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Database Commons - GOLD

GOLD

Citations: 1646

z-index 26.06

Short name GOLD
Full name Genomes On Line Database
Description GOLD is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide.GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata.
URL https://gold.jgi.doe.gov/
Year founded 2006
Last update & version 2017-01-11    v6
Availability Free to all users
University/Institution hosted DOE Joint Genome Institute
Address 2800 Mitchell Drive
City Walnut Creek
Province/State CA
Country/Region United States
Contact name T. B. K. Reddy
Contact email tbreddy@lbl.gov
Data type(s)
Major organism(s)
Keyword(s)
  • metagenome
Publication(s)
  • Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. [PMID: 27794040]

    Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Olena Verezemska, Michelle Isbandi, Alex D Thomas, Rida Ali, Kaushal Sharma, Nikos C Kyrpides, T B K Reddy
    Nucleic acids research 2017:45(D1)
    1 Citations (Google Scholar as of 2017-02-16)

    Abstract: The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects. These are integrated with over 312 metadata fields from which 58 are controlled vocabularies with 2067 terms. The web interface facilitates submission of a diverse range of Sequencing Projects (such as isolate genome, single-cell genome, metagenome, metatranscriptome) and complex Analysis Projects (such as genome from metagenome, or combined assembly from multiple Sequencing Projects). GOLD provides a seamless interface with the Integrated Microbial Genomes (IMG) system and supports and promotes the Genomic Standards Consortium (GSC) Minimum Information standards. This paper describes the data updates and additional features added during the last two years. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  • The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. [PMID: 25348402]

    T B K Reddy, Alex D Thomas, Dimitri Stamatis, Jon Bertsch, Michelle Isbandi, Jakob Jansson, Jyothi Mallajosyula, Ioanna Pagani, Elizabeth A Lobos, Nikos C Kyrpides
    Nucleic acids research 2015:43(Database issue)
    179 Citations (Google Scholar as of 2017-02-16)

    Abstract: The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19,200 studies, 56,000 Biosamples, 56,000 sequencing projects and 39,400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  • The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. [PMID: 22135293]

    Ioanna Pagani, Konstantinos Liolios, Jakob Jansson, I-Min A Chen, Tatyana Smirnova, Bahador Nosrat, Victor M Markowitz, Nikos C Kyrpides
    Nucleic acids research 2012:40(Database issue)
    424 Citations (Google Scholar as of 2017-02-16)

    Abstract: The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2011, GOLD, now on version 4.0, contains information for 11,472 sequencing projects, of which 2907 have been completed and their sequence data has been deposited in a public repository. Out of these complete projects, 1918 are finished and 989 are permanent drafts. Moreover, GOLD contains information for 340 metagenome studies associated with 1927 metagenome samples. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about any (x) Sequence specification and beyond.

  • The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. [PMID: 19914934]

    Konstantinos Liolios, I-Min A Chen, Konstantinos Mavromatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M Markowitz, Nikos C Kyrpides
    Nucleic acids research 2010:38(Database issue)
    373 Citations (Google Scholar as of 2017-02-16)

    Abstract: The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification. GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/

  • The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. [PMID: 17981842]

    Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis, Nikos C Kyrpides
    Nucleic acids research 2008:36(Database issue)
    378 Citations (Google Scholar as of 2017-02-16)

    Abstract: The Genomes On Line Database (GOLD) is a comprehensive resource that provides information on genome and metagenome projects worldwide. Complete and ongoing projects and their associated metadata can be accessed in GOLD through pre-computed lists and a search page. As of September 2007, GOLD contains information on more than 2900 sequencing projects, out of which 639 have been completed and their sequence data deposited in the public databases. GOLD continues to expand with the goal of providing metadata information related to the projects and the organisms/environments towards the Minimum Information about a Genome Sequence' (MIGS) guideline. GOLD is available at http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/

  • The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. [PMID: 16381880]

    Konstantinos Liolios, Nektarios Tavernarakis, Philip Hugenholtz, Nikos C Kyrpides
    Nucleic acids research 2006:34(Database issue)
    291 Citations (Google Scholar as of 2017-02-16)

    Abstract: The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates information on over 1500 sequencing projects, of which 294 have been completed and the data deposited in the public databases. GOLD v.2 has been expanded to provide information related to organism properties such as phenotype, ecotype and disease. Furthermore, project relevance and availability information is now included. GOLD is available at http://www.genomesonline.org. It is also mirrored at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/

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Tags

DNA Metadata
Archaea Bacteria Eukaryota Virus
metagenome

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Shixiang Sun [2017-02-16]
    • Lina Ma [2016-08-16]
    • Lin Liu [2016-03-29]
    • Lin Liu [2016-03-26]
    • Jian Sang [2015-12-05]
    • Jian Sang [2015-06-28]
Stats