Copyright 2006, Ida Sim Ida Sim, MD, PhD Associate Professor of Medicine Associate Director for Medical Informatics Program in Biological and Medical Informatics.

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Presentation transcript:

Copyright 2006, Ida Sim Ida Sim, MD, PhD Associate Professor of Medicine Associate Director for Medical Informatics Program in Biological and Medical Informatics University of California, San Francisco, CA R01-LM Analysis of HIV Trials cBIO Driving Biological Project

Copyright 2006, Ida Sim Outline Background Trial Bank Project DBP Goals

Copyright 2006, Ida Sim Domain Problem Want to advance clinical science and practice evidence-based medicine » based on results from scientific experiments, e.g., from randomized controlled trials (RCTs) » randomization equalizes known and unknown confounders between intervention arms » any observed differences in outcome should be due only to the intervention Drug A Placebo Death at 1 year

Copyright 2006, Ida Sim HIV Trials Two controversial areas of HIV with conflicting RCT evidence » Prevention of mother-to-child-transmission (MTCT) » Structured Treatment Interruption Very complex heterogenous trials » need computational support to visualize, analyze, apply these trials

Copyright 2006, Ida Sim Need Computational KBs of RCTs RCT journal articles not ideal » key descriptors of experimental method not always reported » not easily computable KB of information on RCT » design » execution » results would allow for better computer support for advancing clinical science and practice

Copyright 2006, Ida Sim Outline Background Trial Bank Project DBP Goals

Copyright 2006, Ida Sim Trial Bank Software Bank-a-Trial » web-based program for entering trials into RCT Bank (annotation) » clinical descriptions of trial features (slot values) are in UMLS terms RCT Presenter » web-based browser of RCT Bank entries » SecurePresenter for browsing restricted-access entries RCT Bank Bank-a-TrialRCT Presenter (SecurePresenter)

Copyright 2006, Ida Sim Ontology: RCT Schema Models clinical trials » instantiated using UMLS terms to describe clinical concepts Frame-based model (in Ocelot) » 7 levels deep 188 frames, 601 unique slots » average 9.8 slots/frame » 13 frames (7%) have multiple parents » 187/601 slots (31%) take other frames as values Available at

Copyright 2006, Ida Sim RCT Presenter Demo RCT Presenter is open access »

Copyright 2006, Ida Sim Bank-a-Trial Demo

Copyright 2006, Ida Sim Outline Background Trial Bank Project DBP Goals

Copyright 2006, Ida Sim DBP Goals Trial Bank instances » visualizing collections of related but heterogenous clinical trial instances » using sample HIV medical record to select “applicable” MTCT and STI trials in RCT Bank » meta-analysis RCT Schema » towards a reference ontology for clinical trials

Copyright 2006, Ida Sim Goal 1: Visualization Stage III Breast CA XRT and tamoxifen XRT only tamoxifen only 5 year survival 1 year local recurrence 5 year local recurrence 5 year metastatic dissemination 5 year quality of life OutcomesInterventions

Copyright 2006, Ida Sim Visualization (cont.) RCT BankOBD interventions conditions outcomes number of participants Visualizations! Visualization meta-model Degree of Interest model Core 2 Core 1 Bank-a-Trial MTCT/STI trials WHO/ CDISC XML Stage III Breast CA XRT and tamoxifen XRT only tamoxifen only 5 year survival 1 year local recurrence 5 year local recurrence 5 year metastatic dissemination 5 year quality of life OutcomesInterventions Presenter

Copyright 2006, Ida Sim Goal 2: Identifying Applicable Trials Use case » I have an HIV patient, which STI trials are applicable? –patients in STI trials are “like” this patient » want to “drag and drop” EHR onto Trial Bank to pull out applicable trials » visualize these applicable trials, explore specific details of trials Terminological matching required » sample EHR coded in SNOMED » RCT Bank trials coded in UMLS

Copyright 2006, Ida Sim Identifying Applicable Trials RCT BankOBD Visualizations! Visualization meta-model Degree of Interest model Core 2 Core 1 Bank-a-Trial STI trials WHO/ CDISC XML Stage III Breast CA XRT and tamoxifen XRT only tamoxifen only 5 year survival 1 year local recurrence 5 year local recurrence 5 year metastatic dissemination 5 year quality of life OutcomesInterventions EHR LexGrid UMLS SNOMED Applicability Engine Core 1 Presenter

Copyright 2006, Ida Sim Goal 3: Meta-Analysis Given set of related trials, use statistical routines » explore statistical heterogeneity » perform quantitative meta-analysis

Copyright 2006, Ida Sim Meta-Analysis RCT BankOBD Visualizations! Core 2 Core 1 Bank-a-Trial STI trials WHO/ CDISC XML Stage III Breast CA XRT and tamoxifen XRT only tamoxifen only 5 year survival 1 year local recurrence 5 year local recurrence 5 year metastatic dissemination 5 year quality of life OutcomesInterventions EHR LexGrid UMLS SNOMED Applicability Engine Core 1 Presenter Meta-analysis Core 2?

Copyright 2006, Ida Sim RCT Reference Ontology? Harmonize RCT Schema with CDISC, caBIG, WHO, etc. through BRIDG (outside cBIO) Put into OWL Deposit into OBO Join the “OBO Collaboratory”

Copyright 2006, Ida Sim Timelines Dec 2006 » Visualization Year 2-3 » applicability » meta-analysis » moving towards OBO

Copyright 2006, Ida Sim Summary Clinical trials are valuable source of biomedical knowledge Trial Bank captures RCTs to support understanding, analyzing, applying RCT evidence Drives cBIO on » Core 1: visualization, terminology mapping, Ocelot->OWL, RCT reference ontology » Core 2: OBD, data interchange standard, meta- analysis

Copyright 2006, Ida Sim Questions To group