1. Disease Ontology Workshop The Ontology of Diagnosis (to be quoted as work in progress) Baltimore, MD, USA. November 7, 2006
Werner CEUSTERS
Center of Excellence in Bioinformatics and Life Sciences
Department of Psychiatry, University at Buffalo, NY, USA
National Center for Biomedical Ontology

2. Outline
Background notions on ontology.
What is a diagnosis ?
What is a disease ?
Diagnostic decision making from an ontological and epistemological perspective.
The impact of change on making diagnoses.
(if enough time) Tracking changes in representations.

3. Reality, ontologies, views, …
Part 1: Background
Reality, ontologies, views, …

4. 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
<particular , universal> e.g. is-instance-of,
<particular , particular> e.g. is-member-of
<universal , universal> e.g. isa (is-subtype-of)
Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

5. Three levels of reality
The world exists ‘as it is’ prior to a cognitive agent’s perception thereof;
Cognitive agents build up ‘in their minds’ cognitive representations of the world;
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

6. Representational artifacts
Ideally built out of representational units and relationships that mirror the entities and their relationships in reality.
Non-Formalized
Formalized
Primarily about particulars
Progress notes, discharge letters, medical summaries, maps, ...
Inventories, referent tracking database, ...
Primarily about universals and defined classes
Medical textbooks, scientific theories, ...
Ontologies, terminologies, ...

7. An example: Referent Tracking Now
An example: Referent Tracking Now! That should clear up a few things around here !
Purpose:
explicit reference to the concrete individual entities relevant to the accurate description of each patient’s condition, therapies, outcomes, ...
Method:
Introduce an Instance Unique Identifier (IUI) for each relevant particular (individual) entity
Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records. J Biomed Inform Jun;39(3):

8. From non-formalized to formalized repositories through Referent Tracking
‘John Doe’s
liver
tumor
was treated
with
RPCI’s
irradiation device’
‘John Doe’s ‘John Smith’s
liver liver
tumor tumor
was treated was treated
with with
RPCI’s RPCI’s
irradiation device’ irradiation device’ #1 #3 #2 #4 #5 #6
instance-of at t1
inst-of
at t2
treating
person
liver
tumor
clinic
device
#10
#30
#20
#40 #5 #6

9. Repository – Ontology “collaboration”

10. Ontology of Biomedical Reality (under development)
pathological
anatomical
structure
pathological
formation
caused by
caused by
disease
isa
isa
tumor
aberrant DNA
molecule
Liver cell adenoma
isa
Hepatocellular carcinoma
hepatoblastoma

11. Part 2: What is a diagnosis ?

12. Making a diagnosis (naive view)
instance-of at t
#105
caused by

13. Towards the full picture (1)
Level of biomedical reality:
Persons, diseases, pathological structures and formations,... do exist as particulars (p, d, ps, pf, ... ) and universals (P, D, PS, PF, ...), and are related in specific ways prior to our perception;
Biomedical reality changes:
d’s, p’s, ... come and go; D’s, P’s, ... only come (?)
Level of biomedical science and case perception:
Mirrors reality only partially
Evolves over time towards better understanding

14. Towards the full picture (2)
Level of concretizations
Mirrors biomedical science and case perception only partially
Editing mistakes
Leaving out diseases or pathological behaviours for non-biomedical reasons
Smoking
Adding non-pathological behaviour as a disease
homosexuality

15. My working definition of ‘diagnosis’
Any configuration of representational units
which is believed to mirror the portion of reality consisting of
an organism’s disease and the relationships this disease enjoys with the entities that caused the disease or influence its course,
whereby some part of this configuration of representational units refers to the universal of which that disease is believed to be an instance, or the defined class of which it is believed to be a member.

