SONet: S cientific O bservations Net work
description
Transcript of SONet: S cientific O bservations Net work
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SONet: Scientific Observations Network
Semtools: Semantic Enhancements for Ecological Data Management
Mark Schildhauer, Matt Jones, Shawn Bowers, Huiping Cao
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Outline
• Project overview• Observational data models (SONet)
• OBOE re-factored• O&M• EQ• SONet core - domain ontologies
• Semantic tools for observational data (Semtools)• Semantic annotation• OM Query language• Querying annotated observational metadata and data
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Challenges
• Mark and Matt fill in …
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Our Approach
The SONet Project- Define a core observational model (based on OBOE, O&M,
and others) … progress made on OBOE/O&M alignment- Identify and develop domain-specific vocabularies for
describing observational data semantics- Define a set of scientific use cases for data interoperability- Develop a set of interoperability “demonstration prototypes”
The Semtools Project- Incorporate OBOE and semantic annotations into existing
Metacat and Morpho metadata tools- Focus on ecology data and use cases
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Weight Mass Unit
Biomass
usesStandard
Gram
is-a
Bio.EntityTree
Leaf LitterTree Leaf Wet Weight Dry Weight
Observation
Measurement
Site Species Ind Mass
GCE6 Picea Rubens 1 75.13
GCE6 Picea Rubens 2 179.81
GCE7 Picea Rubens 1 443.20
… … … …
Data
Structural Meatadata
<attribute id=“att.4”> <attributeName> Mass </attributeName></attribute>
hasMeasurement
OBOE Semantic Annotation
Domain-Specific Ontology
is-a is-ais-a
is-a
has-part
hasCharacteristicis-a
part-of is-a
ofEntity
usesS
tandardofCharacteristic
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Observational data models
• OBOE 1.0• O&M (ISO)• EQ• SONet Domain Ontologies
• Plant Traits• SBC• Ongoing
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OBOE Core 1.0
Extensible Observation Ontology (OBOE) [1]
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Entity
Characteristic
Observation
Measurement
Protocol Standard
hasMeasurement
ofCharacteristic
usesProtocol usesStandard
ofEntity
hasContext
1..1*
1..1
*
*
*
1..1 1..1
1..1**
hasValue
1..1
**
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OBOE re-factored (cont.)
• Shawn adds more (2-3 slides) on OBOE …
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O&M ([2])
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• Feature– Abstraction of real world phenomena
(Def. 4.5)– E.g., Tree
• Feature type– Class of features having common
characteristics (Def. 4.6)• Property
– Facet or attribute of an object referenced by name (Def. 4.14)
– E.g., Height• Property-type
– Characteristic of a feature type (Def. 4.15)
Feature
Property
carrierOfCharacteristic
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Feature
Property
OM_Observation
observedProperty
featureOfInterestcarrierOfCharacteristic
OO&M (Cont.)
• Observation– Act of observing a property (Def. 4.10)
• Measurement– Set of operations having the object of determining the value of a quantity (Def.
4.9)
• OM_Observation– An instance of feature type
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Feature
Property
OM_Observation
Result
hasResult
Procedure
usesProcedure
carrierOfCharacteristicobservedPro
perty
featureOfInterest
O&M (cont.)
• Observation procedure– Method, algorithm or instrument, or system of these which may be used
in making an observation (Def. 4.11)– The base class OM_Process
• Observation result– Estimate of the value of a property determined through a known procedure.
Any type
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Feature
ObservationContext
Property
OM_Observation
Result
relatedObservation
hasResult
Procedure
usesProcedure
ObservationContext• Some observations depend on other observations to provide context in
understanding the result. (Sec. 6.2.4)
• Link a OM_Observation to another OM_Observation, with the role name relatedObservation for the target
carrierOfCharacteristicobservedPro
perty
featureOfInterest
O&M (cont.)
