1. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Discovery Seminar 175555/UE 141 M – Fall 2008 Solving Crimes using Referent Tracking Using Aristotelian definitions to build an ontology --- Introduction --- October 1, 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 Correction of homework

3. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Homework of last week Several students gave distinct descriptions of what they understood “killing” to be. Plot the 4 distinctions shown on the next slide on the semantic triangle, PLUS one other description that you find in some dictionary. –This means: give for each meaning an Aristotelian definition which is such that: There is only one interpretation possible For each event which might be a killing, at least one of the definitions is applicable DUE: Monday Sept 29, before 10 PM, by email as usual.

4. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Students found 4 distinct meanings for ‘killing’ time Weiss’ shooting of Long Carl Weiss’ living Bodyguards’shooting of Weiss Weiss’s path. body reactions Long’s pathological body reactions Senator Long’s living k1 k2 k3 k4

5. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Good definitions Give an if-and-only-if condition for when an entity satisfies that definition One type of good definitions: Aristotelian definitions An X is a Y which C where ‘Y which C’ satisfies the if-and-only-if condition

6. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Good definitions A B types particulars Instance-of extension of Aextension of B

7. New York State Center of Excellence in Bioinformatics & Life Sciences R T U S4 This is the entity level image of a killing. This allows one to determine if one was killed or not. An image of a deceased body with multiple bullet wounds would conclude in that person being killed. In our case Weiss’s body after being mutilated by Long’s bodyguards would have one determine that Weiss was killed. This is the actual term “killing.” This is when a person dies from whatever reasons caused by someone else. When a person is shot, he may not die right away, but the wounds they receive from another person will kill them. In our case, Weiss shot Long mortally wounding him. Once Long died, then the killing happened. When Long’s bodyguards shot Weiss, they killed him immediately with an onslaught of bullets. This is type level definition of killing. This will provide characteristics that will separate it from other entities. A killing is where one dies of unnatural causes at the expense of another person. The other person is labeled the killer and is attempting to take the life of another person. In our case Weiss was the killer. He attempted to take the life of Long, and was successful in the end when Weiss was labeled dead or officially killed. Long’s bodyguards are labeled killers as well, because they meant to shoot and kill Weiss. Dictionary: According to Merriam-Webster’s online dictionary, killing can be defined as: kill transitive verb1 a: to deprive of life : cause the death of b (1): to slaughter (as a hog) for food (2): to convert a food animal into (a kind of meat) by slaughtering 2 a: to put an end to b: defeat, veto c: to mark for omission ; also : delete d: annihilate, destroy 3 a: to destroy the vital or essential quality of b: to cause to stop c: to check the flow of current through4: to make a markedly favorable impression on 5: to get through uneventfully ; also : to get through (the time of a penalty) without being scored on 6 a: to cause extreme pain to b: to tire almost to the point of collapse7: to hit (a shot) so hard in various games that a return is impossible.defeatvetodeleteannihilatedestroy Using these definitions in the situation between Long and Weiss only some can apply. Definition “a” can be used in the situation where Weiss caused the death of Long, and where Long’s bodyguards caused the death of Weiss. Def. d can be used as well, Long’s bodyguards destroyed Weiss after he shot Long. All the other definitions are different ways we use kill in everyday language. 10%No single Aristotelian definition is given.

8. New York State Center of Excellence in Bioinformatics & Life Sciences R T U S1 Oxford American dictionary: Killing: cause the death of K1) Killing occurred when Weiss shot at Long, intending to kill him, and ended when the bullets ceased fire. K2) Killing occurred when the bullets were all fired at Long K3) Killing occurred as pathological body reactions occur after he was shot (but not necessarily killing him) K4) Killing occurred when all of Long's organs ceased to function. 10%No single Aristotelian definition is given.

