Redundant Elements in SNOMED CT Concept Definitions

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Redundant Elements in SNOMED CT Concept Definitions

  1. 1. Introduction Materials & methods Results ConclusionRedundant Elements in SNOMED CTConcept DefinitionsKathrin Dentler and Ronald Cornet31. May @ AIME 2013. Paper: http://www.few.vu.nl/~kdr250/publications/AIME2013-Redundant-Elements-SNOMED.pdfKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 1/23
  2. 2. Introduction Materials & methods Results ConclusionOutline1 Introduction2 Materials & methods3 Results4 ConclusionKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 2/23
  3. 3. Introduction Materials & methods Results ConclusionSNOMED CTSystematized Nomenclature Of Medicine Clinical TermsMeaning-based recording & retrieval, reuse,interoperability!Most comprehensive clinical terminology: around 300,000conceptsConcepts are organized in hierarchies with multiple levelsof granularityKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 3/23
  4. 4. Introduction Materials & methods Results ConclusionSNOMED CTSystematized Nomenclature Of Medicine Clinical TermsKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 4/23
  5. 5. Introduction Materials & methods Results ConclusionSNOMED CT Concept Definitions in EL+RoleGroupsFinding X includes an inflamed arm and a broken leg:∃Finding site.Arm∃Associated morphology.Inflammation∃Finding site.Leg∃Associated morphology.Fracture→unclear what belongs together. Therefore, role-value pairscan be grouped in RoleGroups (RG):∃RG(Finding site.ArmAssociated morphology.Inflammation)∃RG(Finding site.Leg Associated morphology.Fracture)Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 5/23
  6. 6. Introduction Materials & methods Results ConclusionSNOMED CT Concept Definitions in EL+Conjunctions ( ) of other concepts (superconcepts) androle-value pairs (∃), ungrouped or grouped in RoleGroups.Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 6/23
  7. 7. Introduction Materials & methods Results Conclusion(Intra-Axiom) RedundanciesRedundant elementStated explicitly even though it is implied by thedefinition of the same concept or a stated superconcept.Can be removed without affecting the logical closure.Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 7/23
  8. 8. Introduction Materials & methods Results Conclusion(Intra-Axiom) RedundanciesConfuse knowledge modellers (Spackman; ChiefTerminologist at IHTSDO)Make a terminology less flexible and harder to maintain(Grimm and Wissmann)Should be recognized & rendered transparent (Cimino)Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 8/23
  9. 9. Introduction Materials & methods Results Conclusion(Intra-Axiom) RedundanciesExampleExample: Two concepts July 2012Non-imaging thyroid uptake testRadionuclide study of endocrine function∃RG(∃Method.Radionuclide imaging∃Procedure site.Thyroid structure∃Using substance.Radioactive isotope)Thyroid uptake with thyroid stimulationStimulation test Non-imaging thyroid uptake testRadionuclide uptake study∃RG(∃Method.Radionuclide imaging∃Procedure site.Thyroid structure∃Using substance.Radioactive isotope)Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 9/23
  10. 10. Introduction Materials & methods Results Conclusion(Intra-Axiom) RedundanciesMight lead to content-related problems when concepts driftExample: Two concepts January 2013Non-imaging thyroid uptake testRadionuclide study of endocrine function∃RG(∃Method.Radionuclide imaging∃Procedure site.Thyroid structure∃Using substance.Radioactive isotope)Thyroid uptake with thyroid stimulationStimulation test Non-imaging thyroid uptake testRadionuclide uptake study∃RG(::::::::::::::::::::::::::::::::∃Method.Radionuclide imaging∃Procedure site.Thyroid structure∃Using substance.Radioactive isotope)Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 10/23
  11. 11. Introduction Materials & methods Results ConclusionApproachSpackman: defined rules to determine and eliminateredundant expressions in concept definitions (2002)We adapted and extended these rules; one rule perelement:1 concepts2 ungrouped exists restrictions3 exists restrictions within rolegroups4 rolegroupsAim: apply the rules to the entire SNOMED CT; supportknowledge modellersKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 11/23
  12. 12. Introduction Materials & methods Results ConclusionFour rules of redundancy detectionConceptA concept is redundant when it is more general than orequivalent to another concept in the definition of the sameconcept or a superconcept.Example: Structure of lobe of brainStructure of lobe of brainBrain part Brain tissue structureBrain tissue structure Brain partKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 12/23
