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Complex Occurrents in Clinical Terminologies

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Title: Complex Occurrents in Clinical Terminologies


1
Complex Occurrents in Clinical Terminologies
  • Stefan Schulz, Kornél Markó
  • Department of Medical Informatics, Freiburg
    University Hospital, Germany
  • Boontawee Suntisrivaraporn
  • Department of Computer Science, Technical
    University of Dresden, Germany

2
Understanding Clinical Terminologies from an
Ontological Point of View
Append-ectomy
  • Terms / Concepts / Nodes represent Types (common
    properties) used to classify

Append-ectomy,open
Append-ectomy,laparo-scopic
Taxonomy(subtype hierarchy)
Individual objects (instances) in clinical
reality An individual object is instance of one
or more concept according to the properties
defined for this concept
3
Understanding Clinical Terminologies from an
Ontological Point of View
Append-ectomy
  • Terms / Concepts / Nodes represent Types (common
    properties) used to classify

Append-ectomy,open
Append-ectomy,laparo-scopic
Taxonomy(subtype hierarchy)
Proc. 62846
Individual objects (instances) in clinical
reality An individual object is instance of one
or more concepts according to the properties
defined for this concept
Proc. 67129
Proc. 81196
Proc. 64518
Proc. 67599
Proc. 87918
Proc. 69129
Proc. 95541
Proc. 15541
Proc. 66629
Proc. 10196
Proc. 87101
Proc. 63281
Proc. 89006
Proc. 68816
Proc. 24095
Proc. 10541
Proc. 12345
Proc. 87888
Proc. 87877
Proc. 22345
Proc. 89201
Proc. 68876
Proc. 20095
Proc. 68881
4
Understanding Clinical Terminologies from an
Ontological Point of View
Append-ectomy
T-BoxTerminological Level Concepts / Types /
Universal Properties General axioms about
individuals
Append-ectomy,open
Append-ectomy,laparo-scopic
Taxonomy(subtype hierarchy)
All open appendectomies are appendectomies All
appendectomies act on some appendix
instance-of
instance-of
Proc. 62846
A-BoxAssertional LevelAssertions about
instances (individuals, tokens) concrete
objects in the world
Proc. 67129
Proc. 81196
Proc. 64518
Proc. 67599
Proc. 87918
Proc. 69129
Proc. 95541
Proc. 15541
Proc. 66629
Proc. 10196
Proc. 87101
Proc. 63281
Proc. 89006
Proc. 68816
Proc. 24095
Proc. 10541
Procedure 67129 is a laparoscopic
appendectomy Procedure 67129 is performed by
Dr. Petersson Procedure 67129 is complicated
by some infection
Proc. 12345
Proc. 87888
Proc. 87877
Proc. 22345
Proc. 89201
Proc. 68876
Proc. 20095
Proc. 68881
5
Understanding Clinical Terminologies from an
Ontological Point of View
Append-ectomy
ClinicalTerminology
Append-ectomy,open
Append-ectomy,laparo-scopic
Taxonomy(subtype hierarchy)
instance-of
instance-of
MedicalRecords
Proc. 62846
Proc. 67129
Proc. 81196
Proc. 64518
Proc. 67599
Proc. 87918
Proc. 69129
Proc. 95541
Proc. 15541
Proc. 66629
Proc. 10196
Proc. 87101
Proc. 63281
Proc. 89006
Proc. 68816
Proc. 24095
Proc. 10541
Proc. 12345
Proc. 87888
Proc. 87877
Proc. 22345
Proc. 89201
Proc. 68876
Proc. 20095
Proc. 68881
6
Understanding Clinical Terminologies from an
Ontological Point of View
Append-ectomy
ClinicalTerminology
Append-ectomy,open
Append-ectomy,laparo-scopic
Taxonomy(subtype hierarchy)
instance-of
instance-of
MedicalRecords
Proc. 62846
Proc. 67129
Proc. 81196
Proc. 64518
Proc. 67599
Proc. 87918
Proc. 69129
Proc. 95541
Proc. 15541
Proc. 66629
Proc. 10196
Proc. 87101
Proc. 63281
Proc. 89006
Proc. 68816
Proc. 24095
Proc. 10541
Proc. 12345
Proc. 87888
Proc. 87877
Proc. 22345
Proc. 89201
Proc. 68876
Proc. 20095
Proc. 68881
7
Thing
Upper Ontology
Occurrent
Continuant
SurgicalProcedure
Phys.Object
  • Taxonomy(subtype hierarchy,is-a hierarchy)
  • All appendectomies are surgical procedures
  • All surgical procedures are occurrents
  • All appendices are body parts
  • All body parts are physical objects
  • All physical objects are continuants
  • ()

