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I. Lumb , J. Lederman, J. Freemantle & K. Aldridge HPCS 2007

Semantically Enabling the Global Geodynamics Project: Incorporating Feature-Based Annotations via XML Pointer Language (XPointer). I. Lumb , J. Lederman, J. Freemantle & K. Aldridge HPCS 2007. Representing GGP Data via ESML and RDF. Lumb & Aldridge (2005, 2006). Involved usage of XSLT

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I. Lumb , J. Lederman, J. Freemantle & K. Aldridge HPCS 2007

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  1. Semantically Enabling the Global Geodynamics Project: Incorporating Feature-Based Annotations via XML Pointer Language (XPointer) I. Lumb, J. Lederman, J. Freemantle & K. Aldridge HPCS 2007

  2. Representing GGP Data via ESML and RDF Lumb & Aldridge (2005, 2006)

  3. Involved usage of XSLT Even more complicated when RDF representations are taken into account Features are difficult to describe Especially those that cross-cut ESML element boundaries Features are difficult to correlate to primary and auxilliary data How is GGP Log Data Handled? Filename ST970910.LOG Station Strasbourg, France Instrument GWR C026 Author (jhinderer@eost.u-strasbg.fr) yyyymmdd hhmmss comment C******************************************** 77777777 ... 19990705 050330 15 microgal offset of unknown origin ... 19990712 220610 power loss due to lightening strike ...

  4. Can GGP Log Data be Better Represented? • Options • Re-purpose existing ESML elements • Extend the ESML Schema • Consequences • Not vanilla ESML anymore • An ‘enhanced ESML’ • ESML gets more complicated • RDF representations are also more complicated • Features aren't necessarily nested • Features cross-cut ESML element boundaries • This is a showstopper!!

  5. Consider Annotation • ESML has a limited ability to represent features • Features (especially complex ones) don’t necessarily obey XML element boundaries • Likely true for all XML dialects - including DFDL • “Annotations are comments, notes, explanations, or other types of external remarks that can be attached to a Web document or a selected part of the document. As they are external, it is possible to annotate any Web document independently, without needing to edit that document. From the technical point of view, annotations are usually seen as [editorial] metadata, as they give additional information about an existing piece of data.” • Amaya 9.52, W3C

  6. http://www.w3.org/Amaya/ See also Annozilla (Annotea on Mozilla), http://annozilla.mozdev.org/

  7. Annotating a Complex Selection (1) <?xml version="1.0" ?> <r:RDF xmlns:r="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:a="http://www.w3.org/2000/10/annotation-ns#" xmlns:t="http://www.w3.org/2001/03/thread#" xmlns:http="http://www.w3.org/1999/xx/http#" xmlns:d="http://purl.org/dc/elements/1.1/"> This is RDF-based!!

  8. Annotating a Complex Selection (2) <r:Description> <r:type r:resource="http://www.w3.org/2000/10/annotation-ns#Annotation" /> <r:type r:resource="http://www.w3.org/2000/10/annotationType#Example" /> <a:annotates r:resource="http://www.eas.slu.edu/GGP/ggpas.html" /> <a:context>http://www.eas.slu.edu/GGP/ggpas.html #xpointer(start-point(string-range(/html[1]/body[1]/table[3]/tr[1]/td[1]/pre[1],"",658,1)) /range-to(end-point(string-range(/html[1]/body[1]/table[3]/tr[1]/td[1]/pre[2],"",65,1)))) </a:context> <d:title>Annotation of Agreements and Standards</d:title> <d:creator>ian@yorku.ca</d:creator> <a:created>2006-10-25T10:31:44+521773:43</a:created> <d:date>2006-10-25T10:32:43+521773:43</d:date> <a:body r:resource="file:///Users/ian/.amaya/annotations/annotj0lF0n.html" /> </r:Description>

  9. XPointer - XML Pointer Language • An extension of XPath • XPath is used by XLink to locate remote link resources • Relative addressing • Allows links to places with no anchors • Flexible and robust • XPointer/XPath expressions often survive changes in the target document • Can point to substrings in character data and to whole tree fragments • Status • The key specification is a Working Draft in the W3C’s Recommendation Track http://www.w3.org/TR/xptr-xpointer/

  10. Representing GGP Data via ESML and RDF Lumb & Aldridge (2005, 2006)

  11. Representing GGP Data via ESML and RDF with Annotation

  12. Self-Contained Annotated Informal Ontology … BUT • The representation will likely require use of OWL Full • Computationally incomplete • May not be able to infer valid conclusions • Undecidable • May not be able to make inferences in a finite amount of time • To ensure OWL Description Logic representation • Ontologies and their external annotations may need to remain separate Lumb et al., submitted to Computers & Geosciences (2007)

