SONet: Scientific Observations Network
Semtools: Semantic Enhancements for
Ecological Data Management
Mark Schildhauer, Matt Jones,
Shawn Bowers, Huiping Cao
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
Challenges
• Mark and Matt fill in …
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
Domain-Specific
Ontology
is-a
Tree
part-of
Weight
hasCharac
teristic
OBOE
Semantic
Annotation
is-a
is-a
is-a
Wet Weight
Dry Weight
is-a
Leaf Litter
has-part
is-a
Biomass
Bio.Entity
is-a
Tree Leaf
usesStandard
Mass Unit
Observation
hasMeasurement
Measurement
Structural
Meatadata
Data
<attribute id=“att.4”>
<attributeName>
Mass
</attributeName>
</attribute>
Site
Species
Ind
Mass
GCE6
Picea Rubens
1
75.13
GCE6
Picea Rubens
2
179.81
GCE7
Picea Rubens
1
443.20
…
…
…
…
Gram
Observational data models
•
•
•
•
OBOE 1.0
O&M (ISO)
EQ
SONet Domain Ontologies
• Plant Traits
• SBC
• Ongoing
OBOE Core 1.0
hasContext
*
*
Observation
ofEntity
*
1..1
1..1
hasMeasurement
Entity
1..1
hasValue
*
Measurement
*
*
ofCharacteristic
1..1
Characteristic
* *
usesProtocol
1..1
Protocol
1..1 usesStandard
Standard
Extensible Observation Ontology (OBOE) [1]
7
OBOE re-factored (cont.)
• Shawn adds more (2-3 slides) on OBOE …
O&M ([2])
•
Feature
– Abstraction of real world phenomena
(Def. 4.5)
– E.g., Tree
•
Feature type
– Class of features having common
characteristics (Def. 4.6)
•
Property
Feature
carrierOfCharacteristic
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)
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O&M (Cont.)
O
Feature
featureOfInterest
OM_Observation
observedProperty
carrierOfCharacteristic
Property
• 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
O&M (cont.)
Feature
featureOfInterest
carrierOfCharacteristic
OM_Observation
usesProcedure
Procedure
observedPro
perty
hasResult
Property
Result
• 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
O&M (cont.)
ObservationContext
Feature
relatedObservation
featureOfInterest
OM_Observation
usesProcedure
Procedure
observedPro
perty
hasResult
carrierOfCharacteristic
Property
Result
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
ObservationContex
hasContext
ofEntity
Observation
hasValue
hasMeasurement
Measurement
Entity
ofCharacteristic
Protocol
featureOfInterest
OM_Observation
Characteristic
usesProcedure
usesProtocol
Feature
relatedObservation
carrierOfCharacteristic
observedProper
ty
Property
hasResult
usesStandard
Standard
Entity
Procedure
Result
Feature
Characteristic
Property
Observation Measurement
OM_Observation
Protocol
Procedure
Standard
Entity
Result
hasContext
ObservationContext
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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
– value. E.g., color = red, means eye’s color is red.
• Character
– Composed of Entity and Quality attributes to
– represent the meaning of which entity's which attribute.
E.g.,
– eye's color.
• Character state
– Quality value. E.g., “red” to represent eye’s color is red).
Comparison
OBOE re-facored
O&M
EQ
Entity
Feature
Entity
Characteristic
Property
Quality attribute
Measurement
OM_Observation
Quality value or Character
state
Protocol
Procedure
Standard + Result
Result
hasContext
ObservationContext
Observation
SONet core - domain ontology: trait
•
Trait group: Centre d'Écologie Fonctionnelle et Évolutive (CÉFÉ) [5]
SONet core -domain ontology: SBC
•
Group: Santa Barbara Coastal (SBC) Lont Term Ecological Research (LTER) [6]
SONet core -domain ontology: ongoing
• Plant
– iPlant group ([7])
• PATO ([8])
– Phenotypic Quality Ontology
– Automatic tool to convert PATO to be compatible with SONet
core model
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!
19
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
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)
22
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
Query 1
Query 2
Result Q1
… ….
