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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: and Diseases in SNOMED CT 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: and Diseases in SNOMED CTcf. 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 and Diseases in SNOMED CT

  • 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

? and Diseases in SNOMED CT

?

?

?

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

? and Diseases in SNOMED CT

?

?

?

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

? and Diseases in SNOMED CT

?

?

?

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


How to semantically relate processes with their subprocesses and Diseases in SNOMED CT

  • 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 process

    …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 subprocesses

    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” ???


    Relationship groups in snomed ct
    Relationship Groups subprocessesin SNOMED CT


    Nesting with relationship groups rgs in dl formalism
    Nesting with relationship subprocessesgroups (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

    process 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 process 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 process

    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 process “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 process “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 process

    • 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

    P and Diseases in SNOMED CT1

    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 and Diseases in SNOMED CT“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

    P and Diseases in SNOMED CT1

    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 and Diseases in SNOMED CT

    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 and Diseases in SNOMED CT

    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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