16. BTW: universal versus defined class
“lung inflammation”
defined class
universal
instance-of at t

17. A well-formed diagnosis of ‘pneumococal pneumonia’
A configuration of representational units;
Believed to mirror the person’s disease;
Believed to mirror the disease’s cause;
Refers to the universal of which the disease is believed to be an instance.
Disease
isa
Pneumococcal pneumonia
Instance-of at t1
#78
John’s portion
of pneumococs
#56
John’s
Pneumonia
caused by

18. Some motivations and consequences (1)
No use of debatable or ambiguous notions such as proposition, statement, assertion, fact, ...
The same diagnosis can be expressed in various forms.
Disease
isa
caused by
Instance-of at t1
#56
#78
Pneumonia
caused by
Portion of pneumococs
#56
#78
Pneumococcal pneumonia
caused by
Instance-of at t1

19. Some motivations and consequences (2)
A diagnosis can be of level 2 or level 3, i.e. either in the mind of a cognitive agent, or in some physical form.
Allows for a clean interpretation of assertions of the sort ‘these patients have the same diagnosis’:
 The configuration of representational units is such that the parts which do not refer to the particulars related to the respective patients, refer to the same portion of reality.

20. Distinct but similar diagnoses
Pneumococcal pneumonia
Instance-of at t1
Instance-of at t2
#78
John’s portion
of pneumococs
#56
John’s
Pneumonia
#956
Bob’s
pneumonia
#2087
Bob’s portion
of pneumococs
caused by
caused by

21. Some motivations and consequences (3)
Allows evenly clean interpretations for the wealth of ‘modified’ diagnoses:
With respect to the author of the representation:
‘nursing diagnosis’, ‘referral diagnosis’
When created:
‘post-operative diagnosis’, ‘admitting diagnosis’, ‘final diagnosis’
Degree of the belief:
‘uncertain diagnosis’, ‘preliminary diagnosis’

22. But the definition requires working out:
At the level of biomedical reality:
What is a disease ?
What are the entities that cause a specific disease to exist or influence its course ?
What are the relationships between these entities and the disease ?
At the level of representational artifacts:
How do they relate to reality ?
How keeping track of changes in reality ?

23. Part 3: What is a disease ?

24. Latest WHO definition A disease is:
an interconnected set of one or more dysfunctions in one or more body systems including:
a pattern of signs, symptoms and findings (symptomatology - manifestations)
a pattern or patterns of development over time (course and outcome)
a common underlying causal mechanism (etiology)
linking to underling genetic factors (genotypes, phenotypes and endophenotypes) and to interacting environmental factors
and possibly: to a pattern or patterns of response to interventions (treatment response).

25. Latest WHO definition I assume ... ‘of one single person’.
A disease is:
an interconnected set of one or more dysfunctions in one or more body systems including:
a pattern of signs, symptoms and findings (symptomatology - manifestations)
a pattern or patterns of development over time (course and outcome)
a common underlying causal mechanism (etiology)
linking to underling genetic factors (genotypes, phenotypes and endophenotypes) and to interacting environmental factors
and possibly: to a pattern or patterns of response to interventions (treatment response).
I assume ...
‘of one single person’.

26. What is referred to by ‘dysfunction’ ? - A non-canonical functioning ?
Latest WHO definition
A disease is:
an interconnected set of one or more dysfunctions in one or more body systems including:
a pattern of signs, symptoms and findings (symptomatology - manifestations)
a pattern or patterns of development over time (course and outcome)
a common underlying causal mechanism (etiology)
linking to underling genetic factors (genotypes, phenotypes and endophenotypes) and to interacting environmental factors
and possibly: to a pattern or patterns of response to interventions (treatment response).
What is referred to by ‘dysfunction’ ?
- A non-canonical functioning ?
- A functioning which may lead to
harming the diseased person ?

27. Is not an ontological entity but a representational entity.
Latest WHO definition
A disease is:
an interconnected set of one or more dysfunctions in one or more body systems including:
a pattern of signs, symptoms and findings (symptomatology - manifestations)
a pattern or patterns of development over time (course and outcome)
a common underlying causal mechanism (etiology)
linking to underling genetic factors (genotypes, phenotypes and endophenotypes) and to interacting environmental factors
and possibly: to a pattern or patterns of response to interventions (treatment response).
Is not an ontological entity but a representational entity.
Better: a disease involves one or more ...
But then it is left open what a disease IS !

28. Or: the processual entity composed of the dysfunctionings ...
Latest WHO definition
A disease is:
an interconnected set of one or more dysfunctions in one or more body systems including:
a pattern of signs, symptoms and findings (symptomatology - manifestations)
a pattern or patterns of development over time (course and outcome)
a common underlying causal mechanism (etiology)
linking to underling genetic factors (genotypes, phenotypes and endophenotypes) and to interacting environmental factors
and possibly: to a pattern or patterns of response to interventions (treatment response).
Or: the processual entity composed of the dysfunctionings ...

