Database Commons a catalog of biological databases

Database Commons - CGHub

CGHub

Citations: 26

z-index 1.24

Short name CGHub
Full name Cancer Genomics Hub
Description The Cancer Genomics Hub (CGHub) is a secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects.
URL https://cghub.ucsc.edu/
Year founded 2014
Last update & version NA    v1.0
Availability Free to all users
University/Institution hosted University of California Santa Cruz
Address Santa Cruz,CA, USA
City Santa Cruz
Province/State CA
Country/Region United States
Contact name Christopher Wilks
Contact email cwilks@soe.ucsc.edu
Data type(s)
Major organism(s)
Keyword(s)
  • cancer genomics
Publication(s)
  • The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. [PMID: 25267794]

    Christopher Wilks, Melissa S Cline, Erich Weiler, Mark Diehkans, Brian Craft, Christy Martin, Daniel Murphy, Howdy Pierce, John Black, Donavan Nelson, Brian Litzinger, Thomas Hatton, Lori Maltbie, Michael Ainsworth, Patrick Allen, Linda Rosewood, Elizabeth Mitchell, Bradley Smith, Jim Warner, John Groboske, Haifang Telc, Daniel Wilson, Brian Sanford, Hannes Schmidt, David Haussler, Daniel Maltbie
    Database : the journal of biological databases and curation 2014:2014
    26 Citations (Google Scholar as of 2016-03-02)

    Abstract: The Cancer Genomics Hub (CGHub) is the online repository of the sequencing programs of the National Cancer Institute (NCI), including The Cancer Genomics Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects, with data from 25 different types of cancer. The CGHub currently contains >1.4?PB of data, has grown at an average rate of 50?TB a month and serves >100?TB per week. The architecture of CGHub is designed to support bulk searching and downloading through a Web-accessible application programming interface, enforce patient genome confidentiality in data storage and transmission and optimize for efficiency in access and transfer. In this article, we describe the design of these three components, present performance results for our transfer protocol, GeneTorrent, and finally report on the growth of the system in terms of data stored and transferred, including estimated limits on the current architecture. Our experienced-based estimates suggest that centralizing storage and computational resources is more efficient than wide distribution across many satellite labs. Database URL: https://cghub.ucsc.edu. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

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Tags

Disease Metadata Standard, Ontology and Nomenclature
Homo sapiens
cancer genomics

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Mengwei Li [2016-04-12]
    • Mengwei Li [2015-12-02]
    • Mengwei Li [2015-06-27]
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