Foundations of Ontology 1
description
Transcript of Foundations of Ontology 1
![Page 1: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/1.jpg)
1
Foundations of Ontology 1
Barry Smith
http://ifomis.org
![Page 2: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/2.jpg)
2
The problem
About 30,000 genes in a humanProbably 100-200,000 proteinsIndividual variation in most genes100s of cell types100,000s of disease types
![Page 3: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/3.jpg)
3
DNA
Protein
Organelle
Cell
Tissue
Organ
Organism
Muscle tissueNerve tissueConnective tissueEpithelial tissueBlood
Musculo-skeletal systemCirculatory systemRespiratory systemDigestive systemNervous systemUrinary systemReproductive systemEndocrine systemLymphoidal system
MitochondriaNucleusEndoplasmic reticulumCell membrane
![Page 4: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/4.jpg)
4
The Challenge
Each (clinical, pathological, genetic, proteomic, pharmacological …) information system uses its own terminology and category systembiomedical research demands the ability to navigate through all such information systems How can we overcome the incompatibilities which become apparent when data from distinct sources is combined?
![Page 5: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/5.jpg)
5
Answer:
“Ontology”
![Page 6: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/6.jpg)
6
Three senses of ontology
1. Philosophical sense: an inventory of the types of entities and relations in reality
2. Knowledge engineering sense: an ontology as a consensus representation of the concepts used in a given domain
3. GO/OBO sense: a controlled vocabulary
![Page 7: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/7.jpg)
7
Ontology as a branch of philosophy
seeks to establishthe basic formal-ontological structuresthe kinds and structures of objects, properties, events, processes and relations in each material domain of reality
![Page 8: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/8.jpg)
8
Formal ontology an analogue of pure mathematics
Can be applied to different domains
![Page 9: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/9.jpg)
9
Material ontology a kind of generalized chemistry or zoology
(Aristotle’s ontology grew out of biological classification)
![Page 10: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/10.jpg)
10
Aristotle
world’s first ontologist
![Page 11: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/11.jpg)
11
World‘s first ontology
(from Porphyry’s Commentary on Aristotle’s Categories)
![Page 12: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/12.jpg)
12
Linnaean Ontology
![Page 13: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/13.jpg)
13
Formal Ontology– theory of part and whole– theory of dependence / unity– theory of boundary, continuity and contact– theory of universals and instances – theory of continuants and occurrents (objects
and processes)– theory of functions and functioning– theory of granularity
![Page 14: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/14.jpg)
14
Formal Ontology
the theory of those ontological structures (such as part-whole, universal-particular) which apply to all domains whatsoever
![Page 15: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/15.jpg)
15
Formal Ontology vs. Formal Logic
Formal ontology deals with the interconnections of thingswith objects and properties, parts and wholes, relations and collectivesFormal logic deals with the interconnections of truthswith consistency and validity, or and not
![Page 16: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/16.jpg)
16
Formal Ontology vs. Formal Logic
Formal ontology deals with formal ontological structuresFormal logic deals with formal logical structures (Epistemology deals with ways of gaining knowledge)
![Page 17: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/17.jpg)
17
Formal-Ontological Categoriessubstanceprocessfunctionunitypluralitysitedependent partindependent part
are able to form complex structures in non-arbitrary ways joined by relations such as part, dependence, location.