Result Q2
… ….
Online query engine
OBOE-aware DB
Offline data processing
Annotation 1
Annotation 2
Annotation 3
Annotation 4
Annotation interface
OBOE domain
model
File 1
File 2
File 3
File 4
…
24
Annotation as a bridge
Map
Measurement
type table
Observation
Type table
Entity type table
Context type
table
OBOE-aware DB
Offline data processing
Annotation 1
File 1
Annotation 2
File 2
Annotation 3
File 3
Annotation 4
File 4
…
25
Annotation as a bridge
Map (for ann1, 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, …)
Annotation 1
File 1
Annotation 2
File 2
OBOE-aware DB
Annotation 3
File 3
Annotation 4
File 4
…
26
Raw data loading
Map (for ann1, 2, …)
Measurement type table
(for ann1, 2, …)
Table 4
Table 3
Observation type table
(for ann1, 2, …)
Table 2
Table 1
Entity type table
(for ann1, 2, …)
…
Context type table
(for ann1, 2, …)
OBOE-aware DB
Offline data processing (raw data loading)
Annotation 1
File 1
Annotation 2
File 2
Annotation 3
File 3
Annotation 4
File 4
…
27
Data materialization
Map (for ann1, 2, …)
Measurement type table
(for ann1, 2, …)
Table 4
Table 3
Observation type table
(for ann1, 2, …)
Table 2
Table 1
…
OBOE-aware DB
Measurement
table
Observation
table
Entity type table
(for ann1, 2, …)
Entity table
Context type table
(for ann1, 2, …)
Context table
Offline data processing (data materialization)
Annotation 1
Annotation 2
Annotation 3 Annotation 4
File 1
File 2
File 3
File 4
…
28
Data materialization
Measurement
Table (for file 1, 2, …)
Map (for ann1, 2, …)
Measurement type table
(for ann1, 2, …)
Table 4
Observation table (for
file 1, 2, …)
Table 3
Observation type table
(for ann1, 2, …)
Table 2
Table 1
Entity table (for file 1, 2,
…)
Entity type table
(for ann1, 2, …)
…
Context table (for file 1,
2, …)
Context type table
(for ann1, 2, …)
OBOE-aware DB
Annotation 1
File 1
Annotation 2
File 2
Annotation 3
File 3
Annotation 4
File 4
…
29
Query strategy 1
Online query engine (query re-writing over raw data)
Map (for ann1, 2, …)
Table 4
Measurement type
table (for ann1, 2, …)
Table 3
Table 2
Table 1
…
Observation type table
(for ann1, 2, …)
Entity type table
(for ann1, 2, …)
Context type table
(for ann1, 2, …)
Measurement
Table (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
30
Query strategy 2
Online query engine (query re-writing over materialized data)
Map (for ann1, 2, …)
Table 4
Measurement type
table (for ann1, 2, …)
Table 3
Table 2
Table 1
…
Observation type table
(for ann1, 2, …)
Entity type table
(for ann1, 2, …)
Context type table
(for ann1, 2, …)
Measurement
Table (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
31
Query strategy n??
Online query engine
Map (for ann1, 2, …)
Table 4
Measurement type table
(for ann1, 2, …)
Table 3
Table 2
Table 1
…
Observation type table
(for ann1, 2, …)
Entity type table
(for ann1, 2, …)
Context type table
(for ann1, 2, …)
Measurement
Table (for file 1, 2, …)
Other
Observation
table (for
filematerialization/de1, 2, …)
normalization??
Entity table (for file 1, 2,
RDF triple store?
…)
Context table (for file 1,
2, …)
OBOE-aware DB
32
Ontology Editing Tools
• Protégé plug-in
- For creating and editing OBOE-compatible ontologies
- Form-based UI
- Generates “low-level” OWL constraints/axioms
References
[1] Shawn Bowers and Joshua S. Madin and Mark P. Schildhauer, A Conceptual
Modeling Framework for Expressing Observational Data Semantic. In ER 2008, 4154.
[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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