1. W. Ceusters1, M. Capolupo2, B. Smith1, G. De Moor3
Medical Informatics Europe – Oral Paper Session 11: Adverse Drug Events An Evolutionary Approach to the Representation of Adverse Events August 31, 2009 Sarajevo, Bosnia - Herzegovina
W. Ceusters1, M. Capolupo2, B. Smith1, G. De Moor3
1 Ontology Research Group, CoE in Bioinformatics & Life Sciences, SUNY at Buffalo
2 Independent consultant, Buffalo, NY
3 RAMIT VZW, Belgium

2. ReMINE Project

3. Ontology development in ReMINE
support annotation
support
reasoning
higher order logic
description logic
ReMINE
Taxonomies
Description of specific adverse event domains (childbirth, patient transfer, ..) as cognized by human beings
Realism-based, purpose independent representation of the portion of reality described in the taxonomies
Purpose dependent reformulations of the parts of RAEDO which are relevant for a specific domain
ReMINE
Taxonomies
ReMINE
Taxonomies
ReMINE
Taxonomies
ReMINE Application
Ontology
ReMINE Application
Ontology
ReMINE
Adverse Event
Domain Ontology
ReMINE Application
Ontology
ReMINE Application
Ontologies

4. Risk Manager’s Event Administration System
ReMINE Taxonomy
Annotated Events
Risk Manager’s Event Administration System

5. The cognitive model underlying the taxonomies
Risky
Parameters
has
Software
Situation
Environment
has_quality
occurs_in
has_role
SHEL entity
Time Interval
Hardware
occurs_in
has_quality
Contributing
Factor
causes
Adverse_Event
Liveware
results_in
Impact on
Patient
prevents
has_quality
Patient
Incident Type
Mitigation
Factor
results_in
occurs_during
has
results_in
Impact on
Organization
Primary
Diagnosis
Process
Problem

6. ReMINE’s notion of adverse event
an ‘incident [that] occurred during the past and [is] documented in a database of adverse events’
Stefano Arici, Paolo Bertele. ReMINE Deliverable D4.1 – RAPS Taxonomy: approach and definition. V1.0 (Final) August 8, (p21)
… which is a ‘perdurant’ - ibidem (p26)
… ‘that occurs to a patient’ - ibidem (p23)
an expectation of some future happening that can be prevented - ibidem (p23)

7. Terminologists agree, ontologists think …
Can something which is an incident be at the same time an expectation ?
Can something which is an incident a time t, later become an adverse event simply because it [?] has been entered in a database ?
Can adverse events really occur in software ? …

8. Intermediate conclusion
The ReMINE taxonomy (and all concept-based terminologies and ‘ontologies’ in general) provides a distorted view of reality.
For good reasons: the distortion is such that
it reflects a pragmatic view on what is relevant for the purposes it is designed,
it does away with complexities that do not help human beings in doing a better job.
But with some negative consequences:
reusability out of the ReMINE context is hampered,
integration with other descriptive systems becomes cumbersome, and
advanced reasoning turns out to be impossible.

9. Solution: bring philosophical realism in play
Basic axioms of realism:
There is an external reality which is ‘objectively’ the way it is;
That reality is accessible to us;
We build in our brains cognitive representations of reality;
We communicate with others about what is there, and what we believe there is there.
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, Biomedical Ontology in Action, November 8, 2006, Baltimore MD, USA

10. What is there ? some continuant universal some occurrent universal
instanceOf at t
instanceOf
some continuant
particular
some occurrent
particular

11. PtoU: instanceOf, lacks,
Sorts of relations
Unconstrained
reasoning
UtoU: isa, partOf, … U1 U2
PtoU: instanceOf, lacks,
denotes…
OWL-DL reasoning
PtoP: partOf, denotes, subclassOf,… P1 P2

12. Universals and Defined Classes
Unconstrained
reasoning
HUMAN BEING
extension_of at t
instance_of at t
E: all human beings at t
DC-x: patients at t
subclass_of at t
I-y
OWL-DL
reasoning
class_member_of at t
class_member_of at t

13. There are way more sorts of classes than universals
Fever
Rash
Tremor
Edema
Quality
Independent
continuant
Process
isa
extension_of
do not have corresponding universals

14. Three levels of reality, two sorts of representations
beliefs L3
symbolizations
‘about’

15. Level 2
Diagnoses
Interpretations
Hypotheses
Risk assessments …
interpretation
documentation
Level 1
Primary care processes
Secondary processes
management
research
Patients
Clinicians
Drugs
Disorders …
Risk
Management
Ontology
Level 3
Patient documentation
Protocols
Guidelines
Event reports
Scientific literature …
guidance

16. Using the 3 levels and the particular/universal/class distinctions
#1: an incident that happened in the past;
Level 2:
#2: the interpretation by some cognitive agent that #1 is an adverse event;
#3: the expectation by some cognitive agent that similar incidents might happen in the future;
Level 3:
#4: an entry in the adverse event database concerning #1;
#5: an entry in some other system about #3 for mitigation or prevention purposes.

17. Allows appropriate error management
Some possibilities:
#1with unjustified absence of #2:
#1 was not perceived at all, or not assessed as being an adverse event
Unjustified presence of #2:
There was no #1 at all, or #1 was not an adverse event
Unjustified absence of #4
Same reasons as under (1) above
Justified presence of #2 but not reported in the database …
Ceusters W, Smith B. A Realism-Based Approach to the Evolution of Biomedical Ontologies.
Proceedings of AMIA 2006, Washington DC, 2006;:

18. Part of the ReMINE Domain Ontology

19. Higher order logical representation
an incident (#1) that happened at time t2 to a patient (#2) after some intervention (#3 at t1)
is judged at t3 to be an adverse event, thereby giving rise to a belief (#4) about #1 on
the part of some person (#5, a caregiver as of time t6).
This requires the introduction (at t4) of an entry (#6) in the adverse event database (#7, installed at t0).

20. Back-linking of the ontology to the taxonomies
‘ReM:Insufficient illumination’ is a ReMINE term representing a defined class whose members are all instances of the universal represented by the ReMINE term ‘ReM:illumination’, that universal enjoying an isa relation with the universal represented by the BFO term ‘BFO:Quality’
‘ReM:international guideline’ is a ReMINE term representing a defined class whose members are all instances of the universal represented by the UCore-SL term ‘UCore:Plan’, that universal enjoying an isa relation with the universal represented by the BFO term ‘BFO:InformationContentEntity’

21. Advantages
Synchronisation of two distinct representations of the same reality:
taxonomies:
user-oriented view
data annotation
Domain ontology compatible with OBO-Foundry ontologies:
no overlap,
easier to re-use.
Not only tracking of incidents, but also:
how well individual clinicians and organizations manage adverse events,
how well one learns from past experiences.
ontologies:
realism-based view
unconstrained reasoning