New caBIG® Knowledge Centers Serve as Hub for Growing Community
Six Knowledge Centers Streamline Access to the Latest Bioinformatics Information
As an expanding number of institutions across the biomedical community deploy and begin using caBIG® tools and resources, the need for consistent access to accurate, up-to-date information is growing dramatically.
To accommodate the community’s needs, the National Cancer Institute Center for Biomedical Informatics and Information Technology (NCICBIIT) recently launched six caBIG® Knowledge Centers designed to promote knowledge exchange regarding the use and development of interoperable biomedical tools, standards, and infrastructure.
The Centers are managed by leading biomedical institutions across the United Sates, and serve as centralized, authoritative hubs for the specific domains in which they have expertise. The resources of each Knowledge Center (KC) are Web-accessible and are staffed by a combination of IT specialists, bioinformaticists, laboratory and clinical researchers, and legal and policy experts who are currently employing and/or developing caBIG® tools, infrastructure, or policies.
The overarching mission of the Knowledge Centers is to provide easily accessible information to IT professionals, senior biomedical decision makers, and end-users of the tools and resources.
“A key aspect to the success of any open source, community-driven project is readily available and easy access to information,” noted Patrick McConnell, vice president of Biomedical Informatics at SemanticBits. “I foresee this open sharing of information to be key in addressing the needs of researchers and clinicians. It allows us as a technical community to bridge the gap with the true end users - cancer researchers.”
There are six caBIG® Knowledge Centers:
- caGrid
- Clinical Trials Management Systems
- Data Sharing and Intellectual Capital
- Molecular Analysis Tools
- Tissue/Biospecimen Banking and Technology Tools
- Vocabulary
caBIG® Knowledge Centers provide:
- Web-based knowledge related to the caBIG® tools in each domain;
- Domain-specific forums for real-time questions and conversations;
- Comprehensive and up-to-date technical and end user documentation and training materials;
- Outreach to existing caBIG® participants and the broader cancer and biomedical research community;
- Administration of source code repository for current caBIG® tools and to promote open development by the community; and
- Collection and monitoring of defect reports, feature requests, and end user requirements and communications to the appropriate caBIG® workspaces.
The first five Knowledge Centers opened for business on August 11, 2008, followed by the launch of the Data Sharing and Intellectual Capital Knowledge Center on September 8, 2008.
The caGrid Knowledge Center is led by The Ohio State University Comprehensive Cancer Center, with University of Chicago and the Argonne National Laboratory. caGrid is the underlying network architecture that provides connectivity among institutions, allowing research groups to exchange data and services while also supporting their individual investigations. The caGrid KC wiki shares information through comprehensive pages called “Community Member Tracks,” which are distinguished by the user audience for ease of access.
“The primary mission [for us] is clearly illustrating the added value provided by a grid computing approach in general, and caGrid specifically, and helping research projects get maximum benefit from caGrid,” said Justin Permar, operations manager for the caGrid KC and technical manager in the Software Research Institute and Department of Biomedical Informatics at the Ohio State University. “Another major utility of the caGrid KC is to provide clear, comprehensive information resources to the caGrid user community. These information resources should efficiently and accurately answer any community questions.”
The Clinical Trials Management Systems Knowledge Center is led by Duke University Comprehensive Cancer Center in collaboration with Northwestern University, Cancer and Leukemia Group B – Information Systems (CALGB-IS), and SemanticBits. The CTMS KC is a resource for organizations using caBIG® tools for the development, management, conduct, and reporting of clinical trials.
“The CTMS KC should be considered a clearing house for CTMS information and tools, with moderated forums and wikis to provide input on issues and solutions,” said Bob Annechiarico, director of the CTMS KC and director of Cancer Center Information Systems at Duke University. “Information collected from these sources would then be evaluated by subject matter experts and software engineers to provide feedback and to form requirements for future releases of core software products.”
The Molecular Analysis Tools Knowledge Center is led by Columbia University Herbert Irving Comprehensive Cancer Center with the Broad Institute of MIT and Harvard, and is a resource for institutions and individuals using caBIG® tools for the management and analysis of genomic and proteomic data.
“One challenge we face as we move forward is to provide the right information so researchers and clinicians find it easy to learn about those tools, quick to align their needs with what the tools offer, and straightforward to use those tools in their research,” said Dr. Zhong Li, director of operations, caBIG® Molecular Analysis Tools Knowledge Center. “We have to establish good structure to convey the information effectively and smooth the learning curve.”
The Tissue/Biospecimen Banking and Technology Tools Knowledge Center is led by Siteman Cancer Center at the Washington University at St. Louis, and is a resource for organizations that are managing, annotating, and tracking biospecimens. The Washington University team developed and supported the caBIG® tissue banking software and uses these tools to manage their own large biospecimen repository.
Dave Mulvihill, operations manager of the Tissue/Biospecimen Banking and Technology Tools (TBBT) KC and IT project manager at the Washington University School of Medicine explained how the TBBT forums are already providing value to users, as well as the KC staff.
“Community forums are an effective way of exchanging questions, answers, and ideas,” said Mulvihill. “This exchange allows the Knowledge Center to keep current with community needs and extract relevant content to the knowledge base.”
The Vocabulary Knowledge Center is led by Mayo Clinic, in collaboration with SemanticBits. The Vocabulary KC is a resource for individuals and organizations using the distributed vocabulary services infrastructure to enable publication of vocabularies. Vocabularies are used throughout the caBIG® community to code biomedical information and to create semantically annotated metadata that allows researchers to integrate information from disparate sources.
According to Dr. Robert Freimuth, director of the caBIG® Vocabulary Knowledge Center and assistant professor of Medical Informatics at the Mayo Clinic, “most end users have not thought about formally creating or managing a controlled terminology even though most are familiar with simple coding schemes, such as the use of "M" for male and "F" for female.”
Dr. Freimuth went on to explain, how, as caBIG® applications become widely adopted and researchers share large, diverse data sets, the need for specialized terminologies will become more prominent, especially in areas such as phenotypes, drug names, and laboratory findings.
“As members of the research community recognize that need, the Vocabulary Knowledge Center will provide the tools and training that they need to create and manage their terminologies as efficiently as possible.”
The Data Sharing and Intellectual Capital (DSIC) Knowledge Center is hosted by the University of Michigan. Unlike the other five Centers, which are focused on supporting caBIG® software and infrastructure, the DSIC KC provides a centralized repository of processes, model agreements, and other resources to encourage and facilitate data sharing to advance scientific discovery consistent with applicable legal, regulatory, ethical, and contractual requirements. The DSIC KC is the first interactive web resource designed to assist individuals and organizations as they navigate both security and policy-related data sharing issues.
“Every institution will have different data sharing and intellectual capital issues,” said Alex Kanous, operations manager for the DSIC KC at the University of Michigan. “One of our responsibilities is to find the common thread in these challenges and create solutions that will help organizations and other stakeholders deal with their specific institutional issues. We’ll look to the cancer research community and other subject matter experts to help us ensure that these solutions keep pace with the rapid evolution of research.”
Learn more:
Click here to visit the caBIG® Knowledge Center Web Infrastructure.
Click here to view a listing of which caBIG® Knowledge Centers are responsible for specific caBIG® tools.
Click here to learn more about the Enterprise Support Network.
