Transcript SOA/OGC Workshop: Demystifying the acronym soup

A standard information transfer model scopes the
ontologies required for observations
Simon Cox, Laurent Lefort
TDWG, Fremantle, 2008-09-30
Science relies on observations
•
•
Provides evidence & validation
Involves sampling
•
A domain-independent terminology and information-model
•
•
Supports data discovery and integration across discipline boundaries
Scopes ontology developments
CSIRO Cox/TDWG 2008
What is “an Observation”
• Observation act involves a procedure applied at a specific time
• The result of an observation is an estimate of some property
• The observation domain is a feature of interest at some time
• After Fowler & Odell ca. 1997
CSIRO Cox/TDWG 2008
Examples
• The 7th banana weighed 270gm on the kitchen scales this morning
• The attitude of the foliation at outcrop 321 of the Leederville Formation was
63/085, measured using a Brunton on 2006-08-08
• Specimen H69 was identified on 1999-01-14 by Amy Bachrach as Eucalyptus
Caesia
• The image of Camp Iota was obtained by Aster in 2003
• Sample WMC997t collected at Empire Dam on 1996-03-30 was found to have
5.6 g/T Au as measured by ICPMS at ABC Labs on 1996-05-31
• The X-Z Geobarometer determined that the ore-body was at depth 3.5 km at
1.75 Ga
• The GCM simulation run today using CMIP3 indicated that the pressure field in
the atmosphere tomorrow will be as given in pf999_20081020_1
CSIRO Cox/TDWG 2008
In “pictures”
:Specimen
H69Banana
7th
: :
Leederville
Iota
BFCamp
Ore Body
:
WMC997t
:
Grid999
AnyFeature
Formation
::
AnyFeature
GeologicUnit
SamplingSolid
Specimen
AnyFeature
sampledFeature
featureOfInterest
featureOfInterest
featureOfInterest
featureOfInterest
featureOfInterest
featureOfInterest
sampledFeature
KitchenScales
Brunton
: ::
Aster
:Process
Bachrach
Amy
X-Z
ICPMS
:Process
CMIP3
:
Process
Process
geobarometer
:
Process
Process
procedure
procedure
procedure
procedure
procedure
procedure
procedure
location
Run999_20081020_1
:
O-LF
:Observation
:Observation
O_SAB
O_I345
:Observation
O7 Observation
:Observation
O_Depth
:Observation
O_Assay689
:Observation
Empire Dam :
EarthAtmosphere
GeologicUnit
notes
notes
notes
notes
notes
notes
notes
samplingTime="2006-08-08"
samplingTime="1999-01-14"
samplingTime="2003"
samplingTime="this
morning"
samplingTime="-1.75Ga"
samplingTime="tomorrow"
samplingTime="1996-03-30"
resultTime="today"
resultTime="1996-04-16"
observedProperty
observedProperty
observedProperty
observedProperty
observedProperty
observedProperty
observedProperty
weight
: :
foliation
species
IR
Radiance
depth
:: :
pressure
gold
PropertyType
orientation
:
PropertyType
PropertyType
PropertyType
PropertyType
concentration
:
PropertyType
PropertyType
CSIRO Cox/TDWG 2008
result
result
result
result
result
result
result
270g
:Measure
63/085
:Record
ASgh67c
3.5km
:Measure
Eucalyptus
5.6 ppm
::Image:
pf999_20081020_1
:
Caesia
Measure
CV_DiscreteGridPointCoverage
AnyDefinition
ABC Labs :
AnyFeature
Name:
Package:
Version:
Author:
Overview: Observation
«Application Schema» OM Observation Core
1.0
Simon Cox
Generic pattern for observation data
OF_AnyFeature
OM_Process
1
featureOfInterest
1
propertyValueProvider
0..*
OM_Observation
+
+
+
+
+
Conformant with
ISO 19100 CSL
and meta-model
generatedObservation
samplingTime
resultTime [0..1]
procedureOperator [0..1]
parameter [0..*]
resultQuality [0..1]
observedProperty
result
1
OF_PropertyType
procedure
0..*
Any
{n}
An Observation is an action whose result is an estimate of the value
of some property of the feature-of-interest, obtained using a specified procedure
Where’s the “observation location”?