![Page 18: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/18.jpg)
18
Example of a Formal-Ontological Structure
D E
A BC
![Page 19: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/19.jpg)
19
Ontological Structure
D E
A BC
two-sided mutual dependence
one-sided dependence
![Page 20: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/20.jpg)
20
Ontological Structure
D E
A B
C
part-whole
relation
F
![Page 21: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/21.jpg)
21
A Network of Domain Ontologies
Material (Regional) Ontologies
Basic Formal Ontology
![Page 22: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/22.jpg)
22
In formal ontologyas in formal logic, we can grasp the properties of given structures in such a way as to establish in one go the properties of all formally similar structures
![Page 23: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/23.jpg)
23
Material Ontology of Social Interaction
oblig-ation
claim
promiser
promisee
act of speaking
act of registering
content
![Page 24: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/24.jpg)
24
A Window on Reality
oblig-ation
claim
promiser
promisee
act of speaking
act of registering
content
![Page 25: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/25.jpg)
25
Universals
oblig-ation
claim
promiser
promisee
act of speaking
act of registering
content
![Page 26: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/26.jpg)
26
Instances
oblig-ation
claim
promiser
promisee
act of speaking
act of registering
content
![Page 27: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/27.jpg)
27
A Window on Reality
![Page 28: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/28.jpg)
28
Medical Diagnostic Hierarchy
a hierarchy in the realm of diseases
![Page 29: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/29.jpg)
29
Dependence Relations
Organisms Diseases
![Page 30: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/30.jpg)
30
A Window on Reality
Organisms Diseases
![Page 31: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/31.jpg)
31
A Window on Reality
![Page 32: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/32.jpg)
32
siamese
mammal
cat
organism
substanceuniversals
animal
instances
frog
![Page 33: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/33.jpg)
33
![Page 34: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/34.jpg)
34
![Page 35: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/35.jpg)
35
Many current standard ‘ontologies’ ramshackle because they have no
counterpart of formal ontologyThe Universal Medical Language System (UMLS)a compendium of source vocabularies including:
HL7 RIMSNOMED International Classification of DiseasesMeSH – Medical Subject HeadingsGene Ontology
![Page 36: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/36.jpg)
36
Problem: The different source vocabularies are incompatible with
each other
![Page 37: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/37.jpg)
37
Problem: They contain bad coding
which often derives from failure to pay attention to simple logical or ontological principles or from principles of good definitions
![Page 38: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/38.jpg)
38
Bad Coding
Plant roots is-a PlantPlant leaves is-a Plant Pollen is-a PlantBoth testes is a testisBoth uterii is a uterus
![Page 39: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/39.jpg)
39
Bad definitions
Heptolysis =def the cause of heptolysis
Biological process =def a biological goal that requires more than one function
![Page 40: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/40.jpg)
40
UMLS Source Vocabularies
HL7 RIMSNOMEDInternational Classification of DiseasesMeSH – Medical Subject HeadingsGene Ontology
![Page 41: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/41.jpg)
41
To reap the benefits of standardization
we need to make ONE SYSTEM out of many different terminologies UMLS Semantic Networknearest thing to an “ontology” of the UMLS134 Nodes, 54 Relationship-Types between these Nodes, forming a graph with 6000 Edges(built by linguists …)
![Page 42: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/42.jpg)
42Fragment of the UMLSemantic Network
![Page 43: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/43.jpg)
43
![Page 44: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/44.jpg)
44
UMLS Semantic Networkentity event
physical conceptual object entity
organism
![Page 45: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/45.jpg)
45
conceptual entity
Organism AttributeFinding
Idea or ConceptOccupation or Discipline
OrganizationGroup
Group AttributeIntellectual Product
Language
![Page 46: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/46.jpg)
46
Idea or ConceptFunctional ConceptQualitative ConceptQuantitative ConceptSpatial ConceptBody Location or RegionBody Space or JunctionGeographic AreaMolecular SequenceAmino Acid SequenceCarbohydrate SequenceNucleotide Sequence
![Page 47: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/47.jpg)
47
Budapest
is an Idea or Concept
![Page 48: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/48.jpg)
48
Idea or ConceptFunctional ConceptQualitative ConceptQuantitative ConceptSpatial ConceptBody Location or RegionBody Space or JunctionGeographic AreaMolecular SequenceAmino Acid SequenceCarbohydrate SequenceNucleotide Sequence
![Page 49: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/49.jpg)
49
Problem: Confusion of concepts and entities in reality
![Page 50: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/50.jpg)
50
Blood Pressure OntologyThe hydraulic equation:
BP = CO*PVRarterial blood pressure (BP) is directly proportional to the product of blood flow (cardiac output, CO) and peripheral vascular resistance (PVR).
![Page 51: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/51.jpg)
51
UMLS-Semantic Types:
blood pressure is an Organism Function,cardiac output is a Laboratory or Test Result
or Diagnostic Procedure
BP = CO*PVR thus asserts that blood pressure is proportional either to a laboratory or test result or to a diagnostic procedure
![Page 52: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/52.jpg)
52
Problem: Confusion of reality with our (ways of gaining) knowledge
about reality
![Page 53: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/53.jpg)
53
What are the terms of ontologies
Concepts?
![Page 54: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/54.jpg)
54
The Concept OrientationWork on biomedical ontologies grew out of work on
medical dictionaries and nomenclaturesHas focused almost exclusively on ‘concepts’ conceived
(sometimes called ‘classes’, sometimes confused with terms/descriptions).
Concept-orientation also common in KR, has led to the entrenchment of an assumption according
to which all that need be said about classes can be said without appeal to time or instances.
This, however, has fostered an impoverished regime of definitions in which the use of identical terms (like ‘part’) in different systems has been allowed to mask underlying incompatibilities.
