The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

By I. Pagani, K. Liolios, Jakob Jansson, I-Min A. Chen, Tatyana Smirnova, Bahador Nosrat, Victor M. Markowitz, Nikos Kyrpides. Nucleic Acids Res., 2011

442 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ceba907545035a894322204da31c59fd580e8e00

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Citations in the corpus

Insights from 20 years of bacterial genome sequencing (2015, methodology): “An urgent future task is the development new tools based on genome sequence analysis for future taxonomy classification (Chun and Rainey 2014; Ozen et al. 2012).”
METAGENassist: a comprehensive web server for comparative metagenomics (2012, methodology): “It is also updated regularly through information drawn from BACMAP (14), GOLD (15) and other NCBI microbial taxonomy resources (16).”
MycoCosm portal: gearing up for 1000 fungal genomes (2013, background): “Combined with other genome projects listed in the GOLD database (36) and other sources, they form a ‘master’ list of fungal genome sequencing projects worldwide (http://1.”
IMG/M 4 version of the integrated metagenome comparative analysis system (2013, methodology): “The GOLD metagenome classiﬁcation and metadata attributes are included into IMG/M where they are essential for selecting metagenome data sets for comparative analysis.”
OMA standalone: orthology inference among public and custom genomes and transcriptomes (2018, background): “The sequencing revolution is yielding a flood of genomes and transcriptomes, with thousands already sequenced and many more underway (Pagani et al., 2012) .”
PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data (2013, methodology): “On 26th Feb. 2012 we queried GOLD for pathogenicity information about organisms that had been published after 5th Nov. 2010 (the date of the latest published bacteria in the training-set).”
A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation (2014, background): “0) [1].”
Genome sequence-based species delimitation with confidence intervals and improved distance functions (2013, methodology): “[6], 31 from the GOLD database [25], and 63 from Richter et al.”
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, background): “With the number of publically available genomes currently doub-ling every 18 months [1], and genome quality improving with the arrival of new technologies, we set out to solve the problem of aligning thousands of closely-related whole genomes.”
GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis (2013, background): “Among bacteria, which are being sequenced faster than any other domain of life (4), a popular heuristic recipe for detecting orthologous sequences is simply looking for reciprocal BLAST hits (5, 6), and different software choices are available for this task (7).”
Genomics-aided structure prediction (2012, background): “This is becoming accessible for many bacterial proteins due to the large number of sequenced bacterial genomes (29), but so far only for few highly amplified eukaryotic proteins.”
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes (2013, methodology): “…3,171 genomes from IMG 3.5 as of February 2012; 566 additional genomes not contained in IMG 3.5 were downloaded from IMG-GEBA 31 as of March 2012, and the genomes of candidate division OP1 34 and Caldiserica 35 were retrieved from the GOLD database 59 (GOLD ids Gc02183 and Gi17125 respectively).”
IMG 4 version of the integrated microbial genomes comparative analysis system (2013, background): “Public and private genomes submitted for annotation and integration by IMG’s pipelines are ﬁrst associated with sequencing projects in GOLD.”
From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction (2012, unknown): “Thanks to the constant progresses in DNA sequencing techniques, by now more than 4,400 full genomes are sequenced [1], resulting in more than 3:6 10(7) known protein sequences [2], which are classified into more than 14,000 protein domain families [3], many of them containing in the range of 10(3){1”