# Presentation: 933723

## Welcome to the caBIGTM Tissue Banks and Pathology Tools (TBPT) Workspace! 

***Introduction for caBIGTM Newcomers******Face-To-Face Meeting, May 2007***

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

***Part 1: caBIGTM Overview***

## caBIGTM Movie

- _[http://](http://cabig.cancer.gov/resources/video.asp)__[cabig.cancer.gov/resources/video.asp](http://cabig.cancer.gov/resources/video.asp)_

## Biomedical information tsunami

**Biomedical information tsunami**

**overwhelming volume of data**
**multitude of sources **

## Informatics tower of Babel

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

## caBIGTM is an innovative bioinformatics program at the NIH’s 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 (caBIGTM) **
**The goal of caBIGTM 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 caBIGTM are:**
- Open Source
- Open Access
- Open Development
- Federated Model

## caBIG will facilitate sharing of infrastructure, applications, and data across multiple cancer research programs

## ...and the realization of that goal

## caBIGTM 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...**

## The caBIGTM approach balances objectives from Bench to Bedside, therefore interlocking both communities to ensure success

**The caBIGTM approach balances objectives from Bench to Bedside, therefore interlocking both communities to ensure success**

## The first three years of caBIGTM had clearly-defined goals and metrics

**The first three years of caBIGTM had clearly-defined goals and metrics**

## Common needs helped shape priority areas for the caBIG pilot activities 

- 0

- 5

- 10

- 15

- 20

- 25

- 30

- 35

**Clinical Data Management Tools**

- Staff Resources

**Distributed Data Sharing/Analysis Tools**

**Translational Research Tools**

**Access to Data**

**Tissue & Pathology Tools**

- Center Integration & Management

- Common Data Elements & Architecture

- Meta-Project

- Vocabulary & Ontology Tools & Databases

- Statistical Data Analysis Tools

- Visualization & Front-End Tools

- Remote/Bandwidth

**Proteomics**

**Microarray & Gene Expression Tools**

- Meeting

- LIMS

- Licensing Issues

**Pathways**

- High Performance Computing

- Integration

- Imaging Tools & Databases

- Database & Datasets

**Number of Needs Reported**

**Clinical Trial Management Systems**

**Tissue ****Banks ****& Pathology**

**Integrative Cancer Research**

## Slide 13

## 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)
- Don’t 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

## Four Domain Workspaces and two Cross Cutting Workspaces have been launched

**DOMAIN WORKSPACE 3**
**Tissue Banks & Pathology Tools**

- provides for the integration, development, and implementation of tissue and pathology tools.

**DOMAIN WORKSPACE 2**
**Integrative Cancer Research**

- provides tools and systems to enable integration and sharing of information.

**DOMAIN WORKSPACE 1**
**Clinical Trial Management Systems**

- addresses the need for consistent, open and comprehensive tools for clinical trials  management.

**CROSS CUTTING WORKSPACE 2**
**Architecture**

- developing architectural standards and architecture necessary for other workspaces.

**CROSS CUTTING WORKSPACE 1**
**Vocabularies & Common ****Data Elements **

- responsible for evaluating, developing, and integrating systems for vocabulary and ontology content, standards, and software systems for content delivery

**DOMAIN WORKSPACE 4**
**Imaging**

- provides for the sharing and analysis of in vivo imaging data.

## Strategic Level Workspaces

**caBIG Strategic Planning**

- Assists in identifying strategic priorities for the development and evolution of the caBIG effort.

**Training**

- Developing strategies for providing training in the use of the caBIG developed resources including on-line turtorials, workshops, training programs.