In the feature-of-interest - this reconciles remote, lab, and in-situ observations
CSIRO Cox/TDWG 2008
Name:
Package:
Version:
Author:
Overview: Observation
«Application Schema» OM Observation Core
1.0
Simon Cox
O&M vs. OBOE
OF_AnyFeature
OM_Process
1
featureOfInterest
1
propertyValueProvider
0..*
OM_Observation
+
+
+
+
+
generatedObservation
samplingTime
resultTime [0..1]
procedureOperator [0..1]
parameter [0..*]
resultQuality [0..1]
observedProperty
result
1
OF_PropertyType
procedure
0..*
Any
{n}
An Observation is an action whose result is an estimate of the value
of some property of the feature-of-interest, obtained using a specified procedure
NCEAS OBOE:
An Observation is the Measurement of the Value
of a Characteristic of some Entity in a particular Context
CSIRO Cox/TDWG 2008
TDWG examples
FlipDibner :
Process
Plot_996 :
OOc2008_786 :
SamplingSurface
OrganismOccurence
procedure
FlipDibner :
Process
FlipDibnersWatch :
Process
procedure
featureOfInterest
featureOfInterest
featureOfInterest
featureOfInterest
procedure
FlipDibnersGPS :
sampledFeature
Survey_2008_996 Process
:
Observation
Ecosystem_abt417h
O2008_786s :Observation
procedure
notes
samplingTime="2008-10-18"
O2008_786t :Observation
O2008_786x :Observation
observedProperty
observedProperty
Taxon :
PropertyType
observedProperty
result
OrganismCount :
PropertyType
E. Caesia : 26 :
ScopedName
Integer
result
Time :
PropertyType
observedProperty
ScopedName
CSIRO Cox/TDWG 2008
2008-10-18T18:17:00.00+08:00 :
DateTime
taxon
Location : E. Caesia :
PropertyType
result
result
-31.5 115,5 :
DirectPosition
Sampling strategies and relationships
Domain feature type
sampledFeature
0..*
Complex
AnyFeature
Intention
SamplingFeature
relatedSamplingFeature 0..*+
samplingTime [0..1]
+ parameter [0..*]
relatedObservation
Observation
0..*
SpatiallyExtensiveSamplingFeature
Specimen
+
+
+
+
+
materialClass
samplingMethod [0..1]
samplingLocation [0..1]
size [0..1]
currentLocation [0..1]
SamplingPoint
Station
SamplingCurve
SamplingSurface
SamplingSolid
+ length [0..1]
+ area [0..1]
+ volume [0..1]
Traverse
Borehole
CSIRO Cox/TDWG 2008
Plot
MapHorizon
Section
Mine
Specimens and “outcrops”
CSIRO Cox/TDWG 2008
What’s this got to do with Ontologies?
• UML is a formal language
• UML vs. OWL … similarly expressive
• Especially if UML profile and «stereotype» used
CSIRO Cox/TDWG 2008
Obrst 2006
- Ontology Spectrum: One View
strong semantics
Modal Logic
First Order Logic
Logical Theory
Is Disjoint Subclass of
Description Logic
with transitivity
DAML+OIL, OWL
property
UML
Conceptual Model
RDF/S
XTM
Extended ER
Thesaurus
ER
Is Subclass of
Has Narrower Meaning Than
Structural Interoperability
DB Schemas, XML Schema
Taxonomy
Relational
Model, XML
Is Sub-Classification of
Syntactic Interoperability
Ontologies for observations
weak semantics
Semantic Interoperability
Obrst 2006
- Ontology Spectrum: One View
strong semantics
Modal Logic
First Order Logic
Logical Theory Problem:
Very General
Is Disjoint
Subclass of
Semantic Expressivity: Very High
Description Logic
with transitivity
DAML+OIL, OWL
property
UML
Conceptual Model
Problem: General
Is Subclass of
Semantic Interoperability
Semantic Expressivity: High
RDF/S
XTM
Extended ER
Thesaurus
Has Narrower Meaning Than
Problem: General
ER
Semantic Expressivity: Medium
Structural Interoperability
DB Schemas, XML Schema
Taxonomy
Is Sub-Classification of
Problem: Local
Relational
Semantic Expressivity: Low
Model, XML
Syntactic Interoperability
Ontologies for observations
weak semantics
What’s this got to do with Ontologies?
• UML is a formal language
• UML vs. OWL … similarly expressive
• Especially if UML profile and «stereotype» used
• ISO 19103 profile models may be transformed into OWL
without too much difficulty
• ISO 19150 will define a UML→OWL rule
• … but converting the O&M model just gives you an OWL
representation of the schema
• Is this useful for reasoning?
