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Gordon Semantic Web 2008

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The document discusses using semantic web technologies to make data transformations and analysis workflows more reusable. It describes how Moby, an open source ontology, allows data transformations to be treated as reusable commodities. This enables moving up an "abstraction gradient" towards more user-friendly workflow systems using techniques like parameterized batch execution that require fewer explicit notations. The goal is to make analysis workflows more accessible and modifiable for researchers.

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How Can We Use This Semantic Web Thing? Paul Gordon Sun Center of Excellence for Visual Genomics University of Calgary
Desiderata ,[object Object],[object Object],[object Object]
Web Services Today
What’s Moby?
Semantics & Semiotics Semiotic Triangle from The Meaning of Meaning (1923) Concept Deoxyribonucleic Acid ADN (French) (Simplified Chinese)... Words Things
Where are we going? Seahawk
traceview vectorstrip trimseq
Paul’s Pragmatic Maxims ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
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
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> … <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;
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
User-Friendly? * Apologies to Aleksi Kallio, presenting tomorrow 12 Actual 148 “User study” 8310 “User friendly”* Source: Google Scholar
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
Viscosity Dimension Consistency Amongst and Between Groups Visibility (2)‏ Story content Modifiability Controllability Referencability Programming salience Provisionality Communicative Cognitive Visibility (1)‏
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.
The Plug ,[object Object],[object Object],[object Object]
Ω

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Gordon Semantic Web 2008

  • 1. How Can We Use This Semantic Web Thing? Paul Gordon Sun Center of Excellence for Visual Genomics University of Calgary
  • 2.
  • 3. Web Services Today
  • 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
  • 8.
  • 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
  • 11. ACDServlet web.xml trimseq.acd Rule selection 2 nd -ary parameter creation mobyInput DNASequence … mobyOutput DNASequence …
  • 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.
  • 23. Ω