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Lexically Suggest, Logically Define:Lexically Suggest, Logically Define:

QA of Qualifiers & QA of Qualifiers & Expected Results of Post-CoordinationExpected Results of Post-Coordination

in SNOMED CTin SNOMED CT

Alan Rector & Luigi Iannone

with thanks to Robert Stevens

BioHealth Informatics GroupSchool of Computer Science &

Northwest Institute of BioHealth InformaticsUniversity of Manchester, Manchester M13 9PL

[email protected]

http://dx.doi.org/10.1016/j.jbi.2011.10.002


Pre-coordination and post-coordinationPre-coordination and post-coordination

► Pre-coordination►SNOMED authors define “Acute bronchitis”

• Classifier creates correct hierarchy

►Clinical user enters “Acute bronchitis” (or its code)

► Post-coordination►Clinical user enters “Bronchitis” + “Acute”

►Classifier finds any equivalent term or places the expression in the right place in the hierarchy

• Concept does not need to exist beforehand, e.g.Might define “Acute” + “Bronchitis” + “Right main stem bronchus”‣ Would still be in the correct place in hierarchy even if no term exists.

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Can SNOMED post-coordination work?Can SNOMED post-coordination work?Do SNOMED authors pre-coordinate consistently?Do SNOMED authors pre-coordinate consistently?

► Two related questions?►Are SNOMED qualified expressions expressed consistently?

• If SNOMED authors don’t do it consistently, can anyone else?

► Proxies: In either case►The definitions should allow the description logic classifier to

organize the hierarchies correctly• Includes determining equivalence between pre- and post- coordinated

forms‣ Necessary but not sufficient for post-coordination to work

►For post coordination, must be well defined consistent patterns that users & software develpers understand

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First tryFirst try

► Take a simple case: “acute” and “chronic”

► Look at the pattern SNOMED uses to defineAcute disease and Chronic disease

► Follow Campbell, Tuttle, & Spackman and see how many diseases named “Acute…” or “Chronic …” are retrieved under the pattern


Definition of acute & chronicDefinition of acute & chronic

► Chronic disease == Disease & (RoleGroup some (Clinical course some Chronic))

broaden to

► Chronic finding == Clinical finding & (RoleGroup some (Clinical course some Chronic))

► … similarly for Acute► fully specified name: “Sudden onset AND/OR short duration”

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Write a script to check for Write a script to check for candidates in OPPL2candidates in OPPL2

► Requires ► Lexical match

► Description logic/OWL semantics -- open world, negation as provably false DL Reasoner

► Query semantics -- closed world, negation as failure over concepts in corpus

► Procedural semantics – add things to ontology

► ?C:CLASS=MATCH("'Chronic.*") LexicalSELECT ?C SubClassOf 'Clinical finding (finding)' DL SemanticsWHERE FAIL ?C SubClassOf ‘Chronic clinical finding (finding)’ Query SemanticsBEGIN

ADD ?C SubClassOf Candidate Procedural END;

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Next, classify candidates;Next, classify candidates;only top-level ones need be examinedonly top-level ones need be examined

► If a concept’s definition is changed, the change will be inherited by all descendants

► What did we find?►25%-30% of all lexical matches were “Candidate” errors,

but there were cases where • “Acute” and “Chronic” clearly no longer can be taken literally

‣ Chronic and acute leukemias and myeloproliferative disorders‣ So exclude them from candidates

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Then remaining candidates not Then remaining candidates not classified as classified as Chronic findingsChronic findings: :

► Why?►Systematic?

…or…

►Accidental?

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Look at definitionsLook at definitions

► Systematic► Chronic duodenal ulcer ==

Duodenal ulcer disease and RoleGroup some ( Associated morphology some Chronic ulcer (morphologic abnormality)

and Finding site some Duodenal structure)))

► Compare with► Chronic disease ==

Disease & (RoleGroup some (Clinical course some Chronic))

► Different qualifiers► Associated morphology

► Clinical course

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Different qualifiersDifferent qualifiers

► User guide says:►Acute & chronic may be morphological

• Chronic inflammation means mononuclear cell infiltration• Acute inflammation means polymorphonuclear cell infiltration

► For ulcers…► Chronic ulcer (morphological abnormality) is a kind of

Chronic inflammation (morphological abnormality)

► But users must understand► Acute and chronic ulcers are defined by Associated morphology,

► Acute obstruction is defined by Clinical course,

► Chronic cholecystitis by both!