• O&M model scopes the (discipline specific) ontologies required
for observational data
• and describes the relationships between them
CSIRO Cox/TDWG 2008
Name:
Package:
Version:
Author:
Overview: Observation
«Application Schema» OM Observation Core
1.0
Simon Cox
Discipline or community profile
OF_AnyFeature
OM_Process
1
featureOfInterest
propertyValueProvider
• feature of interest
0..*
• Types define a
domain-model
(e.g. Plot, Ecosystem,
OrganismOccurence)
0..*
OM_Observation
+
+
+
+
+
generatedObservation
• procedure
samplingTime
resultTime [0..1]
procedureOperator [0..1]
parameter [0..*]
resultQuality [0..1]
observedProperty
• Standard procedures,
suitable for the
property-type
result
1
OF_PropertyType
• observed property
• Belongs to the type of the
feature-of-interest (e.g. organism
count, taxon, time, location)
CSIRO Cox/TDWG 2008
procedure
1
Any
{n}
• result
• Standard scales
suitable for the
property-type
(e.g. taxonomy)
Ontology enabled profiles
• Step one: align ontology and O&M skeleton
• Step two: round trip transformation
• Transform UML model into OWL (done)
• Use OWL to develop vocabularies on top of O&M skeleton
• Use extended UML-based MDA process to generate XML schemas
• Motivations
• Better quality vocabularies
• Greater consistency of the conceptual model
CSIRO Cox/TDWG 2008
Vocabularies dependencies in O&M
N
Observation
Geometry
Featureindependent
parameters
Featuredependent
parameters
WHO
Feature
codes
T
WHA
Result
Observed
property
Features types
Procedure
Semi-primitive concepts
Primitive concepts
Metadata
Institution
and project
Security classif.
O&M amd GFM stereotypes
System
and author
Missing data
Classes w/ ident. instances
Simple classes
Onto category to be defined
Transaction type
Processing
chain type
Semi-abstract concepts
Field & Lab
methods
Procedures
Feature-indep. parameters
Abstract concepts
Temporal types
Geometrical types
Result type
Survey type
Coord. Sys
Vertical
Coord. Sys
Chemistry
Taxa
Quantities
Units
Medium
Fraction
?
?
Processing &
interpolation
?
?
Validation &
quality flag
?
?
Time* : two O&M stereotypes (sampling time and result time)
CSIRO Cox/TDWG 2008
Feature
property
Parameters
Sampled
Feature
Water
Feature
Event
Feature-dep. parameters
UML defs
IN
WHAT
Time*
Multi-dependent concepts
Vocabularies
Sampling
Feature
Station
Site
Platform
Gauge/weir
layout/profile
Generic
type
W
HE
Sensor
(Instrument)
HOW
Observations codes
Action
Event codes
WHERE
Observation
VAL U E
Action codes
Process
Wrap-up
CSIRO Cox/TDWG 2008
Development and validation of “O&M”
• Developed in the context of
• Geochemistry/Assay data
• OGC Sensor Web Enablement – environmental and remote sensing
• Subsequently applied in
•
•
•
•
•
Water resources/water quality
Oceans & Atmospheres
Natural resources
Taxonomic data
Geology field data
CSIRO Cox/TDWG 2008
Scopes the ontologies for domain observations
•
•
•
•
Feature types (feature of interest, sampling features)
Observed properties
Observation procedures, instruments, algorithms
Scales, taxonomies
CSIRO Cox/TDWG 2008
O&M Status
• OGC Standard 2007
• ISO 19156 – upcoming
• Key aspect of GeoSciML
• Basis for WaterML v2
• Basis for Climate Science ML
CSIRO Cox/TDWG 2008
Motivation for developing a common model
• Cross-domain data discovery and fusion
• Re-usable service interfaces
CSIRO Cox/TDWG 2008
Exploration & Mining
Simon Cox
Research Scientist
Phone: +61 8 6436 8639
Email: [email protected]
Web: www.csiro.au/em
Thank you
Contact Us
Phone: 1300 363 400 or +61 3 9545 2176
Email: [email protected] Web: www.csiro.au
Generations of “standards”
& integration complexity
Surface water
& groundwater
“standards”
Integration support
OWL ontologies
WDTF
Registries
Semantic integration
Master Data Managt
GWML
UML &
XML schemas
eWater (EU)
SANDRE XML
WaterML (CUAHSI)
XML schemas
WFD schemas
EPA WQX
XML
ODM
EPA STORET
DB-based
SANDRE
ASCII-based
CSIRO Cox/TDWG 2008
Model-driven generation
