Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
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, 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.
- Authors:
-
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Prokaryotic Super Program
- King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1482516
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 45; Journal Issue: D1; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING
Citation Formats
Mukherjee, Supratim, Stamatis, Dimitri, Bertsch, Jon, Ovchinnikova, Galina, Verezemska, Olena, Isbandi, Michelle, Thomas, Alex D., Ali, Rida, Sharma, Kaushal, Kyrpides, Nikos C., and Reddy, T. B. K. Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. United States: N. p., 2016.
Web. doi:10.1093/nar/gkw992.
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. Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. United States. https://doi.org/10.1093/nar/gkw992
Mukherjee, Supratim, Stamatis, Dimitri, Bertsch, Jon, Ovchinnikova, Galina, Verezemska, Olena, Isbandi, Michelle, Thomas, Alex D., Ali, Rida, Sharma, Kaushal, Kyrpides, Nikos C., and Reddy, T. B. K. 2016.
"Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements". United States. https://doi.org/10.1093/nar/gkw992. https://www.osti.gov/servlets/purl/1482516.
@article{osti_1482516,
title = {Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements},
author = {Mukherjee, Supratim and Stamatis, Dimitri and Bertsch, Jon and Ovchinnikova, Galina and Verezemska, Olena and Isbandi, Michelle and Thomas, Alex D. and Ali, Rida and Sharma, Kaushal and Kyrpides, Nikos C. and Reddy, T. B. K.},
abstractNote = {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.},
doi = {10.1093/nar/gkw992},
url = {https://www.osti.gov/biblio/1482516},
journal = {Nucleic Acids Research},
issn = {0305-1048},
number = D1,
volume = 45,
place = {United States},
year = {Thu Oct 27 00:00:00 EDT 2016},
month = {Thu Oct 27 00:00:00 EDT 2016}
}
Web of Science
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- Mathema, Vivek Bhakta; Dondorp, Arjen M.; Imwong, Mallika
- Evolutionary Bioinformatics, Vol. 15
SamPler – a novel method for selecting parameters for gene functional annotation routines
journal, September 2019
- Cruz, Fernando; Lagoa, Davide; Mendes, João
- BMC Bioinformatics, Vol. 20, Issue 1
Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have
journal, January 2019
- Aslam, Sidra; Lan, Xin-Ran; Zhang, Bo-Wen
- BMC Evolutionary Biology, Vol. 19, Issue 1
bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
journal, February 2019
- DeMaere, Matthew Z.; Darling, Aaron E.
- Genome Biology, Vol. 20, Issue 1
Diversity, evolution, and classification of virophages uncovered through global metagenomics
journal, December 2019
- Paez-Espino, David; Zhou, Jinglie; Roux, Simon
- Microbiome, Vol. 7, Issue 1
metaSNV: A tool for metagenomic strain level analysis
journal, July 2017
- Costea, Paul Igor; Munch, Robin; Coelho, Luis Pedro
- PLOS ONE, Vol. 12, Issue 7
A family of silicon transporter structural genes in a pennate diatom Synedra ulna subsp. danica (Kütz.) Skabitsch
journal, August 2018
- Marchenkov, Artyom M.; Petrova, Darya P.; Morozov, Alexey A.
- PLOS ONE, Vol. 13, Issue 8
Access to Marine Genetic Resources (MGR): Raising Awareness of Best-Practice Through a New Agreement for Biodiversity Beyond National Jurisdiction (BBNJ)
journal, September 2019
- Rabone, Muriel; Harden-Davies, Harriet; Collins, Jane Eva
- Frontiers in Marine Science, Vol. 6
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
journal, April 2017
- Waite, David W.; Vanwonterghem, Inka; Rinke, Christian
- Frontiers in Microbiology, Vol. 8
Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae
journal, December 2017
- Montero-Calasanz, Maria del Carmen; Meier-Kolthoff, Jan P.; Zhang, Dao-Feng
- Frontiers in Microbiology, Vol. 8
Distributions of Extracellular Peptidases Across Prokaryotic Genomes Reflect Phylogeny and Habitat
journal, March 2019
- Nguyen, Trang T. H.; Myrold, David D.; Mueller, Ryan S.
