1. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Discovery Seminar 035158/UE 141 MMM – Spring 2008 Solving Crimes using Referent Tracking Building a Realism-based Crime Ontology - Realism-based Relationships - March 5 through 31, 2008 Werner CEUSTERS Center of Excellence in Bioinformatics and Life Sciences Ontology Research Group University at Buffalo, NY, USA

2. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Three levels of reality 1.The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; 2.Cognitive agents build up ‘in their minds’ cognitive representations of the world; 3.To make these representations publicly accessible in some enduring fashion, they create representational artifacts that are fixed in some medium. Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

3. New York State Center of Excellence in Bioinformatics & Life Sciences R T U R Three levels of reality O B #1 RU 1 B1 RU 1 O1

4. New York State Center of Excellence in Bioinformatics & Life Sciences R T U A realist view of the world The world consists of –entities that are Either particulars or universals; Either occurrents or continuants; Either dependent or independent; and, –relationships between these entities of the form e.g. is-instance-of, e.g. is-member-of e.g. isa (is-subtype-of) Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

5. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Top-Level Ontology (1) Continuant Occurrent (always dependent on one or more independent continuants) Independent Continuant Dependent Continuant RoleFunctionPropensity

6. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Top-Level Ontology (2) Continuant Occurrent (always dependent on one or more independent continuants) Independent Continuant Dependent Continuant RoleFunctionPropensity Spatial Region Temporal Region Process

7. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Relationships The way in which continuants and occurrants stand to each other. Example: –Prisoner:a person who is confined in prison The naïve solution: –Prisoner is-confined-in prison

8. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Problems with ‘Prisoner is-confined-in prison’ Structure of language does most often not reflect the structure of reality –‘is-confined-in’ is not an ontological relation What does it actually mean ? –Some/All prisoners are-confined-in some/all prisons ? Is a prisoner, while transferred from one prison to another one not anymore a prisoner ? Is the van or bus in which a prisoner is transported a prison ? …

9. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Three basic sorts of relationships universal particular humans are mammals Werner Ceusters instance-of human Werner Ceusters’ nose part-of Werner Ceusters

10. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Universals and classes universal PPPP PPPP PPPP instance-of extension-of member-of class Defined class e.g. human e.g. all humans e.g. all humans in this room

11. New York State Center of Excellence in Bioinformatics & Life Sciences R T U General principle about relationships All universal level relationships are defined on the basis of particular level relationships

12. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Primitive instance-level relationships c instance_of C at t - a primitive relation between a continuant instance and a class which it instantiates at a specific time p instance_of P - a primitive relation between a process instance and a class which it instantiates holding independently of time c part_of c1 at t - a primitive relation between two continuant instances and a time at which the one is part of the other p part_of p1, r part_of r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other) c located_in r at t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time r adjacent_to r1 - a primitive relation of proximity between two disjoint continuants t earlier t1 - a primitive relation between two times c derives_from c1 - a primitive relation involving two distinct material continuants c and c1 p has_participant c at t - a primitive relation between a process, a continuant, and a time p has_agent c at t - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process

13. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Is_a is defined over instance-of (1) For continuants C is_a C1 = [definition] for all c, t, if c instance_of C at t then c instance_of C1 at t. For occurrents P is_a P1 = [definition] for all p, if p instance_of P then p instance_of P1.

14. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Is_a is defined over instance-of (2) human being living creature me universals particulars is_a instance-of at t

15. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Is_a is defined over instance-of (3) childadultcaterpillarbutterfly human being living creature animal me More than subset or inclusion ! is_a Instance-of t1t2

16. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Transformation Derivation continuation fusion fission

17. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Part-of different for continuants and occurrents methis walking human being Instance-of at t living creature Is_a walking Instance-of my left leg this leg moving leg moving leg process Instance-of at t Is_a Instance-of part-of at t part-of

18. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Part-of can be generalized, … with care ! me human being Instance-of at t living creature Is_a my left leg part-of at t leg Instance-of at t C part_of C1 = [def] for all c, t, if Cct then there is some c1 such that C1c1t and c part_of c1 at t. Cct = c instance-of C at t

19. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Part-of can be generalized, … with care ! me human being Instance-of at t living creature Is_a my left leg part-of at t leg Instance-of at t C part_of C1 = [def] for all c, t, if Cct then there is some c1 such that C1c1t and c part_of c1 at t. Cct = c instance-of C at t Part-of ?

20. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Part-of can be generalized, … with care ! me human being Instance-of at t living creature Is_a my left leg part-of at t leg Instance-of at t Horse legs are not parts of human beings Amputated legs are not parts of human beings ‘Canonical leg is part of canonical human being’, but…, there are (very likely) no such particulars … Part-of ?

21. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Generalization of temporal parthood this walking walking Instance-of this leg moving leg moving process Is_a Instance-of part-of P part_of P1 = [definition] –for all p, –if Pp –then there is some p1 such that: P1p1 and p part_of p1

22. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Two sorts of temporal parthood (1) methis walking Has-participant at t 2 walking Instance-of my left leg part-of at t this leg moving leg moving part-of process Is_a Instance-of Has- Participant at t ‘longitudinal’: one process evolves as part of another one. May involve stronger relationships of other types, e.g. causal

23. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Two sorts of temporal parthood (2) Cuts cross temporal entities this walking this leg moving this foot moving t

24. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Assignment (1) Analyze ontologically the following: –A prisoner is a person held in confinement against his will. –Prisoners are of two kinds, those lawfully confined, and those unlawfully imprisoned. –Lawful prisoners are either prisoners charged with crimes, or for a civil liability. –Those charged with crimes are either persons accused and not tried, or those who have been convicted of crimes. –Prisoners in civil cases, are persons arrested on original or mesne process, and prisoners in execution.

25. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Assignment (2) Identify: –the minimal numbers of particulars involved for each type of prisoner; –the universals, classes and defined classes involved; –The relationships, drawn from the ones discussed in this presentation. Execution: –Draw schemas as the ones in this presentation. –In group, starting during class of March 19, continued March 26, to be delivered March 31 at the latest.