switch on Webex

1. switch on Webex

2. Examples of new ontologies using BFO • Actionable Intelligence Retrieval System (AIRS) • US Transcom (Transportation Command) Enterprise Ontology (http://www.securboration.com/) • Mental Functioning Ontology (MFO), Emotion Ontology (MFO-EM) • Financial Report Ontology: FRO • here BFO (and IAO) must be under the hood

3. FMA: BFO under the hood

4. Blue Force Overwatch The Plant Ontology

5. cROP: Common Reference Ontologies for Plants

6. Role of BFO in OBO Foundry • OBO Foundry and related suites of ontologies will work only if their component ontologies are orthogonal • Orthogonality can be established only if these ontologies are comparable • BFO is at the core of the strategy to ensure compatibility

7. id: HP:0001943 ! Hypoglycemia = = decreased concentration of glucose in the blood • intersection_of: PATO:0001163 ! decreased concentration • intersection_of: qualifier PATO:0000460 ! abnormal • intersection_of: towards CHEBI:17234 ! glucose • intersection_of: inheres_in FMA:9670 ! Portion of blood Class: Hypoglycemia ≡ decreased concentration & towards some glucose & inheres_in some portion of blood & qualifier some 'abnormal‘ P. Robinson: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224779/ http://www.ncbi.nlm.nih.gov/pubmed/23104991

8.  HP:0001720 ! tachycardia Process: GO:0060048 cardiac muscle contractionQuality: PATO:0000912 increased rate PATO:Rate =def. A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time logically: rate(r,p) =def. p is a process & p consists of a sequence of similar sub-processes & these sub-processes repeat r times per unit time Note that there is no reference to a quality or to inherence here

9. Tachycardi • Thus Tachycardia only exists if there is the sort of cyclical repetition of cardiac muscle contraction that is involved in the heart's beating.Thus Tachycardia is not a rate of cardiac muscle contraction, but rather a rate of cardiac muscle contraction repetition.

10. Treatment of ‘process qualities’ • ‘BFO:quality’ just means: a quality of an independent continuant • PATO:process-quality uses 'quality' in a different sense; providing this sense is well-defined, there is no objection to its use. Unfortunately most PATO:process-quality terms are currently poorly defined. The hope is that use of BFO 2.0 can help to bring improvements.

11. rate (rough version) rate(r,p) =def. p is a process & p consists of a sequence of similar sub-processes & these sub-processes repeat r times per unit time increased-rate(r,p) = def. p is such that r is greater than a certain normal threshold (defined for each particular kind of patient)There are numbers here, and time units, and thresholds for numbers.

12. But there are no extra entities called ‘process qualities’ • If we observe that there are 3 apples in a bowl on Wednesday and 2 apples in the same bowl on Thursday, then we could express this by saying that the apples in the bowl had the quality of threeness on Wednesday and the quality of twoness on Thursday. • People could talk like that if they wanted, butit would be ontologically much less adequate than just the assertion underlined above.

13. Similarly, if we observe that there is a 63 bpm heart rate in a patient on Wednesday and 102 bpm heart rate in the same partient on Thursday, then we could express this by saying that the heart beat process of the patient had the quality of sixtythree-bpm-ness on Wednesday and ofonehundredandtwo-bpm-ness on Thursday. People could talk like that if they wanted, butit would be ontologically much less adequate than just the assertion underlined above/ • 63bpm  Wednesday and 102 bpm in the same patient on Thursdayi.e. more beats per minute on Thursday

14. What BFO is designed to do • BFO is not intending to constrain what people say, merely to provide a formally coherent basis for definitions (for example in PATO). • Given this basis, it should be possible to define all the terms one needs, including all the terms one needs from PATO.

15. Which general terms refer to universals? For some general terms X we can formulate definitions of the following sort:(C) Collection of X’s =def. collection of particulars of type X.How do we determine whether for (C) holds of a given term ‘X’? This is the job of scientists, in an on-going process of terminology evolution through which those terms come to be selected for that are fit to serve in successive formulations of the corresponding scientific theory.

16. Which general terms refer to universals? Each scientific theory as it exists at any given stage will likely be marked by (as yet unidentified) terminologically relevant errors, and these errors will accordingly be carried over into the corresponding ontology. Hence, we cannot embrace any one-one correspondence between scientific general terms and universals in reality. Rather, we should assume, for heuristic purposes only, that at any given stage the terms used by scientists in a given discipline refer to universals, knowing full well that this assumption may be false for any given term.

