complex occurrents in clinical terminologies stefan schulz, kornél markó department of medical...
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Complex Occurrents in Clinical Terminologies
Stefan Schulz, Kornél MarkóDepartment of Medical Informatics,
Freiburg University Hospital, Germany
Boontawee SuntisrivarapornDepartment of Computer Science,
Technical University of Dresden, Germany
Understanding Clinical Terminologies from an Ontological Point of View
Proc. #12345
Proc. #22345
Proc. #24095
Proc. #20095Proc.
#68881
Proc. #63281
Proc. #95541
Proc. #10541
Proc. #15541
Proc. #67599
Proc. #67129Proc.
#69129
Proc. #66629
Proc. #62846
Proc. #68876
Proc. #68816
Proc. #10196
Proc. #81196
Proc. #89006
Proc. #89201
Proc. #87101
Proc. #87877
Proc. #87888
Proc. #87918
Proc. #64518
Append-ectomy,
open
Append-ectomy
Append-ectomy,laparo-scopic
Taxonomy(subtype hierarchy)
T-BoxTerminological LevelConcepts / Types / Universal Properties General axioms about individuals:
A-BoxAssertional Level:Assertions about instances (individuals,tokens) = concrete objects in the world
“All open appendectomies are appendectomies”“All appendectomies act on some appendix”
“Procedure #67129 is a laparoscopic appendectomy”“Procedure #67129 is performed by Dr. Petersson”“Procedure #67129 is complicated by some infection”
instance-of instance-of
Understanding Clinical Terminologies from an Ontological Point of View
Proc. #12345
Proc. #22345
Proc. #24095
Proc. #20095Proc.
#68881
Proc. #63281
Proc. #95541
Proc. #10541
Proc. #15541
Proc. #67599
Proc. #67129Proc.
#69129
Proc. #66629
Proc. #62846
Proc. #68876
Proc. #68816
Proc. #10196
Proc. #81196
Proc. #89006
Proc. #89201
Proc. #87101
Proc. #87877
Proc. #87888
Proc. #87918
Proc. #64518
Append-ectomy,
open
Append-ectomy
Append-ectomy,laparo-scopic
Taxonomy(subtype hierarchy)
ClinicalTerminology
MedicalRecords
instance-of instance-of
Understanding Clinical Terminologies from an Ontological Point of View
Proc. #12345
Proc. #22345
Proc. #24095
Proc. #20095Proc.
#68881
Proc. #63281
Proc. #95541
Proc. #10541
Proc. #15541
Proc. #67599
Proc. #67129Proc.
#69129
Proc. #66629
Proc. #62846
Proc. #68876
Proc. #68816
Proc. #10196
Proc. #81196
Proc. #89006
Proc. #89201
Proc. #87101
Proc. #87877
Proc. #87888
Proc. #87918
Proc. #64518
Append-ectomy,
open
Append-ectomy
Append-ectomy,laparo-scopic
Taxonomy(subtype hierarchy)
ClinicalTerminology
MedicalRecords
instance-of instance-of
Append-ectomy,
open
Append-ectomy
Append-ectomy,laparo-scopic
SurgicalProcedure
Append-ectomy
Occurrent
Thing
Continuant
Phys.Object
BodyPart
AppendixHeart
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• (…)
Upper Ontology
Domain Ontology
Append-ectomy,
open
Append-ectomy
Append-ectomy,laparo-scopic
SurgicalProcedure
Append-ectomy
Occurrent
Thing
Continuant
Phys.Object
BodyPart
AppendixHeart
Upper Ontology
Domain Ontology
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• (…)
Partonomies (Compositional Hierarchies) of Continuants
DigestiveTract
LargeIntestine
SmallIntestine
Ileum
Jejunum
Appendix
Colon
part-of some
part-of some
part-of some
part-of some
part-of some
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• (…)
Partonomies (Compositional Hierarchies) of Continuants
Removal
of Foreign Body
from Stomach by
Gastrotomy
Gastrotomy
Removal of Foreign Body from Stomach
has-part some
has-part someEvery instance of “Removal of Foreign Body from Stomach by Gastrotomy” has as parts:• some Gastrotomy• some Removal of Foreign Body from Stomach