- Frontiers in Microbiology, Vol. 10
Integrating 16S rRNA Sequencing and LC–MS-Based Metabolomics to Evaluate the Effects of Live Yeast on Rumen Function in Beef Cattle
journal, January 2019
- Ogunade, Ibukun; Schweickart, Hank; McCoun, Megan
- Animals, Vol. 9, Issue 1
A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog
journal, January 2017
- Montero-Mendieta, Santiago; Grabherr, Manfred; Lantz, Henrik
- PeerJ, Vol. 5
Genomes OnLine database (GOLD) v.7: updates and new features
journal, October 2018
- Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon
- Nucleic Acids Research, Vol. 47, Issue D1
A global survey of arsenic-related genes in soil microbiomes
journal, May 2019
- Dunivin, Taylor K.; Yeh, Susanna Y.; Shade, Ashley
- BMC Biology, Vol. 17, Issue 1
Towards a balanced view of the bacterial tree of life
journal, October 2017
- Schulz, Frederik; Eloe-Fadrosh, Emiley A.; Bowers, Robert M.
- Microbiome, Vol. 5, Issue 1
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes
journal, July 2020
- Moi, David; Kilchoer, Laurent; Aguilar, Pablo S.
- PLOS Computational Biology, Vol. 16, Issue 7
Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae.
text, January 2019
- Cooper, Matthew B.; Kazamia, Elena; Helliwell, Katherine E.
- Apollo - University of Cambridge Repository
Comparative genomics of Czech vaccine strains of Bordetella pertussis.
text, January 2018
- Dienstbier, Ana; Pouchnik, Derek; Wildung, Mark
- Apollo - University of Cambridge Repository
metaSNV: A tool for metagenomic strain level analysis
text, January 2017
- Costea, Paul I.; Munch, Robin; Coelho, Luis P.
- ETH Zurich
Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats
journal, June 2018
- Moon, Christina D.; Young, Wayne; Maclean, Paul H.
- MicrobiologyOpen, Vol. 7, Issue 5
GSA and BIGD: Filling the Gap of Bioinformatics Resource and Service in China *
journal, February 2017
- Luo, Jingchu
- Genomics, Proteomics & Bioinformatics, Vol. 15, Issue 1
On monospecific genera in prokaryotic taxonomy
journal, September 2017
- Zuo, Guanghong; Hao, Bailin
- Synthetic and Systems Biotechnology, Vol. 2, Issue 3
Infant airway microbiota and topical immune perturbations in the origins of childhood asthma
journal, November 2019
- Thorsen, Jonathan; Rasmussen, Morten A.; Waage, Johannes
- Nature Communications, Vol. 10, Issue 1
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes
journal, July 2019
- Roux, Simon; Krupovic, Mart; Daly, Rebecca A.
- Nature Microbiology
Investigation of recombination-intense viral groups and their genes in the Earth’s virome
journal, July 2018
- Meier-Kolthoff, Jan P.; Uchiyama, Jumpei; Yahara, Hiroko
- Scientific Reports, Vol. 8, Issue 1
From sequencing data to gene functions: co-functional network approaches
journal, January 2017
- Shim, Jung Eun; Lee, Tak; Lee, Insuk
- Animal Cells and Systems, Vol. 21, Issue 2
MPD: a pathogen genome and metagenome database
journal, January 2018
- Zhang, Tingting; Miao, Jiaojiao; Han, Na
- Database, Vol. 2018
Bipartite Network Analysis of Gene Sharings in the Microbial World
journal, January 2018
- Corel, Eduardo; Méheust, Raphaël; Watson, Andrew K.
