GP Vocabulary Project Phase-1 Don Walker Dept General Practice University of Adelaide January 2003

Acknowledgements Commonwealth Department of Health and Ageing GPCG – General Practice Computing Group GPRN – General Practice Research Network NCCH – National Centre for Classification in Health

GP Vocabulary Project What is it? What is its aim? What does it look like? What is delivered? Why was it done? Who might use it? How might it be used? What is its availability? What started it? Who did it? What was it made from? How was it done? What does it need? What comes next? More information?

What is it? A collection of terms “entered” by GPs –About: History, Symptom, Reason, Problem, Diagnoses –Not about: Interventions, Imaging, and Pathology Contents

What is its aim? To capture the many ways GPs enter information in clinical records (including synonyms, acronyms, abbreviations, misspellings Contents

What does it look like? The TermThe Semantic type CHEST PAINSympt/Sign/Diag/Prob PAINSympt/Sign/Diag/Prob SEVERESeverity/Type ACUTECourse CHESTSite/Position CENTRALLaterality WORSENINGStatus TODAYTime Related ISCHAEMIAMorphology REFERALProcess CHEST X-RAYProcedure/Test SPECIALISTPeople/Place/Organisation Contents

What does it look like? – “Term Associations” “LOW” is associated with the following terms… BACK20.52Site/Position PAIN8.73Sympt/Sign/Diag/Prob PAINS7.86Sympt/Sign/Diag/Prob CHRONIC2.62Course B122.18Procedure/Test FOLATE1.75 Procedure/Test SPRAIN1.31Sympt/Sign/Diag/Prob ACUTE 1.31 Course CALCIUM 1.31 Procedure/Test Contents

What is delivered? Several data files in "text-file" format – notably… –“Terms” and their “Semantic-Type” –“Term Associations” and “Frequencies %” Contents

Why do it? Do you mean… –Why “Code”? or –What is the purpose of this project? Contents

Why do it? Why "code"? To enable GPs to enter information in a structured way with minimal effort so that..  Computer may then “understand” the content  Nicer systems – eg. smart pick-lists Decision support – eg drug/disease interactions, reminders Report and analyse – eg. good auto-summaries Clinical review – quality improvement Epidemiological research Contents

What is the project's purpose? This is the first stage of a project to develop a complete approach to GP clinical terminology Facilitate mapping GP terms to SNOMED-CT; ICD-10-AM; ICPC2 & DOCLE (= a later phase of the project) Comparison of the above systems Enhance the user interfaces to the above Identify deficiencies in the above and Improve "terming" software  “Control” of the user vocabulary (…see previous) Contents

Who might use it? GPs when entering diagnosis data into records Software developers – better system interface Knowledge base builders – decision support systems Terminology and Classification system builders Researchers, analysts, epidemiologists Contents

How might it be used? As an interim “controlled vocabulary” As an Interface terminology to a “reference terminology” and “classification system” - when these are mapped to and from it. As a start to “smart pick list” creation As an ingredient for natural language processing research. Contents

What is its availability? General Practice Computing Group & Commonwealth Government funded this project – will dictate availability, however… –Potentially available to anybody –No licence or cost currently considered –Not for sale –Available December 2002 –Available on WWW: Dept GP, University of Adelaide Contents

What started it? Medical record industry – requested a standard codes system or terminology GPCG – produced a strategy Coding Jury – made a recommendation GPCG/Dept.Health – implemented strategy through: "The development of a consolidated GP Vocabulary, covering the domains of diagnosis and problems" Contents

Who did it? Department of General Practice, University of Adelaide (Dr Don Walker – Project Director) With assistance from…. National Centre for Classification in Health, University of Sydney Contents

What was it made from? (1 of 2) De-personalised computer records of GPRN from the “MedicalDirector” software of HCN –Practices 78 –General practitioners 176 –Patients 891,503 Contents

What was it made from? (2 of 2) Computerised medical records 2,360,788 –Past History Problems 866,239 –Diagnoses / Problems 336,744 –Encounter Reasons 1,118,123 –Prescription Reasons 1,568,213 Contents

How? Get computer entries made by GPs Define “semantic-types” “Semantically parse” entries Compile “Vocabulary” Test for parser consistency Contents

How? – Get GP Entries 1.Extract entries for diagnosis, reason prescribing  "Unique Raw Utterances” (177,470 phrases) 2.Tidy punctuation – Using a rule base system  "Unique Clean Utterances" (163,225 phrases) 3. Select working Subset – 3 or more recorded uses (41,908 Phrases) HowContents

