1. Rules for Good Ontology
Rules of thumb:
represent ideals to be approximated to in practice
often with trade-offs

2. The ontologist’s job is not to mimic or replace or usurp science
not to discover statistical or functional laws
it is to establish the categories involved in given domains of reality and the relations between them
via: taxonomies
and: partonomies
and NORMATIVE ISSUES

3. Naturalness
A good ontology should include in its basic category scheme only those categories which are instantiated by entities in reality (it should reflect nature at its joints)

4. A good first test:
the categories in question should be reflected in TEE
(for: Technically Extended English
= English as extended by the various technical vocabularies of medical and scientific disciplines)

5. Basic categories reflected by morphologically simple terms: dog pain
foot
blood
hunger
hot
red
diabetes

6. No theoretical artifacts
A good ontology should not include in its basic category scheme
artifacts of logical, mathematical or philosophical theories (such as: transfinite cardinals, instantaneous rabbit-slices, non-existent golden mountains, functions across possible worlds, and the like).

7. A good category scheme
should not be a mish-mash of natural and philosophical taxa
(keep views separate:
basic views, domain-specific views,
theoretical-artefactual views)

8. Problem of Double-Counting
in realm of substances
foot, arm, nose;
family, patient population
fiat parts and aggregates on the same level of granularity should be explicitly marked as involving double-counting

9. Cheese-paring principle
While a good ontology should use categories which reflect only TEE, it should also have the resources to do justice to the fact that the world can be sliced in many ways, including ways not reflected by TEE

10. Example of cheese-paring
substance
action
(relational
process)
substance
agent
(substance
plus role)
patient
(substance
plus role)
linked by mutual dependence

11. Always ask the question
when is this proposition true?
when does this entity exist?
Two sorts of answers:
at t (for SNAP entities)
over time interval t
looking down on the order of time from the outside (for SPAN entities)

12. John lived in Kansas for 25 years
when is this proposition true?
when does the entity which makes it true exist?

13. Summing within SPAN and summing within SNAP are both acceptable
John plus his role: Major John
John plus his quality: hungry John
The rest of the World Cup

14. Confess Double-Counting
in realm of substances
ear, nose, throat, arm
family, clinical trial population
fiat parts and aggregates on the same level of granularity should be explicitly marked as involving double-counting

15. SNAPshot ONTOLOGY

16. Confess Double-Counting
in realm of processes
beginning, end, first phase
series of clinical trials, World Cup
fiat parts and aggregates on the same level of granularity should be explicitly marked as involving double-counting

17. SPAN ONTOLOGY

18. SPAM ONTOLOGY

19. No Crossing Categories
If C is a major category then an instance of C is always an instance of C whichever VIEW of C we take
If C is a major category then an instance of C is always an instance of C whichever granularity we take

20. If x instances a category under any determinable, then it instances this category under all determinables
John’s temperature is a SNAP entity
The value of John’s temperature is 62 degrees
(The value is changing all the time)

21. No ‘others’
All category labels should be positive

22. Respect Granularity
spatial region
substance
quality
parts of spatial regions are always spatial regions

23. Respect Granularity parts of substances are always substances
spatial region
substance
quality
parts of substances are always substances

24. Respect Granularity parts of qualities are always qualities
spatial region
substance
quality
parts of qualities are always qualities

25. Relations crossing the SNAP/SPAN border are not part-relations
substance John
John’s life
sustaining in existence
physiological processes

26. Rule for Crossing Granularities
For x and y instances of basic categories
If x is part of y, then x is of the same category as y
(if x is substantial, then y is substantial)
(if x is a quality, then y is a quality)
(if x is a process, then y is process)
(if x is a spatial region, then y is a spatial region)
(if x is a spatial boundary, then y is a spatial boundary)

27. Rule for Crossing Granularities
For x an instances of a basic category, x is always an instance of that category in every view or from every perspective
(if x is substantial, then y is substantial)
(if x is a quality, then y is a quality)
(if x is a process, then y is process)
(if x is a spatial region, then y is a spatial region)
(if x is a spatial boundary, then y is a spatial boundary)

28. How to treat cross-categorial structures?
which ontology do they belong to?
How to treat higher-order attributions
Universals have instances
Universal A depends for its instantiation on the instantiation of universal B
Roughly: these are meta-assertions
(that they have special truthmakers of their own is an illusion of language)

29. Universals have instances
is not an extra assertion
rather it is something which shows itself via the syntax of a good ontological language
(cf. Wittgenstein’s Tractatus)

30. Rules for good syntax in formalizing ontology
entities of the same category should be represented in the language of ontology by means of symbols of the same type
some symbols will not represent entities at all (⌐)

31. Tools are just tools
If specific logical or mathematical or conceptual tools are needed, for example for semantic purposes,
then these should be clearly recognized as tools and thus not be seen as having consequences for basic ontology.
(Possible worlds …)