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Entity Feature
Characteristic Property
Observation Measurement OM_Observation
Protocol Procedure
ResultStandardEntity
hasContext ObservationContext
Entity
CharacteristicMeasurement
Observation
Standard
hasMeasurement
ofEntity
Protocol
Feature
ObservationContex
Property
OM_Observation
Result
carrierOfCharacteristicobservedProper
ty
featureOfInterestrelatedObservation
hasResult
Procedure
usesProcedure
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hasValue
usesProtocol usesStandard
ofCharacteristic
hasContext
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EQ ([4])
• Entity– Describes some object in the real world. E.g., eye
• Quality– Describes an entity's attribute and its attribute
• Character – Composed of Entity and Quality attributes to
• Character state– Quality value. E.g., “red” to represent eye’s color is red). - represent the meaning of which entity's which attribute.
E.g.,- eye's color.- value. E.g., color = red, means eye’s color is red.
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Comparison
OBOE re-facored O&M EQ
Entity Feature Entity
Characteristic Property Quality attribute
Observation
OM_ObservationMeasurement Quality value or Character state
Protocol Procedure
Standard + Result Result
hasContext ObservationContext
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SONet core - domain ontology: trait• Trait group: Centre d'Écologie Fonctionnelle et Évolutive (CÉFÉ) [5]
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SONet core -domain ontology: SBC• Group: Santa Barbara Coastal (SBC) Lont Term Ecological Research (LTER) [6]
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• Plant– iPlant group ([7])
• PATO ([8])– Phenotypic Quality Ontology– Automatic tool to convert PATO to be compatible with SONet
core model
SONet core -domain ontology: ongoing
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How to use SONet core model?• SONet-core
• Morpho data annotation tool to generate data instances for you automatically
• OM query language • OM query framework for data discovery
• O&M• Write your own xml file to contain the observation
and measurement data• Write Schematron [3] file to validate whether the
data xml file • No tool report!
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Tools
• Morpho data annotation tool to generate data instances for you automatically
• Observation and Measurement (OM) query language
• Framework for querying annotated observational data
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Semantic Annotation
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OM Query example
• Tree[Height > 5 Meter]- Return datasets that have at least one Tree
observation containing a Height measurement with a value greater than 5 Meters
• Tree[Height > 5 Meter], Soil[Acidity >= 7 pH]- Return datasets that contain at least one Tree
observation (having a measurement where the Height was greater than 5) and at least one Soil observation (having an Acidity measurement of 7 or greater)
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OM Query Example (cont.)
• Tree[Height > 5 Meter] -> Soil[Acidity >= 7pH]- Incorporates context via the "->” (arrow) symbol, which
can be read as "contextualized by" or "has context"- Returns datasets that contain at least one Tree observation
(with the corresponding height value) where the observation was taken within the context of a Soil observation (with the corresponding acidity value)
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Query framework
Annotation 1 Annotation 2 Annotation 3 Annotation 4
File 1 File 2 File 3 File 4
Offline data processing
Result Q1 Result Q2 … ….
OBOE-aware DB
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OBOE domain model
Annotation interface
Query 1 Query 2 … ….
