1. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license Lexically Suggest, Logically Define: QA of Qualifiers & Expected Results of Post-Coordination in SNOMED CT Lexically Suggest, Logically Define: QA of Qualifiers & Expected Results of Post-Coordination in SNOMED CT Alan Rector & Luigi Iannone with thanks to Robert Stevens BioHealth Informatics Group School of Computer Science & Northwest Institute of BioHealth Informatics University of Manchester, Manchester M13 9PL rector@cs.manchester.ac.uk http://dx.doi.org/10.1016/j.jbi.2011.10.002

2. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 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. 2

3. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 3 Can SNOMED post-coordination work? 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

4. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 4 First try ►Take a simple case: “acute” and “chronic” ►Look at the pattern SNOMED uses to define Acute disease and Chronic disease ►Follow Campbell, Tuttle, & Spackman and see how many diseases named “Acute…” or “Chronic …” are retrieved under the pattern

5. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 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” 5

6. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 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 ►?C:CLASS=MATCH("'Chronic.*")  Lexical SELECT ?C SubClassOf 'Clinical finding (finding)'  DL Semantics WHERE FAIL ?C SubClassOf ‘Chronic clinical finding (finding)’  Query Semantics BEGIN ADD ?C SubClassOf Candidate  Procedural END; 6

7. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license Next, classify candidates; only 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 7

8. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license Then remaining candidates not classified as Chronic findings: ►Why? ►Systematic? …or… ►Accidental? 8

9. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 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 9

10. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 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? 10

11. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license Late discovery: Chronic inflammatory disease 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, 11

12. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license … but even authors don’t, 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 12

13. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license One 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 13

14. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 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 14

15. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 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 only 85 (83%) chronic / 92 (85%) Acute Due to simple errors and omissions 18 (17%) chronic / 14 (15%) 15

16. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 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) 16

17. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 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, < 1 min ►SNOROCKET in Protege is very fast and reliable ►But still works better on modules than all of SNOMED 17

18. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 license 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 =< 2 person weeks 18

19. © University of Manchester Creative Commons Attribution-NonCommercial 3.0 unported 3.0 licenseSummary ►Lexical suggest, semantically define works to raise issues ►Post coordination of acute and chronic unlikely to work reliably, 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? 19 http://dx.doi.org/10.1016/j.jbi.2011.10.002