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 · 27 October 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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PATRIC, the bacterial bioinformatics database and analysis resource Wattam, Alice R.; Abraham, David; Dalay, Oral Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1099	journal	November 2013
MycoCosm portal: gearing up for 1000 fungal genomes Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1183	journal	December 2013
IMG/M 4 version of the integrated metagenome comparative analysis system Markowitz, Victor M.; Chen, I-Min A.; Chu, Ken Nucleic Acids Research, Vol. 42, Issue D1, p. D568-D573 https://doi.org/10.1093/nar/gkt919	journal	October 2013
IMG 4 version of the integrated microbial genomes comparative analysis system Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt963	journal	October 2013
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A Catalog of Reference Genomes from the Human Microbiome Nelson, K. E.; Weinstock, G. M.; Highlander, S. K. Science, Vol. 328, Issue 5981 https://doi.org/10.1126/science.1183605	journal	May 2010
Metazen – metadata capture for metagenomes Bischof, Jared; Harrison, Travis; Paczian, Tobias Standards in Genomic Sciences, Vol. 9, Issue 1 https://doi.org/10.1186/1944-3277-9-18	journal	January 2014
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos Standards in Genomic Sciences, Vol. 10, Issue 1 https://doi.org/10.1186/s40793-015-0077-y	journal	October 2015
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0138-x	journal	February 2016
Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A. PLoS Biology, Vol. 12, Issue 8 https://doi.org/10.1371/journal.pbio.1001920	journal	August 2014
ProDeGe: a computational protocol for fully automated decontamination of genomes James, Han,; L., Dangl, Jeff; Scott, Clingenpeel, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/xvw7-9p10	text	January 2016
The State of Standards in Genomic Sciences Garrity, George M. Standards in Genomic Sciences, Vol. 5, Issue 3 https://doi.org/10.4056/sigs.2515706	journal	December 2011
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A. Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.5068949	journal	December 2013
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants Stolze, Yvonne; Bremges, Andreas; Rumming, Madis Figshare https://doi.org/10.6084/m9.figshare.c.3635852	collection	January 2016

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Emergence and features of the multipartite genome structure of the family Burkholderiaceae revealed through comparative and evolutionary genomics diCenzo, George C.; Mengoni, Alessio; Perrin, Elena https://doi.org/10.1101/382267	posted_content	August 2018
bin3C : Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes (MAGs) DeMaere, Matthew Z.; Darling, Aaron E. https://doi.org/10.1101/388355	posted_content	August 2018
Untapped viral diversity in global soil metagenomes Graham, Emily B.; Paez-Espino, David; Brislawn, Colin BioRxiv https://doi.org/10.1101/583997	posted_content	January 2019
Tracking microbial evolution in the human gut using Hi-C Yaffe, Eitan; Relman, David A. Nature Microbiology https://doi.org/10.1101/594903	journal	March 2019
Alpha- and beta-mannan utilization by marine Bacteroidetes: Marine mannan utilization Chen, Jing; Robb, Craig S.; Unfried, Frank Environmental Microbiology, Vol. 20, Issue 11 https://doi.org/10.1111/1462-2920.14414	journal	October 2018
Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations Fuentes-Pardo, Angela P.; Ruzzante, Daniel E. Molecular Ecology, Vol. 26, Issue 20 https://doi.org/10.1111/mec.14264	journal	September 2017
Genome Plasticity of agr -Defective Staphylococcus aureus during Clinical Infection Altman, Deena R.; Sullivan, Mitchell J.; Chacko, Kieran I. Infection and Immunity, Vol. 86, Issue 10 https://doi.org/10.1128/iai.00331-18	journal	July 2018
Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation Silveira, Melise Chaves; Azevedo da Silva, Rangeline; Faria da Mota, Fábio Evolutionary Bioinformatics, Vol. 14 https://doi.org/10.1177/1176934318797351	journal	January 2018
OSTRFPD: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer Mathema, Vivek Bhakta; Dondorp, Arjen M.; Imwong, Mallika Evolutionary Bioinformatics, Vol. 15 https://doi.org/10.1177/1176934319843130	journal	January 2019
SamPler – a novel method for selecting parameters for gene functional annotation routines Cruz, Fernando; Lagoa, Davide; Mendes, João BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-3038-4	journal	September 2019
Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have Aslam, Sidra; Lan, Xin-Ran; Zhang, Bo-Wen BMC Evolutionary Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s12862-019-1365-8	journal	January 2019
bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes DeMaere, Matthew Z.; Darling, Aaron E. Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1643-1	journal	February 2019
Diversity, evolution, and classification of virophages uncovered through global metagenomics Paez-Espino, David; Zhou, Jinglie; Roux, Simon Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0768-5	journal	December 2019
metaSNV: A tool for metagenomic strain level analysis Costea, Paul Igor; Munch, Robin; Coelho, Luis Pedro PLOS ONE, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pone.0182392	journal	July 2017
A family of silicon transporter structural genes in a pennate diatom Synedra ulna subsp. danica (Kütz.) Skabitsch Marchenkov, Artyom M.; Petrova, Darya P.; Morozov, Alexey A. PLOS ONE, Vol. 13, Issue 8 https://doi.org/10.1371/journal.pone.0203161	journal	August 2018
Access to Marine Genetic Resources (MGR): Raising Awareness of Best-Practice Through a New Agreement for Biodiversity Beyond National Jurisdiction (BBNJ) Rabone, Muriel; Harden-Davies, Harriet; Collins, Jane Eva Frontiers in Marine Science, Vol. 6 https://doi.org/10.3389/fmars.2019.00520	journal	September 2019