![Page 55: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/55.jpg)
55
is-aStandard definition:
A is-a B =def every instance of A is an instance of B
= standard definition of computer science
adult is-a childanimal owned by the Emperor is-a animalmammal is-a object weighing less than 200 kg
![Page 56: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/56.jpg)
56
correct reading of is-a1. A and B are natural kinds, 2. there are times at which instances of A exist, 3. at all such times these instances are
necessarily (of their very nature) also instances of B
1. eukaryotic cell is-a cell2. mammal is-a animal3. death is-a biological process
![Page 57: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/57.jpg)
57
Ontologies
Here A and B are universals(= natural kinds, types …, roughly analogous
to biological species)Universals have instances (you and me,
your headache, my coughing)
![Page 58: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/58.jpg)
58
Instances are elite individuals
they are those which instantiate universals (entering into biological laws)
![Page 59: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/59.jpg)
59
Linnaean Ontology
![Page 60: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/60.jpg)
60
Confusion of Ontology and Epistemology
Physical Object
Substance
Food Chemical Body Substance
![Page 61: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/61.jpg)
61
Confusion of Ontology and Epistemology
Chemical
Chemical ChemicalViewed Viewed
Structurally Functionally
![Page 62: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/62.jpg)
62
Chemical
Chemical ChemicalViewed Viewed
Structurally Functionally
Inorganic Organic Enzyme Biomedical or Chemical Chemical Dental Material
![Page 63: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/63.jpg)
63
Chemical
Chemical ChemicalViewed Viewed
Structurally Functionally
Inorganic Organic Biomedical or
Chemical Chemical Dental Material
Enzyme
![Page 64: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/64.jpg)
64
Is biological classification Linnaean?
![Page 65: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/65.jpg)
65
Principle of Single Inheritance
(rule of thumb) no class in a classificatory hierarchy should have more than one parent
![Page 66: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/66.jpg)
66
The Problem of Multiple Inheritance
cars
Buicks blue cars
blue Buicks
![Page 67: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/67.jpg)
67
Principle of Taxonomic Levels
![Page 68: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/68.jpg)
68
Principle of Taxonomic Levels
the terms in a classificatory hierarchy should be divided into predetermined levels (analogous to the levels of kingdom, phylum, class, order, etc., in traditional biology).‘depth’ in GO’s hierarchies not determinate because of multiple inheritance
![Page 69: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/69.jpg)
69
Principle of Exhaustiveness
the classes on any given level should exhaust the domain of the classificatory hierarchy.
![Page 70: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/70.jpg)
70
Single Inheritance + Exhaustiveness = JEPD
Exhaustiveness often difficult to satisfy in the realm of biological phenomena; but its acceptance as an ideal is presupposed as a goal by every scientist.
Single inheritance accepted in all traditional (species-genus) classifications
![Page 71: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/71.jpg)
71
Problems with multiple inheritance
B C is-a1 is-a2
A E D
‘sibling’ is no longer determinate
![Page 72: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/72.jpg)
72
Problems with multiple inheritance
B C is-a1 is-a2
A E D
‘is_a’ is no longer univocal
![Page 73: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/73.jpg)
73
when ‘is-a’ is pressed into service to mean a variety of different things
the resulting ambiguities make the rules for correct coding difficult to communicate to human curators
they also serve as obstacles to integration with neighboring ontologies
![Page 74: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/74.jpg)
74
How are universals and instances related together?
![Page 75: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/75.jpg)
75
Entities
![Page 76: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/76.jpg)
76
Entities
universals (classes, types, taxa, …)
particulars (individuals, tokens, instances …)
Axiom: Nothing is both a universal and a particular
![Page 77: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/77.jpg)
77
Two Kinds of Elite Entities
classes, within the realm of universals
instances within the realm of particulars
![Page 78: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/78.jpg)
78
Entities
classes
![Page 79: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/79.jpg)
79
Entities
classes*
*natural, biological
![Page 80: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/80.jpg)
80
Entities
classes of objects, substances
need modified axioms for classes of functions, processes, pathways, reactions, etc.
