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SONet: S cientific O bservations Net work

SONet: S cientific O bservations Net work 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

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SONet: S cientific O bservations Net work

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  1. SONet: Scientific Observations Network Semtools: Semantic Enhancements for Ecological Data Management Mark Schildhauer, Matt Jones, Shawn Bowers, Huiping Cao

  2. 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

  3. Challenges • Mark and Matt fill in …

  4. 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

  5. usesStandard Domain-Specific Ontology Weight Mass Unit hasCharacteristic is-a is-a is-a Biomass Tree Bio.Entity is-a is-a is-a part-of is-a Tree Leaf Leaf Litter Wet Weight Dry Weight Gram has-part ofEntity ofCharacteristic OBOE Semantic Annotation usesStandard Observation hasMeasurement Measurement Structural Meatadata <attribute id=“att.4”> <attributeName> Mass </attributeName> </attribute> Data

  6. Observational data models • OBOE 1.0 • O&M (ISO) • EQ • SONet Domain Ontologies • Plant Traits • SBC • Ongoing

  7. OBOE Core 1.0 hasContext * ofEntity * Observation Entity * 1..1 1..1 1..1 hasValue hasMeasurement * * ofCharacteristic Measurement Characteristic * 1..1 * * usesProtocol usesStandard 1..1 1..1 Protocol Standard Extensible Observation Ontology (OBOE) [1] 7

  8. OBOE re-factored (cont.) • Shawn adds more (2-3 slides) on OBOE …

  9. 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 • 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 carrierOfCharacteristic Property 9

  10. O&M (Cont.) O Feature featureOfInterest carrierOfCharacteristic OM_Observation Property observedProperty • 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

  11. O&M (cont.) Feature featureOfInterest carrierOfCharacteristic OM_Observation observedProperty Property hasResult usesProcedure Procedure 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

  12. O&M (cont.) ObservationContext Feature relatedObservation featureOfInterest carrierOfCharacteristic OM_Observation observedProperty Property usesProcedure hasResult Procedure 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

  13. ObservationContex hasContext ofEntity Observation Entity Feature relatedObservation featureOfInterest hasValue hasMeasurement carrierOfCharacteristic OM_Observation observedProperty Measurement Characteristic Property ofCharacteristic usesProcedure hasResult usesProtocol usesStandard Result Procedure Protocol Standard Entity Feature Characteristic Property Observation Measurement OM_Observation Procedure Protocol Standard Entity Result 13 hasContext ObservationContext

  14. 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).

  15. Comparison

  16. SONet core - domain ontology: trait • Trait group: Centre d'Écologie Fonctionnelle et Évolutive (CÉFÉ) [5]

  17. SONet core -domain ontology: SBC • Group: Santa Barbara Coastal (SBC) Lont Term Ecological Research (LTER) [6]

  18. 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

  19. 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

  20. Tools • Morpho data annotation tool to generate data instances for you automatically • Observation and Measurement (OM) query language • Framework for querying annotated observational data 20

  21. Semantic Annotation

  22. 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

  23. 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) 23

  24. Query framework Query 1 Query 2 Result Q1 Result Q2 … …. … …. Online query engine File 1 OBOE-aware DB File 2 Offline data processing Annotation 1 Annotation 2 Annotation 4 Annotation 3 File 3 Annotation interface File 4 OBOE domain model 24 …

  25. Annotation as a bridge Map Measurement type table Observation Type table File 1 Entity type table Context type table File 2 OBOE-aware DB File 3 Offline data processing Annotation 1 Annotation 2 Annotation 4 Annotation 3 File 4 25 …

  26. Annotation as a bridge Map (for ann1, 2, …) Measurement type table (for ann1, 2, …) Observation type table (for ann1, 2, …) File 1 Entity type table (for ann1, 2, …) File 2 Context type table (for ann1, 2, …) OBOE-aware DB File 3 Annotation 1 Annotation 2 Annotation 4 Annotation 3 File 4 26 …

  27. 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 File 1 Table 1 Entity type table (for ann1, 2, …) … File 2 Context type table (for ann1, 2, …) OBOE-aware DB File 3 Offline data processing (raw data loading) Annotation 1 Annotation 2 Annotation 4 Annotation 3 File 4 27 …

  28. Data materialization Map (for ann1, 2, …) Measurement type table (for ann1, 2, …) Table 4 Measurement table Table 3 Observation type table (for ann1, 2, …) Observation table Table 2 File 1 Table 1 Entity type table (for ann1, 2, …) Entity table … File 2 OBOE-aware DB Context type table (for ann1, 2, …) Context table File 3 Offline data processing (data materialization) Annotation 1 Annotation 2 Annotation 4 Annotation 3 File 4 28 …

  29. 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 Entity table (for file 1, 2, …) File 1 Table 1 Entity type table (for ann1, 2, …) … Context table (for file 1, 2, …) File 2 Context type table (for ann1, 2, …) OBOE-aware DB File 3 Annotation 1 Annotation 2 Annotation 4 Annotation 3 File 4 29 …

  30. Query strategy 1 Measurement Table (for file 1, 2, …) Online query engine (query re-writing over raw data) 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 Entity table (for file 1, 2, …) Table 1 Entity type table (for ann1, 2, …) … Context table (for file 1, 2, …) Context type table (for ann1, 2, …) OBOE-aware DB 30

  31. Query strategy 2 Measurement Table (for file 1, 2, …) Online query engine (query re-writing over materialized data) 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 Entity table (for file 1, 2, …) Table 1 Entity type table (for ann1, 2, …) … Context table (for file 1, 2, …) Context type table (for ann1, 2, …) OBOE-aware DB 31

  32. Query strategy n?? Measurement Table (for file 1, 2, …) Online query engine 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 Other materialization/de-normalization?? RDF triple store? Entity table (for file 1, 2, …) Table 1 Entity type table (for ann1, 2, …) … Context table (for file 1, 2, …) Context type table (for ann1, 2, …) OBOE-aware DB 32

  33. Ontology Editing Tools • Protégé plug-in • For creating and editing OBOE-compatible ontologies • Form-based UI • Generates “low-level” OWL constraints/axioms

  34. 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 34

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