9. New York State Center of Excellence in Bioinformatics & Life Sciences R T U S10 1. Killing – (linguistics) kill, waste, slay, destroy, put an end to 2. Killing – (ontology) the act of a living thing putting another living thing to death. 3. Killing – (epistemology) the explosion of a person’s head b y another person, destroying their brain and causing death.-the slicing off of a person’s head, causing death. 4. killing – (definition) to deprive of life: cause the death of Reference: http://www.merriam-webster.com/dictionary/kill[1]http://www.merriam-webster.com/dictionary/kill Answer does not address K1, K2, … K2 and K3 are Aristotelian, but do not correspond with what was asked 15%

10. New York State Center of Excellence in Bioinformatics & Life Sciences R T U S14 1.The killing started when Weiss began shooting Long, and ended with the cease fire. It is the act that procedes and causes the fatal wounds. 2.The killing occurred when Weiss finished firing the bullets at Long and had sustained injury. 3.The killing is the pathological body reactions in the time it took after he was shot until is body stopped functioning. 4.The killing occurred when Long's body died. The legal definition of death is “irreversible cessation of all function of the entire brain, including the brain stem.” 5.According to the Oxford American Dictionary – “cause the death of (a person, animal, or other living thing)” K1 is half Aristotelian K3 is “sort of” Aristotelian: definitions are general, never specific. The others are not at all. 15%

11. New York State Center of Excellence in Bioinformatics & Life Sciences R T U S13 K 1: ‘Killing’ is the act of intentionally ending the life of a human that was once alive and conscious of life. –This definition of ‘killing’ applies to when Weiss attempts to terminate the life of Senator Long with the shooting of his gun although Long ‘dies’ hours later. K2: If the ‘Killing’ of Long was done with malice, then when Weiss shot Long it can be considered as manslaughter, even though Long did not die instantly. The death of his body stemmed from the later reactions of his body against his injuries caused by the gun shots. K3: ‘Killing’ occurs after Weiss shot the body of Long and Long, who was once conscious, loses consciousness due to the impacts of his injuries sustained from the shots in his body. K4: Though the person does not ‘die’ instantly after they are ‘killed’ does not mean that the person who shot them are not murderers. When the victim actually ‘dies’ does not determine whether it was a murder because initial events that were triggered by motivations cannot be altered. –Weiss was motivated to shoot Long so he fired the gunshots and ‘killed’ Long however he was also shot by Long’s bodyguards and died before Long died. However, his initial attempt at ‘killing’ Long cannot be changed because he did in fact shoot and injure Long which later caused Long’s body to react and ultimately lose consciousness. Definition of a “killing”: ‘killing’ of a human being, without the authority of law, is justifiable homicide; unless associated otherwise with premeditation and or motivation, malicious intentions. K1 is ok in form, but the restriction to humans is questionable K2, K3 and K4 are not defined. Where did the dictionary definition come from ? That is pure nonsense ! 20%

12. New York State Center of Excellence in Bioinformatics & Life Sciences R T U S12 K1: The attempt to kill someone.. ex: Weiss shoots long but not killing him instantly but causes him to die in the future. K2: The causing of an injury that later causes death. ex: Weiss shoots long later cause it to become a fatal injury. K3: The beginning of the execution. ex: long body reaction to the bullet later cause him to die. K4: killing occur at death. ex: long was killed from his severe body reactions. Dictionary.com "the act of a person or thing that kills" 20% Only K2 is Aristotelian, but unfortunately questionable.

13. New York State Center of Excellence in Bioinformatics & Life Sciences R T U S11 (summarized) According to www.dictionary.refrence.com, "kill" and the verb "killing" has several definitions …www.dictionary.refrence.com K1. "Killing" to deprive of life : cause the death of. ex. Long's bodyguards takings Weiss's life away K2. “Killing” is the act of causing fatal injuries to the victim ex. The injury that Weiss inflicted into Long, which eventually lead to his fatality K3. “Killing” is when the pathological body reactions that result from fatal injuries end in the person’s death ex. After clinging to life for thirty hours the bullet that entered Long lead to his death K4. “Killing” is the death of a person in a case where the death was caused by another person who knowingly caused fatal injuries ex. All the shooters in this senerio were mentally coment man who knew what they were doing they shot to kill in both situations. 30% Only K2 and K4 are Aristotelian, but unfortunately questionable.