**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.

## Many commercial software developers are involved in caBIGTM- 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. **

## The NCI’s 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

## caBIGTM - Interaction Mechanisms

**For all participants:**
- Annual meeting
- Online “Town Hall” quarterly
- Addresses solicited questions
- Monthly program update newsletter (big picture)
- “What’s big this week” weekly newsletter (e.g. workspace meeting schedule)

**For Cancer Center Directors:**
- Director’s newsletter
**For Workspaces participants:**
- Monthly teleconferences (more frequently as needed)
- Quarterly meeting (face to face)
**For all participants and the general public**
- caBIGTM website

## caBIGTM Involves a Large Community with a Wide Range of Interests

**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**

**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**
**Yale UniversityNorthwestern University-Robert H. Lurie**

***Part 2: TBPT Overview***

## What’s 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 caBIGTM compatible tools to advance translational research through cross-disciplinary information integration**

## Why Is TBPT Important? 

**It creates the framework for 21****st**** century biospecimen research**

- Yesterday

- Today

**Notes:**
Advances in molecular technologies and sophistication in clinical trial design have increased the importance of biospecimen banks in collecting, processing, storing, and distribution of human specimens for correlative science cancer research. Once regarded as “wax museums” that simply doled out paraffin tissue sections for immunohistochemical analysis, biospecimen banks are now responsible for collecting and distributing multiple human specimen types for molecular studies.  
In order to accommodate the evolving functional complexity of the 21st century, biospecimen banks and informatics systems need the functionality to track multiple specimens from the same participant, track refined materials (RNA, DNA, and Protein) that are used for molecular analysis, and annotate biospecimens with accumulating experimental data, as they are successively used for clinical correlative studies.
Existing tissue banking systems have some of these features, however no single system currently provides all the features described.  Some perform tracking, some perform financial management, some have automated pathology and clinical annotations, some may have experimental data associated with specimens, but no one system has it all. 

## 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

## We Offer The Following Solutions (1/4)

## We Offer The Following Solutions (2/4)

## We Offer The Following Solutions (3/4)

## We Offer The Following Solutions (4/4)

**Find all cases of prostate ductal carcinoma of Gleason grade 3+4 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

- Accession

- Specimen

- Storage

- Distribution

- Study

- Annotation Event

- Annotation Set

- De-ID

- Pathology Annot.

- Clinical Annot.

- Tumor Registry

- Surgical Pathology

- caTIES

- Core

- CAE

**caTISSUE Suite**** (WU)** – Integrated suite that includes the functionalityof the first three tools plus consent tracking, dynamic vocabulary extension

## For Those New to caBIGTM (1/4)

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

**TBPT Portal:  **_[https://](https://cabig.nci.nih.gov/workspaces/TBPT)__[cabig.nci.nih.gov](https://cabig.nci.nih.gov/workspaces/TBPT)__[/workspaces/TBPT](https://cabig.nci.nih.gov/workspaces/TBPT)_

## For Those New to caBIGTM (2/4)

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

**caTissue Core Online:  **_[http://](http://catissuecore.wustl.edu/catissuecore)__[catissuecore.wustl.edu/catissuecore](http://catissuecore.wustl.edu/catissuecore)_

## For Those New to caBIGTM (3/4)

**Use NCICB’s support helpdesk to get answers to all of your questions about any of our solutions  **

**NCICB support homepage:  **_[http://](http://ncicb.nci.nih.gov/NCICB/support)__[ncicb.nci.nih.gov](http://ncicb.nci.nih.gov/NCICB/support)__[/NCICB/support](http://ncicb.nci.nih.gov/NCICB/support)_

## For Those New to caBIGTM (4/4)

- caBIGTM TBPT Workspace Website (public website with workspace contacts and meeting minutes): _[https://cabig.nci.nih.gov/workspaces/TBPT](https://cabig.nci.nih.gov/workspaces/TBPT)_
- caBIGTM TBPT Listserv (subscribe to get regular announcements): _[https://list.nih.gov/archives/cabig_tbpt-l.html](https://list.nih.gov/archives/cabig_tbpt-l.html)_
- caBIGTM TBPT Workspace calls (every 1st and 3rd Monday of each month, 12:00pm – 1:00pm EST, see announcements on the listserv)
- caBIGTM TBPT GForge Site (includes workspace working documents): _[https://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=340](https://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=340)_
- caBIGTM TBPT CVS Archive (includes distribution of all software packages): _[http://](http://cabigcvs.nci.nih.gov/)__[cabigcvs.nci.nih.gov](http://cabigcvs.nci.nih.gov/)__[/](http://cabigcvs.nci.nih.gov/)_

## 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