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