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UBIOPRED Dr Anthony Rowe, Prof Yike Guo Dept of Computing UBIOPRED - PowerPoint PPT Presentation

Sep 08, 2023 •301 likes •448 views

Knowledge Management in UBIOPRED Dr Anthony Rowe, Prof Yike Guo Dept of Computing UBIOPRED Overview Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes Innovative Medicines Initiative call topic: Understanding Severe

  1. Knowledge Management in UBIOPRED Dr Anthony Rowe, Prof Yike Guo Dept of Computing

  2. UBIOPRED Overview • Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes – Innovative Medicines Initiative call topic: Understanding Severe Asthma – 10 Pharma, 20 Academic Medical Centres, 10 other • Key Highlights – Publication of consensus papers defining 1)severe asthma and 2) systems medicine approach – 1 st patient recruited into the clinical study last week – Cross Industry Data Sharing 2 13/05/2011

  3. U-BIOPRED Aim: Handprint

  4. Three challenges in for Knowledge Management UBIOPRED • Organisational Complexity – Complex consortium • Scientific Complexity – End to End translational Study • Data Complexity – Clinical, Omics (7), Imaging, Histology 4 13/05/2011

  5. Knowledge Production Process Process: Patient Omics Samples Delivery Knowledge Data Data Procedure: Data Analysis Protocol SOP (SRM) KM Manual Plan Technology: KM Governance eCRF LIMS & Standards Files Others? 5 Deploying TranSmart to UBIOPRED 13/05/2011

  6. Knowledge Management Architecture Data Tran- Analytical Analysis Raw Data Processing Registry Engine Store SMART Engine Virtual Machines IC Cloud (Virtualisation Layer) Physical Layer (Imperial Based Data Centre) 6 Deploying TranSmart to UBIOPRED 13/05/2011

  7. Dataflow & Key Transformations 1 Data 5 Analytical Processing eCRF Registry Engine 1 2 2 TSmart 4 DB 4 LIMS 6 TSmart Gene Pattern&R App Omics 3 Raw Data Data Store Files IC Cloud 1. Transform and Load Clinical Data into 4. Load processed Omics Data into Transmart TranSmart using pre-processing functionality in R 2. Transform and Load Inventory Data into 5. Update Completion Information in Analytical TranSmart Registry 3. Upload and Index Raw Data 6. TranSmart application accesses datamart and 7 Deploying TranSmart to UBIOPRED 13/05/2011 R server

  8. TranSmart use in UBIOPRED ECLIPSE pilot • IMI in action (J&J’s Software, GSK’s ECLIPSE data, academic execution) • 3000 Patients, 1800 Clinical Attributes, Blood & Sputum Samples • Data to be provided in 3 Tranches dependent on success – Tranche 1: Clinical Data for 220 Patients that have micro-array data – Tranche 2: The associated micro-array data for 220 group – Tranche 3: Longitudinal data for micro-array data for 220 group – Tranche 4: Full Clinical Data for all patients • 15 days total from install to deploy to users 8 Deploying TranSmart to UBIOPRED 13/05/2011

  9. Recruitment Analysis – Built in less than 5 minutes

  10. UBIOPRED Analytical Register for Managing Study Research Tools to find hypothesis, Activity of people and data people in the within the project project 10 Deploying TranSmart to UBIOPRED 13/05/2011

  11. Drill Down through Study Metadata 11 Deploying TranSmart to UBIOPRED 13/05/2011

  12. Details built up collaboratively Critically linking back to TranSmart 12 Deploying TranSmart to UBIOPRED 13/05/2011

  13. Three challenges in for Knowledge Management UBIOPRED • Organisational Complexity – Analytical Registry Analytical Registry • Data Complexity – TranSMART Other DB Data Analysis • Scientific Complexity TranSMART Engine – New analytic methods under Development 13 13/05/2011

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