# Presentation: 933724

## A Newcomer’s Quick Guide to caBIGTM 

***Prepared by the caBIGTM Documentation and Training (D&T)  Workspace - June 2007***

## Defining the Problem...

**Together, we face: **
**A Biomedical Information Tsunami**
- Overwhelming volume of data
- Multitude of sources
**AND **
**An 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 led by NIH’s National Cancer Institute

**The mission of caBIGTM is to provide infrastructure for creating, communicating and sharing bioinformatics tools, data and research results, using shared data standards and shared data models. **
**caBIGTM encourages researchers to focus on endeavors such as: **
- Analyzing and integrating the vast amounts of information generated in the areas of genomics and proteomics.
- Identifying and applying information from clinically and molecularly annotated biospecimens in research data.
- Integrating information from a wide range of sources, in support of translational and personalized medicine.
**The caBIGTM initiative will produce these results: **
- A shared interoperable infrastructure facilitating researcher collaboration.
- A set of common data elements, data models, vocabulary standards and standards to better enable data sharing and integration.
- Tools for analyzing information associated with cancer research and care.

## caBIGTM: Organizational Overview

**caBIGTM is organized around workspaces.  Domain workspaces focus on specific areas of cancer research. Cross-cutting and Strategic workspaces support these groups by developing standards and infrastructure.**

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

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

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

**Vocabularies & ****Common Data Elements **

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

**caBIG Strategic ****Planning**

**Documentation ****&Training**

**Data Sharing and ****Intellectual Capital**

**Domain** **Workspaces**

**Cross Cutting** **Workspaces**

**Strategic** **Workspaces**

**Architecture**

## Clinical Trials Management Systems (CTMS)

**Primary Mission:**
- Facilitate the planning, instantiation and monitoring of clinical trials
- Facilitate the conduct of clinical trials
- Facilitate the reporting and sharing of clinical trial data to existing/new destinations,
- Achieve interoperability by: (1) Increasing the ability of systems to access and use the data and functionality of other systems; (2) Facilitating the integration of new sources and destinations of data.
**CTMS serves Clinicians, Investigators, Data Managers, and Statisticians by supporting an end-to-end data pipeline, from Point-of-Care Systems (Clinical and Scientific) through sponsor submission, to regulatory submission.**

## CTMS Tools in Development

**Interoperability**** **
**System Interoperability and Harmonization**
**Structured Protocol Representation (BRIDG)**
**Clinical Trials Interoperability Project**

**Planning/**
**Monitoring**** **
**Investigator and Site Credential Repository**
**Study Initiation Tool**
**Protocol Lifecycle Tracking **
**FIREBIRD**
**DCP/DESK**

**Conduct**
**Standardized Case Report Forms**
**Cancer Central Clinical Database (C3D)**
**Participant Registry **
**Laboratory Interface**
**Financial/Billing**
**Study Calendar**
**Subject Prescreening**
**Vendor Systems**

**Reporting/**
**Sharing**** **
**Clinical Trials Database**
**Routine Data Exchange**
**Clinical Trials Object Model**
**Janus (FDA Repository)**
**Adverse Event Reporting and Collection**

## Integrative Cancer Research (ICR)

**Primary Mission:  **
- Produce modular and interoperable tools and interfaces that provide for integration between biomedical informatics applications and data.
- Enable translational and integrative research by providing for the integration of clinical and basic research data.
**Primary Users of ICR Tools: **** **
- Informatics researchers
- Bench researchers
- Clinical researchers
**ICR is the “Bench” in “Bench-to-Bedside”**

## ICR Tools

**Data and Analytical Services**

| Microarray Data and Analysis | Genome Annotation | Pathways | Proteomics |
| --- | --- | --- | --- |
| caArray
GenePattern
geWorkbench
Bioconductor
DWD
VISDA
webGenome
 | GeneConnect
Seed
TrAPSS
caFE
GoMiner
Cancer Molecular Pages
gridPIR | Reactome
Cytoscape
cPath | RProteomics
ProtLIMS
Q5 |

**Translational / Integrative**
- caTRIP
- caIntegrator
- caB2B

## Tissue Banks and Pathology Tools (TBPT)

**Primary Mission:**
- Develop biobanking and pathology solutions,
- Grow an adopter community that employs these solutions, and
- Foster a collaborative culture to collect, integrate, and share data
**For Bio-Bankers TBPT Provides:  **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 TBPT Provides:  **A solution to conduct federated queries across available databases and to order and manage biospecimen for research activities.

## TBPT Tools

## Imaging

**Primary Mission:  **
- Advance imaging informatics for treatment of patients with cancer.
- Leverage caBIGTM technology to share images in a variety of settings.
- Move towards a standardized way to evaluate tumor change.
- Facilitate secure and easy sharing of images within the cancer community.
**Primary Users: Clinicians and Researchers who would benefit from sharing images and their related contextual information (e.g., image markups).  **

## Imaging Projects In Development

**Cancer**
**Imaging**
**Archive (NCIA)**

**Imaging Middleware**

**caGrid**

**Vocabularies**

**XIP Application**

**Imaging Projects In Development**

**Annotations **
**and ****Imaging****Markup**

**Notes:**
Projects are designed to be interoperable.   Software projects (AIM/XIP)Connected to the grid via Middleware.
NCIA-resource for archive and retrieval of images (stored at NCI-and is in active).  Though the projects are designed to facilitate storage, sharing & retrieval of images from any archive, the NCIA has been a good use case for the Imaging WS projects.  