of XML schemas
Reuseable XML schema stack
Custom XSL transfo. & web services
Distributed systems with same db schema
Observations
CSIRO Cox/TDWG 2008
Our Science is changing: scale
Planet
Continent
Mountain
Section
Outcrop
Rock
Mineral
Molecule
Atom
CSIROof
Cox/TDWG
2008 Activities NSF
Source: Office
Integrative
Our Science is changing: interdisciplinary
Source: US Global Change Research Program
CSIRO Cox/TDWG 2008
Ontological value of the
Observations & Measurements standard
• Two user-managed class hierarchies in GFM-based specs:
• Feature and FeaturesCollection: a Feature-type is characterized by a specific set of
properties
• Up to five user-managed class hierarchies in O&M-based specs
• Observation, SamplingFeature, PropertyType, Procedure and Result
• An Observation is an Event whose result is an estimate of the value of some Property of the
Feature-of-interest, obtained using a specified Procedure
• Stronger ontological value for O&M
• More branches and separation of concern:
• Example: Difference between Feature and SamplingFeature
• Feature for the real world objects e.g. an aquifer
• SamplingFeature to characterise how a measure is done e.g. along a borehole
CSIRO Cox/TDWG 2008
Normalised ontology skeleton for water
observation vocabularies
Define the right
branches at the top
Isolate unambiguous
primitives (e.g. units)
Use modules/namespace/URIs to position source-specific
definitions against common ones
CSIRO Cox/TDWG 2008
Observation data interface
• OGC “Sensor Observation Service”
• http interface to sensor observations
• c.f. WFS, WCS, WMS
• Request parameters scoped by O&M model
• featureOfInterest
• observedProperty
• Procedure
• Response is XML-encoded O&M
CSIRO Cox/TDWG 2008
Sampling features
CSIRO Cox/TDWG 2008
Proximate vs ultimate feature-of-interest
Ultimate (“project”) thing of interest often not directly or fully
accessible
1. Proximate feature of interest embodies a sample design
•
•
•
•
Rock-specimen samples an ore-body or geologic unit
Well samples an aquifer
Profile samples an ocean/atmosphere column
Cross-section samples a rock-unit
2. Sensed property is a proxy
•
e.g. want land-cover, but observe colour
Some sampling designs are common across disciplines
CSIRO Cox/TDWG 2008
Examples
CSIRO Cox/TDWG 2008
Nam e:
Package:
Version:
Author:
Well&Intervals
Examples
1. 0
Simon Cox
Water quality of aquifers observed in wells
NWC200 7/WQ :
Observ ationCollection
EW/E W1 :
SamplingFeatureRelation
relatedSamp lingFeature
member
relatedOb servation
WQ3/1 :
Observ ation
notes
role="intervalHost"
featureOfInterest
Interv a lEW1 :
SamplingCurv e
relatedOb servation
sampledFeature
proce dure
member
relatedOb servation
Fooglemeter 2000 : proce dure
Observ ati onProcess
WQ2/1 :
Observ ation
Leederv ill eFormation
target
Ev er tsWell
relatedOb servation
sampledFeature
sampledFeature
target
Cottesl oeWedge
member
relatedOb servation
WQ2/2 :
Observ ation
featureOfInterest
Interv a lEW2 :
featureOfInterest SamplingCurv e
relatedOb servation
sampledFeature
proce dure
Farkleme ter XP : proce dure
Observ ati onProcess
relatedSamp lingFeature
member
WQ3/1 :
Observ ation
EW/E W2 :
SamplingFeatureRelation
notes
role="intervalHost"
relatedOb servation
featureOfInterest
RobsWe ll
sampledFeature
Gnangar aMound
observedProperty
observedProperty
observedProperty
WaterQuality :
Proper tyType
CSIRO Cox/TDWG 2008
observedProperty
result
WQ3/1/r :
CV_DiscreteTime InstantCov erage
Water quality measured along a ferry track
Nam e:
Package:
Version:
Author:
FerrySam pling-C
Examples
1. 0
Simon Cox
Albemarle -Pamlico
sampledFeature Sound :AnyFeature
FerryTrack 20071113 :
SamplingCurv e
notes
shape=Curve987:GM_LineString
featureOfInterest
relatedOb servation
proce dure Fooglemeter 2000 :
Observ ati onProcess
WQ200711113 :
Observ ation
observedProperty
WQ/C-9 (Water Quality) :
Proper tyType
result
WQ20071113/r :
CV_DiscreteP ointCov erage
CSIRO Cox/TDWG 2008
Patterns?
