A Newcomer s Quick Guide to caBIG

A Newcomer’s Quick Guide to caBIG™ Prepared by the caBIG™ 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 caBIG™ is an innovative bioinformatics program led by NIH’s National Cancer Institute • The mission of caBIG™ is to provide infrastructure for creating, communicating and sharing bioinformatics tools, data and research results, using shared data standards and shared data models. caBIG™ 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 caBIG™ 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. • • caBIG™: Organizational Overview caBIG™ 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 1 Clinical Trial Management Systems DOMAIN WORKSPACE 3 Tissue Banks & Pathology Tools DOMAIN WORKSPACE 2 Integrative Cancer Research DOMAIN WORKSPACE 4 Imaging Domain Workspaces Cross Cutting Workspaces Vocabularies & Common Data Elements Architecture Strategic Workspaces Data Sharing and Intellectual Capital Documentation &Training caBIG Strategic Planning 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 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 Interoperability •System Interoperability and Harmonization •Structured Protocol Representation (BRIDG) •Clinical Trials Interoperability Project 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 caArray GenePattern geWorkbench Bioconductor DWD VISDA webGenome Genome Annotation GeneConnect Seed TrAPSS caFE GoMiner Cancer Molecular Pages gridPIR Pathways Reactome Cytoscape cPath Proteomics 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 biobanking 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 caBIG™ 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 National Cancer Imaging Archive (NCIA) XIP Application Annotations and Imaging Markup Imaging Middleware caGrid Vocabularies Vocabularies and Common Data Elements (VCDE) • Primary Mission: Ensure semantic interoperability • Develop caBIG™ compatibility guidelines in the areas of information modeling, metadata and vocabularies • Provide mentors to caBIG™-funded development projects • Facilitate development of caBIG™ 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 caBIG™ compatibility guidelines for interface integration • Provide mentors to caBIG™ 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://cagridportal.nci.nih.gov/portal/ ) Data Sharing & Intellectual Capital (DSIC) • Primary Mission: • Facilitate data sharing between and among caBIG™ participants by addressing legal, regulatory, policy, proprietary, and contractual barriers to data exchange • Goals and activities include: • Address issues confronted by caBIG™ participants, and • Provide education and outreach to caBIG™ 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 caBIG™-related projects • General training opportunities • Community-wide resources • By doing this, we facilitate widespread adoption, dissemination, and use of caBIG™ interoperable tools, standards, and data sets, and increase awareness of caBIG™ within the larger cancer and biomedical communities. • Visit the Training Portal at https://cabig.nci.nih.gov/training Strategic Planning • Mission: • Assist caBIG™ 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, caBIG™ Workspaces Connect Bench to Bedside Communities caBIG WORKSPACES & WORKING GROUPS 1 2 3 4 5 6 7 8 9 Clinical Trial Management Systems (CTM) Tissue Banks & Pathology Tools (TBPTP) Integrative Cancer Research (ICR) Vocabularies & Common Data Elements (VCDE) Architecture Data Sharing & Intellectual Capital (DSIC) Training Strategic Planning Future Planned Workspace (FPW) How Do I Learn More? Resources for Newcomers There are many ways to learn about and get involved with caBIG™ • • caBIG™ Website: https://cabig.nci.nih.gov offers overview materials about caBIG™ as well as community products. LISTSERVS - caBIG™ 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 browse other lists at https://list.nih.gov • • GForge – Many workspaces post working documents in GForge, an online collaboration tool. Visit http://gforge.nci.nih.gov/ Workspace Teleconferences - One way to get a sense of the caBIG™ 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 caBIG™ 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 caBIG™ • Town Hall Meetings - Periodically, the caBIG™ community gathers for a teleconference "town hall meeting” providing updates and addressing issues or questions about caBIG™. See website for announcements. Annual Meeting - The caBIG™ community gathers annually to celebrate successes; address caBIG™-wide and cross-workspace topics; and demonstrate emerging and available products including software tools, databases, prototypes, white papers, and development models. Contact with the caBIG™ Team - The caBIG™ website contact page lists the leads and contact information for all caBIG™ workspaces: https://caBIG.nci.nih.gov/contact_us. For help with caBIG™ tools, contact NCICB applications support at ncicb@pop.nci.nih.gov; Telephone: 301-451-4384; Toll free: 888-478-4423 • • • Closer Look at caBIG™ Website: caBIG™ Primer • The caBIG™ 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 caBIG™ Website: caBIG™ Tools Pages • Tools pages on caBIG™ website help connect you to caBIG™ 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! • caBIG™ 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 caBIG™ provide the opportunity for collaborative solutions that, over time, will reshape the overall cancer research and treatment paradigm. 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