Integration and Representation of Geological Knowledge with Semantic Web Technologies

1. Integration and Representation of Geological Knowledge with Semantic Web Technologies Hassan BabaieDepartments of Geosciences & Computer Science, GSU www.gsu.edu/~geohab

2. Outline of the talk • Define the Semantic Web (SW) and its benefits • Ontological view to the world • Categorize real entities into two disjoint sets • Define taxonomy and meronomy of processes and events and their relational semantics • How knowledge is modeled in an ontology • What is a knowledge base • Semantic Web languages – geological examples

3. Present Web • Most of the resources on the current Web are available in weakly structured form such as text, audio, and video, making it difficult to search, extract, maintain, discover, and view the information content embedded in them • The main aspect of the current document-centric Webis that the information sources which are presented on it, including those automatically generated from databases, often lack semantics, and understanding the meaning of the terms is the responsibility of the knowledgeable human users • These users interpret the meaning of the terms and sentences based on their context and own experience and know-how

4. Knowledge infrastucture • The Semantic Web is transforming the role of the current Web from carrier of data to consumer and transformer of information and knowledge “Learning is less about getting data than it is about using the knowledge behind the data!” • We have entered a decade that brings us an era in which societies of ontology-based software agents • Automatically collect Web content through Semantic Web services provided by diverse global sources • Process the information coming from distributed knowledge bases and databases, and • Exchange the results with other agents

5. Semantic Web • Semantic Web helps building models, applying taxonomies and partonomies, to understand a complex reality, constructing reasoning machines that can draw conclusions from formalized, encoded knowledge (applying language inference rules), and exchanging distributed knowledge on a global scale (applying URI) Complex geological reality Globally exchange knowledge A Encode Knowledge B C D E F Structure the reality Reason Infer

6. Current state of affairs • Compounded on the lack of accuracy and inefficiency in linking the data, the sheer volume of Earth data, collected by modern instruments, requires machine processing, which can be provided with the Semantic Web technologies • Currently, changes that occur in the dataof one sub-community or department are commonly not traceable in other parts of the community

7. How can the Semantic Web help? • Inference, i.e., extracting implicit data from what is explicitly asserted, is very difficult and challenging using traditional databases, because the semantics of the data is not globally defined • Semantic web can help linking disconnected data, collected by different individuals or groups • In the Semantic Web model, as is in scientific research, “Anyone can say Anything about Any topic” [AAA]

8. SW is a specification for data modeling • Semantic Web languages, such as OWL and RDF/S, conform to a well defined set of theorems, with clear meanings (semantics) that are founded on the set theory • So, how can the Semantic Web help? It would allow all data sources and applications, and domain rules to have an RDF (a graph data model) interface, practically providing them with cheaper and automatic global (Web-scale) exposure and integration capability, powerful search, and inherent inference-based reasoning

9. Knowledge is the key! • Geoscientific knowledge will be structured to provide meaning for the immense volumes of seemingly unrelated data and information on the web • The Semantic Web technologies allow us to formally structure the knowledge in every discipline as a series of integrable ontologies

10. Ontological view to the world • Each part of the Earth system includes material, concrete things (objects) that exist, at specific times independent and outside of our minds, as substantial individuals(e.g., Brevard Fault zone) • Each object (individual), including the Earth itself, denoted by a special signorsymbol (e.g., a term in natural languages such as ‘fault’), is referenced by a concept that instantiates a universal type (e.g., Fault)

11. Individual vs. Universal • While objects exist in space and time (e.g., Brevard Fault), the universal is a construct (e.g., Fault) that exists only in our mind • ‘Brevard Fault’ (a symbol), which refers to a specific, real fault (an object) in SE USA, instantiates the universal type ‘Fault’

12. Properties • Every part of the Earth system, as a substantial object, is endowed with a series of properties, which represent relationships among objects, and their attributes • The real, individual Brevard Fault is one of many objects in the Fault class, which conform to this universal type by possessing the set of properties that characterizes Fault

13. Properties are related  = Ee • Scientists have discovered that properties in a given type are related to each other through physical (natural) lawsthat are defined for the universal type, and that are themselves complex properties • For example, the linear law of elasticity, that relates stress () and strain (e), applies to rocks deforming at shallow depths, under a restricted range of mechanical and environmental conditions (e.g., low e, , T)

