Welcome to the caBIG

1
Welcome to the caBIG Tissue Banks and Pathology
Tools (TBPT) Workspace!

• Introduction for caBIG NewcomersFace-To-Face
  Meeting, May 2007

Workspace Lead Juergen Klenk, PhD NCI
Facilitator Ian Fore, PhD May 2007
2

• Part 1 caBIG Overview

3
caBIG Movie
http//cabig.cancer.gov/resources/video.asp
4
Biomedical information tsunami

• overwhelming volume of data
• multitude of sources

5
Informatics tower of Babel

• Each cancer research community speaks its own
  scientific dialect
• Integration critical to achieve promise of
  molecular medicine

6
caBIG is an innovative bioinformatics program at
the NIHs National Cancer Institute

• 50 Cancer Centers are working towards a common
  goal of integrated data, tools and methodologies
  to accelerate cancer research goals at the
  National Cancer Institute for Bioinformatics
  (NCICB), the cancer Biomedical Informatics Grid
  (caBIG)
• The goal of caBIG is to create a virtual web of
  interconnected data, individuals, and
  organizations which will
• redefine how research is conducted
• care is provided
• patients / participants interact with the
  biomedical research enterprise
• The principles driving caBIG are
• Open Source
• Open Access
• Open Development
• Federated Model

7
caBIG will facilitate sharing of infrastructure,
applications, and data across multiple cancer
research programs
8
and the realization of that goal
9
caBIG Pilot action plan

• Establish pilot network of NCI Cancer Centers
• Groups agreeing to caBIG principles
• Mixture of capabilities
• Mixture of contributions
• Expanding collection of participants
• Establish consortium development process
• Collecting and sharing expertise
• Identifying and prioritizing community needs
• Expanding development efforts
• Moving at the speed of the internet

10
The caBIG approach balances objectives from
Bench to Bedside, therefore interlocking both
communities to ensure success
11
The first three years of caBIG had
clearly-defined goals and metrics
12
Common needs helped shape priority areas for the
caBIG pilot activities
Database Datasets
Imaging Tools Databases
Integration
High Performance Computing
Clinical Trial Management Systems
Pathways
Licensing Issues
LIMS
Meeting
Microarray Gene Expression Tools
Tissue Banks Pathology
Proteomics
Remote/Bandwidth
Visualization Front-End Tools
Statistical Data Analysis Tools
Vocabulary Ontology Tools Databases
Integrative Cancer Research
Meta-Project
Common Data Elements Architecture
Center Integration Management
Tissue Pathology Tools
Access to Data
Translational Research Tools
Distributed Data Sharing/Analysis Tools
Staff Resources
Clinical Data Management Tools
0
5
10
15
20
25
30
35
Number of Needs Reported
13
(No Transcript)
14
Cancer Center Roles in caBIG

• Developer (20 of centers)
• Key is to create an environment for sharing tools
  with other centers
• One of the most important issues is not to ignore
  the need for common data elements and vocabulary
  services
• Adopter (20 of centers)
• Key is to understand the needs at local center
  (and be vocal)
• Dont abandon other development efforts think
  modular
• When adopting tools make sure they talk to
  legacy systems
• Working Group Strategic Planning (60 of
  centers)
• These are not soft roles
• Critical to the success of the program
• White paper development will guide caBIG
  successes
• Make sure to communicate internally to all parts
  of the Cancer Center