14. New York State Center of Excellence in Bioinformatics & Life Sciences R T U S7 K1: Linguistics: a killing is an act which is also known as manslaughter or, in some cases, murder (when the perpetrator intends for the victim to die) –Ontology: a killing is an act which causes fatal injuries to the victim –Epistemology: a killing is an act in which the victim receives wounds from the perpetrator, the wounds result in the victim’s death. –Example: A person is killed by a mugger who stabs the victim in order to secure time to run away. The killing happens when the stabbing does. K2 Linguistics: a killing is an act which is also known as manslaughter or, in some cases, murder (when the perpetrator intends for the victim to die) –Ontology: a killing is the action that happens after a person is fatally injured and just before the body’s pathological reactions (causing death) occur –Epistemology: a killing is a completed act in which the perpetrator causes injuries to the victim; injuries will directly result in the victim’s death (no way for the victim to survive, even with medical help) –Example: Bobby is hit in the head with a baseball bat. He falls into a coma and then dies one week later. The killing occurred when he was hit. K3 Linguistics: a killing is an act which is also known as manslaughter or, in some cases, murder (when the perpetrator intends for the victim to die) –Ontology: a killing is an action that occurs when the pathological body reactions that result from fatal injuries end in the person’s death –Epistemology: a killing is an act in which injuries received result in pathological body reactions that end in the victim’s death –Example: Jane is in a car accident with a drunk driver and bleeds to death from her injuries. The killing occurs as she loses the blood. K4 Linguistics: a killing is an act which is also known as manslaughter or, in some cases, murder (when the perpetrator intends for the victim to die) –Ontology: a killing is an act in which the death of a person is caused by another person who knowingly caused fatal injuries –Epistemology: a killing is an intentional act in which the injuries result in victim’s death –Example: Billy, a soldier, is shot while fighting in a war. The person who shot him knew that the shot would kill Billy and still pulled the trigger. K5 Linguistics: a killing is an act which is also known as manslaughter or, in some cases, murder (when the perpetrator intends for the victim to die) –Ontology: a killing is an act that causes death or extinction; is fatal –Epistemology: a killing is an act in which something or someone causes the victim’s death –Example: Joy pushes Claire off of a cliff. Claire dies immediately upon hitting the ground. She was therefore killed by Joy because the fall resulted in her death. Citation: killing. (n.d.). The American Heritage® Dictionary of the English Language, Fourth Edition. Retrieved September 11, 2008, from Dictionary.com website: http://dictionary.reference.com/browse/killinghttp://dictionary.reference.com/browse/killing 90%

15. New York State Center of Excellence in Bioinformatics & Life Sciences R T U S2 (summarized) 1.Merriam-Webster Dictionary definition of killing is: … 2.K1: ‘Killing’ is an action that an individual attempts to extinguish life of another; consequences, disregarded. 3.K2 defined ‘killing’ as, ‘an act where the murderer implants wound-potential cause of death by means of pathological reaction- to the victim; result, disregarded.’ 4.K3 definition of ‘killing’ is ‘a resulting process of murderer’s action in which an individual’s life is extinguished by the means of body’s pathological reaction.’ 5.K4 definition of ‘killing’ is strict and factual. ‘Killing’ is an action in which the consequence is absolute and certain death of the victim. 99% This is excellent and exemplatory work. Only minus is that the dictionary definition is not translated in Aristotelian form.

16. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Building an Ontology

17. New York State Center of Excellence in Bioinformatics & Life Sciences R T U ‘Ontology’ in philosophy = the study of what exists Key questions: –What exists ? –How do things that exist relate to each other ? Some hypotheses: –An external reality, time, space –Particulars, universals, objects, processes –Ideas, concepts –God Ontologists from distinct ‘schools’ differ in opinion about the existence of some of the above: –Realism, nominalism, conceptualism, monism, …

18. New York State Center of Excellence in Bioinformatics & Life Sciences R T U ‘Ontology’ in software engineering = an explicit formal representation of entities that are assumed to exist in some area of interest Come in various flavors: –Reference ontologies –Application ontologies –Domain ontologies –Top-level ontologies

19. New York State Center of Excellence in Bioinformatics & Life Sciences R T U However … Although (almost) everybody (knowledgeable) agrees that –an ontology is a representation, there is a huge variety in –what the representational units in an ontology stand for, if anything at all, –the degree to which the structure of the ontology corresponds with the structure of that part of reality it intends to represent.

20. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Major problems 1.A mismatch between what is - and has been - the case in reality, and representations thereof in: a)(generic) Knowledge repositories, and b)(specific) Data and Information repositories. 2.An inadequate integration of a) and b). Solutions Philosophical realism Realism-based Ontology Referent Tracking PhilosophyHITPhilosophyHIT

21. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Philosophical Realism Basic assumptions: 1.reality exists objectively in itself, i.e. independent of the perceptions or beliefs of cognitive beings; 2.reality, including its structure, is accessible to us, and can be discovered; Various forms, e.g. –Naive realism: things really are as they seem –Scientific realism: things really are as science determines (or ultimately will determine) them to be; science discovers objective truths; mistakes can be made, but don’t invalidate the enterprise.

22. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Realism-based ontology Three levels of reality: 1.First-order reality: what is on the side of persons, organizations, … 2.Cognitive representations: what cognitive agents assume to observe and know ‘in their mind’ 3.Representational artefacts for communication, documentation, … Terms, definitions, drawings, images, … Assumption: The quality of an ontology is at least determined by the accuracy with which its structure mimics the pre-existing structure of reality. 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

23. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Compare with Alberti’s grid reality representation Ontological theory

24. 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; 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

25. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Reality exist before any observation R

26. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Reality exist before any observation R And also most structures in reality are there in advance.

27. 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; 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

28. New York State Center of Excellence in Bioinformatics & Life Sciences R T U The ontology author acknowledges the existence of some Portion Of Reality (POR) R B

29. New York State Center of Excellence in Bioinformatics & Life Sciences R T U R B Some portions of reality escape his attention.

30. 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

31. New York State Center of Excellence in Bioinformatics & Life Sciences R T U R He represents only what he considers relevant O B #1 RU 1 B1 RU 1 O1 Both RU 1 B1 and RU 1 O1 are representational units referring to #1; RU 1 O1 is NOT a representation of RU 1 B1 ; RU 1 O1 is created through concretization of RU 1 B1 in some medium.

32. 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

33. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Continuants (aka endurants) –have continuous existence in time –preserve their identity through change –exist in toto whenever they exist at all Occurrents (aka processes) –have temporal parts –unfold themselves in successive phases –exist only in their phases Continuants versus Occurrents

34. New York State Center of Excellence in Bioinformatics & Life Sciences R T U You are a continuant Your life is an occurrent You are 3-dimensional Your life is 4-dimensional

35. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Dependent entities require independent continuants as their bearers There is no run without a runner There is no grin without a cat

36. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Dependent vs. independent continuants Independent continuants (persons, knifes, buildings) Dependent continuants –qualities : sharp, red –shapes : round, square –roles: judge –propensities: breakable –functions: to make noise

37. New York State Center of Excellence in Bioinformatics & Life Sciences R T U All occurrents are dependent entities They are dependent on those independent continuants which are their participants (agents, patients, media...) –Stabbing –Punching –Running

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