17. Qualities determinable and determinate temperature blood pressure mass ... are continuants they exist through time while undergoing changes

18. Qualities temperature / blood pressure / mass ... are dimensions of variation within the structure of the entity; a quality is something which can change while its bearer remains one and the same

19. A Chart representing how John’s temperature changes

20. Qualities temperature / blood pressure / mass ... are dimensions of variation within the structure of the entity; a quality is something which can change while its bearer remains one and the same hence only independent continuants may have qualities

21. John’s temperature the temperature John has throughout his entire life, cycles through different determinate temperatures from one time to the next John’s temperature is a physiology variable which, in thus changing, exerts an influence on other physiology variables through time

22. temperature 37ºC 37.1ºC 37.2ºC 37.3ºC 37.4ºC 37.5ºC instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John’s temperature

23. One issue Chris Mungall: BFO should have some documented position as to • determinables are still present when their value is zero • OR physics is such that no true determinable can take on a zero value.

24. a quality is something which can change while its bearer remains one and the same hence only independent continuants may have qualities for suppose q were a quality of a process then q would have to be something which could change while the process, its bearer, would remain one and the same – and this is not possible

25. temperature course increasing temperature course constant temperature course decreasing temperature course instantiates at t1 instantiates at t4 instantiates at t5 John’s temperature

26. information artefact temperature unit of measurement measures 37.2ºC measurement record instantiates at t3 ºC John’s temperature instantiates uses inheres_in “John has temperature 37.2ºC at t3” John about

27. note re IAO aboutness information artefact temperature unit of measurement about 37.2ºC temperature measurement record measures ºC about instantiates instantiates at t3 uses John’s temperature “37.2ºC at t3” about

28. BFO: The Very Top continuant occurrent independent continuant dependent continuant quality temperature

29. Blinding Flash of the Obvious independent continuant dependent continuant quality organism temperature types instances John John’s temperature

30. Blinding Flash of the Obvious independent continuant dependent continuant quality organism temperature types instances John John’s temperature

31. independent continuant dependent continuant quality organism temperature types instances John John’s temperature

32. Can sites have histories? Full process(p) =def. there is some spatiotemporal regions r & p is the sum of all processes occurring in r A history is a full process Participants of a history: independent continuant, site – but what if they coincide spatio-temporally

33. Process profiles Full process(p) =def. there is some spatiotemporal regions r & p is the sum of all processes occurring in r Example of full process: history Process profile = a process that is less than a full process

34. Canonical example • A spinning top is spinning • A spinning top is simultaneously warming The spinning and the warming are both proper parts of the full process (= all the processes taking place within the

35. Families of process profiles • Quality process profiles • Measurement/assay process profiles • Scientific discipline demarcated process profiles • Diseases • Speech, music, thinking, writing, dancing …

36. Relative process profiles

37. independent continuant dependent continuant occurrent process quality organism life of an organism temperature John John’s temperature John’s life

38. quality process profile occurrent dependent continuant process independent continuant process profile quality course of temperature changes organism temperature John John’s temperature John’s temperature history

39. independent continuant dependent continuant occurrent process quality organism life of an organism temperature John John’s temperature John’s life

40. independent continuant dependent continuant occurrent process quality process profile organism metabolism of an organism temperature John John’s temperature John’s metabolism

41. independent continuant dependent continuant occurrent process quality process profile organism growth of an organism temperature John John’s temperature John’s growth

42. independent continuant dependent continuant occurrent process quality process profile organism development of an organism temperature John John’s temperature John’s development

43. temperature 37ºC 37.1ºC 37.2ºC 37.3ºC 37.4ºC 37.5ºC instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John’s temperature

44. human embryo fetus neonate infant child adult instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John

45. human in nature, no sharp boundaries here embryo fetus neonate infant child adult instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John

46. Phase transitions portion of water portion of ice portion of liquid water portion of gas instantiates at t1 instantiates at t2 instantiates at t3 this portion of H20

47. temperature in nature, no sharp boundaries here in nature, no sharp boundaries here 37ºC 37.1ºC 37.2ºC 37.3ºC 37.4ºC 37.5ºC instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John’s temperature

49. heart disease disease with early lesions and small fibrous plaques disease with asymptomatic disease, silent infarction disease with surface disruption of plaque disease with unstable angina disease with stable angina instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John’s heart disease (continuant)

50. What is the course of John’s heart disease?