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Semantic Clarification of the Representation of Procedures and Diseases in SNOMED CT. Stefan Schulz. Jeremy Rogers. Udo Hahn. Medical Informatics University of Manchester (UK). Medical Informatics, Freiburg University Hospital (Germany). Computational Linguistics Jena University (Germany).

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semantic clarification of the representation of procedures and diseases in snomed ct

Semantic Clarification of the Representation of Procedures and Diseases in SNOMED CT

Stefan Schulz

Jeremy Rogers

Udo Hahn

Medical Informatics University of Manchester(UK)

Medical Informatics, Freiburg University Hospital (Germany)

Computational Linguistics Jena University (Germany)

context snomed ct clinical terms
Context: SNOMED CT (Clinical Terms)
  • Comprehensive clinical terminology system
  • Constructed by merging, expanding, and restructuring SNOMED RT and Clinical Terms Version 3 (former Read Codes).
  • 364,000 concepts, 984,000 terms, 1.45 million defined relationships between concepts
  • Government agreements in U.S. & U.K.
  • Increasing interest into SNOMED CT in other countries
snomed ct oav and dl notation
Description Logics (DL) representation:cf. Kent Spackman, AMIA 2002Renal glomerular disease ⊑Renal diseaseRenal glomerular disease ⊑  has_finding_site.KidneyGlomerulum ⊑  part-of.Kidney

Syntax Semantics

cf. Baader et al. Description Logics Handbook

SNOMED CT OAV and DL notation
  • Object – Attribute – Value (OAV) Triplets
  • Objects and Values are SNOMED “concepts”
  • Attributes are SNOMED “relations”
objective of this talk
Objective of this talk
  • Ontological Inquiry of the representation of Processes in SNOMED CT
  • Clarification of the meaning of the “relationship group” attribute in SNOMED CT
  • „Process“ in the sense of
    • Diagnostic or Therapeutic Procedures
    • Pathological and Physiological Processes

Removal of foreign body from stomach by incision

hierarchichal arrangement of processes
?

?

?

?

Hierarchichal Arrangement of Processes

Medical Procedure

?

Surgical Procedure

?

?

Removal of foreign body from stomachby endoscopy

Removal of foreign body

from stomach by incision

EndoscopicExploration

Removal offoreign body

Removal offoreign body

Incision ofStomach

parent and child processes
?

?

?

?

Parent and Child Processes

Medical Procedure

is-a

Taxonomy of Processes:

is-a relation between parent and

child processes

Surgical Procedure

is-a

is-a

Removal of foreign body from stomachby endoscopy

Removal of foreign body

from stomach by incision

EndoscopicExploration

Removal offoreign body

Removal offoreign body

Incision ofStomach

processes and subprocesses
?

?

?

?

Processes and Subprocesses

Medical Procedure

is-a

Surgical Procedure

is-a

is-a

Removal of foreign body from stomachby endoscopy

Removal of foreign body

from stomach by incision

Processes/

Subprocesses

EndoscopicExploration

Removal offoreign body

Removal offoreign body

Incision ofStomach

slide8
How to semantically relate processes with their subprocesses
  • A (complex) process is subsumed by its subprocesses:
      • Subprocesses do not exist simultaneously. An instance of Removal of foreign body from stomach by incision is first an instance of Incision of stomach and then becomes an instance of Removal of foreign body
  • Subprocesses are temporal parts of a (complex) process :
      • A complex process can be aborted before completion. The complex process Removal of foreign body from stomach by incision can only be instantiated if the subprocesses have been completed.
theory 1 a complex process is subsumed by its subprocesses
Theory 1: A (complex) process is subsumed by its subprocesses

Surgical Procedure

is-a

is-a

is-a

Incision ofStomach

EndoscopicExploration

Removal of foreign body from stomach

is-a

is-a

is-a

is-a

Removal of foreign body from stomachby endoscopy

Removal of foreign body from stomach by incision

theory 2 subprocesses are temporal parts of a complex process
Theory 2: Subprocesses are temporal parts of a (complex) process

Surgical Procedure

is-a

is-a

Removal of foreign body from stomach by endoscopy

Removal of foreign body from stomach by incision

 has-part

 has-part

 has-part

 has-part

EndoscopicExploration

Removal offoreign bodyfrom Stomach

Incision ofStomach

representation in snomed ct
Representation in SNOMED CT

…compatible with Theory 1

theory 1 a complex process is subsumed by its subprocesses1
Theory 1: A (complex) process is subsumed by its subprocesses

Surgical Procedure

is-a

is-a

is-a

Incision ofStomach

EndoscopicExploration

Removal of foreign body from stomach

is-a

is-a

is-a

is-a

Removal of foreign body from stomachby endoscopy

Removal of foreign body from stomach by incision

na ve dl transcription
Naïve DL Transcription

RemovalOfForeignBodyFromStomachByIncision

RemovalOfForeignBodyFromDigestiveSystem AND

RemovalOfForeignBodyFromStomach AND

IncisionOfStomach AND

Method.RemovalAction AND

DirectMorphology.ForeignBody AND

Method.IncisionAction AND

ProcedureSite.stomachStructure

…indistinguishable from “incision of foreign body and removal of stomach” ???

nesting with relationship groups rgs in dl formalism
Nesting with relationship groups (RGs) in DL formalism

RemovalOfForeignBodyFromStomachByIncision

RemovalOfForeignBodyFromDigestiveSystem AND

RemovalOfForeignBodyFromStomach AND

IncisionOfStomach AND

 RG.(Method.RemovalAction AND

DirectMorphology.ForeignBody) AND

 RG.(Method.IncisionAction AND

ProcedureSite.stomachStructure)

RG1

RG2

Mix-up prevented. Compatible with which theory ?