![Page 81: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/81.jpg)
81
Entities
classes
instances
![Page 82: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/82.jpg)
82
Classes are natural kinds
Instances are natural exemplars of natural kinds(problem of non-standard instances) Not all individuals are instances of classes
![Page 83: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/83.jpg)
83
Entities
classes
instancesinstances
penumbra of borderline cases
![Page 84: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/84.jpg)
84
Entities
classes
instancesjunkjunk
junk
example of junk: beachball-desk
![Page 85: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/85.jpg)
85
Primitive relations: inst and part
inst(Jane, human being)part(Jane’s heart, Jane’s body)
A class is anything that is instantiatedAn instance as anything (any individual) that
instantiates some class
![Page 86: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/86.jpg)
86
Entities
human
Jane
inst
![Page 87: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/87.jpg)
87
Entities
human
Jane’s heart part Jane
![Page 88: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/88.jpg)
88
part as a relation between individuals
subject to the usual axioms of mereology
![Page 89: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/89.jpg)
89
Two primitive relations: inst and part
inst(Jane, human being)part(Jane’s heart, Jane’s body)
A universal is anything that is instantiatedAn instance is anything (any individual) that
instantiates some class
![Page 90: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/90.jpg)
90
Two primitive relations: inst and part
Axioms governing inst : (1) it holds in every case between an instance and a
class, in that order; (2) that nothing can be both an instance and a class.
Axioms governing part (= ‘proper part’) (1) it is irreflexive (2) it is asymmetric (3) it is transitive (4) it holds only between individuals (usual mereological axioms)
![Page 91: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/91.jpg)
91
Part_for and Has_Part
A part_for B =def given any x, if inst(x, A) then there is some y such that inst(y, B) and part(x, y)
B has_part A =def given any y, if inst(y, B) then there is some x such that inst(x, A) and part(x, y)
human testis part_for human being, But not: human being has_part human testis. human being has_part heart, But not: heart part_for human being.
![Page 92: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/92.jpg)
92
The usual part_of relation as a relation between universals
A part_of B =def A part_for B & B has_part A As exist only as parts of Bs and Bs are structurally organized in such a way that As must appear in them as parts.
![Page 93: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/93.jpg)
93
Analogous problems for nearly all foundational relations of ontologies and semantic networks:
A causes BA is associated with BA is located in Betc.
Reference to instances is necessary to clear up these problems
![Page 94: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/94.jpg)
94
if they can be cleared up at all …
![Page 95: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/95.jpg)
95Fragment of the UMLSemantic Network
![Page 96: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/96.jpg)
96
![Page 97: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/97.jpg)
97
Mental Process precedes Molecular Function Mental Process precedes Genetic FunctionExperimental Model of Disease precedes Cell or
Molecular DysfunctionAcquired Abnormality affects BirdExperimental Model of Disease affects FungusPhysiologic Function affects ReptileAntibiotic causes Experimental Model of DiseaseBiomedical or Dental Material causes Mental or
Behavioral DysfunctionManufactured Object causes Disease or SyndromeVitamin causes Injury or PoisoningFungus location_of VitaminOrganization location_of Diagnostic Procedure
![Page 98: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/98.jpg)
98
What are universals?
invariants in reality
satisfying biological laws(there are truths about universals in
biological textbooks)
![Page 99: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/99.jpg)
99
Universals are Not SumsUniversals are distinguished by granularity: they divide up the corresponding domain into whole units or members, whose interior parts and structure are traced over. The universal human being is instantiated only by human beings as single, whole units.
A mereological sum is not granular in this sense(molecules are parts of the mereological sum of human beings)
![Page 100: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/100.jpg)
100
Universals are Not SetsBoth universals and sets are marked by
granularity – but universals are timelessBoth a universal and a set is laid across reality like
a grid consisting (1) of a number of slots or pigeonholes each (2) occupied by some member.
But a set is determined by its members. This means that it is (1) associated with a specific number of slots, each of which (2) must be occupied by some specific member.
A universal survives the turnover in its instances: it is specified neither (1) what the number of associated slots should be nor (2) what individuals should occupy these slots. Both may vary with time.
![Page 101: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/101.jpg)
101
A universal is not determined by its instances as a state is not determined by its citizens
A universal may vary with time as an organism may vary with time (by gaining and losing molecules)
![Page 102: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/102.jpg)
102
Universals are Not Sets
A set is an abstract structure, existing outside time and space. The set of Romans timelessly has Julius Caesar as a member.Universals exist in time.
![Page 103: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/103.jpg)
103
![Page 104: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/104.jpg)
104
Two Questions
1. What does “Functional” mean in expressions like “Functional Genomics” ?
2. How can we use the answer to this question to help us understand notions fundamental to medicine such as “health” and “disease” ?
![Page 105: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/105.jpg)
105
Towards an Tri-Categorial Ontology
of Structures, Functions and Processes
![Page 106: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/106.jpg)
106
Definition of Function in UMLS Semantic Network
Functional Concept =df A concept which is of interest because it pertains to the carrying out of a process or activity.
Function Functional ConceptFunction Realization of a Function
![Page 107: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/107.jpg)
107
What do the kidneys do?
