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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).

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

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  1. 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)

  2. 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

  3. 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”

  4. 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

  5. ? ? ? ? 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

  6. ? ? ? ? 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

  7. ? ? ? ? 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

  8. 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.

  9. 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

  10. 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

  11. Representation in SNOMED CT …compatible with Theory 1

  12. 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

  13. 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” ???

  14. Relationship Groupsin SNOMED CT

  15. 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 ?

  16. 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

  17.  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)

  18. 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

  19. 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

  20. 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)

  21. 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)

  22. 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.

  23. 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)

  24. 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

  25. 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)

  26. 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

  27. 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

  28. 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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