► Are these the consequences we want?►Does this correspond to use in clinical care?

• Do we have evidence?• Should pathology take precedence over clinical observation?

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Late discovery:Late discovery:

Chronic inflammatory diseaseChronic inflammatory diseaseis defined as have both qualifiers! is defined as have both qualifiers!

► Chronic inflammatory disease == Chronic disease & RoleGroup some ( Associated morphology some Chronic inflammatory morphology) & RoleGroup some ( Clinical course some Chronic )

► Means:

►Classifier will chronic inflammatory disease only if you have both • Or that author asserts directly is a descendant of Chronic inflammatory

disease

►To get post-coordination to work you have to use both!• Will anyone remember to do so?• Obviously not all SNOMED authors,

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… … but even authors don’t, so but even authors don’t, so Many inflammations (…itis) are missed Many inflammations (…itis) are missed

► Authors have done some directly and not others►“Helter skelter” / “Mish mash” modelling

• Systematic inconsistency• What using a description logic is meant to avoid

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One solutionOne solution

► Change the axioms so that any disease with chronic inflammatory morphology has a chronic course

►Still within SNOMED’s DL EL++/OWL-EL• SNOROCKET still classifies it efficiently

► Or vice versa for all inflammatory diseases with chronic course

►Chronic course & inflammatory morphology Chronic inflammatory morphology

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How should the decision be made?How should the decision be made?How monitored?How monitored?

► New axiom may or may not be strictly “true”, but…

► What are the consequences?►For accuracy of authoring?

►For accuracy of retrieval?

►For consistency of setting value sets?

►For post-coordination?

►For meaninful use?

► Base decisions on evidence of consequences►Evidence-based terminologies / ontologies

► Whatever the decision, need a QA process to enforce and check it

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How big is the problem?How big is the problem?

► In a “module” based on the UMLS CORE Problem list subset:

►368 total chronic; 450 total acute

►103 (28%) chronic / 92 ( 20%) Acute were “candidates”,of these:

• Due to use of morphology only85 (83%) chronic / 92 (85%) Acute

• Due to simple errors and omissions18 (17%) chronic / 14 (15%)

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Other issues (See paper)Other issues (See paper)

► Hierarchy of qualifiers►Should Intermittent (course) be a kind of chronic (course)?

• What about “intermittent acute pain”?

►Pressure ulcers and decubitous ulcers are all chronic by definition

• Can there be an acute pressure ulcer?

► Odd anatomy►Lower back pain is a kind of Abdominal pain

• Because the lower back is part of the abdominal wall is part of the abdomen‣ (Anatomy under review by SNOMED)

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You have to use a classifierYou have to use a classifier

► This work can only be done by using a classifier to find inferences

►Post-coordination depends on the classifier

► To work efficiently, the classifier must be fast►For iterative analysis, < 1 min

► SNOROCKET in Protege is very fast and reliable►But still works better on modules than all of SNOMED

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Use of “modules” makes this possibleUse of “modules” makes this possible

► A “signature” is a subset of the entities in a description logic/OWL KB

► A “module” for a “signature” is a subset of the axioms & entities in the KB such that

► All inferences amongst entities in the signature can be inferred from the module

► For the UMLS CORE Problem List Subset► SNOMED Size ~300,000

• Classification time 2-8 minutes

► Signature (UMLS CORE Subset) ~8500

► Module extracted ~35,000• Classification time .25 – 2 minutes

► Also methods for extracting the changes and applying them to the whole

► Re-apply final methods to whole corpus if require

► Total effort for this study =< 2 person weeks

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SummarySummary► Lexical suggest, semantically define works to raise issues

► Post coordination of acute and chronic unlikely to workreliably, unless

►SNOMED makes pattern consistent

►Bases decisions on consequences for use in patient care• Are patient care clinicians likely to align with pathology in the ED?

► Other Findings►Working on modules makes analysis of SNOMED practical

►There are problems in the anatomy and qualifier hierarchies

► Questions►How many other such problems are there?

• How do they affect post-coordination?

►How to establish QA procedures to find out and prevent recurrence?

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http://dx.doi.org/10.1016/j.jbi.2011.10.002

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