15
Four Domain Workspaces and two Cross Cutting
Workspaces have been launched
DOMAIN WORKSPACE 1 Clinical Trial Management
Systems
addresses the need for consistent, open and
comprehensive tools for clinical trials
management.
DOMAIN WORKSPACE 2 Integrative Cancer Research
provides tools and systems to enable integration
and sharing of information.
DOMAIN WORKSPACE 3 Tissue Banks Pathology Tools
provides for the integration, development, and
implementation of tissue and pathology tools.
DOMAIN WORKSPACE 4 Imaging
provides for the sharing and analysis of in vivo
imaging data.
responsible for evaluating, developing, and
integrating systems for vocabulary and ontology
content, standards, and software systems for
content delivery
CROSS CUTTING WORKSPACE 1 Vocabularies Common
Data Elements
developing architectural standards and
architecture necessary for other workspaces.
CROSS CUTTING WORKSPACE 2 Architecture
16
Strategic Level Workspaces
Data Sharing and Intellectual Capital
Addresses issues related to the sharing of data,
applications and infrastructure both within the
consortium and in the larger cancer research
community.
Training
Developing strategies for providing training in
the use of the caBIG developed resources
including on-line turtorials, workshops, training
programs.
caBIG Strategic Planning
Assists in identifying strategic priorities for
the development and evolution of the caBIG effort.
17
Many commercial software developers are involved
in caBIG- Examples

• Velos Comprehensive clinical trials system in
  widespread use in the extramural Cancer Centers
  throughout the country.
• PercipEnz A comprehensive solution for managing
  all aspects of clinical research study setup
  and activation, scientific reviews, subject
  registration, compliance tracking, visit
  tracking, data collection, data and safety
  monitoring, financials management, data
  extraction, regulatory reporting, and outreach.
• Akaza Rsch web-based, open source software
  platform for managing multi-site clinical
  research studies. It facilitates protocol
  configuration, design of case report forms,
  electronic data capture, retrieval, and
  management.

18
The NCIs General Contractor

• Responsible for coordination of Workspace
  activities
• Provides funding through contracts to
  participating centers
• Provides a channel for communication of guidance
  and priorities
• Provides a measure of participant progress (e.g.,
  contract milestones)
• Fosters accountability and provides mechanisms
  for conflict resolution

The NCI is investing resources for administration
and support of the caBIG project, decreasing the
burden on the participating community
19
caBIG - Interaction Mechanisms

• For all participants
• Annual meeting
• Online Town Hall quarterly
• Addresses solicited questions
• Monthly program update newsletter (big picture)
• Whats big this week weekly newsletter (e.g.
  workspace meeting schedule)

• For Cancer Center Directors
• Directors newsletter
• For Workspaces participants
• Monthly teleconferences (more frequently as
  needed)
• Quarterly meeting (face to face)
• For all participants and the general public
• caBIG website

20
caBIG Involves a Large Community with a Wide
Range of Interests
Ohio State University-Arthur G. James/Richard
Solove Oregon Health and Science
University Roswell Park Cancer Institute St Jude
Children's Research Hospital Thomas Jefferson
University-Kimmel Translational Genomics Research
Institute Tulane University School of
Medicine University of Alabama at
Birmingham University of Arizona University of
California Irvine-Chao Family University of
California, San Francisco University of
California-Davis University of Chicago University
of Colorado University of Hawaii University of
Iowa-Holden University of Michigan University of
Minnesota University of Nebraska University of
North Carolina-Lineberger University of
Pennsylvania-Abramson University of
Pittsburgh University of South Florida-H. Lee
Moffitt University of Southern
California-Norris University of
Vermont University of Wisconsin Vanderbilt
University-Ingram Velos Virginia Commonwealth
University-Massey Virginia Tech Wake Forest
University Washington University-Siteman Wistar Ya
le UniversityNorthwestern University-Robert H.
Lurie
9Star Research Albert Einstein Ardais Argonne
National Laboratory Burnham Institute California
Institute of Technology-JPL City of Hope
Clinical Trial Information Service (CTIS) Cold
Spring Harbor Columbia University-Herbert
Irving Consumer Advocates in Research and
Related Activities (CARRA) Dartmouth-Norris
Cotton Data Works Development Department of
Veterans Affairs Drexel University Duke
University EMMES Corporation First Genetic
Trust Food and Drug Administration Fox Chase
Fred Hutchinson GE Global Research
Center Georgetown University-Lombardi IBM Indiana
University Internet 2 Jackson Laboratory Johns
Hopkins-Sidney Kimmel Lawrence Berkeley
National Laboratory Massachusetts Institute of
Technology Mayo Clinic Memorial Sloan
Kettering Meyer L. Prentis-Karmanos New York
University
21