32. Trade off between cheese-paring and sake-mongering
We say
“For Pierre’s sake …, for Heinrich’s sake …”
But
There are no sakes in this room
This is so however we slice the cheese

33. Problems arise for partial ontologies
only if they come along with the claim to be complete
(reductionists are nearly always correct in what they hold to exist --
but incorrect when they hold that nothing else exists)

34. Even reductionists are right as far as they go
(even their peculiar maps of reality,
as consisting of processes,
or of spacetime worms,
are transparent to reality)
The only problem with such maps is that they are not complete

35. Rules Governing Taxonomies
Every (coherent, tested) ontology for a given domain at a given level of granularity
should be representable as a tree in the mathematical sense

36. Natural scientific classifications are principled

37. Principled classifications satisfy the no-diamonds rule:
A E
F G
B C D H
Good
Bad

38. Counterexample in the realm of artifacts ?
urban structures
buildings
car parks
multi-story car-parks

39. Eliminating counter-examples
urban structures
buildings
parking areas
multi-story car-parks
“Ontoclean”

40. No ‘others’
A good taxonomy should contain no taxons labeled
‘others’

41. Representations
A representation is never identical with the object which it is a representation of

42. Fallibilism
Ontologists are seeking principles that are true of reality,
but this does not mean that they have special powers for discovering the truth.
Ontology is, like physics or chemistry, part of a piecemeal, on-going process of exploration, hypothesis-formation, testing and revision.

43. Fallibilism
Ontological claims advanced as true today may well be rejected tomorrow in light of further discoveries or new and better arguments
Ontology is like a small window on reality which, in fits and starts, gets bigger and more refined as we proceed

44. Adequatism A good ontology should be adequatist:
its taxonomies and partonomies should comprehend the entities in reality at all levels of aggregation,
from the microphysical to the cosmological,
and including also the middle world (the mesocosmos) of human-scale entities in between.
Adequatists: Aristotle, Ingarden, Chisholm

45. Nothing in life is certain
except
death
and taxes
Fictionalism is always wrong
Either an entity exists, or it does not exist
Either an entity type exists, or it does not exist

46. Quine is wrong There is no entity without identity
We have no identity criteria for
people
taxes
plans
diseases

47. A good category scheme
should not be a mish-mash of individuals and universals
Universals are not extra types of entities
Types of entities ARE universals
Boxes in category diagrams represent universals
The instances are what the boxes contain

48. SNAPshot ONTOLOGY

49. SNAPshot ONTOLOGY

50. Tree structure
Higher nodes within the tree represent more general universals, lower nodes represent less general universals.

51. Branches connecting nodes represent the relations of inclusion of a lower category in a higher:
man is included in mammal
mammal is included in animal
and so on.

52. An Ontology (Taxonomy) should be Principled
Suppose that in counting off the cars passing beneath you on the highway, your checklist includes one box labeled red cars and another box labeled Chevrolets.
The resultant inventory will be unprincipled;
you will almost certainly be guilty of counting some cars twice.
Unprincipled = the two modes of classification belong to two distinct classifications made for two distinct purposes

53. Tree structure implies:
A good ontology should satisfy certain well-formedness rules

54. Well-formedness rule Each tree is unified
in the sense that it has a single top-most or maximal node, representing the maximum category
comprehending all the categories represented by the nodes lower down the tree

55. Why trees?
A taxonomy (ontology) with two maximal nodes would be in need of completion by some extra, higher-level node representing the union of these two maxima.
Otherwise it would not be one taxonomy at all, but rather two separate taxonomies (e.g. SNAP and SPAN)

56. ‘Entity’ = label for the highest-level category of ontology.
Everything which exists is an entity
Alternative top-level terms favored by different ontologists: ‘thing,’ ‘object,’ ‘item,’ ‘element,’ ‘existent.’
Use of ‘entity’ is dangerous (see Frege)

57. Basis in minimal nodes (leaves)
Leaves of the tree represent the lowest categories (infima species)
= categories in which no sub-categories are included.
‘Has a basis in minimal nodes’ = the categories at the lowest level of the tree exhaust the maximum category

58. Exhaustiveness
The chemical classification of the noble gases is exhausted by:
Helium, Neon, Argon, Krypton, Xenon and Radon.
…normally very hard to achieve

59. For a taxonomy with a basis in minimal nodes
every intermediate node in the tree is identifiable as a combination of minimal nodes.

60. More well-formedness principles
There should be a finite number of steps between the maximal category and each minimal category.
There should be the same number of steps between the topmost node of the tree and all its lowest-level nodes.

61. Well-Formedness
The taxonomy as a whole is thereby divided into homogeneous levels,
each level represents a jointly exhaustive and pairwise disjoint partition of the corresponding domain of categories on the side of objects in the world.

