1. Simon Cox Research Scientist 16 April 2008
Standards-based methodology for developing a geoscience markup language
Markup languages have been developed for data transfer in a variety of earth science disciplines. Most of these have been developed using an informal methodology – typically guided by a data model implicitly defined in some existing document or database, but with the XML schema often designed directly using ad-hoc patterns, or sometimes created automatically by some proprietary toolkit. This often leads to a language that is efficient for a single application or within a workgroup or community, but with limited scope for interoperability across domain boundaries. The latter is a serious constraint to the use of data from diverse sources in cross-disciplinary investigations.
A uniform methodology, based on standards published by Open Geospatial Consortium and ISO, has been developed and applied in the design of GeoSciML. The method is based on the Object Management Group’s Model Driven Architecture (MDA), with model design in UML using the General Feature Model from ISO 19109, the use of components from other standards in the ISO series, and production of the XML schema following the encoding rules specified in ISO The resultant encoding shows a literal and explicit relationship to the UML model. This is unlikely to be as compact as hand-coded special cases, but is consistently structured across similar models. Full structure and meaning is preserved, and compactness is easily dealt with using standard compression techniques. Furthermore, the use of standard components for elements that are common across domains ensures maximum interoperability.
To assist in the use of this methodology, we have developed two tools:
“HollowWorld” – a UML template with ISO components, stereotypes, and tags pre-loaded, plus some other cross-domain components;
“FullMoon” – a UML processing framework, based on application of sets of rules against the XMI representation of a model.
We use a UML design tool that allows direct binding to one or more SVN repositories. These host the various UML packages that are under separate governance arrangements. This overcomes an important limitation of most UML-based methodologies, which effectively treat the entire model as a single artefact.
Three rule-sets are available For FullMoon:
validating the UML model with respect to the profile described in ISO 19136
generating GML-conformant XML schema according to the rules in ISO 19136
generating human-readable documentation of the model, in the form of an HTML frameset.
Use of these tools has allowed the GeoSciML team to develop and maintain the model as a single normative artefact (XMI). Implementation views in XML Schema and HTML documentation are generated automatically at significant release points. This addresses two key issues with ad-hoc approaches: ensuring normative and descriptive content are consistent across maintenance activities, and the ability to support convenient cross-reference between the conceptual model and the XML encoding.
Simon Cox
Research Scientist
16 April 2008

2. Outline The problem GeoSciML Re-use and delegation patterns
Tooling to support methdology
Summary
CSIRO EGU-2008-A Cox Standards-based methodology

3. The problem
CSIRO EGU-2008-A Cox Standards-based methodology

4. The problem Typical markup language strategy: XML is a meta-language
Manually crafted schema
Implicit data model from existing db or processing service
Ad-hoc xml patterns
Single use-case
 no interoperability
XML is a meta-language
Syntactic vs structural or semantic interoperability
CSIRO EGU-2008-A Cox Standards-based methodology

5. A better way Model-driven, standards-based
UML formalization
Automatic transformation to implementation platform (e.g. XML)
Standard meta-model
ISO General Feature Model + Coverage
Standard X-domain components
Geometry, CRS, Temporal
Observations, Sampling Features
Formally governed vocabularies
Published in online registers
CSIRO EGU-2008-A Cox Standards-based methodology

6. GeoSciML
CSIRO EGU-2008-A Cox Standards-based methodology

7. GeoSciML A language for exchange of geoscience information
UML logical model
XML transfer encoding
Scope: interpreted geology and supporting observations
MappedFeature, GeologicUnit, GeologicStructure, Fossil, Geologic timescale, Borehole, Observation, etc
i.e. information required to maintain geologic maps
Design in pictures – but using a formal notation: Unified Modeling Language UML
Automatic transformation into an XML Schema
XML document format is for data transfer uses
Geology model, not geological-map model
Maps are views of the world, projected or sampled on a particular plane etc.
CSIRO EGU-2008-A Cox Standards-based methodology

8. GeologicUnit A core part of the model: Geologic Unit
Some “simple” attributes, plus some complex properties (associations).
Specializations as LithologicUnit, ChronostratigraphicUnit, DeformationUnit (maybe more to come).
CSIRO EGU-2008-A Cox Standards-based methodology

9. Use of standards
CSIRO EGU-2008-A Cox Standards-based methodology

10. MappedFeature ISO 19109 Feature Model ISO 19107 Geometry
ISO Metadata
OGC Sampling Model
How does the use of this framework show up?
Click
Use of standard UML stereotypes ( specific encoding patterns)
Reference to standard external components
E.g. Geometry GM_Object (from ISO 19107), metadata MD_Metadata (from ISO 19115), SamplingFeatures (from OGC O&M)
CSIRO EGU-2008-A Cox Standards-based methodology

11. Boreholes, outcrops and specimens
ISO/OGC Sampling Model
ISO/OGC Observation model
CSIRO EGU-2008-A Cox Standards-based methodology