  13. 13. Introduction Materials & methods Results ConclusionFour rules of redundancy detectionUngrouped exists restrictionAn ungrouped exists restriction is redundant when it is moregeneral than or equivalent to another ungrouped existsrestriction within the definition of the same concept or asuperconcept.Example: Parenteral form thymoxamineThymoxamine (product)Alpha blocking vasodilator Alpha 1 blocking agent∃Has active ingredient.Thymoxamine (substance)Parenteral form thymoxamine (product) ≡Thymoxamine (product)∃Has active ingredient.Thymoxamine (substance)Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 13/23
  14. 14. Introduction Materials & methods Results ConclusionFour rules of redundancy detectionExists restriction within rolegroupAn exists restriction is redundant within a rolegroup when it ismore general than or equivalent to another exists restriction inthe same rolegroup.Example: Closed skull fracture with intracranial injuryClosed skull fracture with intracranial injury ≡Fracture of skull∃RG(∃Finding site.Intracranial structure∃Associated morphology.Traumatic abnormality∃Associated morphology.Closed traumatic abnormality )Closed traumatic abnormality Traumatic abnormalityKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 14/23
  15. 15. Introduction Materials & methods Results ConclusionFour rules of redundancy detectionRolegroupA rolegroup is redundant when all its exists restrictions aremore general than or equivalent to those contained in anotherrolegroup in the definition of the same concept or asuperconcept.Example: Brain stem contusion with open intracranial woundBrain stem contusion with open intracranial wound ≡Contusion of brain with open intracranial wound∃RG(∃Associated morphology.Open wound∃Finding site.Intracranial structure)∃RG(∃Associated morphology.Open contusion∃Finding site.Brainstem structure)Open contusion Open woundBrainstem structure Intracranial structureKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 15/23
  16. 16. Introduction Materials & methods Results ConclusionFour rules of redundancy detectionApproachApplied the four rules of redundancy detection to eachconcept and recursively all its stated (direct and indirect)superconcepts in the stated form of SNOMED CT.Eliminated all identified redundant elements.Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 16/23
  17. 17. Introduction Materials & methods Results ConclusionDetected redundanciesApplying the four rules of redundancy detection, 35,010 of the296,433 SNOMED CT concepts (12%) were identified tocontain redundant elements in their definitions.Overview of all identified redundant elements:Rule All Percentagerolegroup 50,680 41%ungrouped exists restriction 13,808 54%concept 842 0.024%grouped exists restriction 6 0.00026%Sum 65,336Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 17/23
  18. 18. Introduction Materials & methods Results ConclusionCategories of concepts with redundanciesfindingprocedureproductbody structuresituationspecimenorganismsubstancephysical objectNumber of Concepts05000100001500020000Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 18/23
  19. 19. Introduction Materials & methods Results ConclusionDistancesDefined as steps in the concept hierarchyKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 19/23
  20. 20. Introduction Materials & methods Results ConclusionEvaluation of ResultsPartial completeness by comparison to Cornet and Abu-HannaCornet and Abu-Hanna (2008) designed a method to identifyunderspecified concepts, which can also identify special casesof redundantly defined concepts.→We compare the results of the two methods.Partial completeness: All redundantly defined conceptsidentified by applying the Cornet and Abu-Hanna methodmust also be identified by the application of the four rules ofredundancy detection.Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 20/23
  21. 21. Introduction Materials & methods Results ConclusionEvaluation of ResultsPartial completeness by comparison to Cornet and Abu-HannaKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 21/23
  22. 22. Introduction Materials & methods Results ConclusionEvaluation of ResultsSoundnessClosure of manipulated, redundancy-free version of SNOMEDCT equivalent to closure of original version.Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 22/23
  23. 23. Introduction Materials & methods Results ConclusionQuestions?Overview of redundantelements in SNOMED CTRules could help toremove existingredundancies and toprevent futureredundanciesadvantage: explanations!IHTSDO: redundancy-freenormal formsFuture: Generalisation ofmethodKathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 23/23

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