Your entire blood volume flows through your kidneys every few minutes, leaving behind excess water, solutes and waste materials
The KidneyFrom Andrew Lonie, University of Melbourne
![Page 108: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/108.jpg)
108
How does a kidney work?
Essentially a massively parallel filter composed of 105 to 106 nephrons
The nephron is the functional unit of the kidney
Each nephron is a very convoluted, long, thin tube lined with biochemical pumps
![Page 109: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/109.jpg)
109
Nephron Functions10 functional segments15 different cell types
![Page 110: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/110.jpg)
110
QualitativefunctionalontologyNormal PhysiologyDisease StatesGenetics/MutationsSpecies Differences
Structural ontology
KidneyRenal architecture
Tubule section/Glomerulus
Cell= ANATOMY AT
DIFFERENT LEVELS OF GRANULARITY
Structural and functional representation
process ontology(molecular, cellular, organ-level …)
![Page 111: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/111.jpg)
111
UMLS Semantic Networkentity event
physical conceptual object entity
organism
![Page 112: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/112.jpg)
112
Tri-Categorial Ontology present also in GO: The Gene Ontology
3 ‘ontologies’ (large telephone directories) of standardized designations for gene functions and products
![Page 113: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/113.jpg)
113
RUMLS Semantic Networkentity event
structures functions processes
![Page 114: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/114.jpg)
114
GO’s three disjoint term hierarchies
the cellular component (structure) ontology,e.g. flagellum, chromosome, cell
the biological process ontology,e.g. glycolysis, death
the molecular function ontology, e.g. ice nucleation, binding, protein stabilization
![Page 115: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/115.jpg)
115
RUMLS Semantic Networkentity event
structures functions processes
![Page 116: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/116.jpg)
116
Functional Genomics
What does “Functional“ mean?
![Page 117: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/117.jpg)
117
The Problem
The tumor developed in John’s lung over 25 years
![Page 118: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/118.jpg)
118
The Problem
____ developed in _____ over 25 years
process
![Page 119: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/119.jpg)
119
The Problem
The tumor developed in the lung over 25 years
substances things objects continuants
![Page 120: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/120.jpg)
120
The Problem
The tumor developed in John’s lung over 25 years
PARTHOOD NOT DETERMINATE
![Page 121: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/121.jpg)
121
The Problem
The tumor developed in the lung over 25 years
substances
GLUING THESE TOGETHER YIELDS ONTOLOGICAL MONSTERS
processes
![Page 122: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/122.jpg)
122
Substances and processes exist in time in different ways
substance
t i m
e
process
![Page 123: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/123.jpg)
123
SNAP vs SPAN
Endurants vs perdurantsContinuants vs occurrents
In preparing an inventory of realitywe keep track of these two different kinds of entities in two different ways
![Page 124: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/124.jpg)
124
Fourdimensionalism
– only processes exist– time is just another dimension, analogous
to the three spatial dimensions– substances are analyzed away as
worms/fibers within the four-dimensional plenum
![Page 125: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/125.jpg)
125
There are no substances
Bill Clinton does not existRather: there exists within the four-
dimensional plenum a continuous succession of processes which are similar in a Billclintonizing way
![Page 126: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/126.jpg)
126
Fourdimensionalism (the SPAN perspective) is right in
everything it says
But incomplete
![Page 127: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/127.jpg)
127
Need for Two Orthogonal, Complementary Perspectives
SNAP and SPAN
![Page 128: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/128.jpg)
128
Snapshot Video ontology ontology
substance
t i m
e
process
![Page 129: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/129.jpg)
129
SNAP and SPAN
stocks and flowscommodities and services
product and process
anatomy and physiology
![Page 130: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/130.jpg)
130
SNAP and SPAN
SNAP entities- have continuous existence in time- preserve their identity through change- exist in toto if they exist at all
SPAN entities- have temporal parts- unfold themselves phase by phase- exist only in their phases/stages
![Page 131: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/131.jpg)
131
You are a substance
Your life is a process
You are 3-dimensionalYour life is 4-dimensional
![Page 132: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/132.jpg)
132
Many SNAP Ontologies
t1
t3
t2
here time exists outside the ontology, as an index or time-stamp
![Page 133: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/133.jpg)
133
each SNAPi section through reality
includes everything which exists (present tense)
![Page 134: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/134.jpg)
134
mereology works without restriction (parthood is everywhere determinate) in
every SNAPi ontology
![Page 135: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/135.jpg)
135
Three kinds of SNAP entities