29. Latest WHO definition
A disease is:
an interconnected set of one or more dysfunctions in one or more body systems including:
a pattern of signs, symptoms and findings (symptomatology - manifestations)
a pattern or patterns of development over time (course and outcome)
a common underlying causal mechanism (etiology)
linking to underling genetic factors (genotypes, phenotypes and endophenotypes) and to interacting environmental factors
and possibly: to a pattern or patterns of response to interventions (treatment response).
Violates the principle of the a priori reality: diseases would only exist if we look for them.

30. ‘Ontology inspired’ definition
An organism (or part of an organism) is diseased if and only if
it includes among its parts pathological anatomical structures which compromise the organism’s physiological processes to the degree that they give rise to symptoms and signs.
An anatomical structure is pathological whenever:
it has come into being as a result of changes in some pre-existing canonical anatomical structure
through processes other than the expression of the normal complement of genes of an organism of the given type, and
is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs.
Smith B, Kumar A, Ceusters W, Rosse C. On carcinomas and other pathological entities. Comparative and Functional Genomics, Volume 6, Issue 7-8 (October - December 2005), p

31. Some origines of pathological structures
At molecular level
Defective piece of DNA (“gene”)
Transcription mistakes or mutations
Random event
Environmental effect (radiation, chemical, virusses...)
Results in cellular dysfunction or structural damage
At higher levels of granularity
Traumatic
 Results in cellular, organ or system damage

32. ‘Ontology inspired’ definition
An organism (or part of an organism) is diseased if and only if
it includes among its parts pathological anatomical structures which compromise the organism’s physiological processes to the degree that they give rise to symptoms and signs.
An anatomical structure is pathological whenever:
it has come into being as a result of changes in some pre-existing canonical anatomical structure
through processes other than the expression of the normal complement of genes of an organism of the given type, and
is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs.
A clever trick for not having us to commit at that time what a disease IS.
Smith B, Kumar A, Ceusters W, Rosse C. On carcinomas and other pathological entities. Comparative and Functional Genomics, Volume 6, Issue 7-8 (October - December 2005), p

33. 1st tentative definition of disease
a disposition which, when realized, has health-related consequences for the well-being of the organism or any of its parts.

34. Somewhat problematic
Notion of “well-being” easily leads into circularity when associated with ‘non-diseased’.
‘having health-related consequences’ may also be positive.
It says very little about the nature of the disposition.

35. 2nd tentative definition of disease
A disease is a disposition acquired by a relatively isolated causal system (RICS) to have its external membrane or covering damaged through the coming into existence of a pathological structure.

36. An entity is a relatively isolated causal system iff (1)
The entity has an external boundary which is established via a physical covering or membrane which extends continuously across all or almost all of its surface.
The events transpiring within the entity have characteristic magnitudes which either fall or fall not within a certain spectrum of allowed values. The latter are distinguished by the fact that they will, in cumulation, lead to the entity’s ceasing to exist.
Barry Smith and Berit Brogaard. Sixteen Days. Journal of Medicine and Philosophy 2003, Vol. 28, No. 1, pp. 45–78

37. An entity is a relatively isolated causal system iff (2)
The external membrane or covering serves as a shield to protect the entity from those causal influences deriving from its exterior which are likely to give rise to events which are outside its spectrum of allowed values.
The entity contains within itself its own mechanisms which are able to maintain (or, in cases of disturbance, to re-establish) sequences of events falling within the spectrum of allowed values. The entity also contains within itself mechanisms for reconstituting or replacing its external membrane or covering in case of damage.
Barry Smith and Berit Brogaard. Sixteen Days. Journal of Medicine and Philosophy 2003, Vol. 28, No. 1, pp. 45–78

38. Entities qualifying as relatively isolated causal system
Organisms
Human beings
Unicellular organisms
...
Certain parts of organisms
Cells
Organ systems
Some organs
Maximal portions of tissues
Opens the possibility for an entity to be a disease of a body part without being a disease of the organism of which that body part is a part, yet being a disease in that organism.