  13. Summary • Automate the introduction of a self-describing representation • Use an XML-based approach • Automate the extraction of relationships • Use RDF to represent relationships • Use GRDDL to extract relationships • Describe and relate features via annotation • XPointer is a standards-based vehicle • Use annotation tools (like Amaya or Annozilla) to automate wherever possible • Integrate annotations into ontology (?) • Transform data into information into knowledge

  14. Future Work • Replace ESML by DFDL (?) • Develop single schema for annotation types/properties • XPointer and OWL each have their own • Semantically base annotations • Automate annotation • Transform RDF to OWL • Extract OWL classes, properties and individuals from RDF-based representations • Develop tools • W3C strategy specified • Ontology/annotation integration

  15. Questions?

  16. Additional Slides

  17. Earth Science Markup Language (ESML) • Makes use of XML Schema • Supports semi-structured ASCII format files • Includes Earth-Science affinities • Being used in various projects • GGP to LEAD • On track for standards compliance • Data Format Description Language (DFDL) • An Open Grid Forum (OGF) Working Group and emerging recommendation http://esml.itsc.uah.edu http://forge.gridforum.org/projects/dfdl-wg

  18. ESML Handles GGP Data via a Template • <Array occurs = “2” > • <Header name = “_Filename” format = “%20s” /> • <Header name = “Filename” format = “%20s” /> • </Array> • : • . • <Array occurs = “FROM PREPROCESSOR”> • <Array occurs = “4”> • <Field name = “TimeYMD” format = “%8d” /> • <Field name = “TimeHMS” format = “%6d” /> • <Field name = “Gravity” format = “%10.6f” /> • <Field name = “Pressure” format = “%10.6f” /> • </Array> • </Array> Filename ST970910.GGP Station Strasbourg, France Instrument GWR C026 Phase Lag (deg/cpd) 0.1500 0.0100 nominal N Latitude (deg) 48.6220 0.0010 estimated E Longitude (deg) 7.6840 0.0010 estimated Height (m) 180.0000 1.0000 estimated Gravity Cal (mgal/v) -792.0000 1.0000 measured Pressure Cal(mbar/v) 200.0000 1.0000 nominal Author (jhinderer@eost.u-strasbg.fr) yyyymmdd hhmmss gravity(V) pressure(V) C******************************************** 77777777 19970901 000000 0.075913 0.420192 ...

  19. Consider an External Scheme via Annotation • ESML has a limited ability to represent features • Features don’t necessarily obey XML element boundaries • Likely true for all XML dialects • Including DFDL (!) • “Annotation is the linking of a new commentary node to someone else's existing node. It is the essence of a collaborative hypertext.” • TBL, W3 Archive, c. 1990 • "... the addition of information to existing documents without changing the originals.” • Passin, Explorer’s Guide to the Semantic Web, 2004 • Editorial metadata • Current work

  20. ‘infer’ ‘compare’ ‘relate’ ‘describe’ The stack of expressive power After http://www.w3.org/2005/Talks/0517-boit-tbl/#[27]

  21. Automating Annotation • Quick-and-dirty solution • Perl script • CPAN offers a number of XML-targeted Perl modules … • More-appropriate solution • Leverage the XML family • XPath/XQuery • To help ‘place’ the selection in the document to be annotated • XPointer my also be useful here • XPointer • To annotate the selection

  22. 3C454.3 http://www.aoc.nrao.edu/aips/

  23. Courtesy Ross Baker, York University

  24. Annotations are Everywhere! • Analog • Post-its • Digital • Productivity software • Office Comments • Microsoft Word (Live), Open Office, Google Docs … • Web • Browser-based mouse-overs • Google Notebook, Google Earth • Amaya • Source code • OpenMP directives

  25. Lumb et al. (2007)

  26. Mozilla DOM Inspector

  27. Modeling with Formal Ontologies • Seek to make use of OWL Description Logic • Maximally expressive • Computational complete • All valid conclusions can be inferred • Decidable • The inferences take a finite amount of time • OWL DL constrains annotation properties • Annotations are well-behaved comments • Caution • XPointer-based annotations are highly likely to violate OWL DL constraints on integration tnto ontologies • Results in OWL Full Lumb et al. (2007)

  28. Origin/Destination: ESML vs. XPointer

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