• Much of the interest concerns
• relations between sampling features,
• associations with the domain (sampled) features
• i.e. sampling regimes are core
CSIRO Cox/TDWG 2008
Governance
CSIRO Cox/TDWG 2008
OGC Sensor Web Enablement
• OGC Web Services testbeds
• OWS-1 2001 – OWS-5 2007
• Core elements of OGC SWE suite
•
•
•
•
•
SensorML – provider-centric information viewpoint
O&M – consumer-centric information viewpoint
SOS, SAS – http interface to observations
SPS – tasking interface
sweCommon – data-types & encodings, including coverage
encoding
• TML – low-level sensor streams
CSIRO Cox/TDWG 2008
Accessing data using the “Observation” viewpoint
getFeature,
type=Observation
WFS/
Obs
getObservation
getCoverage
(result)
getCoverage
getResult
describeSensor
WCS
SOS
getFeatureOfInterest
getRecordById
Sensor
Register
getFeature
WFS
e.g. SOS::getResult == “convenience” interface for WCS
CSIRO Cox/TDWG 2008
Accessing data using the “Sampling Feature Service”
viewpoint
WFS
getFeature
getFeature
(sampling Feature)
getCoverage
getFeature
(coverage property value)
getFeature
(relatedObservation)
getCoverage
(property value)
getObservation
(relatedObs)
WFS/
SFS
WCS
getResult
(property value) Common
data
source
getFeature
(featureOfInterest)
getObservation
getCoverage
(result)
SOS
getRecordById
(procedure)
Sensor
Register
CSIRO Cox/TDWG 2008
Accessing data using the “Domain Feature” viewpoint
getResult
(property value)
SOS
getFeature
??
WFS
getCoverage
(property value)
WCS
The “George Percivall preferred™” viewpoint #1
– observations are property-value-providers for features
CSIRO Cox/TDWG 2008
Accessing data using the “just the data” viewpoint
getResult (lots of ‘em)
(range values)
SOS
getCoverage
WCS
getFeature/geometry
(domain exent)
WFS
The “George Percivall preferred™” viewpoint #2
– observations are range-value-providers for coverages
CSIRO Cox/TDWG 2008
Application to other science disciplines
• need information transfer standards for
•
•
•
•
•
•
•
•
•
Geochemistry
Geochronology
Geophysics
Geodesy
Seismology
Hydrogeology
Marine
Ecology
Biogeology
http://www.datastrategyjournal.com/index.php?option=com_content&task=view&id=18&Itemid=1
• But need to coordinate these standards (including ontologies) to avoid
uncontrolled growth of YAML (Yet Another Markup Language)
CSIRO Cox/TDWG 2008
Procedure vs. observedProperty
• observedProperty supports discovery by observation users
• “show me all the observations of temperature and wind-speed”
• procedure provides strict definition
• “how was that value obtained?”
• …or provider-centric discovery
• “show me all the data collected by instrument X”
CSIRO Cox/TDWG 2008
Some properties vary within a feature
•
•
•
•
colour of a Scene or Swath varies with position
shape of a Glacier varies with time
flow at a Station varies with time
rock density varies along a Borehole
• Variable values may be described as a Function on some axis of
the feature
• Corresponding Observation/result is a Function
• If domain is spatio-temporal, also known as coverage or map
CSIRO Cox/TDWG 2008
Variable property  coverage valued result
«FeatureType»
Observ ation
«FeatureType»
DiscreteCov erageObserv ation
CV_Coverage
result
CV_DiscreteCov erage
{n}
«FeatureType»
PointCov erageObserv ation
result
CV_DiscretePointCov erage
{n}
CSIRO Cox/TDWG 2008
«FeatureType»
TimeSeriesObserv ation
result
CV_DiscreteTimeInstantCov erage
«FeatureType»
ElementCov erageObserv ation
result
CV_DiscreteElementCov erage