Redundant Elements in SNOMED CT Concept Definitions

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

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Introduction Materials & methods Results Conclusion

Outline

1 Introduction

2 Materials & methods

3 Results

4 Conclusion

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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

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SNOMED CTSystematized Nomenclature Of Medicine Clinical Terms

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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)

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SNOMED CT Concept Definitions in EL+

Conjunctions (u) of other concepts (superconcepts) androle-value pairs (∃), ungrouped or grouped in RoleGroups.

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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.

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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)

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(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)

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(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)

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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

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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

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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)

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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

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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

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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.

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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

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Categories of concepts with redundancies

findingprocedure

productbody structure

situationspecimenorganism

substancephysical object

Number of Concepts

0

5000

1000

0

1500

0

2000

0

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DistancesDefined as steps in the concept hierarchy

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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.

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Evaluation of ResultsPartial completeness by comparison to Cornet and Abu-Hanna

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Evaluation of ResultsSoundness

Closure of manipulated, redundancy-free version of SNOMEDCT equivalent to closure of original version.

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Questions?

Overview of redundantelements in SNOMED CT

Rules could help toremove existingredundancies and toprevent futureredundancies

advantage: explanations!

IHTSDO: redundancy-freenormal forms

Future: Generalisation ofmethod

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