Domain Ontology
Append-ectomy
Append-ectomy
BodyPart
Append-ectomy,open
Append-ectomy,laparo-scopic
Appendix
Heart
8
Thing
Upper Ontology
Occurrent
Continuant
SurgicalProcedure
Phys.Object
  • Taxonomy(subtype hierarchy,is-a hierarchy)
  • All appendectomies are surgical procedures
  • All surgical procedures are occurrents
  • All appendices are body parts
  • All body parts are physical objects
  • All physical objects are continuants
  • ()

Domain Ontology
Append-ectomy
Append-ectomy
BodyPart
Append-ectomy,open
Append-ectomy,laparo-scopic
Appendix
Heart
9
Partonomies (Compositional Hierarchies) of
Continuants
Appendix
part-of some
  • General axioms about parts and holes
  • All appendices are part of some large
    intestine
  • All colons are part of some large intestine
  • All large intestines are part of
  • some digestive tract
  • ()

LargeIntestine
Colon
part-of some
part-of some
DigestiveTract
Ileum
part-of some
SmallIntestine
part-of some
Jejunum
part-of some
10
Partonomies (Compositional Hierarchies) of
Continuants
Gastrotomy
has-part some
  • Every instance of Removal of Foreign Body from
    Stomach by Gastrotomy has as parts
  • some Gastrotomy
  • some Removal of Foreign Body from Stomach

Removal of Foreign Body from Stomach
by Gastrotomy
Removal of Foreign Body from Stomach
has-part some
has-part some in SNOMED CT expressed as Role
Groups (Schulz et al, Meth Inf Med 2006)
11
Problems with Complex Occurrents in Clinical
Terminologies
Running Example
  • Brain Concussion ( ) With Loss Of
    Consciousness ( ) BCLOC

accident
admission
12
Brain Concussion With Loss Of Consciousness
(BCLOC) Different interpretations
  • BCLOC One complex event which is the sum of two
    simple events, a BC and a LOC
  • BCLOC One (simple) BC event which is followed by
    a LOC event
  • BCLOC One (simple) LOC event which is preceded
    by a BC event
  • Instances of BCLOC are not instances of BCLOC,
    they are BCs ontologically dependent on LOCs
  • Instances of BCLOC are not instances of BCLOC,
    they are LOCs ontologically dependent on BCs

13
Brain Concussion With Loss Of Consciousness
(BCLOC) and related types
Occurrent
subtype-of
has-part some
has-part some
BC
LOC
BCLOC
subtype-of
subtype-of
part-of some
part-of some
BCLOC
BCLOC
14
Analogy Sums are not subtypes of their summands

