How Can We Use This Semantic Web Thing? Paul Gordon Sun Center of Excellence for Visual Genomics University of Calgary
Desiderata <ul><li>Something that doesn’t require reprogramming my business logic:  notations </li></ul><ul><li>Something ...
Web Services  Today
What’s Moby?
Semantics  &  Semiotics Semiotic Triangle from  The Meaning of Meaning  (1923) Concept Deoxyribonucleic Acid ADN  (French)...
Where are we going?  Seahawk
traceview vectorstrip trimseq
Paul’s Pragmatic Maxims <ul><li>You cannot get rid of work </li></ul><ul><li>Redistribute work amongst parties </li></ul><...
Obsoleted User domain knowledge HTML Form input restrictions SAWSDL markup ACD command-line spec Moby Ontology Leveraged S...
MobyServlet
ACDServlet web.xml trimseq.acd Rule selection 2 nd -ary parameter creation mobyInput  DNASequence … mobyOutput DNASequence …
MOB rules
WSDLServlet
WSDL Notation
bioxml.info
CGIServlet <form   …> … <textarea name=&quot;input_text&quot; cols=&quot;61&quot; rows=&quot;5&quot;  ></textarea> … <inpu...
PBEServlet: user-driven examples Legacy non-XML apps HTML + declarative “MOB” and “DEM” rules  + user drag ‘n’ drop Seahaw...
User-Friendly? * Apologies to Aleksi Kallio, presenting tomorrow 12 Actual 148 “User study” 8310  “User friendly”* Source:...
Abstraction Gradient Closeness of Mapping Consistency Diffuseness Error-Proneness Hard Mental Operations Hidden Dependenci...
Viscosity Dimension Consistency Amongst and Between Groups Visibility (2)‏ Story content Modifiability Controllability Ref...
Interest in the Given Workflows Seeing analysis workflow descriptions in  published research you read? Using a library of ...
The Plug <ul><li>Increasingly abstract notations, until no notations at all (PBE) </li></ul><ul><li>Made possible by Moby ...
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Gordon Semantic Web 2008

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Gordon Semantic Web 2008

  1. 1. How Can We Use This Semantic Web Thing? Paul Gordon Sun Center of Excellence for Visual Genomics University of Calgary
  2. 2. Desiderata <ul><li>Something that doesn’t require reprogramming my business logic: notations </li></ul><ul><li>Something that lets me reuse others’ code: commoditization </li></ul><ul><li>Something my lets my users bug me less: workflows </li></ul>
  3. 3. Web Services Today
  4. 4. What’s Moby?
  5. 5. Semantics & Semiotics Semiotic Triangle from The Meaning of Meaning (1923) Concept Deoxyribonucleic Acid ADN (French) (Simplified Chinese)... Words Things
  6. 6. Where are we going? Seahawk
  7. 7. traceview vectorstrip trimseq
  8. 8. Paul’s Pragmatic Maxims <ul><li>You cannot get rid of work </li></ul><ul><li>Redistribute work amongst parties </li></ul><ul><ul><li>Who’s most motivated? </li></ul></ul><ul><ul><li>Who’s most knowledgeable? </li></ul></ul><ul><li>Avoid repetition of work </li></ul><ul><ul><li>Accessibility of code </li></ul></ul><ul><ul><li>Reusability of code </li></ul></ul><ul><li>Self-containment (~10MB WAR) via custom ClassLoader </li></ul>
  9. 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. 10. MobyServlet
  11. 11. ACDServlet web.xml trimseq.acd Rule selection 2 nd -ary parameter creation mobyInput DNASequence … mobyOutput DNASequence …
  12. 12. MOB rules
  13. 13. WSDLServlet
  14. 14. WSDL Notation
  15. 15. bioxml.info
  16. 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. 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. 18. User-Friendly? * Apologies to Aleksi Kallio, presenting tomorrow 12 Actual 148 “User study” 8310 “User friendly”* Source: Google Scholar
  19. 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. 20. Viscosity Dimension Consistency Amongst and Between Groups Visibility (2)‏ Story content Modifiability Controllability Referencability Programming salience Provisionality Communicative Cognitive Visibility (1)‏
  21. 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. 22. The Plug <ul><li>Increasingly abstract notations, until no notations at all (PBE) </li></ul><ul><li>Made possible by Moby ontology, turning data transformations into reusable commodities (open source) </li></ul><ul><li>A gentle slope into workflows, with user-defined functions </li></ul>
  23. 23.

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