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.) Waite, David W.; Vanwonterghem, Inka; Rinke, Christian Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00682	journal	April 2017
Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae Montero-Calasanz, Maria del Carmen; Meier-Kolthoff, Jan P.; Zhang, Dao-Feng Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02501	journal	December 2017
Distributions of Extracellular Peptidases Across Prokaryotic Genomes Reflect Phylogeny and Habitat Nguyen, Trang T. H.; Myrold, David D.; Mueller, Ryan S. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00413	journal	March 2019
Integrating 16S rRNA Sequencing and LC–MS-Based Metabolomics to Evaluate the Effects of Live Yeast on Rumen Function in Beef Cattle Ogunade, Ibukun; Schweickart, Hank; McCoun, Megan Animals, Vol. 9, Issue 1 https://doi.org/10.3390/ani9010028	journal	January 2019
A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog Montero-Mendieta, Santiago; Grabherr, Manfred; Lantz, Henrik PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3702	journal	January 2017
Genomes OnLine database (GOLD) v.7: updates and new features Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky977	journal	October 2018
A global survey of arsenic-related genes in soil microbiomes Dunivin, Taylor K.; Yeh, Susanna Y.; Shade, Ashley BMC Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s12915-019-0661-5	journal	May 2019
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/s40168-017-0360-9	journal	October 2017
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes Moi, David; Kilchoer, Laurent; Aguilar, Pablo S. PLOS Computational Biology, Vol. 16, Issue 7 https://doi.org/10.1371/journal.pcbi.1007553	journal	July 2020
Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae. Cooper, Matthew B.; Kazamia, Elena; Helliwell, Katherine E. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.28008	text	January 2019
Comparative genomics of Czech vaccine strains of Bordetella pertussis. Dienstbier, Ana; Pouchnik, Derek; Wildung, Mark Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.43799	text	January 2018
metaSNV: A tool for metagenomic strain level analysis Costea, Paul I.; Munch, Robin; Coelho, Luis P. ETH Zurich https://doi.org/10.3929/ethz-b-000191622	text	January 2017
Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats Moon, Christina D.; Young, Wayne; Maclean, Paul H. MicrobiologyOpen, Vol. 7, Issue 5 https://doi.org/10.1002/mbo3.677	journal	June 2018
GSA and BIGD: Filling the Gap of Bioinformatics Resource and Service in China * Luo, Jingchu Genomics, Proteomics & Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1016/j.gpb.2017.02.001	journal	February 2017
On monospecific genera in prokaryotic taxonomy Zuo, Guanghong; Hao, Bailin Synthetic and Systems Biotechnology, Vol. 2, Issue 3 https://doi.org/10.1016/j.synbio.2017.08.004	journal	September 2017
Infant airway microbiota and topical immune perturbations in the origins of childhood asthma Thorsen, Jonathan; Rasmussen, Morten A.; Waage, Johannes Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12989-7	journal	November 2019
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes Roux, Simon; Krupovic, Mart; Daly, Rebecca A. Nature Microbiology https://doi.org/10.1038/s41564-019-0510-x	journal	July 2019
Investigation of recombination-intense viral groups and their genes in the Earth’s virome Meier-Kolthoff, Jan P.; Uchiyama, Jumpei; Yahara, Hiroko Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-29272-2	journal	July 2018
From sequencing data to gene functions: co-functional network approaches Shim, Jung Eun; Lee, Tak; Lee, Insuk Animal Cells and Systems, Vol. 21, Issue 2 https://doi.org/10.1080/19768354.2017.1284156	journal	January 2017
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
Bipartite Network Analysis of Gene Sharings in the Microbial World Corel, Eduardo; Méheust, Raphaël; Watson, Andrew K. Molecular Biology and Evolution, Vol. 35, Issue 4 https://doi.org/10.1093/molbev/msy001	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
Genomes OnLine database (GOLD) v.7: updates and new features Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky977	journal	October 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
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes Alneberg, Johannes; Karlsson, Christofer M. G.; Divne, Anna-Maria https://doi.org/10.1101/219295	posted_content	November 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
Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have Aslam, Sidra; Lan, Xin-Ran; Zhang, Bo-Wen BMC Evolutionary Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s12862-019-1365-8	journal	January 2019
bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes DeMaere, Matthew Z.; Darling, Aaron E. Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1643-1	journal	February 2019
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
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.) Waite, David W.; Vanwonterghem, Inka; Rinke, Christian Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00682	journal	April 2017
Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae Montero-Calasanz, Maria del Carmen; Meier-Kolthoff, Jan P.; Zhang, Dao-Feng Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02501	journal	December 2017
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
Distributions of Extracellular Peptidases Across Prokaryotic Genomes Reflect Phylogeny and Habitat Nguyen, Trang T. H.; Myrold, David D.; Mueller, Ryan S. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00413	journal	March 2019
Integrating 16S rRNA Sequencing and LC–MS-Based Metabolomics to Evaluate the Effects of Live Yeast on Rumen Function in Beef Cattle Ogunade, Ibukun; Schweickart, Hank; McCoun, Megan Animals, Vol. 9, Issue 1 https://doi.org/10.3390/ani9010028	journal	January 2019
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
metaSNV: A tool for metagenomic strain level analysis Costea, Paul I.; Munch, Robin; Coelho, Luis P. ETH Zurich https://doi.org/10.3929/ethz-b-000191622	text	January 2017

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