- Molecular Biology and Evolution, Vol. 35, Issue 4
The MAR databases: development and implementation of databases specific for marine metagenomics
journal, November 2017
- Klemetsen, Terje; Raknes, Inge A.; Fu, Juan
- Nucleic Acids Research, Vol. 46, Issue D1
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes
journal, November 2018
- Paez-Espino, David; Roux, Simon; Chen, I-Min A.
- Nucleic Acids Research, Vol. 47, Issue D1
CSAR-web: a web server of contig scaffolding using algebraic rearrangements
journal, May 2018
- Chen, Kun-Tze; Lu, Chin Lung
- Nucleic Acids Research, Vol. 46, Issue W1
Genomes OnLine database (GOLD) v.7: updates and new features
journal, October 2018
- Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon
- Nucleic Acids Research, Vol. 47, Issue D1
Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments
journal, February 2017
- Munoz, Samuel L. Diaz
- Virus Evolution
A Robust Framework for Microbial Archaeology
journal, August 2017
- Warinner, Christina; Herbig, Alexander; Mann, Allison
- Annual Review of Genomics and Human Genetics, Vol. 18, Issue 1
Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have
journal, January 2019
- Aslam, Sidra; Lan, Xin-Ran; Zhang, Bo-Wen
- BMC Evolutionary Biology, Vol. 19, Issue 1
bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
journal, February 2019
- DeMaere, Matthew Z.; Darling, Aaron E.
- Genome Biology, Vol. 20, Issue 1
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
journal, February 2020
- Adeyemi, James A.; Peters, Sunday O.; De Donato, Marcos
- Journal of Animal Science and Biotechnology, Vol. 11, Issue 1
Correction to: Towards a balanced view of the bacterial tree of life
journal, November 2017
- Schulz, Frederik; Eloe-Fadrosh, Emiley A.; Bowers, Robert M.
- Microbiome, Vol. 5, Issue 1
Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica
journal, October 2017
- Choi, Dong Han; Jang, Gwang II; Lapidus, Alla
- Standards in Genomic Sciences, Vol. 12, Issue 1
Cyberbiosecurity Challenges of Pathogen Genome Databases
journal, May 2019
- Vinatzer, Boris A.; Heath, Lenwood S.; Almohri, Hussain M. J.
- Frontiers in Bioengineering and Biotechnology, Vol. 7
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
journal, April 2017
- Waite, David W.; Vanwonterghem, Inka; Rinke, Christian
- Frontiers in Microbiology, Vol. 8
Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae
journal, December 2017
- Montero-Calasanz, Maria del Carmen; Meier-Kolthoff, Jan P.; Zhang, Dao-Feng
- Frontiers in Microbiology, Vol. 8
A Genomic Outlook on Bioremediation: The Case of Arsenic Removal
journal, April 2018
- Plewniak, Frédéric; Crognale, Simona; Rossetti, Simona
- Frontiers in Microbiology, Vol. 9
Distributions of Extracellular Peptidases Across Prokaryotic Genomes Reflect Phylogeny and Habitat
journal, March 2019
- Nguyen, Trang T. H.; Myrold, David D.; Mueller, Ryan S.
- Frontiers in Microbiology, Vol. 10
Integrating 16S rRNA Sequencing and LC–MS-Based Metabolomics to Evaluate the Effects of Live Yeast on Rumen Function in Beef Cattle
journal, January 2019
- Ogunade, Ibukun; Schweickart, Hank; McCoun, Megan
- Animals, Vol. 9, Issue 1
Insights into Xylan Degradation and Haloalkaline Adaptation through Whole-Genome Analysis of Alkalitalea saponilacus, an Anaerobic Haloalkaliphilic Bacterium Capable of Secreting Novel Halostable Xylanase
journal, December 2018
- Liao, Ziya; Holtzapple, Mark; Yan, Yanchun
- Genes, Vol. 10, Issue 1
metaSNV: A tool for metagenomic strain level analysis
text, January 2017
- Costea, Paul I.; Munch, Robin; Coelho, Luis P.
- ETH Zurich