The National Cancer Institute (NCI) will deploy an integrating biomedical informatics infrastructure, the cancer Biomedical Informatics Grid (caBIGTM), to expedite the cancer research community's access to key bioinformatics platforms. In partnership with the cancer research community, the NCI is creating a common, extensible informatics platform that integrates diverse data types and supports interoperable analytic tools. This platform will allow research groups to tap into the rich collection of emerging cancer research data while supporting their individual investigations.
This Integrative Cancer Research Workspace will provide tools and systems to enable integration and sharing of information among cancer researchers. These tools will facilitate the integration of data not only from different centers, but also data of different types, thereby enabling translational and integrative research, These tools also provide for the integration of clinical and basic research data. The Workspace is tasked to develop a well-documented and validated toolset for use throughout the cancer research community. Workspace activities will include platforms and standards to facilitate the sharing of datasets and repositories, and those appropriate for testing the caBIGTM infrastructure are being asked to participate. A major goal of this workspace will be a demonstration of how a shared informatics platform can allow a comprehensive, federated grid of information to be made available to the cancer research community.
The main goal of the Integrative Cancer Research Workspace is to assemble data, tools, and infrastructure that facilitate the cross silo use of cancer biology information to promote integrated cancer research. Working towards this goal, the NCICB is developing an integrative application framework, known as caintegrator, designed to facilitate cross data analysis in support of ongoing cancer research.
2.0 Objectives
This SOW is intended to cover three major projects/initiatives at the NCI Center for Bioinformatics:
Computational Portal and Analysis System (CPAS), Cancer Genetic Markers of Susceptibility
(CGEMS) and caintegrator.
The following high level objectives are intended to be achieved by the work described herein.
CPAS: The Computational Portal and Analysis System is part of deliverable from the mouse Biomarker
Discovery Project (BDI), funded by Nd. Data generated under the BDI contract is to be delivered to
NCICB in addition to the CPAS system. NCICB will make the data accessible to the public via an NCBI
proteomics portal, based on CPAS. Several enhancements are planned to adapt CPAS from pipeline
based system to a public repository. Support is also required to
(a) verify and ensure caBIG Silver-level compatibility (https://cabig.nci.nih.gov/quidelines documentation)
(b) Get the mouse BDI data (including mass spectrometry and 2D gel) loaded into NCICB's installation of
CPAS;
(c) Load proteomics data from other studies, as these become available;
(d) Fix bugs;
(e) Install and maintain the caBIG Silver-level API when this becomes available.
CGEMS: The Cancer Genetic Markers of Susceptibility project is an effort to identify germ-line singleżnucleotide polymorphisms (SNPs) that correlate with disease. As currently scoped, the CGEMS project will conduct two genotyping studies: one for prostate cancer and one for breast cancer. For each study,
1200 cases and 1200 controls will be genotyped for 500,000 SNPs. The goal is to identify SNPs that predispose a person to disease.
The CGEMS project is coordinated by the Office of Cancer Genomics (OCG), Division of Cancer Epidemiology and Genetics (DCEG), and the Core Genotyping Facility (CGF). Initial analysis of the data will be performed by CGF. All data to be made public will be delivered to NCICB. NCICB is responsible for long-term storage and presentation of the data through a publicly-accessible portal. This will consist of:
(a) a caBlG object API to the data,
(b) a web interface |