl:part name=&quot; in4 &quot; type=&quot;xsd:string&quot;/> <wsdl:part name=&quot; in5 &quot; type=&quot;xsd:string&quot;/> <wsdl:part name=&quot; in6 &quot; type=&quot;xsd:string&quot;/> <wsdl:part name=&quot; in7 &quot; type=&quot;xsd:int&quot;/> <wsdl:part name=&quot;i n8 &quot; type=&quot;xsd:string&quot;/> Motivations e.g. a WSDL document
  5. 5. 3-Existing annotation frameworks <ul><li>SAWSDL (Semantic Annotations for WSDL) </li></ul><ul><li>WSMO (Web Service Modeling Ontology) </li></ul><ul><li>OWL-S </li></ul><ul><li>Feta </li></ul>Motivations
  6. 6. <ul><li>Annotation at the interface level </li></ul><ul><li>Tied to the service technology </li></ul><ul><li>Difficult for user to understand </li></ul><ul><li>Wrong level of abstraction </li></ul>Motivations 4-Shortcoming Existing frameworks
  7. 7. The BioCatalogue
  8. 8. The BioCatalogue <ul><li>A means to pool metadata about services </li></ul><ul><li>A means to discover and reuse services </li></ul><ul><li>A means to curate services </li></ul><ul><li>A platform for service monitoring and analytics </li></ul><ul><li>A generic service annotation model for community annotation </li></ul>
  9. 9. Truth about web services <ul><li>Different types and different behaviors: </li></ul><ul><li>Each operation performs a single domain related task e.g. KEGG web service </li></ul><ul><li>A single operation performs several domain related tasks => Polymorphic services e.g. searchSimple operation from BLAST web service by DDBJ </li></ul><ul><li>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 </li></ul>
  10. 10. FU by example <ul><li>1- One operation, one FU </li></ul><ul><li>1 Operation performs 1 domain related task </li></ul><ul><ul><li>KEGG </li></ul></ul><ul><ul><li>SABIO-RK </li></ul></ul><ul><ul><li>BioMoby </li></ul></ul><ul><ul><li>Etc… </li></ul></ul>Inputs Outputs Data resources FU aligned with service operation
  11. 11. FU by example <ul><li>2-One operation multiple FUs </li></ul><ul><li>e.g. SearchSimple from blast web service by DDBJ </li></ul>searchSimple PD: protein sequence database ND: nucleotide sequence database 5 FU for searchSimple query database program proteinBlast blastp protein PD nucleotideBlast blastn nucleotide ND proteinNucleotideBlast tblastn nucleotide ND nucleotideProteinBlast blastx protein PD nucleotideBlastFrameTranslation tblastx nucleotide ND
  12. 12. FU by example <ul><li>Multiple operation, one FU </li></ul><ul><li>Operations orchestration or pattern based </li></ul><ul><li>Asynchronous service </li></ul><ul><li>Server like services (e.g soaplab) </li></ul>FU for InterProScan Inputs Outputs Data resources Protein Motifs analysis Protein sequence Protein Motifs InterProScan FUNCTIONAL UNIT SOAP runInterProScan CheckStatus Get_XML_Result
  13. 13. FU by example <ul><li>Composite FUs </li></ul><ul><li>Task A + Task B = Task C </li></ul><ul><li>2 or more Functional Units </li></ul><ul><li>when combined can produce </li></ul><ul><li>another Functional Unit </li></ul>Inputs Outputs Data resources
  14. 14. <ul><li>Composite of the service properties </li></ul><ul><li>Input </li></ul><ul><li>Task </li></ul><ul><li>Output </li></ul><ul><li>Underlying data resources </li></ul>FU defined Inputs Outputs Data resources
  15. 15. Specifying the FU <ul><li>We used: </li></ul><ul><li>An OWL-based semantic annotation </li></ul><ul><li>The myGrid ontology for core annotation vocabulary </li></ul>
  16. 16. Specifying the FU by example <ul><li>Describing a KEGG operation (getEnzymeByGene) as FU </li></ul>
  17. 17. Specifying the FU by example <ul><li>Describing a pattern based service (e.g. interProScan) as FU </li></ul>
  18. 18. FU usefulness <ul><li>Identify domain relevant operations from a given service </li></ul><ul><li>Same level of abstraction as the user </li></ul><ul><li>Enhance service discovery </li></ul><ul><li>Conceal service technology </li></ul><ul><li>Workflow composition </li></ul>
  19. 19. Cost of identifying the FU <ul><li>Yet another ‘thing’ to annotate </li></ul><ul><li>triple the curation effort </li></ul><ul><li>Rely on the curators to identify the FUs </li></ul><ul><li>Domain knowledge required </li></ul>
  20. 20. To reduce the cost <ul><li>Use existing pool of workflows available at myExperiment </li></ul> <ul><li>Use existing tool such as QuASAR </li></ul><ul><li>Encourage Web Service providers </li></ul>
  21. 21. Summary <ul><li>Abstraction handle the diversity of service type (SOAP, REST) and behaviors </li></ul><ul><li>Concrete example of how to use the service </li></ul><ul><li>Enhance web service annotation </li></ul><ul><li>Enhance web service discovery </li></ul><ul><li>Development of FU by the BioCatalogue team ongoing </li></ul>
  22. 22. Acknowledgments <ul><li>Jiten Bhagat </li></ul><ul><li>School of Computer Science, University of Manchester (UK) </li></ul><ul><li>Eric Nzuobontane, Thomas Laurent, Rodrigo Lopez </li></ul><ul><li>EMBL European Bioinformatics Institute, Cambridge (UK) </li></ul>