The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

By K. Liolios, I-Min A. Chen, Konstantinos Mavrommatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M. Markowitz, Nikos Kyrpides. 2007

912 citations recorded by the source corpus.

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/

Subfields: Genetics, Molecular Biology

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Citations in the corpus

Direct-coupling analysis of residue coevolution captures native contacts across many protein families (2011, methodology): “fill ! h ˜ i (q)=h ˜ j (q)=0. Note that the auxiliary fields have to be determined for each pair ! (i,j) independently to fit Eq. (12). Finally, we define the direct information DI as the MI of model (11), ! DI ij =P ij (dir)(A,B)ln AB " P ij (dir)(A,B) f i (A)f j (B) . (13) Algorithmic impleme”
Identification of direct residue contacts in protein–protein interaction by message passing (2009, methodology): “∑ [ 4 ] is calculated using the contribution Pij (dir) (Ai,Aj) of the direct coupling eij(Ai,Aj) between”
Clustering metagenomic sequences with interpolated Markov models (2010, background): “Over the last 15 years, DNA sequencing technologies have advanced rapidly, allowing sequencing of over one thousand microbial genomes [1].”
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison (2010, methodology): “This was done by reconciling the Genomes On Line Database [30] and the DSMZ database (http://www.dsmz.de/microorganisms/); and by (ii) International Journal of Systematic and Evolutionary Microbiology screening the (http://ijs.sgmjournals.org/) for articles containing DDH values of these strains.”
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata (2011, background): “Several other resources are collecting and presenting bio-molecular projects but all of them are limited in scope either by speciﬁc organism group [MicrobesOnline (9), IMG (10), GDR (11)] or by project type [GOLD (12)].”
Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. (2014, background): “Currently, the Genomes Online Database (Pagani et al. 2012; http://www.genomesonline.org/, July 2013) lists a total of 5159 whole genome or transcriptome sequencing projects almost 60% of which are in progress, clearly documenting the trend of more and more genomes being sequenced in the near future”
PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data (2013, methodology): “From January 2012, NCBI removed pathogenicity information from its pages, redirecting the users to Genomes Online Database (GOLD) [58].”