ICD 11 and SNOMED CT common ontology : Circulatory system Jean-Marie Rodrigues, Stefan Schulz, Alan Rector, Kent Spackman, Jane Millar, James Campbell, Bedirhan Üstün, Christopher Chute, Harold Solbrig, Vincenzo Della Mea, Kristina Brand Persson. rodrigues@univ-st-etienne.fr MIE 2014 1st september 2014 Istanbul Turkey 31-August/03 1 rodrigues mie 2014 September 2014
Plan Ø SNOMED CT and ICD11 Ø Common Ontology and multilayered ICD 11 Ø Circulatory system pilot Ø Conclusion 2 rodrigues mie 2014
SNOMED CT and ICD11 Ø SNOMED CT Ø standardized health terminology that provides clinical terms for health records. SNOMED CT concepts provide standardized meaning by logic descriptions Ø ICD 11 Ø delivering summary high level aggregations Ø a multi-layered disease classification system. • Foundation Component, Common ontology plus queries • Purpose-specific linearizations (mortality, morbidity, primary care) with jointly exhaustive and mutually exclusive classes 3 rodrigues mie 2014
Common Ontology definition Ø The Common Ontology is a set of ICD Foundation Component terms harmonised with a subset of SNOMED CT and formulated in SNOMED CT’s description logic. Ø OWL/DL SubClass/SuperClass Ø Non Is_A Definition relations (axioms) l Fully defined terms (necessary and sufficient) l Partially defined terms (necessary plus manual assertion) l Poly-hierarchy 4 rodrigues mie 2014
Simplified Architectural Diagram ICD-11 Foundation Component Foundation Ontology Foundation Scaffold Common Ontology Common Ontology Subset of SNOMED CT0 Linking Query Library SNOMED CT Linearization A Linearizations
Architectural Diagram ICD-11 Foundation Component ICD11 Foundation External Additional External External ontology sources External sources links sources Content Content Common Model Model Foundation Ontology (with Schema Contents Scaffold value SNOMED CT) Common sets Subset of Ontology ICD-11 Non- (with ICD-11) ontological Subset of primitives SNOMED CT Linking Query Library SNOMED CT Linearization B Linearization set Linearization A (un-nested) A (nested)
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FC non in CO - Headers that aggregate entities of vocabulary, typically using plurals (“Diseases of … ”) - Fine-grained parts of ICD, more specific than SNOMED CT - Queries for Exclusion statements for linearizations - Non-ontological content (Icat content model) (signs, symptoms, diagnostic criteria) 8 rodrigues mie 2014
Linearizations differences with the common ontology Ø Mono-hierarchy ( different from Co Is_a) Ø Specific preferred term Ø Inclusion/exclusion Ø Residuals Ø Related to Common Ontology by Ø a disjunction of terms in the Common Ontology Ø Queries 9 rodrigues mie 2014
the basic structure of most queries Ø the basic structure of most queries are of the form “A but not B or C or … ”, i.e. Ø LinearizationClass à BaseOntologyClassExpression MINUS OntExpression1 MINUS OntExporession2 Ø where “MINUS” can be read as “not classified under”. rodrigues mie 2014 10
Ø ICD:’Hypertensive diseases’ à FROM sct: Findings SELECT sct: ‘Hypertensive Disease’ Ø MINUS sct:’Metabolic disorder’ // from Dis of Circ System MINUS sct:’Endocrine disorder’ // from Dis of Circ System MINUS sct:’Infectious and parasitic // as above MINUS sct:’Poisoning’ // as above MINUS sct:’Diseases of Puerperium’ // from self MINUS sct:’Disorders of Pregnancy’ // from self rodrigues mie 2014 11
Circulatory system pilot Ø Workflow Ø Material Ø Method Ø Results rodrigues mie 2014 12
Workflow 1 Ø identify candidate SCT concepts for FC classes. Ø Construct valid SCT formal expressions for ICD-11 textual definitions, Ø Specify the queries for ICD-11 FC classes Ø Assure that all expressions in SCT representing subchapters in ICD-11 aggregate to the SCT pre-coordinated expression for the ICD-11 chapter concept. rodrigues mie 2014 13
Workflow 2 Ø When necessary, submit potential revisions to the SCT concepts model and expansions of SCT content Ø Add all SCT editorial expansions into the common ontology. rodrigues mie 2014 14