Online query engine
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Offline data processing
Annotation as a bridge
…
Annotation 1 Annotation 2 Annotation 3 Annotation 4
File 1 File 2 File 3 File 4
Measurement type table
Observation Type table
Entity type table
Context type table
Map
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OBOE-aware DB
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Annotation as a bridge
…
Annotation 1 Annotation 2 Annotation 3 Annotation 4
File 1 File 2 File 3 File 4
Measurement type table (for ann1, 2, …)
Observation type table (for ann1, 2, …)
Entity type table (for ann1, 2, …)
Context type table (for ann1, 2, …)
Map (for ann1, 2, …)
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OBOE-aware DB
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Offline data processing (raw data loading)
Observation type table (for ann1, 2, …)
Entity type table (for ann1, 2, …)
Context type table (for ann1, 2, …)
Map (for ann1, 2, …)
Measurement type table (for ann1, 2, …)
Raw data loading
…
Annotation 1 Annotation 2 Annotation 3 Annotation 4
File 1 File 2 File 3 File 4
Table 4
Table 3
Table 2
Table 1
…
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OBOE-aware DB
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Offline data processing (data materialization)
Measurementtable
Observation table
Entity table
Context table
Measurement type table (for ann1, 2, …)
Observation type table (for ann1, 2, …)
Entity type table (for ann1, 2, …)
Context type table (for ann1, 2, …)
Map (for ann1, 2, …)
Table 4
Table 3
Table 2
Table 1
…
Data materialization
…
Annotation 1 Annotation 2 Annotation 3 Annotation 4
File 1 File 2 File 3 File 428
OBOE-aware DB
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MeasurementTable (for file 1, 2, …)
Observation table (for file 1, 2, …)
Entity table (for file 1, 2, …)
Context table (for file 1, 2, …)
Measurement type table (for ann1, 2, …)
Observation type table (for ann1, 2, …)
Entity type table (for ann1, 2, …)
Context type table (for ann1, 2, …)
Map (for ann1, 2, …)
Table 4
Table 3
Table 2
Table 1
…
Data materialization
…
Annotation 1 Annotation 2 Annotation 3 Annotation 4
File 1 File 2 File 3 File 429
OBOE-aware DB
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Measurement type table (for ann1, 2, …)
Observation type table (for ann1, 2, …)
Entity type table (for ann1, 2, …)
Context type table (for ann1, 2, …)
Map (for ann1, 2, …)
Table 4
Table 3
Table 2
Table 1
…
Query strategy 1
Online query engine (query re-writing over raw data)
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MeasurementTable (for file 1, 2, …)
Observation table (for file 1, 2, …)
Entity table (for file 1, 2, …)
Context table (for file 1, 2, …)
OBOE-aware DB
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Measurement type table (for ann1, 2, …)
Observation type table (for ann1, 2, …)
Entity type table (for ann1, 2, …)
Context type table (for ann1, 2, …)
Map (for ann1, 2, …)
Table 4
Table 3
Table 2
Table 1
…
Query strategy 2
Online query engine (query re-writing over materialized data)
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MeasurementTable (for file 1, 2, …)
Observation table (for file 1, 2, …)
Entity table (for file 1, 2, …)
Context table (for file 1, 2, …)
OBOE-aware DB
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Measurement type table (for ann1, 2, …)
Observation type table (for ann1, 2, …)
Entity type table (for ann1, 2, …)
Context type table (for ann1, 2, …)
Map (for ann1, 2, …)
Table 4
Table 3
Table 2
Table 1
…
Query strategy n??
Online query engine
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MeasurementTable (for file 1, 2, …)
Observation table (for file 1, 2, …)
Entity table (for file 1, 2, …)
Context table (for file 1, 2, …)
Other materialization/de-
normalization??
RDF triple store?
OBOE-aware DB
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Ontology Editing Tools
• Protégé plug-in - For creating and editing OBOE-compatible ontologies- Form-based UI- Generates “low-level” OWL constraints/axioms
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References[1] Shawn Bowers and Joshua S. Madin and Mark P. Schildhauer, A Conceptual
Modeling Framework for Expressing Observational Data Semantic. In ER 2008, 41-54.
[2] OpenGIS observations and measurements encoding standard (O&M): http://www.opengeospatial.org/standards/om
[3] Schematron ISO standard: http://www.schematron.com/
[4] EQ: https://www.phenoscape.org/wiki/EQ_for_character_matrices
[5] CECF: http://www.cefe.cnrs.fr/ecopar/
[6] SBC LTER: http://sbc.lternet.edu/
[7] iPlant: http://www.iplantcollaborative.org/
[8] PATO: http://obofoundry.org/wiki/index.php/PATO:Main_Page
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