Realist Ontology for Electronic Healthcare Records

1
Realist Ontology forElectronic Healthcare Records

• Dr. Werner Ceusters, MD
• European Centre for Ontological Research
• Universität des Saarlandes
• Saarbrücken, Germany

2
Electronic Healthcare Record

• A collection of electronic data about a single
  patient relevant for his health.
• Exists in many forms with various degrees of
  automation
• Scanned documents
• Machine readable documents (text, XML,...)
• Personal (GP), departmental, hospital wide, ...
• Multiple challenges
• Deontological safety, security, confidentiality
• Technical structure and architecture,
  communication
• Pragmatic getting them used
• Machine interpretable triggering and allerts

3
Focus of this presentation

• Role of ontology in maximizing the potential uses
  of the EHCR ...
• For the patients own benefit
• For the advance of science
• Hence, for the health of the population
• ... by making the contents understandable both
  for humans and machines.

4
Understanding content (1)
John Doe has a pyogenic granuloma of the left
thumb
John Doe has a pyogenic granuloma of the left
thumb
5
Understanding content (2)
ltrecordgt ltpatientgtJohn Doelt/patientgt ltdiagnosisgtpy
ogenic granuloma of the left thumblt/diagnosisgt lt/r
ecordgt
ltrecordgt ltsubjectgt John Doe lt/subjectgt ltdiagnosisgt
pyogenic granuloma of the left thumb
lt/diagnosisgt lt/recordgt
6
Understanding content (3)
lt129465004gt lt116154003gtJohn Doelt/116154003gt lt
8319008 gt 17372009 ltfinding sitegt 76505004
ltlateralitygt7771000lt/lateralitygt lt/finding
sitegt lt/ 8319008 gt lt/129465004gt
7
Current state of the art onmeaning in
healthcare informatics

• A pervasive bias towards concepts
• Content wise
• Work based on ISO/TC37 that advocates the
  Ogden-Richards theory of meaning
• Corresponds with a linguistic reading of
  concept
• Architecture wise
• In Europe work based on CEN/TC251 WG1 WG2 that
  follow ISO/TC37
• In the US HL7, inspired by Speech Act Theory
• Concepts used as elements of information
  models, hence mixing a linguistic and engineering
  reading.

8
Topics

• Meaning and understanding
• Biomedical terminologies and concept systems
• EHCR architecture
• Problems of the concept-based approach
• Ontology as part of the solution

9
Dyadic models of meaning

• Saussure (language philosopher)
• signe / signifiant (sign/concept)
• Ron Stamper (information scientist)
• thing-A STANDS-FOR thing-B
• Major drawback
• excludes the referent from the model, i.e. that
  what the sign/symbol/word/... denotes

10
Triadic models of meaning The Semiotic/Semantic
triangle
Reference Concept / Sense / Model / View /
Partition
Sign Language/ Term/ Symbol
Referent Reality/ Object
11
Aristotles triadic meaning model
Words spoken are signs or symbols (symbola) of
affections or impressions (pathemata) of the soul
(psyche) written words (graphomena) are the
signs of words spoken (phoné). As writing
(grammatta), so also is speech not the same for
all races of men. But the mental affections
themselves, of which these words are primarily
signs (semeia), are the same for the whole of
mankind, as are also the objects (pragmata) of
which those affections are representations or
likenesses, images, copies (homoiomata).
Aristotle, 'On Interpretation', 1.16.a.4-9,
Translated by Cooke Tredennick, Loeb Classical
Library, William Heinemann, London, UK, 1938.
pathema
semeia ? gramma/ phoné
pragma
12
Richards semantic triangle

• Reference (concept) indicates the realm of
  memory where recollections of past experiences
  and contexts occur.
• Hence as with Aristotle, the reference is
  mind-related thought.
• But not the same for all, rather individual
  mind-related

reference
symbol
referent
13
Dont confuse with homonymy !
mole
14
Different thoughts Homonymy
R2
R3
R1
mole skin lesion
mole unit
mole
mole animal
15
And by the way, synonymy...
the Aristotelian view
Richards view
sweat
sweat
perspiration
perspiration
16
Freges view

• sense is an objective feature of how words are
  used and not a thought or concept in somebodys
  head
• 2 names with the same reference can have
  different senses
• 2 names with the same sense have the same
  reference (synonyms)
• a name with a sense does not need to have a
  reference (Beethovens 10th symphony)

sense
name
reference (referent)
17
Tetrahedric extensions
CEN/TC251 ENV 12264
FRISCO model (information science)
18
The theory in practice
He wants me to hold that kocher
Oops, this is too slippery to hold any longer
Take this, please !
19
Issues in communication
Take the kocher, please.
20
Concept-based Terminology
kocher
21
Kocher clamp in SNOMED-CT
22
From Speech Acts to Information Model
HL7-RIM
23
CENs view on reality andthe healthcare record
CEN ENV 13606

• The real world of health and health care is made
  up of individual clinical situations
• (of which the participants are called associate
  topics), that are described by an EHCR author as
  clinical statements.
• Within an EHCR system each clinical statement
  will be expressed as an elementary healthcare
  record entry.

