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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.

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

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Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

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


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

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


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Sharing data, tools, analysis & knowledge

statistical & modeling tools

sample collection

lab analysis pipelines

clinical data collection

lab data collection


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

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


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

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


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

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


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

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


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Clinical and sample data collection & processing


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Clinical data views


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

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


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

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


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

  • ”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


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Laboratory knowledge base


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Laboratory knowledge base


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Laboratory data flow, standards, data annotations & upload


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Laboratory data repository views


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Laboratory data : some stats


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

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


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Tools to support data exploration and synthesis


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Tools for physician decision support


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Tool Results Collections and Analysis Browser


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Collaboration for Cancer Care Engineering Research


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

ITMIG Global Prospective Database just underway …


Ccehub sharing exploring and analyzing data an environment for collaborative cancer research

Our technology extends to other cancer research workflows

Using the HUB cyber infrastructure

and cceHUB data technology

to further collaborative

Cancer Care Engineering Research


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