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

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Representing GGP Data via ESML and RDF

Lumb & Aldridge (2005, 2006)

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Filename ST970910.LOGStation Strasbourg, FranceInstrument GWR C026Author (jhinderer@eost.u-strasbg.fr)yyyymmdd hhmmss commentC********************************************77777777...19990705 050330 15 microgal offset of unknown origin...19990712 220610 power loss due to lightening strike...

How is GGP Log Data Handled?

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

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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!!

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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

http://www.w3.org/Amaya/

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

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<?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/">

Annotating a Complex Selection (1)

This is RDF-based!!

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<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>

Annotating a Complex Selection (2)

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XPointer - XML Pointer Language

An extension of XPath – XPath is used by XLink to locate remote link

resourcesRelative addressing

– Allows links to places with no anchorsFlexible 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/

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Representing GGP Data via ESML and RDF

Lumb & Aldridge (2005, 2006)

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Representing GGP Data via ESML and RDF with Annotation

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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)

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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

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Future Work

Replace ESML by DFDL (?)Develop single schema for annotation types/properties

– XPointer and OWL each have their own

Semantically base annotationsAutomate annotationTransform RDF to OWL

– Extract OWL classes, properties and individuals from RDF-based representations

– Develop tools • W3C strategy

specified

Ontology/annotation integration

Questions?

Additional Slides

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Makes use of XML SchemaSupports semi-structured ASCII format filesIncludes Earth-Science affinitiesBeing 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

Earth Science Markup Language (ESML)

http://forge.gridforum.org/projects/dfdl-wg

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Filename ST970910.GGPStation Strasbourg, FranceInstrument GWR C026Phase Lag (deg/cpd) 0.1500 0.0100 nominalN Latitude (deg) 48.6220 0.0010 estimatedE Longitude (deg) 7.6840 0.0010 estimatedHeight (m) 180.0000 1.0000 estimatedGravity Cal (mgal/v) -792.0000 1.0000 measuredPressure Cal(mbar/v) 200.0000 1.0000 nominalAuthor (jhinderer@eost.u-strasbg.fr)yyyymmdd hhmmss gravity(V) pressure(V)C********************************************77777777 19970901 000000 0.075913 0.420192...

<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>

ESML Handles GGP Data via a Template

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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, 2004Editorial metadata

– Current work

‘describe’

‘relate’

‘compare’

‘infer’The stack of expressive power

After http://www.w3.org/2005/Talks/0517-boit-tbl/#[27]

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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

http://www.aoc.nrao.edu/aips/

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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

Lumb et al. (2007)

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Mozilla DOM Inspector

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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)

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Origin/Destination: ESML vs. XPointer