cceHUB Sharing , Exploring and Analyzing Data An Environment for Collaborative Cancer Research

1. clinical data observational & scientific data computation & visualization decision support cceHUB Sharing , Exploring and Analyzing Data An Environment for Collaborative Cancer Research Ann Christine Catlin HUBbub 04-06-2011

2. Master plan for the Cancer Care Engineering Colorectal Cancer Study 3. Predictive Modeling Data Synthesis & Analysis Knowledge Acquisition Zhang Group Integrative ModelsPurdue ShererPopulation-based ModelsVA Hospital ChenBiological Network ModelsIUPUI • Blood Sample Acquisition • Sample Processing, Annotation, Distribution • Clinical Patient Data Collection • IU Simon Cancer Center 2. OMIC Laboratory Analysis Data & Knowledge Acquisition XuLab LipidomicsIUSchool of Medicine Raftery Lab MetabolomicsPurdue Regnier Lab GlycoproteomicsPurdue Bindley LabGlobal ProteomicsPurdue Teegarden Lab Vitamin DPurdue Klaunig Lab Oxidative StressIU School of Medicine 4. Visual Analytics Data Exploration & Analysis Knowledge Acquisition EbertGroupPURVACPurdue • Iterative Feedback & Validation • CCEResearchCommunity molecular signatures for colorectal cancer that predict susceptibility, treatment response and ultimate treatment outcome

3. Sharing data, tools, analysis & knowledge statistical & modeling tools sample collection lab analysis pipelines clinical data collection lab data collection

4. A single portal : sharing data, tools, analysis & knowledge statistical & modeling tools sample collection lab analysis pipelines clinical data collection lab data collection cancer research groups worldwide

5. A single portal: sharing data, tools, analysis & knowledge a web environment with that supports data flow data sharing data analysis for the collaborating cancer research groups of CCE

6. Support for clinical data Clinical Research Team and Physicians clinical data Data contribution from clinical team Patients Diagnosis, Treatments, Surgeries, Lifestyle, Diet, Demographics, … Samples Collection, Processing, Protocols, Distribution, Tracking, … Data Workflow laboratory analysis Automatic Metadata Processing Sample Data Patient Data Clinical Metadata predictive modeling tools cceHUB Database

7. Support for clinical data Clinical Research Team Physicians • nightly pull from hospital e-records • patient data collection • sample tracking • data annotation • clinical data archive • blood sample bio-repository • patient and sample linkage • data viewing • data search, filter & explore Clinical Data Flow clinical data Data contribution from clinical team Patients Diagnosis, Treatments, Surgeries, Lifestyle, Diet, Demographics, … Samples Collection, Processing, Protocols, Distribution, Tracking, … Data Flow laboratory analysis Automatic Metadata Processing Sample Data Patient Data Clinical Metadata predictive modeling tools cceHUB Database

8. Clinical and sample data collection & processing

9. Clinical data views

10. Clinical data : some stats First patient CCE001 enrolled on 04/02/2009 (the day cceHUB went live) Most recent patient CC285 enrolled on 02/15/2011 Most recent data : neoadjuvant chemoradiation treatment for patient CCE156 on 04/02/2011 Maximum patients enrolled on a single day 09/23/2009 = 9 # web-forms to track patient and sample data flow : 12 # accesses to clinical data viewer 04/02/2009 – 05/25/2010 : > 15,000

11. Support for laboratory data Lab Workflow Knowledge clinical data Sample-Dataset tracking Massive instrument- generated datasets Research Labs Metabolomics, Lipidomics, Global Proteomics, Glycoproteomics, Vitamin D, Oxidative Stress, Genomics laboratory analysis Data Upload Clinical Data Lab Knowledge Base Repository Metadata predictive modeling tools cceHUB Database cceHUB Lab Instrument Data Repository

12. ”knowledge base” resources • (protocols, sample preparation, instruments, standards, file formats, analysis) • annotation for lab data files • lab data files tracked to samples/patients • data files upload with provenance • metadata processing • lab data collections • data view & explore • data access for analysis tools Laboratory Data Flow Support for laboratory data Lab Workflow Knowledge clinical data Sample-Dataset tracking Massive instrument- generated datasets Research Labs Metabolomics, Lipidomics, Global Proteomics, Glycoproteomics, Vitamin D, Oxidative Stress, Genomics laboratory analysis Data Upload Clinical Data Lab Knowledge Base Repository Metadata predictive modeling tools cceHUB Database cceHUB Lab Instrument Data Repository

13. Laboratory knowledge base

14. Laboratory knowledge base

15. Laboratory data flow, standards, data annotations & upload

16. Laboratory data repository views

17. Laboratory data : some stats

18. Support for modeling and analysis GCxGC MS Classification and Alignment clinical data LC-MS Discovery Pipeline: Spectrum Deconvolution Data to Tools Data from Tools laboratory analysis Clinical Data Lab Knowledge Base Repository Metadata Modeling Groups Visual Analytics Data Synthesis & Analysis Knowledge Acquisition predictive modeling tools cceHUB Database cceHUB Lab Instrument Data Repository

19. Tools to support data exploration and synthesis

20. Tools for physician decision support

21. Tool Results Collections and Analysis Browser

22. Collaboration for Cancer Care Engineering Research

23. ITMIG Global Prospective Database just underway …

24. Our technology extends to other cancer research workflows Using the HUB cyber infrastructure and cceHUB data technology to further collaborative Cancer Care Engineering Research