62. Which rules satisfied by BFO?

63. Types of Formal Relation
Intracategorial
Mereological (part)
Topological (connected, temporally precedes)
Dependency
Intercategorial
Inherence (quality of)
Location
Participation (agent)

64. Relations can also hold across granularities
Microbial processes in the human body sustain the human body in existence
Neurophysiological processes in the brain cause and provide the substratum for cognitive processes

65. Trees of universals (species-genus hierarchies)
capture the way the world is (realism)
– they depict the invariant structures/patterns/regularities in reality

66. or: species-genus hierarchies
may capture the way the world should be
– by depicting the structures/patterns/regularities in the realm of standards, ideal cases, recipes
(a hierarchy of medical therapies)

67. Anglocentric (Aristotelian) Realism
The general terms of TEE (or many of them),
including terms like ‘Coca Cola’,
correspond to universals (species and genera, invariant patterns) in reality

68. Two distinct realms of being
universals
particulars
general
individual
types
tokens
species
instances
essence
fact

69. species, genera instances substance organism animal mammal cat frog
siamese
frog
instances

70. common nouns proper names substance organism animal mammal cat
pekinese
mammal
cat
organism
substance
animal
common
nouns
proper names
Common nouns

71. types
substance
organism
animal
cat
mammal
siamese
frog
tokens

72. Accidents: Species and instances
substance
animal
mammal
human
Irishman
Accidents: Species and instances
types
this individual token man
tokens

73. There are universals both among substances (man, mammal)
and among qualities (hot, red)
and among processes (run, movement)
There are universals also among spatial regions (triangle, room, cockpit)
and among spatio-temporal regions (orbit)

74. Substance universals
pertain to what a thing is at all times at which it exists:
cow man rock planet
VW Golf

75. red hot suntanned spinning
Quality universals
pertain to how a thing is at some time at which it exists:
red hot suntanned spinning
Clintophobic Eurosceptic

76. Process universals
reflect invariants in the spatiotemporal world taken as an atemporal whole
football match
course of disease
exercise of function
(course of) therapy

77. Processes and qualities, too, instantiate genera and species
Thus process and quality universals form trees

78. Accidents: Species and instances
quality
color
red
scarlet
R232, G54, B24
this individual accident of redness
(this token redness – here, now)

79. - IS-WE-STATE-OF
This is a link which relates a STATE of a PROPERTY to the element where this STATE inherence.
Example: TEMPERATURE (is the property)
               HIGH TEMPERATURE (is a state of the property TEMPERATURE)
               HOT WATER   [HAS-WE-STATE]   HIGH TEMPERATURE (But at the level of the instance the reverse link can also be applied "high temperature 1" IS-WE-STATE-OF "hot water 1”)

80.   HAS-EXISTENT
This link relates a process of existence to the entity that exists.
Example: MEDICAL HISTORY (is considered an EXISTANCE IN THE PAST) and HAS-EXISTENT a HEALTHCARE PHENOMENOM
So "history of diabetes" is (for us) an "existence of diabetes in the past" and "diabetes" is the entity which existed.

81. -         HAS-SAYING
This is a link which relates a COMMUNICATIVE PROCESS (mental process) to the element which is communicated.
Ex: MENTION OF ABSCESS [HAS-SAYING] ABSCESS
 -        HAS- SENSOR
Relates an INTERNAL MENTAL PROCESS ( thinking, observation...) to the person/animal who performs this action
Ex: (at instance level) "John recognizes Mary." becomes "recognizing process 1" HAS-SENSOR "John 1"

82. -  HAS-PHENOMENON
Also for  INTERNAL MENTAL PROCESS, but phenomenon is the entity which has been "perceived". (Mary in the example above)
Ex: DETERMINATION OF PROGNOSIS [HAS-PHENOMENON] PROGNOSIS

83. -        HAS-SYSTEMIC-MEDIUM
Relates a MATERIAL PROCESS to an entity which participates is the process in an active and passive way at the same time
EX: ARM INFLAMMATION [HAS-SYSTEMIC-MEDIUM] ARM or CHANGE IN WEIGHT [HAS-SYSTEMIC-MEDIUM] WEIGHT

84. -       HAS-CEN-OCCURENCE-DURING
Temporal link that indicates the event in question has happened (begun and ended) during the reference event.
Ex: INFARCT DURING SURGERY [HAS-CEN-OCCURENCE-DURING] SURGICAL DOING

85. Perspectivalism
Perspectivalism
Different partitions may represent cuts through the same reality which are skew to each other

86. Ontology like cartography
must work with maps at different scales and with maps picking out different dimensions of invariants

88. Varieties of granular partitions
Partonomies: inventories of the parts of individual entities
Maps: partonomies of space
Taxonomies: inventories of the universals covering a given domain of reality