• Part 2 TBPT Overview

22
Whats the Workspace Mission?

• The primary mission of the Tissue Banks and
  Pathology Tools (TBPT) Workspace is to
• Develop biobanking and pathology solutions,
• Grow an adopter community that employs these
  solutions, and
• Foster a collaborative culture to collect,
  integrate, and share data
• TBPT solutions support interoperability with
  other caBIG compatible tools to advance
  translational research through cross-disciplinary
  information integration

23
Why Is TBPT Important?

• It creates the framework for 21st century
  biospecimen research

Yesterday
Today
24
We Serve Two Primary Audiences

• For Bio-Bankers We Provide
• A solution to capture all bio-banking related
  workflows and information, including participant,
  collection protocol, biospecimen, storage,
  annotation data, consent tracking, and
  distribution protocol.
• For Researchers We Provide
• A solution to conduct federated queries across
  available caTissue databases and to order and
  manage biospecimen for research activities

25
We Offer The Following Solutions (1/4)
26
We Offer The Following Solutions (2/4)
27
We Offer The Following Solutions (3/4)
28
We Offer The Following Solutions (4/4)
caTISSUE Suite (WU) Integrated suite that
includes the functionalityof the first three
tools plus consent tracking, dynamic vocabulary
extension

• Find all cases of prostate ductal carcinoma of
  Gleason grade 34 for which there are frozen
  tissue samples containing at least 50 neoplastic
  cellularity available.
• Find all cases of squamous cell carcinoma of the
  tongue base with perineural invasion for which
  there is at least 5 ug of matching RNA from
  non-malignant tissue and tumor with at least 50
  neoplastic cellularity.

Participant
Annotation Event
De-ID
Accession
Annotation Set
Surgical Pathology
Specimen
Pathology Annot.
Storage
Clinical Annot.
Distribution
Tumor Registry
Study
caTIES
Core
CAE
29
For Those New to caBIG (1/4)

• Check out detailed information about our
  workspace, activities, and all of our solutions
  on the TBPT Portal

TBPT Portal https//cabig.nci.nih.gov/workspaces
/TBPT
30
For Those New to caBIG (2/4)

• From our TBPT Portal you can follow the links to
  try out online versions of our solutions

caTissue Core Online http//catissuecore.wustl.e
du/catissuecore
31
For Those New to caBIG (3/4)

• Use NCICBs support helpdesk to get answers to
  all of your questions about any of our solutions
  

NCICB support homepage http//ncicb.nci.nih.gov/
NCICB/support
32
For Those New to caBIG (4/4)

• caBIG TBPT Workspace Website (public website
  with workspace contacts and meeting minutes)
  https//cabig.nci.nih.gov/workspaces/TBPT
• caBIG TBPT Listserv (subscribe to get regular
  announcements) https//list.nih.gov/archives/cabi
  g_tbpt-l.html
• caBIG TBPT Workspace calls (every 1st and 3rd
  Monday of each month, 1200pm 100pm EST, see
  announcements on the listserv)
• caBIG TBPT GForge Site (includes workspace
  working documents) https//gforge.nci.nih.gov/sof
  twaremap/trove_list.php?form_cat340
• caBIG TBPT CVS Archive (includes distribution of
  all software packages) http//cabigcvs.nci.nih.go
  v/

33
Ongoing Workspace Activities

• Workspace members are working on the following
  projects
• Developing solutions for TBPT, specifically
  within the caTissue Suite project
• Shaping the future of our solutions (at
  face-to-face meetings)
• Adopting our solutions to satisfy a variety of
  needs (individual adopters, group adopters, pilot
  enterprise adopters)
• Sharing best practices with the community (in
  regular calls)
• Sharing data (as permitted) and consuming data
• Growing our community
• Interacting with other workspaces to start
  realizing the paradigm of translational medicine