Bride Groom
Couple
summands
sum
  • An instance of Bride is not an instance of
    Couple, but for every instance of Bride there is
    some instance of Couple and some instance of
    Groom
  • An instance of Groom is not an instance of
    Couple, but for every instance of Groom there is
    a some instance of Couple and some instance of
    Bride

cf. Straub et al. From Terminologies to
Classifications FCTC 2006
15
Couple, Woman, Man, Bride, Groom
Continuant
subtype-of
has-part some
Man
Woman
Couple
has-part some
subtype-of
subtype-of
part-of some
part-of some
Groom
Bride
16
Continuant
Occurrent
subtype-of
subtype-of
has-part some
has-part some
has-part some
has-part some
Man
Woman
Couple
BC
LOC
BCLOC
subtype-of
subtype-of
subtype-of
subtype-of
part-of some
part-of some
part-of some
part-of some
Groom
Bride
BCLOC
BCLOC
17
T-Box
Occurrent
subtype-of
has-part some
has-part some
BC
LOC
BCLOC
subtype-of
subtype-of
part-of some
part-of some
BCLOC
BCLOC
A-Box
Patient 1
Patient 2
18
Brain Concussion With Loss Of Consciousness
(BCLOC) More interpretations
19
Brain Concussion With Loss Of Consciousness
(BCLOC) More interpretations
  • BC?LOC complex event constituted by a BC being
    followed by a LOC
  • LOC?BC complex event constituted by a LOC
    followed by a BC
  • AnalogouslyBCLOC, LOCBC, BCLOC, , LOCBC

20
Occurrent
has-part some
has-part some
BC
LOC
BCLOC
BC?LOC
LOC?BC
part-of some
part-of some
LOCBC
LOCBC
BCLOC
BCLOC
21
Occurrent
has-part some
has-part some
BC
LOC
BCLOC
BC?LOC
LOC?BC
precedessome
precedes some
follows some
follows some
LOCBC
BCLOC
BCLOC
LOCBC
22
Brain Concussion Without Loss Of Consciousness
(BC-LOC)
  • Brain Concussion ( ) With Period Without Loss
    Of Consciousness ( )

accident
admission
23
Brain Concussion Without Loss Of Consciousness
(BC-LOC)
?
  • Brain Concussion ( ) With Period Without Loss
    Of Consciousness ( )

?
accident
admission
24
Brain Concussion Without Loss Of Conscious-ness
(BC-LOC) and related types
Occurrent
subtype-of
allhas-partnot
has-part some
BC
LOC
BC-LOC
  • Problems - Temporal Context must be
  • considered
  • Negation or at least
  • disjointness must be
  • supported

subtype-of
part-of some
BC- LOC
25
Workaround Without Negation
Occurrent
absence of loss of consciousness between
traumatic event and examination
subtype-of
has-part some
has-part some
BC
ALOCBTEE
BC-LOC
subtype-of
part-of some
BC- LOC
26
How Complex Occurrents can be expressed in SNOMED
CT
  • SNOMED supports
  • by underlying description logics
  • ontological dependence by existential quantified
    roles (exists some)
  • complex definitions by implicit conjunction (RG)
  • context dependence by context model
  • SNOMED does not support
  • temporal reasoning
  • temporal relations such as follows, precedes
  • negations

27
How Complex Occurrents are currently expressed in
SNOMED CT
  • heterogeneous picture
  • some are represented as sums (BCLOC)
  • some are represented specialized concepts (BCLOC)
  • post-coordination does not always allow to infer
    the pre-coordinated concept
  • Definitions of simple occurrents exhibit
    unnecessary complexity (RG nesting)
  • Conclusion
  • Revision necessary !
  • Examples

28
Occurrent
Gastrotomy
(Group)has-part some
Removal of Foreign Body from Stomach
by Gastrotomy
Removal of Foreign Body from Stomach
(Group)has-part some
29
Occurrent
subtype-of
has-part some
has-part some
BC
LOC
BCLOC
subtype-of
subtype-of
part-of some
part-of some
BCLOC
BCLOC
30
Complex Occurrents in Clinical Terminologies
and their Representation in a Formal Language
  • Stefan Schulz, Kornél Markó
  • Department of Medical Informatics, Freiburg
    University Hospital, Germany
  • Boontawee Suntisrivaraporn
  • Department of Computer Science, Technical
    University of Dresden, Germany

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