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Gordon Semantic Web 2008

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  • 1. How Can We Use This Semantic Web Thing? Paul Gordon Sun Center of Excellence for Visual Genomics University of Calgary
  • 2. Desiderata
    • Something that doesn’t require reprogramming my business logic: notations
    • Something that lets me reuse others’ code: commoditization
    • Something my lets my users bug me less: workflows
  • 3. Web Services Today
  • 4. What’s Moby?
  • 5. Semantics & Semiotics Semiotic Triangle from The Meaning of Meaning (1923) Concept Deoxyribonucleic Acid ADN (French) (Simplified Chinese)... Words Things
  • 6. Where are we going? Seahawk
  • 7. traceview vectorstrip trimseq
  • 8. Paul’s Pragmatic Maxims
    • You cannot get rid of work
    • Redistribute work amongst parties
      • Who’s most motivated?
      • Who’s most knowledgeable?
    • Avoid repetition of work
      • Accessibility of code
      • Reusability of code
    • Self-containment (~10MB WAR) via custom ClassLoader
  • 9. Obsoleted User domain knowledge HTML Form input restrictions SAWSDL markup ACD command-line spec Moby Ontology Leveraged Semantic monitoring of user actions Auto-spec of secondaries, rule lookup Concept-URN to schema-mapping res. MOB & DEM rules Moby-specific Java annotations New Tech. MOB rules + user hints MOB rules + HTML class attributes* MOB or XSLT on returned XML MOB rules on returned data files N/A Legacy-to-Moby data DEM rules DEM rules DEM rules DEM rules N/A Moby-to-legacy data HTTP CGI HTTP CGI HTTP SOAP Command-line jMoby API I/O Exec. Example usage with typed data HTML form fields’ class attribute Extra tags in WSDL Servlet web.xml properties Java annotation Semantics Specific legacy formats (implicit) Specific legacy formats (implicit) Schema-defined XML in the WSDL Specific legacy formats (explicit in ACD file) Moby types, as specified by the Java annotation Expected I/O HTML form HTML form WSDL file ACD file Java code Source Spec. ← (-) External code reuse (+) -> PBEServlet CGIServlet WSDLServlet ACDServlet MobyServlet Easier for na ïve users -> Skeleton code generation Custom data parsers “ Shim” Services Screen scrapers Explicit semantic markup
  • 10. MobyServlet
  • 11. ACDServlet web.xml trimseq.acd Rule selection 2 nd -ary parameter creation mobyInput DNASequence … mobyOutput DNASequence …
  • 12. MOB rules
  • 13. WSDLServlet
  • 14. WSDL Notation
  • 15. bioxml.info
  • 16. CGIServlet <form …> … <textarea name=&quot;input_text&quot; cols=&quot;61&quot; rows=&quot;5&quot; ></textarea> … <input type=&quot;text&quot; size=&quot;7&quot; name=&quot;salt_conc&quot; value=&quot;0.05&quot; /> … </form> <html xmlns:moby=“http://www.biomoby.org/moby”…> <head> … … <meta name=&quot;moby:service&quot; scheme=&quot;http://moby.ucalgary.ca/moby/MOBY-Central.pl&quot; content=&quot;Primers,moby.ucalgary.ca,CalcPCRPrimers: Takes a DNA sequence and calculates PCR probes satisfying a given set of conditions &quot;/> class=&quot;moby:CalcPCRPrimers:primers:Collection(DNASequence)” class=&quot;moby:sequence:DNASequence:fasta&quot; class=&quot;moby::Float::[0,10]&quot; alt=&quot;Na+ concentration (molar)&quot;
  • 17. PBEServlet: user-driven examples Legacy non-XML apps HTML + declarative “MOB” and “DEM” rules + user drag ‘n’ drop Seahawk Proxied Web page Seahawk AJAX prompting Drag ‘n’ drop
  • 18. User-Friendly? * Apologies to Aleksi Kallio, presenting tomorrow 12 Actual 148 “User study” 8310 “User friendly”* Source: Google Scholar
  • 19. Abstraction Gradient Closeness of Mapping Consistency Diffuseness Error-Proneness Hard Mental Operations Hidden Dependencies Premature Commitment Progressive Evaluation Role-Expressiveness Secondary Notation Cognitive Dimension Consistency Amongst and Between Groups Agree Disagree Neither
  • 20. Viscosity Dimension Consistency Amongst and Between Groups Visibility (2)‏ Story content Modifiability Controllability Referencability Programming salience Provisionality Communicative Cognitive Visibility (1)‏
  • 21. Interest in the Given Workflows Seeing analysis workflow descriptions in published research you read? Using a library of pre-built workflows to Run your analysis in this tool? Developing your own workflows again, with this tool? Modifying pre-built workflows in this tool, for your own purpose? Despite general lacklustre interest in EUD, interest in domain specific workflows is high.
  • 22. The Plug
    • Increasingly abstract notations, until no notations at all (PBE)
    • Made possible by Moby ontology, turning data transformations into reusable commodities (open source)
    • A gentle slope into workflows, with user-defined functions
  • 23.

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