”has-part some” in SNOMED CT expressed as Role Groups (Schulz et al, Meth Inf Med 2006)
Problems with Complex Occurrents in Clinical Terminologies
Brain Concussion ( ) With Loss Of Consciousness ( ) = BCLOC
accident admission
Running Example:
Brain Concussion With Loss Of Consciousness (BCLOC): Different interpretations
1. BCLOC: One complex event which is the sum of two simple events, a BC and a LOC
2. BCLOC: One (simple) BC event which is followed by a LOC event
3. 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
BC LOC
Occurrent
BCLOC
has-part some
has-part some
BCLOC BCLOC
part-of some
part-of some
subtype-of
subtype-ofsubtype-of
Brain Concussion With Loss Of Consciousness (BCLOC) and related types
Analogy: Sums are not subtypes of their summands
+ =
Bride Groom Couple
• 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
summands sum*
*cf. Straub et al. From Terminologies to Classifications – FCTC 2006
Couple, Woman, Man, Bride, Groom
Man Woman
Continuant
Couple
has-part some
has-part some
Groom Bride
part-of some
part-of some
subtype-of
subtype-ofsubtype-of
Man Woman
Continuant
Couple
has-part some
has-part some
Groom Bride
part-of some
part-of some
subtype-of
subtype-ofsubtype-of
BC LOC
Occurrent
BCLOC
has-part some
has-part some
BCLOC BCLOC
part-of some
part-of some
subtype-of
subtype-ofsubtype-of
BC LOC
Occurrent
BCLOC
has-part some
has-part some
BCLOC BCLOC
part-of some
part-of some
subtype-of
subtype-ofsubtype-of
Patient #1
Patient #2
A-Box
T-Box
Brain Concussion With Loss Of Consciousness (BCLOC): More interpretations
• BCLOC: complex event constituted by a BC being followed by a LOC
• LOCBC: complex event constituted by a LOC followed by a BC
• Analogously:
BCLOC, LOCBC, BCLOC, , LOCBC
Brain Concussion With Loss Of Consciousness (BCLOC): More interpretations
BC LOC
Occurrent
BCLOC
has-part some
has-part some
LOCBC LOCBC
part-of some
BCLOC LOCBC
BCLOC BCLOC
part-of some
BC LOC
Occurrent
BCLOC
has-part some
has-part some
LOCBC BCLOC
BCLOC LOCBC
BCLOC LOCBC
precedessome
followssome
followssome
precedes some
Brain Concussion ( ) With “Period Without Loss Of Consciousness” ( )
Brain Concussion Without Loss Of Consciousness (BC-LOC)
accident admission
Brain Concussion ( ) With “Period Without Loss Of Consciousness” ( )
accident admission
?
?
Brain Concussion Without Loss Of Consciousness (BC-LOC)
BC LOC
Occurrent
BC-LOC
has-part some
allhas-part
not
BC- LOC
part-of some
subtype-of
subtype-of
Brain Concussion Without Loss Of Conscious-ness (BC-LOC) and related types
Problems: - Temporal Context must be considered-Negation or at least disjointness must be supported
BCALOCBTEE
Occurrent
BC-LOC
has-part some
BC- LOC
part-of some
subtype-of
subtype-of
“Workaround” Without Negation
has-part some
absence of loss of consciousness
between traumatic event and
examination
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
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:
Removal
of Foreign Body
from Stomach by
Gastrotomy
(Group)has-part some
(Group)has-part some
Occurrent
Gastrotomy
Removal of Foreign Body from Stomach
BC LOC
Occurrent
BCLOC
has-part some
has-part some
BCLOC BCLOC
part-of some
part-of some
subtype-of
subtype-ofsubtype-of
Complex Occurrents in Clinical Terminologies…
…and their Representation in a Formal Language
Stefan Schulz, Kornél MarkóDepartment of Medical Informatics,
Freiburg University Hospital, Germany
Boontawee SuntisrivarapornDepartment of Computer Science,
Technical University of Dresden, Germany