The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

By T. Reddy, Alex D. Thomas, Dimitrios Stamatis, J. Bertsch, Michelle Isbandi, Jakob Jansson, Jyothi K. Mallajosyula, I. Pagani, E. Lobos, Nikos Kyrpides. Nucleic Acids Res., 2014

338 citations recorded by the source corpus.

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/298decd07895b3d3775157949bdbdad926c8a192

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Citations in the corpus

IMG/M: integrated genome and metagenome comparative data analysis system (2016, background): “5 supports more extensive metadata definition and better provenance for output of complex analysis pipelines, such as combined assembly of metagenomes and single cell genomes or genomes extracted from metagenomes (3).”
Genomes OnLine Database (GOLD) v.8: overview and updates (2020, background): “Now in its eighth release since its first publication (6) followed by regular updates (7–9), GOLD has been instrumental in providing a rich and reliable resource of meta-data that is widely used by the genomics community.”
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data (2017, methodology): “The 105 strain sets were obtained mainly from the Genomes Online Database (GOLD) database (29) and the Pathosystems Resource Integration Center (PATRIC) (30), organized primarily based on their phenotypic traits.”
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming (2018, methodology): “Chimeric sequences were screened using UCHIME [80] against the GOLD database [81] and removed.”
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) (2015, methodology): “In addition, each sequence dataset submitted for annotation needs to be associated with an analysis project that has already been specified in the Genomes OnLine Database [2].”
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis (2016, background): “The availability of thousands of sequenced genomes (12), thanks to next-generation sequencing techniques, enables the application of much finer-scale statistical modeling approaches, which take into account the full sequence (13).”
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database (2015, methodology): “Due to the sparse amount of information on some isolates, we also manually curate metadata using the Minimum Information about any (X) Sequence (MIxS) specification developed by the Genomic Standards Consortium (43) and used by the Genomes Online database (44) as a guide.”
MeDuSa: a multi-draft based scaffolder (2015, background): “This latter point is of great importance in practice since, in current public databases, the availability of draft genomes greatly exceeds that of completely sequenced ones (Reddy et al., 2014).”
Uncovering Earth’s virome (2016, methodology): “These include: (1) alkyl hydroperoxide reductase system in Dehalogenimonas lykanthroporepellens, Desulfococcus biacutus and Geobacter sulfurreducens, (2) efflux ABC transporter in Desulfoarculus baarsii and Desulfobacterium anilini, (3) possible secondary metabolite biosynthesis genes in Desulfovibr”