24
EHR Extended Architecture
CEN ENV 13606
Elementary healthcare record entries
25
Types of Original Component Complexes
CEN ENV 13606
26
Architectural Component Attributes
CEN ENV 13606
Refer to situations and statements and rely on
terminology
27
Archetypes
CEN ENV 13606

• clinical situation
• pertains to body component, product, environment
• has context facet subject of information,
  process status, role for dates
• has information qualifier knowing mode
• has information source actor
• has qualifier communication modality
• has qualifier relevance
• has role role for clinical situation
• Is stated by actor, healthcare organisation
• has temporal marker timing marker

To be used to build terminologies that may be
used for the EHR
28
Structure of concept-based terminologies
29
Axiom

• Concept-based terminology (and standardisation
  thereof) is there as a mechanism to improve
  understanding of messages, originally by humans,
  now also by machines.
• It is NOT the right device to explain why reality
  is what it is, how it is organised, etc.,
  (although it is needed to allow us to communicate
  on insights thereof).

30
Why not ?

• Ad hoc readings of statements of the type
  C1-relationship-C2
• Human has-part head // Human has-part
  finger
• California is-part-of United States //
  California isa name
• labial vein isa vein of head // labial vein
  isa vulval vein
• Concepts not necessarily correspond to something
  that (will) exist(ed)
• Sorcerer, unicorn, leprechaun, ...
• Definitions set the conditions under which terms
  may be used, and may not be abused as conditions
  an entity must satisfy to be what it is
• Language can make strings of words look as if it
  were terms
• Middle lobe of left lung

31
What is then the right way ?

• Realist Ontology !

32
If, later, you can remember just one thing of
this presentation, then make sure it is this one

• If somebody uses the word ontology, ALWAYS let
  him be specific about what he understands by it.

33
The O-word
N. Guarino, P. Giaretta, "Ontologies and
Knowledge Bases Towards a Terminological
Clarification". In Towards Very Large Knowledge
Bases Knowledge Building and Knowledge Sharing,
N. Mars (ed.), pp 25-32. IOS Press, Amsterdam,
1995.
34
Ontology

• In Information Science
• An ontology is a description (like a formal
  specification of a program) of the concepts and
  relationships that can exist for an agent or a
  community of agents.
• In Philosophy
• Ontology is the science of what is, of the kinds
  and structures of objects, properties, events,
  processes and relations in every area of reality.

35
My use of the word ontology

• a for a computer understandable representation
  of some pre-existing domain of REALITY,
  reflecting the properties of the objects within
  its domain in such a way that there obtain
  substantial and systematic correlations between
  reality and the ontology itself.
• modified from Barry Smith

36
Back to to the operating theatre
A lot of objects present
37
Back to to the operating theatre
A lot of processes going on
Haydom Lutheran Hospital, Tanzania
38
Axiom

• If the picture is not a fake, we (i.e., me and
  this audience) KNOW that that hand, that surgeon,
  ... EXIST(ed), i.e. ARE (were) REAL.
• But importantly that hand, surgeon, kocher,
  mask, ... EXIST(ed) independent of our knowledge
  about them and also the part-relationship
  between that hand and that surgeon, and the
  processes going on, are (were) equally real.

39
(Simplified) Logic of classes

• primitive
• entities particulars versus universals
• relation inst such that
• all classes are universals all instances are
  particulars
• some universals are not classes, hence have no
  instances pet, adult, physician
• some particulars are not instances e.g. some
  mereological sums
• subsumption defined resorting to instances

40
Basic Formal Ontology

• Basic Formal Ontology consists in a
  series of sub-ontologies (most properly conceived
  as a series of perspectives on reality), the most
  important of which are
• SnapBFO, a series of snapshot ontologies (Oti ),
  indexed by times
• SpanBFO a single videoscopic ontology (Ov).
• Each Oti is an inventory of all entities
  existing at a time. Ov is an inventory
  (processory) of all processes unfolding through
  time.

41
(No Transcript)
42
Take home messagea need for a clean separation
of knowledge AND ontology
Pragmatic knowledge what users usually say or
think, what they consider important, how to
integrate in software
Alan Rector
Knowledge of classification and coding systems
how an expression has been classified by such a
system
Knowledge of definitions and criteria how to
determine if a concept applies to a particular
instance
Surface linguistic knowledge how to express the
concepts in any given language
Conceptual knowledge the knowledge of sensible
domain concepts
Ontology what exists and how what exists relates
to each other