12. Borehole logs ISO/OGC Sampling Model ISO/OGC Coverage Model
CSIRO EGU-2008-A Cox Standards-based methodology

13. Orderly delegation of responsibility
Interoperability levels:
Schematic/model – common XML Schema
GeoScML v2.0 - see other paper in this conference
Semantic – common vocabularies
CGI GeoSciML provides the data structure
E.g. LithostratigraphicUnit is a kind of GeologicFeature with the properties “preferredAge”, “classifier”, “beddingPattern” etc
Data providers use appropriate vocabs and reference systems
See SOA/Registry paper
GeoSciML model/schema defines a the data structures – to quite a high degree of detail,
But the data values in many cases can be scoped “at run time” to a specific vocabulary, scale, etc
i.e. the governance of scales, vocabularies, etc are delegated to the data provider
Though for maximum interoperability it is recommended to use published, well-governed vocabularies etc.
CSIRO EGU-2008-A Cox Standards-based methodology

14. Example Most property values are references to registers
<MappedFeature>     …     <observationMethod> <CGI_TermValue>
            <value codeSpace="urn:cgi:classifierScheme:GA:1MillionGeology_ObservationMethods“ >GSNSW785</value>
        </CGI_TermValue></observationMethod>     <positionalAccuracy> <CGI_NumericValue>
            <principalValue uom="urn:ogc:def:uom:UCUM:m">500</principalValue>
        </CGI_NumericValue> </positionalAccuracy>
    <samplingFrame xlink:href="urn:cgi:classsifier:GA:SurfaceGeologyOfEasternAustralia_1MillionScale"/>
     <specification>         <LithologicUnit >             <gml:description>Mafic volcaniclastic sandstone, siltstone, shale, chert; minor limestone, conglomerate</gml:description>
            <gml:name codeSpace="urn:cgi:classifierScheme:GA:StratigraphicLexicon:Unitname“ >Kabadah Formation</gml:name>
            <gml:name codeSpace="urn:cgi:classifierScheme:GA:StratigraphicLexicon:Map_symbol“ >Ojck</gml:name>             <gml:name codeSpace="urn:ietf:rfc:2141">urn:cgi:feature:GA:Stratno:29570</gml:name>
            <observationMethod> <CGI_TermValue>
                    <value codeSpace="urn:cgi:classifierScheme:GA:ObservationMethods“ >published description</value>
                </CGI_TermValue> </observationMethod>             <purpose>typicalNorm</purpose>             <preferredAge> <GeologicEvent> <eventAge> <CGI_TermValue>
                            <value codeSpace="urn:cgi:classifierScheme:ICS:StratChart:2004“ >urn:cgi:classifier:ICS:StratChart:2004:Ordovician</value>
                        </CGI_TermValue> </eventAge>  <eventProcess> <CGI_TermValue>
                            <value codeSpace="urn:cgi:classifierScheme:GA:Process">unspecified</value>
                        </CGI_TermValue> </eventProcess>  </GeologicEvent> </preferredAge> …
Most property values are references to registers
Common values  interoperability
CSIRO EGU-2008-A Cox Standards-based methodology

15. Extensibility
Related communities are already building specializations on top of GeoSciML
GroundWaterML
GeochronML
Mineral Occurrences ML
As well as internal extensibility, GeoSciML is designed to be extended or specialized by sub-domains within, and related to, geosciences
For example, two papers in this afternoon’s session describe languages explicitly derived from GeoSciML.
CSIRO EGU-2008-A Cox Standards-based methodology

16. Extensibility methodology
Same pattern as GeoSciML’s specialization of ISO & O&M …
The pattern used to accomplish this follows exactly the same method as the basic GeosciML design
i.e. specialization-of, and reference-to externally governed components. (the blue classes are in the GWML domain).
(N.B. this is enforced within the development environment by the use of “controlled packages” in a variety of SubVersion code repositories).
CSIRO EGU-2008-A Cox Standards-based methodology

17. Tooling
CSIRO EGU-2008-A Cox Standards-based methodology

18. Tooling to support standards-based approach
UML for design, XML for transfer
HollowWorld UML template
Standard UML profile
ISO components
OGC Observation & Sampling components
FullMoon XMI processor to automate
XML schema
documentation production
GeoSciML documentation
CSIRO EGU-2008-A Cox Standards-based methodology

19. Delegation
CSIRO EGU-2008-A Cox Standards-based methodology

20. Benefits of delegating governance
Platform supports governance arrangements
UML packages (XML namespaces) reflect system boundaries  discrete governance arrangements
Markup conventions support late-binding of selected elements (esp. vocabularies and scales)
Understand the scope and reach of your community
Only maintain the elements that are:
important to you
not governed by someone else
Enable extensions to your model
Publish re-usable components in http repository
e.g. XMI of UML model; XML Schema
Maintain your components in an orderly way
Don’t cause surprises!
CSIRO EGU-2008-A Cox Standards-based methodology

21. Summary
CSIRO EGU-2008-A Cox Standards-based methodology

22. Key points Methodology for information communities to reach consensus
UML design stays close to conceptual level
Re-use of cross-domain components and standard applications
Patterns enable delegation to the appropriate authority
Enhanced interoperability
GeoSciML is an example of a community agreement developed using a standards-based methodology
Specialized schemas are being built on top of GeoSciML
Standards build on standards
Don’t re-invent unnecessarily - its easier (and more interoperable) to borrow elements already managed by someone else
Allow others to borrow yours
But this imposes an obligation on you to maintain an orderly governance process.
CSIRO EGU-2008-A Cox Standards-based methodology

23. Thank you Exploration & Mining Simon Cox Research Scientist
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Simon Cox
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