1. SNAP Independent Entities (you and me)2. SNAP Dependent Entities3. Spatial regions
![Page 136: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/136.jpg)
136
SNAP dependent entities
States, powers, qualities, functions, dispositions, plans, shapes, liabilities,
propensities…
![Page 137: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/137.jpg)
137
SNAP dependent entities:
one-place:
your temperature, color, heightmy knowledge of French
the whiteness of this cheese the warmth of this stone
the fragility of this glass
![Page 138: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/138.jpg)
138
relational SNAP dependent entities
John Mary
love
stand in relations of one-sided dependence to a plurality of substances simultaneously
one-sided dependence
![Page 139: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/139.jpg)
139
A Window on Reality
oblig-ation
claim
promiser
promisee
act of speaking
act of registering
content
![Page 140: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/140.jpg)
140
Spatial regions + sites (contexts, niches, environments)
Organism species evolve into environments Domesticated spatial regions: rooms,
nostrils, your alimentary tractFiat spatial regions: JFK designated
airspace
![Page 141: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/141.jpg)
141
SNAP: Entities existing in toto at a time
http://ontology.buffalo.edu/bfo
![Page 142: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/142.jpg)
142
The SPAN Ontology
t i m e
![Page 143: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/143.jpg)
143
here time exists as part of the domain of the ontology
The SPAN ontology
![Page 144: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/144.jpg)
144
mereology works without restriction everywhere here
t i m e
clinical trial
![Page 145: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/145.jpg)
145
mereology works without restriction everywhere here
t i m e
course of a disease
![Page 146: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/146.jpg)
146
Processes, too, are dependent on substances
One-place vs. relational processes
One-place processes:your getting warmeryour getting hungrier
![Page 147: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/147.jpg)
147
Relational processes
kissings, thumpings, conversations, dancings, promisings, infectings, bindings
join their carriers together into collectives of greater or lesser duration
![Page 148: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/148.jpg)
148
SPAN: Entities extended in time
SPANEntity extended in time
Portion of Spacetime
Fiat part of process *First phase of a clinical trial
Spacetime worm of 3 + Tdimensions
occupied by life of organism
Temporal interval *projection of organism’s life
onto temporal dimension
Aggregate of processes *Clinical trial
Process[±Relational]
Circulation of blood,secretion of hormones,course of disease, life
Processual Entity[Exists in space and time, unfolds
in time phase by phase]
Temporal boundary ofprocess *
onset of disease, death
http://ontology.buffalo.edu/bfo
![Page 149: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/149.jpg)
149
Two kinds of SPAN entities
1. Processes (including events: process-boundaries, settings)
2. Spatio-temporal regions
![Page 150: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/150.jpg)
150
How do you know whether an entity is SNAP or SPAN?
![Page 151: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/151.jpg)
151
problem cases
forest firehurricane Maria
traffic jamocean wave
diseaseanthrax epidemic
![Page 152: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/152.jpg)
152
forest fire:
a processa pack of monkeys jumping from tree to tree
and eating up the trees as they gothe Olympic flame:
a process or a thing?(anthrax spores are little monkeys)
![Page 153: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/153.jpg)
153
A disease
The course/history of a disease
![Page 154: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/154.jpg)
154
The Epidemic (SNAP)
The Spread of an Epidemic (SPAN)
![Page 155: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/155.jpg)
155
Material examples:
performance of a symphonyprojection of a filmexpression of an emotionutterance of a sentenceapplication of a therapyincrease of temperature
![Page 156: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/156.jpg)
156
The Tri-Categorial Ontology SNAP SPAN
structures functions processes= independent = dependent continants continuants
![Page 157: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/157.jpg)
157
The Tri-Categorial Ontology continuants occurrents
structures functions processes= independent = dependent continants continuants
![Page 158: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/158.jpg)
158
A Window on Reality continuants occurrents
structures functions processes= independent = dependent continants continuants
Entities in all three categories exist both as universals and as instances (as tokens and as types)
The function of your heart is: to pump bloodThe function of my heart is: to pump blood
![Page 159: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/159.jpg)
159
Functions are continuants
The function of your heart begins to exist with the beginning to exist of your heart, and continues to exist, self-identically, until (roughly) your heart ceases to be able to respond if stimulated by your sympathetic and parasympathetic nervous systems
![Page 160: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/160.jpg)
160
Functions have bearers
The bearer of the function of your heart is: your heart.Functions are dependent continuants. The bearers of functions are independent continuants (hearts, screwdrivers …)
