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The Cancer Biomedical Informatics Grid (caBIG‚): An Evolving Community for Cancer Research

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Biomedical Informatics for Cancer Research

Abstract

This chapter describes the Cancer Biomedical Informatics Grid (caBIG®) project, a collaboration among the National Cancer Institute (NCI) and numerous discovery organizations, mostly NCI-designated cancer centers. The rationale for the caBIG® project opens the review, followed by description and analysis of the pilot phase (2004–2007). Changes in caBIG® as it transitions to an enterprise phase are evaluated. The chapter concludes with a review of important papers that either describe caBIG® components or are based on the initiative.

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Author information

Authors and Affiliations

  1. Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA

    J. Robert Beck

Authors
  1. J. Robert Beck
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Corresponding author

Correspondence to J. Robert Beck .

Editor information

Editors and Affiliations

  1. Sydney Kimmel Comprehensive, Cancer Center, John Hopkins University, N. Broadway 550, Baltimore, 21205-2011, USA

    Michael F. Ochs

  2. USC / Norris Comprehensive Cancer Ctr., Eastlake Ave. 1441, Los Angeles, 90033, USA

    John T. Casagrande

  3. Wistar Institute, Spruce Street 3601, Philadelphia, 19104, USA

    Ramana V. Davuluri

Appendix: caBIG‚ Tools and Technologies at the End of the Pilot Phase

Appendix: caBIG‚ Tools and Technologies at the End of the Pilot Phase

1.1 Clinical Trials Management

  • Cancer Central Clinical Database (C3D): a clinical trials data management system based on Oracle Clinical, including protocol building, remote data capture, and review.

  • Cancer Central Clinical Participant Registry (C3PR): a web-based application for patient trial registry.

  • Clinical Data Exchange/Lab Integration Hub (caXchange): an open-source software tool used to manage laboratory data during a clinical trial.

  • Clinical Trials Object Data System (CTODS): a virtual data warehouse for clinical trials data that can capture trial information and deliver it de-identified.

  • Clinical Data System (CDS): a stand-alone data submission infrastructure for NCI-supported clinical trials.

  • Patient Study Calendar (PSC): an open-source application that can create and edit study calendar templates and manage them during a study.

  • Cancer Adverse Event Reporting System (caAERS): an open-source software tool that is used to collect process and report adverse events that occur during clinical trials.

  • caTRIP: a meta-system that allows users to query across a number of caBIG data services, based on Common Data Elements (CDEs) and integrate results for viewing and further analysis.

  • Federal Investigator Registry of Biomedical Information Research Data (FIREBIRD): a system that automates the Form 1572 registration process for clinical trials investigators.

1.2 Biospecimen Banking

  • caTissue Core: a tissue bank repository tool for biospecimen inventory, tracking, and basic annotation.

  • Cancer Text Information Extraction System (caTIES): a system to extract coded cancer information from free-text surgical pathology reports.

  • caTissue Clinical Annotation Engine (CAE): a web-based user interface for standards-based manual annotation of biospecimens.

1.3 Image Analysis

  • National Cancer Imaging Archive (NCIA): a searchable national repository of cancer images, integrated with clinical and genomic data.

1.4 Data Mapping

  • caAdapter: an open-source tool set that facilitates data mapping, validation, and transformation among various data sources and standard formats.

1.5 General Research Tools

  • Electronic Laboratory Management Information Resource (caELMIR): a Laboratory Information Management System (LIMS) for recording experimental data.

  • geWorkbench: an open-source software platform for genomic data integration.

  • GenePattern: another software platform for genomic data integration.

  • caIntegrator: a translational informatics platform that can integrate clinical and molecular information across patients and trials.

  • caBench-to-Bedside (caB2B): a caGrid client that permits users to search caGrid data services.

  • caArray: an open-source microarray data management system, that supports other caBIG® tools like geWorkbench and GenePattern.

  • Protein Information Resource (gridPIR): a data resource for genomic and proteomic resource that connects to relevant PIR databases.

  • Cancer Models Database (caMOD): a resource for animal models for human cancer, involving submission and search capabilities.

  • Bioconductor: an established open-source collection of software packages for high-throughput genome analysis.

1.6 Genome Analysis

  • SEED: a tool for making and sharing genomic annotations, and for access and analysis of annotations.

  • Transcript Annotation Prioritization and Screening System (TRAPSS): an analytical tool for screening gene sequences for mutations, including notable ones.

  • Function Express (caFE): a tool for annotation of probes on microarrays.

  • GoMiner: a tool for biological interpretation using the Gene Ontology.

  • GeneConnect: a caBIG® mapping service that interlinks various genomic identifiers.

1.7 Protein Analysis

  • RProteomics: a package for analyzing mass spectrometry proteomics data.

  • Q5: a classification tool for expression-dependent proteomic data.

  • Proteomics Laboratory Information Management System (protLIMS): a prototype LIMS for proteomics.

  • Cancer Molecular Pages (CMP): an automated annotation system for cancer-related proteins.

  • Computational Proteomics Analysis System (CPAS): an open-source tool for peptide scoring based on the Trans Proteomics Pipeline.

1.8 Pathway Analysis

  • Quantitative Pathway Analysis in Cancer (QPACA): a tool that provides a set of routines for analysis of microarray data in the context of genetic pathways.

  • Reactome: a service that establishes the Reactome system as a caGrid service.

  • Pathway Interaction Database: a curated database of information about known biomolecular interactions and cellular signaling processes.

  • Pathway Tools: a suite of tools that interact on an open-source pathway database.

1.9 Statistical Analysis

  • Visual Statistical Data Analyzer (VISDA): an analytical tool for cluster modeling and visualization.

  • Distance Weighted Discrimination (DWD): a tool that corrects microarray analyses by reducing systematic bias.

1.10 Core Infrastructure

  • caGrid: the underlying network architecture, based on the Globus toolkit, that balances local access control and central services.

  • BRIDG Model: a collaborative data model for clinical research.

  • caCORE: an open source group of software products developed by NCICB that provide the tools for open source, interoperable applications that are caGrid compliant.

  • Cancer Bioinformatic Infrastructure Objects (caBIO): a set of software objects that provide a programming interface to caCORE.

  • NCI Enterprise Vocabulary Server (EVS): a service that produces metathesaurus entities to support standard controlled vocabularies for caBIG® projects and products.

  • caDSR: a metadata registry in caCORE that stores and manages CDEs developed by participants and NCI-supported organizations.

  • caCORE Software Development Kit (caCORE SDK): a set of tools designed to aid in a caBIG® compliant, semantically integrated system.

1.11 Vocabularies

  • LexBIG: a set of software and services to load, publish, and access caBIG® compliant vocabulary.

  • Mouse–Human Anatomy Mapping Ontology (MHAP): a mapping and harmonization of murine and human anatomical descriptors.

  • Cancer Nutrition Ontology: a unified set of Nutrition vocabularies and mappings.

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Beck, J.R. (2010). The Cancer Biomedical Informatics Grid (caBIG‚): An Evolving Community for Cancer Research. In: Ochs, M., Casagrande, J., Davuluri, R. (eds) Biomedical Informatics for Cancer Research. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-5714-6_9

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  • DOI: https://doi.org/10.1007/978-1-4419-5714-6_9

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  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4419-5712-2

  • Online ISBN: 978-1-4419-5714-6

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