SEMCARE – Semantic Data Platform for Healthcare

1. SEMCARE – Semantic Data Platform for Healthcare Demo – 24.8.2016 Stefan Schulz, Markus Kreuzthaler, Pablo López-García MUG – IMI Philipp Daumke, Kornél Markó Averbis GmbH

2. Vision and Aims of SEMCARE SEMCARE aims to promote better patient care by supporting patient diagnosis and identifying patients for optimal treatment. • Multiple languages, multiple data privacy regulations • European FP7 project, 2014-2015, 1.5 Mio EUR budget   • Different use cases in cardiology • Identify patient cohorts based on patient-level criteria   • Gain insights in (un)structured data • Open infrastructure, easy 3rd party integration (e.g. tranSMART)  

3. Most EHR Information in Unstructured Texts • Characteristics: • "telegram style" (incomplete sentences) • abundance of potentially ambiguous acronyms and abbreviations (HT, "Amp.digg") • Jargon ("Cor normokard") • Spelling variants ("Systolicum") • Spelling errors ("Symtomatik") "Zuweisungzu RR-EinstellungbeiSt.p. HTX AnamneseDyspnoe NYHA II, keine AP, keine Vertigo, US-Ödeme re > li, keineNykturie Klin.-phys. SymtomatikCornormokard, etwasarrhythmisch, HT rein, (leises) Systolicum; US- Ödeme re > li beiSt.p. Amp.digg. II+III ped.dext."

4. Use cases (examples) • Patient recruitment • With no searchable patient database, identifying and recruiting suitable patients delay clinical trials • Delayed trials waste resources and slow access to new therapies • Decision support for genetic and rare diseases • deficient knowledge about rare diseases, although as a whole represent a large medical challenge • Combined with the lack of incentives to treat or cure them , serious public health problems may arise • Other potential use cases • Administrative coding support • Predictive analytics • Quality assessment • Patient summary

5. SEMCARE Components SEMCARE aims to promote better patient care by supporting patient diagnosis and identifying patients for optimal treatment. • Services • Terminology Management • Text Mining • Search & Analytics • ETL, Data Integration • Data Privacy, Anonymization • 3rd party applications (i2b2) 3rd

6. Terminology Management

7. Terminology Management • Term • Removal • Too general terms • Mapping Mode • Abbreviations • Acronyms • Short terms • Term • Enrichment • Missing Synonyms • Missing Concepts

8. Text Mining Preprocessing Information Extraction Writer Diagnosis File Readers File Consumer Document Zoning Search Engine Medication Laboratory Values Sentence Detection I2B2/tranSMART ECG results Tableau, Pentaho, Spotfire, Qlikview Tokenizing Abbreviations POS-Tagging Negation Detection Chunking Date Recognizer Stemming Decompounding …

9. Text Mining

10. Observables, Numbers, Units

11. ECG Annotation Example

12. Diagnosis

13. Other Findings

14. Numbers and Units

15. Modifiers (incl. Leads)

16. = ECG Type

17. SEMCARE Demo Use Casesbased on sample of 31921 clinical texts from Cardiology department) * Acknowledgements: Daniel Scherr, Cardiology of the University Hospital Graz, Medical University Graz

18. Use Case: Implantable Cardioverter Defibrillator • Identify those who maybe suitable for implantable cardiac device (ICD) therapy according to NICE1 guidelines (and therefore at high risk of sudden death or worsening heart failure) • NICE guideline: Implantable cardioverter defibrillators and cardiac re-synchronisation therapy for arrhythmias and heart failure (review of TA95 and TA120) | NICE technology appraisal guidance 314 | Issued June 2014 • Maybe suitable for “Implantable Cardioverter Defibrillator (ICD)”: EF ≤35% AND Class I-III Heart Failure Symptoms AND QRS duration 120–149ms but NOT with LBBB 1National Institute for Health & Care Excellence https://www.nice.org.uk/guidance

19. Use Case CRT-P • Identify those who maybe suitable for implantable cardiac device therapy according to NICE1 guidelines (and therefore at high risk of sudden death or worsening heart failure) • NICE guideline: Implantable cardioverter defibrillators and cardiac resynchronisation therapy for arrhythmias and heart failure (review of TA95 and TA120) | NICE technology appraisal guidance 314 | Issued June 2014 • Maybe suitable for cardiac resynchronization therapy pacemaker (CRT-P): EF ≤35% AND Class IV Heart Failure Symptoms but NOT QRS duration <120ms

20. Use Case Loss of Consciousness • Identify Miscellaneous High Risk Loss of Consciousness patients • Have had syncope AND FHx of sudden death AND/OR FHx of Brugada syndrome AND/OR Brugada type pattern on ECG AND/OR prolonged QTc (adjusted range for sex)

21. Use Case CPVT • Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT) • Based on Executive summary: HRS/EHRA/APHRS expert consensus statement on the diagnosis and management of patients with inherited primary arrhythmia syndromes • Structurally normal heart AND normal ECG AND [ exertional AND/OR stress-induced bidirectional VTAND/OR polymorphic ventricular premature beats AND/OR VT ] AND under 40 years old

22. Use Case Lab Values • Cholesterol > 300 mg/dl • Hämoglobinerhöht • Kalium > 5 mmol/l

23. Gold Standard Creation • brat rapid annotation tool

24. Automatic Annotations

25. Indexing Performance • Total time for add: 11,7845 minutes, average documents per minute 2708,7330 • Process finished, committed 31921 documents

26. Outlook CBmed project IICCAB "Innovative use of Information for Clinical Care and Biomarker Research" • Closely related topic • Main target: Re-use of clinical data for biomarker research (cancer / metabolism) • Secondary targets: Re-use of clinical data for patient quick view, coding support, and predictive analytics (KAGes) • Same text processing / information extraction tools: Averbis • SAP tools for semantic data warehouse and query interface • Ultimate goal: • large-scale semantic processing of textual content of patient records in order no develop novel tools and interfaces for clinical care and secondary use of clinical data for research • Multiple challenges, especially resource generation (user interface terminology)