39. But the definition requires working out:
At the level of biomedical reality:
What is a disease ?
What are the entities that cause a specific disease to exist or influence its course ?
What are the relationships between these entities and the disease ?
At the level of representational artifacts:
How do they relate to reality ?
How keeping track of changes in reality ?

40. How to come to a diagnosis ?
Part 4: Diagnostic decision making from an ontological and epistemological perspective
How to come to a diagnosis ?

41. Some common notions given an ontological flavor
Clinical picture:
A spatiotemporal entity
Comparable to a theatre play
Which has temporal parts which form the course of the disease
Which has spatial parts which are the pathological formations and pathological anatomical structures.
Pathological entity:
Any part of a clinical picture.
Pathological process:
an organismal process that contributes to the dysfunctioning of the organism or any of its parts.

42. Disease and course of disease
processual entity
disposition ?
actualized in
Joe’s disease
Joe’s disease’s course
caused by
part-of
Creations of pathological formations and of pathological anatomical structures in Joe

43. Some counterintuitive aspects (1)
If in a RICS a disposition is realized in such a way that it can’t get that type of disease anymore (because the RICS will certainly die or becomes immune), then the “disease” would have come to an end, but it’s course not.
We tend to say “the disposition for the disease”, while the disposition IS the disease.
Thus perhaps better (?):
‘Disease’  ‘disease-disposition’
‘Course of disease’  ‘disease’

44. Some counterintuitive aspects (2)
The creations of pathological formations and of pathological anatomical structures in Joe lead to new dispositions but are these dispositions distinct diseases ?
A virus enters one cell in Joe  1 disease ?
The virus enters a second cell  2nd disease ? …
But ! 1) The absence of counterintuitive notions associated with colloquial use of the word ‘disease’ is an illusion. They are there, but unnoticed.
2) Word usage is such that language treats disease as continuant.

45. Beliefs about diseases and clinical pictures (1)
A particular person may exhibit particular pathological entities.
A particular clinical picture starts to exist at the time the first pathological process that is a realization of a particular disease starts to exist.
A particular clinical picture ceases to exist when the last pathological process that is a realization of a particular disease comes to an end, and when there are no more pathological formations or pathological anatomical structures that were formed by the course of the disease.

46. Beliefs about the relevant portion of reality (2)
A particular disease exists in a particular person before a particular clinical picture is present in that person.
There can be no clinical picture without a disease.
A person may exhibit different particular diseases during his lifetime, some or all of them of the same disease type, and some or all of them at the same time or during overlapping time spans.

47. Beliefs about diseases and clinical pictures (3)
A clinical picture can continue to exist although its disease ceased to exist:
Remaining scars
Healthy carriers of virusses
Instances of the same disease may lead to non-similar clinical pictures, even in the same person.

48. Beliefs about the relevant portion of reality (4)
The course of some particular disease may lead to other particular diseases of the same or different disease types in a particular person.
Varicella (?) as a child, zoster as an adult
A particular disease of type A in one person may lead to a particular clinical picture of type B, while a particular disease of that same type A in another person may lead to a clinical picture of a totally different type. …

49. On ‘findings’ and ‘observations’ (1)
A particular pathological entity may at a certain time be undetectable by any observation method or technique available to an observer, including the person exhibiting the pathological entity itself.
A particular observation may produce false results and thus simulate the existence of a pathological entity.
An observer may observe or fail to observe a detectable particular pathological entity.

50. On ‘findings’ and ‘observations’ (2)
When an observer perceives a particular pathological entity, he might judge it
(1) to be an instance of the universal of which it is indeed an instance in reality,
(2) to be an instance of another universal (and thus be in error), or
(3) he might be not able to make an association with any universal at all.
Distinct manifestations of ‘the same type’ may be pathological or not:
Singing naked under the shower versus in front of The White House
...

51. Part 5: Making diagnoses in an ever changing world

52. Reality versus beliefs, both in evolutionp3
Reality
IUI-#3
O-#0
O-#2
Belief
O-#1
= “refers to”
= what constitutes the meaning of representational units
…. Therefore: O-#0 is meaningless

53. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
Total ignorance

54. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
False belief in the existence of a type, e.g. unicorns
Note: happens also at the level of particulars: e.g. the planet ‘Vulcan’

55. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
The coming into existence of a new universal remains unnoticed: ‘AIDS’ existed before being discovered.

56. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
The coming into being of a new particular remains unnoticed: e.g. John Doe’s colonic polyp, which from that time on, is an instance of U1.

57. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
An advance in science: the existence of U1 is acknowledged.

58. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
The existence of John Doe’s benign colonic polyp is discovered, however, without being recognized as such. Rather, it is believed to be an instance of what in reality is a fantasy.

59. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
Another advance in science: the ‘concept’ O-#0 is rightfully abandoned, necessitating therefor to reconsider of what p3 must be believed to be an instance of.

60. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
It is, rightfully believed that p3 is an instance of U1.
It raises, amongst other things, the question to what point in history this belief can be extended.

61. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
p3 changes from a benign into a malignant tumor, at a time that science did not discover malignancy yet.
p3 is now wrongly believed to be an instance of U1.

62. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
Advance in science: “malignancy” is discovered.
However, that it applies to John Doe’s polyp has not yet been noticed.

63. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
John Doe’s polyp becomes recognized as an instance of a malignant tumor.

64. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
John Doe’s polyp was irradiated and believed to have vanished, while in reality, it isn’t.

65. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
John Doe is lucky: his tumor indeed disappeared.
His physicians who believed it was already gone, are lucky also: they escape a law suite.

66. Reality versus beliefs, both in evolutionp3
IUI-#3
O-#0
O-#2 B
O-#1
For ‘utilitarian’ reasons, the “pragmatic engineers” remove malignant tumors from their ontology: if it is not believed to exist, you can’t get law suites for failures in recognizing instances.

67. Some other possible situations
IUI-#3
IUI-#3
O-#0
O-#2 B
O-#1
A particular is believed to exist longer than it really does.
e.g. “Elvis is not dead”, or the innumerous EHRs that state the patient taking some drug while he stopped.

68. Some other possible situations
IUI-#3
O-#0
O-#2 B
O-#1
Artifacts on radiographic images

69. And in this, I thus far ignored …p3
IUI-#3
O-#0
O-#2 B
O-#1
Relationships amongst universals (R) or beliefs therein (B)

70. Mistakes, discoveries, being lucky, having bad luckp3
IUI-#3
O-#0
O-#2 B
O-#1

71. A crucial question …
Do we have some means to assess how good we are doing in our understanding of reality ?
Some might argue: no, because every representational unit will always rest on a belief !
My belief is: yes, if one keeps track of the reasons, in function of the three levels discussed earlier, for which one’s beliefs have changed.

72. Part 6: tracking changes in representations
Ceusters W, Smith B. Towards A Realism-Based Metric for Quality Assurance in Ontology Matching. Forthcoming in Proceedings of FOIS-2006, Baltimore, Maryland, November 9-11, 2006.
Ceusters W, Smith B. A Realism-Based Approach to the Evolution of Biomedical Ontologies. Forthcoming in Proceedings of AMIA 2006, Washington DC, November 11-15, 2006.

73. Remember our 3 fundamentally different levels
the reality on the side of the patient;
the cognitive representations of this reality embodied in observations and interpretations on the part of clinicians and others;
the publicly accessible concretizations of such cognitive representations in representational artifacts of various sorts, of which ontologies and terminologies are examples.

74. Example: a person (in this room) ’s phenotypic gender
Reality:
Male
Female
Cognitive representation
[male]
[female]
In the EHR:
“male”
“female”
“unknown”
Other types of phenotypic gender ?

75. The specification bias in ontology evolution (1)
Ontology versions exhibit differences of the following sorts:
Add a subtree
Delete a subtree
Move a subtree to a different location
Move a set of sibling classes to a different location
Create a new abstraction and move a set of siblings down in a class hierarchy, creating a new superclass.
Delete a class, moving its subclasses to become subclasses of its superclass.
Split a class
Merge classes
Noy, N.F., Kunnatur, S., Klein, M., and Musen, M.A. Tracking changes during ontology evolution. In Proceeding of the 3rd International Semantic Web Conference (ISWC2004), Hiroshima, Japan, November 2004.

