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Introduction Materials & methods Results Conclusion
Redundant Elements in SNOMED CT
Concept Definitions
Kathrin Dentler and Ronald Cornet
31. May @ AIME 2013. Paper: http://www.few.vu.nl/~kdr250/
publications/AIME2013-Redundant-Elements-SNOMED.pdf
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 1/23
Introduction Materials & methods Results Conclusion
Outline
1 Introduction
2 Materials & methods
3 Results
4 Conclusion
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 2/23
Introduction Materials & methods Results Conclusion
SNOMED CTSystematized Nomenclature Of Medicine Clinical Terms
Meaning-based recording & retrieval, reuse,interoperability!
Most comprehensive clinical terminology: around 300,000concepts
Concepts are organized in hierarchies with multiple levelsof granularity
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 3/23
Introduction Materials & methods Results Conclusion
SNOMED CTSystematized Nomenclature Of Medicine Clinical Terms
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 4/23
Introduction Materials & methods Results Conclusion
SNOMED CT Concept Definitions in EL+
RoleGroups
Finding X includes an inflamed arm and a broken leg:
∃Finding site.Arm u∃Associated morphology.Inflammation u∃Finding site.Leg u∃Associated morphology.Fracture
→unclear what belongs together. Therefore, role-value pairscan be grouped in RoleGroups (RG):
∃RG(Finding site.Arm uAssociated morphology.Inflammation) u
∃RG(Finding site.Leg u Associated morphology.Fracture)
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 5/23
Introduction Materials & methods Results Conclusion
SNOMED CT Concept Definitions in EL+
Conjunctions (u) 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
Introduction Materials & methods Results Conclusion
(Intra-Axiom) RedundanciesRedundant element
Stated 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
Introduction Materials & methods Results Conclusion
(Intra-Axiom) Redundancies
Confuse 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
Introduction Materials & methods Results Conclusion
(Intra-Axiom) RedundanciesExample
Example: Two concepts July 2012
Non-imaging thyroid uptake test vRadionuclide study of endocrine function u∃RG(∃Method.Radionuclide imaging u
∃Procedure site.Thyroid structure u∃Using substance.Radioactive isotope)
Thyroid uptake with thyroid stimulation vStimulation test u Non-imaging thyroid uptake test uRadionuclide uptake study u∃RG(∃Method.Radionuclide imaging u
∃Procedure site.Thyroid structure u∃Using substance.Radioactive isotope)
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 9/23
Introduction Materials & methods Results Conclusion
(Intra-Axiom) RedundanciesMight lead to content-related problems when concepts drift
Example: Two concepts January 2013
Non-imaging thyroid uptake test vRadionuclide study of endocrine function u∃RG(∃Method.Radionuclide imaging u
∃Procedure site.Thyroid structure u∃Using substance.Radioactive isotope)
Thyroid uptake with thyroid stimulation vStimulation test u Non-imaging thyroid uptake test uRadionuclide uptake study u∃RG(
::::::::::::::::::::::::::::::::∃Method.Radionuclide imaging u∃Procedure site.Thyroid structure u∃Using substance.Radioactive isotope)
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 10/23
Introduction Materials & methods Results Conclusion
Approach
Spackman: 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 rolegroups
Aim: apply the rules to the entire SNOMED CT; supportknowledge modellers
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 11/23
Introduction Materials & methods Results Conclusion
Four rules of redundancy detectionConcept
A 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 brain
Structure of lobe of brain vBrain part u Brain tissue structure
Brain tissue structure v Brain part
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 12/23
Introduction Materials & methods Results Conclusion
Four rules of redundancy detectionUngrouped exists restriction
An 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 thymoxamine
Thymoxamine (product) vAlpha blocking vasodilator u Alpha 1 blocking agent u
∃Has active ingredient.Thymoxamine (substance)
Parenteral form thymoxamine (product) ≡Thymoxamine (product) u
∃Has active ingredient.Thymoxamine (substance)
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 13/23
Introduction Materials & methods Results Conclusion
Four rules of redundancy detectionExists restriction within rolegroup
An 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 u∃RG(∃Finding site.Intracranial structure u∃Associated morphology.Traumatic abnormality u∃Associated morphology.Closed traumatic abnormality )
Closed traumatic abnormality v Traumatic abnormality
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 14/23
Introduction Materials & methods Results Conclusion
Four rules of redundancy detectionRolegroup
A 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 u∃RG(∃Associated morphology.Open wound u
∃Finding site.Intracranial structure) u∃RG(∃Associated morphology.Open contusion u∃Finding site.Brainstem structure)
Open contusion v Open wound
Brainstem structure v Intracranial structure
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 15/23
Introduction Materials & methods Results Conclusion
Four rules of redundancy detectionApproach
Applied 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
Introduction Materials & methods Results Conclusion
Detected redundancies
Applying 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 65,336
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 17/23
Introduction Materials & methods Results Conclusion
Categories of concepts with redundancies
findingprocedure
productbody structure
situationspecimenorganism
substancephysical object
Number of Concepts
0
5000
1000
0
1500
0
2000
0
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 18/23
Introduction Materials & methods Results Conclusion
DistancesDefined as steps in the concept hierarchy
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 19/23
Introduction Materials & methods Results Conclusion
Evaluation of ResultsPartial completeness by comparison to Cornet and Abu-Hanna
Cornet 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
Introduction Materials & methods Results Conclusion
Evaluation of ResultsPartial completeness by comparison to Cornet and Abu-Hanna
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 21/23
Introduction Materials & methods Results Conclusion
Evaluation of ResultsSoundness
Closure 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
Introduction Materials & methods Results Conclusion
Questions?
Overview of redundantelements in SNOMED CT
Rules could help toremove existingredundancies and toprevent futureredundancies
advantage: explanations!
IHTSDO: redundancy-freenormal forms
Future: Generalisation ofmethod
Kathrin Dentler and Ronald Cornet — Redundant Elements in SNOMED CT Concept Definitions 23/23
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