14. Entity Types of entities Endurant Perdurant • Entities occupy space and time • Entities on the surface of the Earth, below its surface, and in the atmosphere around it, can be grouped, based on their mode of existence and persistence, into two general, non-overlapping (i.e., disjoint) categories: • Enduring entities (endurants, continuants) • Perduring entities (perdurants, occurrents)

15. Enduring entities • Include substantial objects (both material and immaterial) such as: • fault, water, gas, subduction zone, • mylonite, and cave (an immaterial entity) • Occur in all Earth’s subsystems • Have spatial parts that exist at all time instants, ti • All ordinary things, e.g., fault, rock • Database record of an outcrop or a mineral

16. Endurants keep identity • Continuants endure by preserving their(same but not necessarily exact) identitythrough time despite the continuous change in their property, e.g., , in their length, density, and temperature • Occur as complete wholes, in spatial regions • This means that, at each instant of time, an endurant object occurs in its entirety, i.e., it persists as a self-connected mereological whole(e.g., Brevard Fault, Chattahoochee River)

17. Perdurant entities • The perdurant (occurrent) Earth objects such as processes, events, on the other hand, occur in intervals of time (ti+n-ti) through a succession of temporal parts(phases, stages), which are different from the whole • An example is a video of a hurricane or tsunami, taken over a period of time by a satellite, showing different phases of the same hurricane or tsunami

18. An earlier temporal part (phase, stage) of the perdurant Katrina Hurricane

19. A later temporal part (phase, stage) of the perdurant Katrina Hurricane

20. Perdurants … • Perdurants such as processes(e.g., eruption) unfold themselves over time and, at each time slice (t)they present an incomplete part of the whole, meaning that they are mereologically incomplete (i.e., does not occur in its entirety) • A perdurant whole unfolds over a time interval by adding temporal parts • Past parts do not exist anymore!

21. Two types of perdurant • Event • Happens in an instant of time, t • Defines the boundaries of states of entities • Start and end processes and subprocesses • e.g., the beginning/ending instants of a volcanic eruption

22. Process • Is an spatio-temporal that brings state change to the endurants (Folding deforms Bedding) • May occur over several spatial and temporal regions, e.g., landslide, deformation, hurricane • May not be a whole (e.g., sub-process) • A complex process is an inhomogeneous aggregate of two or more processes of different types (e.g., parts of an eruption include pyroclastic flow, mudflow)

23. Need ontologies • For spatial and spatio-temporal entities, a database or knowledge base should be able to answer the questions of the following types: • Where were the P- & S-waves5 s after a seismic rupture? • Which process followed the melting of ice on a volcano 10 minutes after the eruption of lava? • Was pyroclastic flow partially synchronous with lahar? • The answers require time and process ontologies

24. Values for the properties of classes and their properties store into a knowledge base An ontology is a formal model of reality, i.e., of objects and their relations TimeInstant begins-at/ends-at Event TimeInterval bounded-by occurs-in causes involves Process Process Object participates-in is-a is-a p Sub-Process Object Object Fold has Axial Plane A knowledge base instantiates an ontology, such as the above, with values

25. Ontologies are based on logic e.g. formalizing a sub-process ending a process • End of pyroclastic ejection (i) ending a period of volcanic eruption (j) • i is a final sub-interval of j • i and j end together beg(j) < beg(i)  end(i) = end(j) occursi(E, i) = e (type (e, E)  time(e) = i) Meaning: Event E occurs in interval i if there exists e, an occurrence of E, whose time of occurrence is interval i Pyroclastic ejection beg(i) end (i) beg(j) end (j) Eruption

26. We acquire data about individuals • The reality is populated by the instancesof the universal types, e.g.: San Andreas Fault, Idaho batholith • To gain and improve knowledge about the universals, geologists acquire data about the instances of the spatial and process entitiesin the field and laboratory, and through experimentation, simulation, and computation

27. Information makes sense with knowledge • A collection of datamay become meaningful and useful, i.e., become information, when they are put together, e.g., in a plot or map • Same information may be interpreted differently applying different knowledge based on different truths, beliefs, perspectives, judgments, and know-how! • Information, is therefore, the meaning of the data based on background knowledge