theory 2 subprocesses are temporal parts of a complex process1
Theory 2: Subprocesses are temporal parts of a (complex) process

Surgical Procedure

is-a

is-a

Removal of foreign body from stomach by endoscopy

Removal of foreign body from stomach by incision

 has-part

 has-part

 has-part

 has-part

EndoscopicExploration

Removal offoreign body

Incision ofStomach

theory 2 subprocesses are temporal parts of a complex process2
 has-part.(Method.Removal AND

DirectMorphology.ForeignBody)

Theory 2: Subprocesses are temporal parts of a (complex) process

Removal of foreign body from stomach by incision

 has-part

 has-part

Removal offoreign body

Incision ofStomach

Incision

Removal

 method

 method

Stomach Structure

Foreign Body

 procedure site

 direct morphology

 has-part.(Method.Incision AND

ProcedureSite.stomachStructure)

nesting with relationship groups rgs in dl formalism1
Nesting with relationship groups (RGs) in DL formalism

RemovalOfForeignBodyFromStomachByIncision

RemovalOfForeignBodyFromDigestiveSystem AND

RemovalOfForeignBodyFromStomach AND

IncisionOfStomach AND

 RG.(Method.RemovalAction AND

DirectMorphology.ForeignBody) AND

 RG.(Method.IncisionAction AND

ProcedureSite.stomachStructure)

RG1

RG2

snomed relation groups can be re interpreted as has part
SNOMED relation groups can be re-interpreted as has-part

RemovalOfForeignBodyFromStomachByIncision

RemovalOfForeignBodyFromDigestiveSystem AND

RemovalOfForeignBodyFromStomach AND

IncisionOfStomach AND

has-part.(Method.RemovalAction AND

DirectMorphology.ForeignBody) AND

has-part.(Method.IncisionAction AND

ProcedureSite.stomachStructure)

RG1

RG2

difference between x and x action in snomed ct
Difference between “X” and “X-Action” in SNOMED CT

RemovalOfForeignBodyFromStomachByIncision

RemovalOfForeignBodyFromDigestiveSystem AND

RemovalOfForeignBodyFromStomach AND

IncisionOfStomach AND

 has-part.(Method.RemovalAction AND

DirectMorphology.ForeignBody) AND

 has-part.(Method.IncisionAction AND

ProcedureSite.stomachStructure)

difference between x and x action in snomed ct1
Difference between “X” and “X-Action” in SNOMED CT

RemovalOfForeignBodyFromStomachByIncision

RemovalOfForeignBodyFromDigestiveSystem AND

RemovalOfForeignBodyFromStomach AND

IncisionOfStomach AND

 has-part.(Method.RemovalAction AND

DirectMorphology.ForeignBody) AND

 has-part.(Method.IncisionAction AND

ProcedureSite.stomachStructure)

conclusions
Conclusions
  • Relationship groups in SNOMED CT may represent the mereological relation between procedures / actions / processes and their parts.
  • Suggest: Rename the relationship group attribute RG by has-part or has-subprocess in these cases.
  • Make a clearer distinction between atomic classes (such as IncisionAction) and those classes which have atomic classes as parts (such as IncisionProcess). The present names are misleading.
semantic clarification of the representation of procedures and diseases in snomed ct1

Semantic Clarification of the Representation of Procedures and Diseases in SNOMED CT

Stefan Schulz

Jeremy Rogers

Udo Hahn

Medical Informatics University of Manchester(UK)

Medical Informatics, Freiburg University Hospital (Germany)

Jena University, Language & Information Engineering (Germany)

theory 1 process is instantiated by its subprocesses
P1

P2

P3

P4

P

Theory 1: Process is instantiated by its subprocesses

P1

P2

P3

P4

P1

P2

P3

P4

P1

P2

P3

P4

P1

P2

P3

P4

    

P

P

P

P

instance-of

instance-of

instance-of

instance-of

p

p

p

p

t

t1

t2

t3

t4

Acknowledgements: Boris Hennig, unpublished

difference between x and x action in snomed ct2
Difference between “X” and “X-Action” in SNOMED CT

RemovalOfForeignBodyFromStomachByIncision

RemovalOfForeignBodyFromDigestiveSystem AND

RemovalOfForeignBodyFromStomach AND

IncisionOfStomach AND

 has-part.(Method.RemovalAction AND

DirectMorphology.ForeignBody) AND

 has-part.(Method.IncisionAction AND

ProcedureSite.stomachStructure)

theory 2 subprocesses are parts of their parent processes
P1

P1

P1

P1

P4

P2

P3

P2

P2

P3

P‘‘‘

P‘‘

P‘

P

Theory 2: Subprocesses are parts of their parent processes

 has-part

is-a

 has-part

is-a

 has-part

is-a

 has-part

instance-of

instance-of

instance-of

instance-of

p

p

p

p

t

t1

t2

t3

t4

parent and child processes1
Parent and Child Processes

Surgical Procedure

Taxonomy of Processes:

is-a relation between parent and

child processes

Removal of foreign body from stomach

Removal of foreign body from stomachby endoscopy

Removal of foreign body from stomachby incision

Preparationfor Surgery

Closure

Preparationfor Endoscopy

Extraction of Endoscope

Incision

Introduction of Endoscope

Removal offoreign body

Removal offoreign body

Exploration

Exploration

t

t

processes and subprocesses1
Processes and Subprocesses

Surgical Procedure

Removal of foreign body from stomach

Removal of foreign body from stomachby endoscopy

Removal of foreign body from stomachby incision

Preparationfor Surgery

Closure

Preparationfor Endoscopy

Extraction of Endoscope

Incision

Introduction of Endoscope

Removal offoreign body

Removal offoreign body

Partonomy of Processes

Exploration

Exploration

t

t

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