Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon; Ovchinnikova, Galina; Verezemska, Olena; Isbandi, Michelle; Thomas, Alex D.; Ali, Rida; Sharma, Kaushal; Kyrpides, Nikos C.; Reddy, T.  B.  K.

doi:10.1093/nar/gkw992

Title: Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

Journal Article · Thu Oct 27 00:00:00 EDT 2016 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkw992· OSTI ID:1482516

Mukherjee, Supratim ^[1]; Stamatis, Dimitri ^[1]; Bertsch, Jon ^[1]; Ovchinnikova, Galina ^[1]; Verezemska, Olena ^[1]; Isbandi, Michelle ^[1]; Thomas, Alex D. ^[1]; Ali, Rida ^[1]; Sharma, Kaushal ^[1]; Kyrpides, Nikos C. ^[2]; Reddy, T. B. K. ^[1]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Prokaryotic Super Program
King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences

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, singlecell 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. Here, this paper describes the data updates and additional features added during the last two years.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1482516

Journal Information:: Nucleic Acids Research, Vol. 45, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 111 works

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MPD: a pathogen genome and metagenome database Zhang, Tingting; Miao, Jiaojiao; Han, Na Database, Vol. 2018 https://doi.org/10.1093/database/bay055	journal	January 2018
The MAR databases: development and implementation of databases specific for marine metagenomics Klemetsen, Terje; Raknes, Inge A.; Fu, Juan Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1036	journal	November 2017
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes Paez-Espino, David; Roux, Simon; Chen, I-Min A. Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1127	journal	November 2018
CSAR-web: a web server of contig scaffolding using algebraic rearrangements Chen, Kun-Tze; Lu, Chin Lung Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky337	journal	May 2018
Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments Munoz, Samuel L. Diaz Virus Evolution https://doi.org/10.1101/038877	journal	February 2017
A Robust Framework for Microbial Archaeology Warinner, Christina; Herbig, Alexander; Mann, Allison Annual Review of Genomics and Human Genetics, Vol. 18, Issue 1 https://doi.org/10.1146/annurev-genom-091416-035526	journal	August 2017
Effects of a blend of Saccharomyces cerevisiae-based direct-fed microbial and fermentation products on plasma carbonyl-metabolome and fecal bacterial community of beef steers Adeyemi, James A.; Peters, Sunday O.; De Donato, Marcos Journal of Animal Science and Biotechnology, Vol. 11, Issue 1 https://doi.org/10.1186/s40104-019-0419-5	journal	February 2020
Correction to: Towards a balanced view of the bacterial tree of life Schulz, Frederik; Eloe-Fadrosh, Emiley A.; Bowers, Robert M. Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0367-2	journal	November 2017
Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica Choi, Dong Han; Jang, Gwang II; Lapidus, Alla Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0275-x	journal	October 2017
Cyberbiosecurity Challenges of Pathogen Genome Databases Vinatzer, Boris A.; Heath, Lenwood S.; Almohri, Hussain M. J. Frontiers in Bioengineering and Biotechnology, Vol. 7 https://doi.org/10.3389/fbioe.2019.00106	journal	May 2019
A Genomic Outlook on Bioremediation: The Case of Arsenic Removal Plewniak, Frédéric; Crognale, Simona; Rossetti, Simona Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00820	journal	April 2018
Insights into Xylan Degradation and Haloalkaline Adaptation through Whole-Genome Analysis of Alkalitalea saponilacus, an Anaerobic Haloalkaliphilic Bacterium Capable of Secreting Novel Halostable Xylanase Liao, Ziya; Holtzapple, Mark; Yan, Yanchun Genes, Vol. 10, Issue 1 https://doi.org/10.3390/genes10010001	journal	December 2018

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