28. Knowledge • Knowledge is a collection or total sumof true beliefs (statements) about real objects in a field (domain), which can be used to make a decision. True statements: • Clay has low permeability • Rocks are made of one or more minerals • Cleavage is a planar structure • The true beliefs are mainly about universals (i.e., types of things such as fault, mineral), but also include facts about individuals

29. Knowledge fragments • Knowledge, which is stored in people’shead, books, and scientific journals, is a collection of true statements: • Rock is made of one or more minerals x y [Rock (x)  Mineral (y)  has-Part (x, y)] • Thrusting moves older rocks on younger rocks x y z [Rock (x)  Rock (y)  Thrusting (z)  older (age(x), age(y))  involves (z, x)  involves (z, y)  moves (onTop (x, y))] • Mylonite forms in some ductile shear zone x y [Mylonite (x)  DuctileShearZone (y)  forms-in (x, y)]

30. What is knowledge base (KB)? • A knowledge-base uses an ontology to translate the knowledge fragments into a machine-understandable and processable code CataclasticFlow forms Gouge • Ontology is a formal, explicit model of the domain knowledge, which describes the terms and their relationships, and is built using semantic languages of RDF, RDFS, and OWL

31. KB has explicit assertions • LaramideOrogeny deformed most rocks in Wyoming during the Late Cretaceous period: x y i [Orogeny (x) Laramide (x)  Rock (y)  located-in (y, Wyoming)  TimeInterval (i)  Deformed (x, y) during (Period (i, “Late Cretaceous”))] • Crystal-plastic deformation involves recrystallization, recovery, or both: x y z [CrystalPlasticDeformation (x) has-Part (Recrystallization (y)  Recovery (z))]

32. Inference Rules • Computers can also make use of information through inference rules if we explicitly formalize our knowledge with specific rule-based machine language and logic • Automatic processing of information and performing inference about it requires specific languages (e.g., RDF, RDFS, and OWL) with built-in inference rules

33. FaultRock Entailment forms CataclasticFlow CataclasticRock Gouge • Knowledge-based model of reality (ontology), represent the semanticsof our knowledge by identifying real domain objects, and modeling the relationships among these objects and processes that involve them • Ontologies have embedded metadata and inference rules, that can be used to draw implicit entailments from the explicitly asserted facts

34. Benefits of Inference Rules • The inference-based semantics is very powerful for the integration of heterogeneous data coming from autonomous, distributed sources on the Web • The reason is that RDFS and OWL inferencing query engines, that know OWL inference rules, will infer (during a query) unasserted information from the directly asserted triples in the RDF store

35. KB returns inferred statements struc:FaultRockrdfs:subClassOfpetr:Rock. struc:Myloniterdf:typestruc:FaultRock. • SPARQL query: Find things that are of type Rock ?x rdf:typepetr:Rock. • Despite the fact that there is no statementin the above triple store, with predicate rdf:type and object petr:Rock, the query will return the following inferred result using the • RDFS’s inference query engine: ?x = struc : Mylonite. (i.e., the reasoner infers: Mylonite) Rock FaultRock Mylonite

36. AccretionaryPrism Accretion occursDuring forms An ontology Subduction is-a Endurant objectNankai Accretionary PrismPerdurant (process): AccretionSub-processes: Offscraping, underplating, subduction erosion Offscraping Underplating SubductionErosion

37. Formal temporal relations

38. Life of an Endurant • Endurants (e.g., lava) are created(P1: eruption), transformed(P2: cooling), or destroyed (P3: erosion) by perdurants (processes, Pi) • e.g., in the case of an eruption (P1), the change occurs between the instant the lava starts to erupt (event E1) and the instant it completely freezes (event E2) • Perdurants change the state of the endurants over time intervals • Endurants keep their state between start & end events • But begin to change their properties at events

39. State • At any instant of time, the state of any object (e.g., rock) that participates in a process (e.g., deformation), defined by the collection of values for its properties, is in constant flux • The change of state (e.g., crystallization of magma), a subject of study by Earth scientists, occurs in a lawful state space, which is constrained by the properties, the physical laws, and environmental conditions

