The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

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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/

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The minimum information about a genome sequence (MIGS) specification.

Dawn Field, George Garrity, Tanya Gray … (2008)

With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

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GenBank

Dennis A Benson, Ilene Karsch-Mizrachi, David Lipman … (2006)

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage ().

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The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis … (2008)

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/

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Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (iso-abbrev): Nucleic Acids Res

Journal ID (publisher-id): nar

Journal ID (hwp): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date (Print): January 2010

Publication date (Electronic): 13 November 2009

Publication date PMC-release: 13 November 2009

Volume: 38

Issue: Database issue , Database issue

Pages: D346-D354

Affiliations

¹Genome Biology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, ²Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA, ³Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece and ⁴Microbial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, USA

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*To whom correspondence should be addressed. Tel: +1 925 296 5718; Fax: +1 925 296 5850; Email: nckyrpides@ 123456lbl.gov

Article

Publisher ID: gkp848

DOI: 10.1093/nar/gkp848

PMC ID: 2808860

PubMed ID: 19914934

SO-VID: 1d14cc87-4743-457c-9c08-f16efbc4b685

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This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

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Most cited references 16

The minimum information about a genome sequence (MIGS) specification.

GenBank

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

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