Abstract
The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal.Database URL: http://dcc.icgc.org
Highlights
One of the major goals of International Cancer Genome Consortium (ICGC) is to rapidly bring these data to the cancer research community in order to accelerate studies on the discovery of cancer causes, to enhance the accuracy of diagnoses and to improve treatments
The scalability of the system is improved by having each member institution store and process data locally; the data federation software presents these separate sources as a single access point for remote data access
In order to link individual BioMart databases into a unified system, each of the ICGC member institutions maintains an instance of the BioMart server
Summary
International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data. The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and search and analyze the available data.
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