![Page 161: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/161.jpg)
161
Functions are realized
in special sorts of processes called functioningsThe processes taking place in or involving entities which are bearers of functions can be divided into two types: those which are realizations of their functions (also called functionings) and processes of other types (junk processes)
![Page 162: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/162.jpg)
162
Functions can exist even when they are not being realized
![Page 163: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/163.jpg)
163
Processes (realizations) are causal-energetic
time
![Page 164: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/164.jpg)
164
Functions are historical (they exist in time)
but they are also quasi-Platonic
time
![Page 165: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/165.jpg)
165
Compare the relation between temperature,
which is quasi-Platonicand Brownian motion, which is causal-energetic
Your temperature at t vs. the value of your temperature at t
![Page 166: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/166.jpg)
166
Your temperature is quasi-Platonic
Your temperature as a determinable is identical from one moment of your existence to the next
This determinable takes on different values at different times
![Page 167: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/167.jpg)
167
Biological functions are always constituent functions
If X has a biological function then there is some Y of which X is a part and X’s functioning is in the service of / for the benefit of Y
![Page 168: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/168.jpg)
168
Functions are beneficial
If an organism has a constituent part X, and if X is the bearer of a function Z, then those processes which are the realizations of the function Z are (in normal circumstances) beneficial to the organism ( such as to sustain the organism in existence)
![Page 169: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/169.jpg)
169
Functional Genomics= study of what the genes contribute to the
organism in the way of survival(Bad genes do not have functions)
Every oncogene is a proto-oncogene
There is functioning, poor functioning, malfunctioning
There is not having a function at all (and this can be either neutral in the stakes of beneficiality or also positively malignant)
![Page 170: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/170.jpg)
170
Does this sense of ‘function’ correspond to the way biologists talk?
![Page 171: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/171.jpg)
171
Clinical vs. biological sense of ‘function’
Biologists sometimes talk about biological structures ‘gaining function’ (= being switched on) even where their functioning is not beneficial
Are all functions associated with malfunctionings?
![Page 172: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/172.jpg)
172
Health – Disease – Illness
Diseased organ = organ predisposed to malfunctionIts functioning is defective
![Page 173: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/173.jpg)
173
![Page 174: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/174.jpg)
174
Part Four: Definitions of Health
World Health Organization:Health is the state of psychological and physical well-being of humans
![Page 175: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/175.jpg)
175
Biostatistical TheoryChristopher Boorse
Health is conformity to normal species design (as statistically determined).
Abnormally healthy people are therefore in fact sick (?)
![Page 176: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/176.jpg)
176
The Vital Goal Theory Lennart Nordenfelt
Health is the bodily and mental state of a person which is such that he or she has an ability to realize vital goals, given standard or otherwise accepted circumstances.
Disease is a state or process of a person’s body or mind that tends to cause ill health in the bearer.
![Page 177: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/177.jpg)
177
The Ordinary Action TheoryK.W.M. Fulford
Health is being able to do what one ordinarily does in the absence of obstruction or opposition.
Illness is failing to do what one ordinarily does in the absence of obstruction or opposition.
![Page 178: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/178.jpg)
178
The Abnormality TheoryLawrie Reznek
Disease is a state of a person which issues in abnormal behavior; something is an abnormal bodily or mental process if it does standard members of the human species some harm in standard circumstances;something does a person harm if it makes the person less able to live a good or worthwhile life.
![Page 179: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/179.jpg)
179
Problems with standard definitions
1. Circularity2. Make health a social construction3. Make health a Cambridge property4. Confuse state and process, disposition
and realization, potentiality and actuality5. Do not apply to organisms other than
humans
![Page 180: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/180.jpg)
180
Circularity
Health is ... well-beingHealth is ... being able to live a good or worthwhile lifeDisease is a state … that tends to cause ill health in the bearer
![Page 181: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/181.jpg)
181
Health a social construction
Health is …the ability to realize vital goals, given standard or otherwise accepted circumstancesIllness = what the insurance company will pay to treat
![Page 182: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/182.jpg)
182
Health a Cambridge Property
Health is conformity to normal species design (as statistically determined).
