openEHR in Research: Linking Health Data with Computational Models
- 1. Koray Atalag MD, PhD, FACHI k.atalag@auckland.ac.nz Senior Research Fellow, ABI Chief Information Officer, The Clinician Management Board Member, openEHR Foundation openEHR in Research Linking Health Data with Computational Models
- 3. Human Physiome Project and Virtual Physiological Human (VPH) a methodological and technological framework that will enable collaborative investigation of the human body as a single complex system Descriptive, Integrative And Predictive
- 4. What’s Computational Physiology Governing equations (laws of physics) Anatomy & structure High-performance computing Software Material properties from measurement Observed function Validation Predicted function Mechanistic insight
- 5. Tissue Osteon NephronAcinus Liver lobuleLymph nodeCardiac sheets Organ Heart Lungs Diaphragm Colon EyeKnee Liver Environment Organ system Organism Cell Protein Gene Atom Network
- 6. (www.cellml.org) Cuellar AA, Lloyd CM, Nielsen PF, Halstead MDB, Bullivant DP, Nickerson DP, Hunter PJ. An overview of CellML 1.1, a biological model description language.SIMULATION: Transactions of the Society for Modeling and Simulation, 79(12):740-747, 2003 Physiome Standards and Tooling
- 7. Why Linked Health Data?
- 8. Secondary Use of EHR using openEHR Single Content Model CDA FHIR HL7 v2/3 EHR Extract UML XSD/XMI PDF Mindmap PAYLOAD System A Data Source A Map To Content Model System B Data Source B Native openEHR Repository Secondary Use Map To Content Model Automated Transforms No Mapping Atalag K. Using a single content model for eHealth interoperability and secondary use. Stud Health Technol Inform. 2013;193:282–96
- 9. Realising the Physiome / VPH
- 11. SNOMED-CT (Systematized Nomenclature of Medicine) • >300,000 biomedical concepts • ~800,000 English language descriptions (terms) • ~1.4 million semantic relationships (i.e. IS_A) • Hierarchically organised in multiple axes • Addressing the whole EHR space • National licensing (NZ +) • Mapped to ICD and through UMLS to 100s others • Aligned/harmonised with LOINC and HL7 The single most important terminology now
- 12. Coronary arteriosclerosis Structural disorder of heart Heart disease Cardiac finding Cardiovascular finding Finding by site Clinical finding SNOMED CT Concept Mediastinal finding Finding of region of thorax Finding of trunk structure Finding of body region Viscus structure finding Disorder of mediastinum Disorder of thorax Disorder of trunk Disorder by body site Disease Disorder of body system Disorder of body cavity Disorder of cardiovascular system Disorder of coronary artery Coronary artery finding Arterial finding Blood vessel finding General finding of soft tissue Disorder of soft tissue of thoracic cavity Disorder of soft tissue of body cavity Disorder of soft tissue Disorder of artery Vascular disorder Arteriosclerotic vascular disease Soft tissue lesion Degenerative disorder
- 13. UMLS: Integrating Biomedicine Unified Medical Language System Biomedical literature MeSH Genome annotations GO Model organisms NCBI Taxonomy Genetic knowledge bases OMIM Clinical repositories SNOMED CTOther subdomains … Anatomy FMA UMLS By NLM - UMLS integrates and distributes key terminology and ontology (knowledge sources)
- 14. Semantics in openEHR • Whole-of-model meta-data: – Description, concept references (terminology/ontology), purpose, use, misuse, provenance, translations • Item level semantics (Schema level) – Trees/Clusters (Structure) – Leaf nodes (Data Elements) Formally: different types of terminology bindings: 1) linking an item to external terminology/ontology for the purpose of defining its real-world clinical/biological meaning 2) Linking data element values to external terminology (e.g. a RefSet or terminology query) AlsoInstance level semantic annotations – applies to actual data collected
- 15. 15
- 16. mindmap representation of openEHR Archetype 1) Linking items to SNOMED to define clinical meaning
- 17. 2) Linking data element values to external terminology
- 18. Bridging Semantics using Archetypes e.g. Pseudohypoaldosteronism (PHA) as a disease (Diagnosis) • Has biophysical, genomic and clinical models • But all encoded using different terminology/ontology
- 19. NZ Cardiac Registry 80k Patients 1000+ data points! 100+ terminology bindings 19Screenshot of openEHR Template
- 20. Do you think it’s all Star Trek Stuff?
- 21. 21
- 23. INNOVATION CONFERENCE IDEAS TO LIFE 2017 www.uoainnovation.com.cn WeChat ‘pauxmg’ 梅保 HANGZHOU, CHINA 12-14 December 2017