Lexically Suggest, Logically Define: QA of Qualifiers

1
Lexically Suggest, Logically DefineQA of
Qualifiers Expected Results of
Post-Coordinationin SNOMED CT
http//dx.doi.org/10.1016/j.jbi.2011.10.002

• Alan Rector Luigi Iannonewith thanks to Robert
  Stevens
• BioHealth Informatics GroupSchool of Computer
  Science Northwest Institute of BioHealth
  InformaticsUniversity of Manchester, Manchester
  M13 9PLrector_at_cs.manchester.ac.uk

2
Pre-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.

3
Can SNOMED post-coordination work?Do SNOMED
authors pre-coordinate consistently?

• Two related questions?
• Are SNOMED qualified expressions expressed
  consistently?
• If SNOMED authors dont 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

4
First 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

5
Definition 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

6
Write a script to check for candidates 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
• ?CCLASSMATCH("'Chronic.")
  ? LexicalSELECT ?C SubClassOf
  'Clinical finding (finding)' ? DL
  SemanticsWHERE FAIL ?C SubClassOf Chronic
  clinical finding (finding) ? Query
  SemanticsBEGIN ADD ?C SubClassOf Candidate
  ?
  Procedural END
  
  

7
Next, classify candidatesonly top-level ones
need be examined

• If a concepts 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

8
Then remaining candidates not classified as
Chronic findings

• Why?
• Systematic?
• or
• Accidental?

9
Look 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
  

10
Different 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?

11
Late discoveryChronic inflammatory diseaseis
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,

12
but even authors dont, so 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

13
One solution

• Change the axioms so that any disease with
  chronic inflammatory morphology has a chronic
  course
• Still within SNOMEDs 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

14
How should the decision be made?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

15
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)

16
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)

17
You 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, lt 1 min
• SNOROCKET in Protege is very fast and reliable
• But still works better on modules than all of
  SNOMED

18
Use 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 lt 2 person weeks

19
Summary

• 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?

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