If everyone in society becomes sicker and you remain the same, then you are the person who becomes unhealthy
![Page 183: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/183.jpg)
183
Ontology of Disease
Diseases are, like functions, dependent continuants
They are states or conditions which endure for a certain time and have a course or history, which is an occurrent
Disease tokens, like roles and functions, do not change through their existence over time
![Page 184: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/184.jpg)
184
Diseases are both historical and quasi-Platonic
time
![Page 185: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/185.jpg)
185
FunctionsThis is a screwdriverThis is a good screwdriverThis is a broken screwdriverThis is a heartThis is a healthy heartThis is an unhealthy heart
![Page 186: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/186.jpg)
186
Functions are associated with certain characteristic process shapes
Screwdriver: rotates and simultaneously moves forward simultaneously transferring torque from hand and arm to screw
Heart: performs a contracting movement inwards and an expanding movement outwards simultaneously transferring hydraulic pressure to the blood stored within its chambers
![Page 187: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/187.jpg)
187
For each function
there is an associated family of (four-dimensional) process shapes, organized around a core of prototypical process shapes representing good functioning
The prototypes play a role analogous to the standard meter rule in the organization of those one-dimensional shapes we call lengths
![Page 188: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/188.jpg)
188
![Page 189: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/189.jpg)
189
Outside the core
are process shapes which are not instances of functioning at all
![Page 190: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/190.jpg)
190
![Page 191: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/191.jpg)
191
![Page 192: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/192.jpg)
192
Normal functioning
= functioning (realizing a four-dimensional shape) at or close to the prototype
![Page 193: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/193.jpg)
193
Prototypes
good functioning
![Page 194: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/194.jpg)
194
Prototypes
reasonable functioning
![Page 195: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/195.jpg)
195
Poor functioning
poor functioning
![Page 196: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/196.jpg)
196
Malfunctioning
malfunctioning
![Page 197: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/197.jpg)
197
Death?
not functioning at all
![Page 198: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/198.jpg)
198
Not functioning at all
leads to death modulo internal factors:plasticity redundancy (2 kidneys)criticality of the system involved
external factors:prosthesis (dialysis machines, oxygen tent)special environmentsassistance from other organisms
![Page 199: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/199.jpg)
199
Relevance of Millikan
Prototypical functioning = exercising what Millikan calls ‘proper function’
(defined historically)X is the proper function of Y means: 1) Y
performs X and 2) Y exists because its predecessors’ performing the function X is responsible for my existing
It is not the function of the nose to hold up spectacles because this was not selected for
![Page 200: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/200.jpg)
200
Millikan = backward looking, focused on whole species
This account = forward looking, focused on single organism
X has a function = (1) X’s functioning is beneficial to the organism of which X is a part
![Page 201: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/201.jpg)
201
Boorse’s Internal Impairment Theory
Disease is an internal state which is an impairment or limitation of normal functional ability.
![Page 202: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/202.jpg)
202
Disease
![Page 203: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/203.jpg)
203
Disease = remoteness from prototypical functioning
disease
![Page 204: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/204.jpg)
204
Disease = remoteness from prototypical functioning
disease
1 2 3 1 = not functioning at all
2 = malfunctioning
3 = functioning poorly
![Page 205: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/205.jpg)
205
Not functioning at all
= death modulo:criticality of the system involved
![Page 206: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/206.jpg)
206
Biological entities have biological functions only as parts of organisms
An organic entity functions in the service of the organism of which it is a part
There are immediate parts of the organism – the bodily systems – which function directly in the service of the organism.
And there are mediate (= smaller) parts of the organism – cells, tissues, organs … -- which function in the service of larger parts
![Page 207: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/207.jpg)
207
Immediate parts of the organism are more critical
![Page 208: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/208.jpg)
208
Bodily Systems
respiratorydigestive skeletal circulatorymusculatory immune
![Page 209: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/209.jpg)
209
ENDOCRINE
SYSTEM
![Page 210: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/210.jpg)
210
What do the kidneys do?KIDNEY
![Page 211: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/211.jpg)
211
How does a kidney work?NEPHRON
![Page 212: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/212.jpg)
212
Nephron FunctionsFUNCTIONAL SEGMENTS
![Page 213: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/213.jpg)
213
DNA
Protein
Organelle
Cell
Tissue
Organ
Organism
![Page 214: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/214.jpg)
214
Coda on ‘Normal’
Normal functioning of the pancreasNormal functioning of the sexual organs
On the several senses of ‘normal’ in biology
![Page 215: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/215.jpg)
215
Problem: The Sexual Organs do not have Biological Functions
A constituent part of an organism has a function = its functioning is beneficial to the survival of the host organism
– this does not hold for the reproductive system and its parts
![Page 216: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/216.jpg)
216
Hence the sexual organs do not have functions
Alternatively they have functions in relation to some larger whole (the family, the dynasty …)
Compare the role of worker bees in bee colonies …
![Page 217: Foundations of Ontology 1](https://reader031.fdocuments.us/reader031/viewer/2022033100/56816093550346895dcfb8e8/html5/thumbnails/217.jpg)
217
The End