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Database information

GOLD (Genomes On Line Database)

General information

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.
Year founded: 2006
Last update: 2017-01-11
Version: v6
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Joint Genome Institute
Address: 2800 Mitchell Drive
City: Walnut Creek
Province/State: CA
Country/Region: United States
Contact name (PI/Team): T. B. K. Reddy
Contact email (PI/Helpdesk): tbreddy@lbl.gov

Record metadata

Created on: 2015-06-20
Curated by:
Dong Zou [2019-01-04]
Rabail Raza [2018-12-26]
huma shireen [2018-08-28]
Shixiang Sun [2017-02-16]
Lina Ma [2016-08-16]
Lin Liu [2016-03-29]
Lin Liu [2016-03-26]
Jian SA [2015-12-05]
Jian SA [2015-06-28]

Ranking

All databases:
133/4692 (97.187%)
Metadata:
8/445 (98.427%)
133
Total Rank
1,242
Citations
65.368
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Word cloud

Publications

30357420
Genomes OnLine database (GOLD) v.7: updates and new features. [PMID: 30357420]
Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Katta HY, Mojica A, Chen IA, Kyrpides NC, Reddy T.

The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project. Currently GOLD hosts information on 33 415 Studies, 49 826 Biosamples, 313 324 Organisms, 215 881 Sequencing Projects and 174 454 Analysis Projects with a total of 541 metadata fields, of which 80 are based on controlled vocabulary (CV) terms. GOLD provides a user-friendly web interface to browse sequencing projects and launch advanced search tools across four classification levels. Users submit metadata on a wide range of Sequencing and Analysis Projects in GOLD before depositing sequence data to the Integrated Microbial Genomes (IMG) system for analysis. GOLD conforms with and supports the rules set by the Genomic Standards Consortium (GSC) Minimum Information standards. The current version of GOLD (v.7) has seen the number of projects and associated metadata increase exponentially over the years. This paper provides an update on the current status of GOLD and highlights the new features added over the last two years.

Nucleic Acids Res. 2019:47(D1) | 17 Citations (from Europe PMC, 2020-09-12)
27794040
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. [PMID: 27794040]
Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Verezemska O, Isbandi M, Thomas AD, Ali R, Sharma K, Kyrpides NC, Reddy TB.

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.

Nucleic Acids Res. 2017:45(D1) | 68 Citations (from Europe PMC, 2020-09-19)
25348402
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. [PMID: 25348402]
Reddy TB, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC.

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.

Nucleic Acids Res. 2015:43(Database issue) | 142 Citations (from Europe PMC, 2020-09-19)
22135293
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. [PMID: 22135293]
Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC.

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.

Nucleic Acids Res. 2012:40(Database issue) | 264 Citations (from Europe PMC, 2020-09-19)
19914934
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. [PMID: 19914934]
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC.

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/

Nucleic Acids Res. 2010:38(Database issue) | 278 Citations (from Europe PMC, 2020-09-19)
17981842
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. [PMID: 17981842]
Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC.

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/

Nucleic Acids Res. 2008:36(Database issue) | 221 Citations (from Europe PMC, 2020-09-19)
16381880
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. [PMID: 16381880]
Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC.

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/

Nucleic Acids Res. 2006:34(Database issue) | 117 Citations (from Europe PMC, 2020-09-19)
11125068
Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. [PMID: 11125068]
Bernal A, Ear U, Kyrpides N.

GOLD is a comprehensive resource for accessing information related to completed and ongoing genome projects world-wide. The database currently provides information on 350 genome projects, of which 48 have been completely sequenced and their analysis published. GOLD was created in 1997 and since April 2000 it has been licensed to Integrated Genomics. The database is freely available through the URL: http://igweb.integratedgenomics.com/GOLD/.

Nucleic Acids Res. 2001:29(1) | 135 Citations (from Europe PMC, 2020-09-12)