76. The specification bias in ontology evolution (2)
Yaozhong David Liang. Enabling Active Ontology Change
Management within Semantic Web-based
Applications
PhD thesis
October 2, 2006

77. They don’t care about the reasons for the changes
changes in the underlying reality (does the appearance or disappearance of an entry in a new version of an ontology relate to the appearance or disappearance of entities or of relationships among entities?);
changes in our scientific understanding;
reassessments of what is relevant for inclusion in an ontology;
encoding mistakes introduced during ontology curation (for example through erroneous introduction of duplicate entries reflecting lack of attention to differences in spelling).

78. An “optimal” ontology (1)
Because ontologies, as conceived on realist terms,
are artifacts created for some purpose (e.g. to serve as controlled vocabulary, or to provide domain knowledge to a software application),
are at the same time intended to mirror reality,
should allow reasoning which is efficient from a computational point of view,
we argue that an optimal ontology should constitute a representation of all and only those portions of reality that are relevant for its purpose.

79. An “optimal” ontology (2)
Each term in such an ontology would designate
(1) a single portion of reality (POR), which is
(2) relevant to the purposes of the ontology and such that
(3) the authors of the ontology intended to use this term to designate this POR, and
(4) there would be no PORs objectively relevant to these purposes that are not referred to in the ontology.

80. But things may go wrong …
assertion errors: ontology developers may be in error as to what is the case in their target domain;
relevance errors: they may be in error as to what is objectively relevant to a given purpose;
encoding errors: they may not successfully encode their underlying cognitive representations, so that particular representational units fail to point to the intended PORs.

81. Key requirement for versioning
Any change in an ontology or data repository should be associated with the reason for that change to be able to assess later what kind of mistake has been made !

82. Example: a person (in this room) ’s gender in the EHR
In John Smith’s EHR:
At t1: “male” at t2: “female”
What are the possibilities ?
Change in reality:
transgender surgery
change in legal self-identification
Change in understanding: it was female from the very beginning but interpreted wrongly
( No change in relevance )
Correction of data entry mistake
(was understood as male, but wrongly transcribed)

83. Ways representational units do or do not refer
OE: objective existence; ORV: objective relevance;
BE: belief in existence;
BRV: belief in relevance;
Int.: intended encoding;
Ref.: manner in which the expression refers;
G: typology which results when the factor of external reality is ignored.
E: number of errors when measured against the benchmark of reality.
P/A: presence/absence of term.

84. Ways representational units do or do not refer
OE/BE value pairs
Y/Y: correct assertion of the existence of a POR;
Y/N: lack of awareness of a POR, reflecting an assertion error;
N/N: correct assertion that some putative POR does not exist ;
N/Y: the false belief that some putative POR exists.

85. Ways representational units do or do not refer
Ref.: manner in which the expression refers
R+: the encoding of the belief is correct
R: the encoding is incorrect because it does not refer
R-: it does refer, but to a POR other than the one which was intended.

86. Possible evolutions through versions

87. Possible evolutions through versions
An entity ceases to exist, but the representation is not updated:

88. Updating is an active process
authors assume in good faith that all included representational units are of the P+1 type, and all they are aware of, but not included, of A+1 or A+2.
If they become aware of a mistake, they make a change under the assumption that their changes are also towards the P+1, A+1, or A+2 cases.
Thus at that time, they know of what type the previous entry must of have been under the belief what the current one is, and the reason for the change.

89. This leads to a calculus …
NOT:
to demonstrate how good an individual version of an ontology is,
But rather
to measure how much it is believed to have been improved (hopefully) as compared to its predecessors.

90. Chains of changes Belief at t reality at t
at t+1: unintended encoding corrected
 If assumed that this is correct, then the unit at t must have been of type P-4, rather than P+1
a gain of +1 is assumed
at t+2: the unit is assumed to refer to nothing, thus is
removed from the representation
 assumption at t+2
then at t+1 it was
then at t it was

91. Additional goodie
Measures also the quality/skills of the ontology / repository authors

92. Can this be implemented ?
Manual burden: documenting the reason for a change  clicking one radio button.
Note: additions require no extra effort
The change of belief revisions is computable
The proof of the pudding is in the eating:
Would SNOMED be a candidate (new grant)
For PHRs (one proposal written)