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4 th Summer Health IT Showcase -2009

4 th Summer Health IT Showcase -2009. Health Information Technologies Research Laboratory School of IT University of Sydney. HITRL Objectives. Research in Natural Language processing for medical content Research into Clinical Information Systems

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4 th Summer Health IT Showcase -2009

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  1. 4th Summer Health IT Showcase -2009 Health Information Technologies Research Laboratory School of IT University of Sydney 4th Health IT Summer Showcase

  2. HITRL Objectives • Research in Natural Language processing for medical content • Research into Clinical Information Systems • Research into the use of terminologies -SNOMED CT, Apache IV, NIC, NOC, etc. • We are learning how to build such functionality 4th Health IT Summer Showcase

  3. Current Enhancement Technologies • Clinical Data Analytics Language (CliniDAL) • Generative Clinical Information Management Systems (GCIMS) • Bolt-on to existing systems 4th Health IT Summer Showcase

  4. 1st Session • Pathology Research and Clinical Data Analytics Language - Cleverer interfaces for research on clinical databases • Visual Annotator - getting at the correct language - clinical notes, synoptic reports - automating annotation • Generating Interoperable Clinical Information Systems - Multidisciplinary & Nursing CIS, Trauma CIS • Intelligent Notes System - Automatic text correction with information retrieval on the ward rounds Health Information Technologies Research Laboratory 4th Health IT Summer Showcase

  5. 2nd Session • Identifying SNOMED CT codes in clinical notes • Identifying medical concepts in published papers • Recognising co-morbidities in clinical notes of Obesity patients • Unpacking clinical notes - recognising words and non-words 4th Health IT Summer Showcase

  6. Other Projects in 2008 • Semester 1 • CLINIDAL installed on SWAPS AP data warehouse • Pathology Classification on SWAPS AP database • Handovers generating system for the ICU • Semester 2 • Graphical viewer for SNOMED CT on Term Server • Workflow on General Medical Wards - BMDH • Software testing for CliniDAL • CLINIDAL installed in CareVue data warehouse • Intelligent Notes for ICU 4th Health IT Summer Showcase

  7. Structured Reporting for Pathology Results • Melanoma - supported by QUPP in collaboration with Dr Richard Scolyer and Dr Raj Murali at the RPAH • Breast Cancer - supported by the BCI Westmead with Dr John Boyages and Dr Nehmat Houssami 4th Health IT Summer Showcase

  8. Melanoma-Executive Summary • Project objectives achieved • 477 histopathology reports annotated for 22 concepts of data by four annotators • Linguists missed 6.0% on average of pathologists labels • 19 fields appear to be reliably computable • Gold-standard set of reports assembled • By-products: advice and training materials on presentation of reports. 4th Health IT Summer Showcase

  9. Ultimate Goals of Project A. provide feedback to pathologists re the content of their reports - are they including all the key information that: i. determines the patients prognosis and ii. directs their management The key features that determine i & ii are: a. Breslow thickness b. mitotic rate c. Clark level d. ulceration e. margins (all of them)  4th Health IT Summer Showcase

  10. Ultimate Goals B. data extraction for i. cancer registries ii. research  C. automated generation of synoptic reports from text reports i. could be done when the pathologist has constructed the narrative report and included in the final report that is sent to the requesting clinician   ii. performed at a later date 4th Health IT Summer Showcase

  11. BACKGROUND TO THE STUDY • Materials • 477 histopathology reports • Photocopied • Scanned • OCRed • Spell checked/ proof read • Anonymised • Stored and maintained in a revision repository • Annotated by pathologist and linguists 4th Health IT Summer Showcase

  12. Annotation Discrepancies Involving Language • Noun Phrase vs Verb phase usage • Arising in a dysplastic naevus (useful verb) • Patchy regression was seen (not useful) • Interpretive Annotations • Early, Intermediate, Late changed to • TILS, Fibrosis, Loss of Rete Ridges 4th Health IT Summer Showcase

  13. Concept Set 4th Health IT Summer Showcase

  14. Results of the Annotations • Most important Concepts accurately identified • Linguists had better agreement than the pathologists • Three codes were not reliable • TILS, Fibrosis, Rete Ridges • Reliable Computation of important elements achievable 4th Health IT Summer Showcase

  15. Figure 3 - Comparative second round inter-annotator agreement, scaled by number of annotations. 4th Health IT Summer Showcase

  16. Tags annotated by Pathologists missed by Linguists 4th Health IT Summer Showcase

  17. Comparison of Gold Standard and Linguists 4th Health IT Summer Showcase

  18. Observations about the corpus contents • Occasional inconsistencies between report body and conclusions, e.g. size = .1mm vs 1mm • Highly variable standard of contents • Lateral margins not well reported 4th Health IT Summer Showcase

  19. Results of simple extraction for a Structured Report • Breslow Thickness simple classifier 4th Health IT Summer Showcase

  20. Summary of the Project Results • Reliable annotations can be made for all the important concepts in melanoma pathology reports. • The prospect of building very reliable computational aides for automatically generating structured reports are high. • The most uncertain aspect of the study is to understand the smallest training set that is needed to build an effective structured report computational populator. • This approach can be used ot identify what is needed in any structured report - “the text tells more than the experts” 4th Health IT Summer Showcase

  21. Breast Cancer Synoptic Reports • 33 categories • 120+ reports • Information extraction 4th Health IT Summer Showcase

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  24. Projects for 2009 • Snomed CT subset for ICU • Snomed CT subset for ED • Multiple CIS for Aged Care demonstrated • Trauma CIS verified and tested • First version of IC Realtime Audit IS (ICRAIS) • Automatic post co-ordination of clinical notes • Lexical and morphological disambiguation of clinical notes • Automatic computation of structured reports for melanoma and breast cancer • Proven use of CLINIDAL for pathology & ICU CIS • Mapping SNOMED CT to ICD 10 AM for ICU notes • Design of Information Model for ICD 11 (WHO) 4th Health IT Summer Showcase

  25. Partners • Breast Cancer Institute • RPAH - ICU, ED, AP • SWAPS • Blacktown-Mt Druitt Hospital - Nursing & Midwifery • QUPC • SEALS • Concorde - ED • NEHTA 4th Health IT Summer Showcase

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