## Vocabularies and Common Data Elements (VCDE)

**Primary Mission:  Ensure semantic interoperability**
- Develop caBIGTM compatibility guidelines in the areas of information modeling, metadata and vocabularies
- Provide mentors to caBIGTM-funded development projects
- Facilitate development of caBIGTM CDE and Vocabulary Standards
- Perform silver compatibility reviews to ensure compliance with compatibility guidelines for semantics.
**Development Activities:  **LexBIG 1.0.1 released Jan. 2007; LexBIG 2.0 to be released March 2008; Compatibility Review Software 1.0 to be released July 2007

## Architecture

**Primary Mission:  Ensure syntactic interoperability**
- Develop caBIGTM compatibility guidelines for interface integration
- Provide mentors to caBIGTM funded development projects in the area of interface integration
- Perform silver compatibility reviews to ensure compliance with compatibility guidelines for interface integration
**Development Activities: **caGrid 1.0 released Dec. 2006; caGrid 1.1 to be released July 2007; caGrid 2.0 to be released Dec. 2007
**Adoption Activities:  **Currently 66 services on caGrid 1.0 linking together 82 organizations via the caGrid 1.0 Portal (http://cagrid-portal.nci.nih.gov/portal/ )

## Data Sharing & Intellectual Capital (DSIC)

**Primary Mission:**** **
- Facilitate data sharing between and among caBIGTM participants by addressing legal, regulatory, policy, proprietary, and contractual barriers to data exchange
**Goals and activities include: **** **
- Address issues confronted by caBIGTM participants, and
- Provide education and outreach to caBIGTM participants, their IRBs and their technology transfer offices
- Develop recommendations for policies and best practices; prepare white papers and model documents; and assist in the development of software tools on regulatory and security policy issues

## Documentation and Training (D&T)  

**The primary mission of the Documentation and Training (D&T) Workspace is to support the creation and dissemination of:**** **
- Documentation and training materials for caBIGTM-related projects
- General training opportunities
- Community-wide resources
**By doing this, we facilitate widespread adoption, dissemination, and use of caBIGTM interoperable tools, standards, and data sets, and increase awareness of caBIGTM within the larger cancer and biomedical communities.**
**Visit the Training Portal at **_**[https://cabig.nci.nih.gov/training](https://cabig.nci.nih.gov/training)**__** **_** **

## Strategic Planning

**Mission: **
- Assist caBIGTM Leadership with strategic planning and vision development activities.
**Participants provide strategic insights regarding caBIG’s potential role and interface with other initiatives. **** **
**The products of these endeavors include white papers and planning documents that help identify and prioritize additional activities for caBIG as a whole. **

## Together, caBIGTM Workspaces Connect Bench to Bedside Communities

**Together, caBIGTM Workspaces Connect Bench to Bedside Communities**

## How Do I Learn More? 

***Resources for Newcomers***

## There are many ways to learn about and get involved with caBIGTM

**caBIGTM Website: **_**[https://cabig.nci.nih.gov](https://cabig.nci.nih.gov/)**_**  offers overview materials about caBIGTM as well as community products. **
**LISTSERVS - caBIGTM workspaces and project teams use these to announce upcoming events and new products. Sign up for general announcements at **_**[https://list.nih.gov/archives/cabig_announce.html](https://list.nih.gov/archives/cabig_announce.html)**_** - browse other lists at **_**[https://list.nih.gov](https://list.nih.gov/)**_**  **
**GForge – Many workspaces post working documents in GForge, an online collaboration tool.  Visit **_**[http://gforge.nci.nih.gov/](http://gforge.nci.nih.gov/)**_** **
**Workspace Teleconferences - One way to get a sense of the caBIGTM project, and to help shape its direction, is to identify a workspace of interest and then request access to the next teleconference.  Look for upcoming calls on caBIGTM Website. **
**Face-to-Face Meetings - Workspaces gather for face-to-face meetings periodically over the course of the year. **

## There are many ways to learn about and get involved with caBIGTM

**Town Hall Meetings - Periodically, the caBIGTM community gathers for a teleconference "town hall meeting” providing updates and addressing issues or questions about caBIGTM.  See website for announcements. **
**Annual Meeting - The caBIGTM community gathers annually to celebrate successes; address caBIGTM-wide and cross-workspace topics; and demonstrate emerging and available products including software tools, databases, prototypes, white papers, and development models. **** **
**Contact with the caBIGTM Team - The caBIGTM website contact page lists the leads and contact information for all caBIGTM workspaces: **_**[https://caBIG.nci.nih.gov/contact_us](https://cabig.nci.nih.gov/contact_us)**_**.  **** **
**For help with caBIGTM tools, contact NCICB applications support at ncicb@pop.nci.nih.gov; Telephone: 301-451-4384; Toll free: 888-478-4423 **

## Closer Look at caBIGTM Website: caBIGTM Primer

**The caBIGTM Primer provides a next step overview of the program for Newcomers.    **

**Also access through the Training Portal:  http://cabig.nci.nih.gov/training**

## Closer Look at caBIGTM Website: caBIGTM Tools Pages

**Tools pages on caBIGTM website help connect you to caBIGTM tools and information to support the use of those tools   **

**Also access through the Training Portal:  http://cabig.nci.nih.gov/training**

## There’s a Place for YOU!

**caBIGTM has accomplished great achievements, yet challenges remain: **** **
- Educating the broader community about available tools and their uses
- Creating methods and a useful workflow for data sharing between basic science and clinical research.
- Reconciling data models and terminology across traditionally separate areas of science and clinical practice.
- Addressing issues of data sharing, including ensuring data security, patient privacy, and intellectual capital.
- Marshalling diverse resources and standards, and organizing them to address the common problem of cancer research and care.
- Coordinating and correctly sequencing multiple interdependent software and standards development projects to meet broader community needs.
**The challenges of caBIGTM provide the opportunity for collaborative solutions that, over time, will reshape the overall cancer research and treatment paradigm.  Join Us!  **