40. Lawful State Space • An endurant object X(e.g., fault) has a lawful state space SL(X), which represents the collection of its possible states (e.g., sliding, stuck, but not swimming!) over time (through its properties) • The lawful state space is a subset of a larger conceivable state space: SL(X)  S (X) • For every object, there is a series of lawful states: Si(x), Sj(X), …  SL(X)

41. State Trajectory • Every possible state of a thing is givenby a point Siin the lawful state space SL(X) • The trajectoryof the actual state of a thing at a given time and space, represents the actual change (due to processes between events) for the individual • FunctionF(e.g., constitutive law) maps the states (Si) w.r.t. a reference frame, along the state trajectory • History is a segment of the trajectory between Si • Transition from state S1 to S2 occurs in a possible event space, E(x), which starts a series of processes characterized by specific functions

42. Fault_Rock is_a How does science advance? forms Crystal Plastic Deformation Mylonite • For example, the state space for rock deformation (a process) is within the range of pressure and temperature (conditions) in which rocks (endurants) remain solid (state) • Science progresses by discovering new properties and laws that restrict the relationship among properties for a given universal type, and the processes that change the state of objects that conform to the type

43. Spatial and Temporal Regions Temporal Region: interval of time in which active processes (tsunami) act on the interacting endurant objects that happen to be present in the spatial region where the starting/ending events occur Spatial Region: space in which the objects of our interest (e.g. tsunami) occupy a specific interval of time Sumatra Tsunami 120 0 60 180 Time (min) Temporal region

44. Representing spatial and temporal regions • Depending on granularity of our study, the spatial region can be represented as: • a point, with long/lat or KML point • a polygon on a GIS layer • an address (e.g., Fernbank Museum) • Temporal data can refer to: • instants (e.g., October 18, 2009 at 10:00 AM) • Discrete interval of time (Thanksgiving) • Continuous period of time (Century, Triassic)

45. Handling spatio-temporal knowledge • Geological processes occur in spatial and temporal regions, i.e. spacetime • For example, the seismic rupture that started the tsunami, initiated the propagation of a series of different types of seismic and tsunami waves, which occupied different spatial regions at different time intervals Sumatra tsunami in spacetime

46. Process Relations • Processes can occur synchronically (i.e., within same time intervals) or polychronically, involving same or different endurant objects, in the same or different spatial regions • The temporal region of an aggregate process (e.g., deformation) may be divided into several sub-intervals within which unique, but possibly (causally) related, sub-processes occurred

47. Processes and spacetime

48. Taxonomy of Processes • Processes can be organized in hierarchical structures using the ‘is-a’ and ‘part-of’ relations, reflecting specialization and part-whole relations • If a process P subsumes another process P1(i.e., P1 is-a P), then for all x, if x is an occurrence ofP1, x is also an occurrence of P x P1(x)  P(x) • Oxidation is-a Weatheringor Folding is-a Deformation, states that instances of Oxidation or Folding are also instances of the Weatheringor Deformationprocesses, respectively P BrittleDeformation is-a P1 Cataclasis

49. OWL (Web Ontology Language) <ow:Classrdf:about=“BrittleDeformation”/> <owl:Classrdf:about=“Cataclasis”> <rdfs:subClassOfrdf:resource=“BrittleDeformation”/> </owl:Class> BrittleDeformation is-a Cataclasis OWL code snippet, part of Structural Geology ontology, asserting that Cataclasis is a type of Brittle Deformation

50. The actual (individual) occurrences of grain boundary migration recrystallization that occur during an actual mylonitization in a specific shear zone, are also occurrences of dynamic recrystallization which is a mechanism of crystal plasticity These explicit assertions imply (through OWL’s inference rules) that the actual (individual) mylonite that participated in the sub-process also participated in the super-process (i.e., crystal plasticity) CrystalPlasticDeformation is-a DynamicCrystallization is-a GrainBoundaryMigration • <owl:Classrdf:about=“CrystalPlasticDeformation”/> • <owl:Classrdf:about=“DynamicRecrystallization"> • <rdfs:subClassOfrdf:resource=“CrystalPlasticDeformation”/> • </owl:Class> • <owl:Classrdf:about=“GrainBoundaryMigration"> • <rdfs:subClassOfrdf:resource="DynamicRecrystallization”/> • </owl:Class>