How? – Define “Semantic-Types” Symptom/Sign/ Diagnosis/Problem Severity/Type Course Site/Anatomy Laterality/Position Status Time related Morphology Physiological Function Related Reason Causative Agent Process Drug/Subs/Appliance Procedure/Test Certainty/Confidence People/Place/ Organisation Other Comment Text; and Junk data. ContentsHow

How? “Semantically Parse” A manual task – team of 6 Divide “Clean-Utterances” into their “Themes” [e.g.][e.g.] Subdivide themes into their “Semantic-Contents” [e.g.][e.g.] Specific software tool created [e.g.][e.g.] NextContentsHow

e.g. “Clean-Utterances”  “Themes” “chronic productive cough, headache worse”  2 themes: (a) “chronic productive cough” (b) “headache worse " BackContentsHow

e.g. Themes  “Semantic-Contents” “chronic productive cough”  –(1) “chronic” = “Course” –(2) “productive cough ” = “Sympt/Sign/Diag/Prob” –(3) “productive” = “Severity/Type” –(4) “cough” = “Sympt/Sign/Diag/Prob” “headache worse” –(1) “headache” = “Sympt/Sign/Diag/Prob” –(2) “worse” = “Status” BackContentsHow

e.g. Specific software tool created BackContentsHow

How? – Compile “Vocabulary” Extract “Unique-Terms” Allocate “Top-Semantic-Type” to each [e.g.][e.g.] Compile “Associated-Terms” & their “Frequencies” [e.g.][e.g.] NextContentsHow

e.g. “Semantic-Types” for the term “LOW” Back Semantic-TypeType-CountType % Status Laterality/Position Symptom/Sign/Diag/Prob21.8 Comment text10.9 e.g. ScreenContentsHow The most common or “top semantic type”

e.g. “Top-Types” for “LOW” BackPreviousContentsHow

e.g. “Associated Terms” for “LOW” BACK20.52Site/Position PAIN8.73Sympt/Sign/Diag/Prob PAINS7.86Sympt/Sign/Diag/Prob CHRONIC2.62Course B122.18Procedure/Test FOLATE1.75 Procedure/Test SPRAIN1.31Sympt/Sign/Diag/Prob ACUTE 1.31 Course CALCIUM 1.31 Procedure/Test WCA 1.31 People/Place/Org TermAssoc-CountType Backe.g. ScreenContentsHow

e.g. “Associated Terms” for “LOW” BackPreviousContentsHow

How? – Test Consistency Four passes were made over 41,908 entries. Consistency testing –Same random 10% “parsed” by all –Done at 1 week from start & again at the end –Both “inter-” and “intra-” consistency tests –“Unique-terms” and their “Top-Semantic-type” were examined and compared ContentsHow

What does it need? Identify spelling errors for exclusion. Link terms to a “reference terminology” –which in turn is mapped to (or contains) classifications of relevance. Add terms from – Other records –“Interventions/Procedures” –“Diagnostic Imaging” –“Laboratory Tests”. Contents

What comes next? Stage 1 = development of a consolidated GP Vocabulary, covering the domains of diagnosis and problems (Current); Stage 2 = the mapping of a sub-set of the GP Vocabulary to terminologies & classifications such as SNOMED CT, ICD-10-AM, ICPC2 and DOCLE (Next); and Stage 3 = the completion of the remainder of the terminology (Later). Contents

Where is there more? (1 of 2) Dept. of General Practice, University of Adelaide… –“010 Introduction to Building a GP Vocabulary” –“020 GP Terminology Project Communiqué” - A General Practice Vocabulary for Australia" - a document providing the project's background, introduction and methodology. –“030 GP Vocab Project 01” - This PowerPoint slide show –“040 Getting Started with the Semantic Parser for GP Terms" – a user document for the software tools Contents

Where is there more? (2 of 2) –“050 Demo Semantic Parser & Browser" - a working demonstration of the software tools used in the project –“060 Data Structure & Sample Data" - a more technical document for industry. –“070 Demo Data files" – samples of preliminary data in text- file format. –“080 Removal of unwanted punctuation from GP terms" – a somewhat technical document describing a rule based system –090: Unique Identifiers document –100: SemParser Browser –110: Data and Documentation –110: Data Documentation document – & related documents…all available from Contents