WHO Material Ø ICD11 Chapter Ø Circulatory Ø Ear & mastoid process Ø Respiratory Ø Infectious diseases Ø Dermatology Ø GURM – genitourinary & reproductive medicine Ø URL: http://mitel.dimi.uniud.it/whotools/ mappingTools/mappet/ rodrigues mie 2014 15
Common Ontology data base Ø SQL database Ø Lexical matches Ø Automatic input of SCT terms and Short Norms Form Ø Import export process via WHO URL Ø References Ø e.g. Medscape/OMIM/Orphanet Ø Internal review approach Ø External review Ø American College of Cardiology for circulatory
Identifying SCT candidates to CO Map Type Description Common Ontology(CO) SCTID ICD11 maps to existing Short Normal Form SNOMED CT, synonymous 0/A pre-coordinated concept Definition using SNOMED CT without change concepts and compositional grammar 0/E post-coordinated Definition using SCT attributes only expression without e.g. site, morphology, expression change in the model of provided in SNOMED CT meaning compositional grammar 0/R residual phrase Not in CO but queries 0/X pre-coordinated concept Change to SCT model of meaning with changes 0/EX post-coordinated Change to content – object/value expression with changes rodrigues mie 2014 17
– Exact match examples Map Type ICD11 Rubric Common Ontology (Short Normal Form) SCTID Cerebral venous 95464572001|Disease (disorder)|: thrombosis {116676008|Associated morphology (attribute)|=396339007|Thrombus (morphologic abnormality)|363698007| Finding site (attribute)|=68351006| Structure of cerebral vein (body structure)|} SCTID Coronary vaso spastic 194828000|Angina (disorder)| with angina +23687008|Coronary artery spasm (disorder)|:{363698007|Finding site (attribute)|=74281007|Myocardium structure (body structure)|} rodrigues mie 2014 18
– Pre coordination examples Map Type ICD11 Rubric Common Ontology 0/A Aldosterone-producing 116680003 | Is a |88213004 | carcinoma Hyperaldosteronism, |42752001 | Due to| 255035007 | Adrenal carcinoma 0/A Acute myocardial infarction, STEMI, 401303003 | Acute ST segment elevation anterior wall myocardial infarction | + 54329005 | Acute anterior myocardial infarction rodrigues mie 2014 19
Post coordination – examples Map Type ICD11 Rubric Common ontology 0/E Asymptomatic stenosis of 116680003 | Is a |230738008 | extracranial carotid artery Asymptomatic cerebrovascular disease, |363698007 | Finding site|17999001 | Structure of cervical portion of internal carotid artery, |116676008 | Associated morphology|415582006 | Stenosis 0/E internal auditory artery 116680003 | Is a |2929001 | occlusion Occlusion of artery, |363698007 | Finding site|89471000 | Structure of labyrinthine artery
Results rodrigues mie 2014 21
Cerebrovascular disease
Results Map Type Number Common Ontology SCTID 792 (50.1%) Short Normal Form 0/A 534 (33.8%) To be developped with SCT grammar 0/E 86 (5.4%) To be developped with SCT grammar 0/EX 16 (1.0%) To be developped with changes SCT values 0/X 12 (0.8%) To be developped with changes in SCT model of meaning 0/R 116 (7.3%) Not in CO but queries Unclear definition 26 (1.6%) Definition by domain experts
Outcomes– ICD11 SCT coordination Mappings -overall Map Circ Ear Resp Inf All % SCTID 792 146 594 1459 2291 58 0/A and 648 29 391 664 1734 34 0/E Residual 116 27 93 35 269 5 Unclear 26 7 47 49 129 3 definition Total 1582 209 1125 2207 5123 100
Conclusion (1) Ø Around 84 % of circulatory chapter ICD11 codes can be represented by a subset of existing SCT concepts and pre- coordination Ø 5,4 % can be represented with SCT attributes (or defining relations or model of meaning) Ø 1,8 % needs modification of the model of meaning (attribute or values sets) Ø 7,3 % and 1,6 % cannot be represented in CO rodrigues mie 2014 25
Conclusion 2 Ø Further steps of the workflow are Ø Validating the formal SCT representations Ø Adressing the pre-coordination issue Ø Modify the SCT model of meaning when necessary Ø Develop the queries Ø Extend the method to other chapters rodrigues mie 2014 26
Questions? Tak Vielen Dank für Ihre Aufmerksamkeit Terima Kashi Thank you Merci rodrigues@univ-st-etienne.fr Tak Grazie Gracias Obrigado Efcharisto ARIGATO GOZAIMA SU Multumesc. 27 rodrigues mie 2014
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