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      Genomes OnLine database (GOLD) v.7: updates and new features

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          Abstract

          The Genomes Online Database (GOLD) ( https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project. Currently GOLD hosts information on 33 415 Studies, 49 826 Biosamples, 313 324 Organisms, 215 881 Sequencing Projects and 174 454 Analysis Projects with a total of 541 metadata fields, of which 80 are based on controlled vocabulary (CV) terms. GOLD provides a user-friendly web interface to browse sequencing projects and launch advanced search tools across four classification levels. Users submit metadata on a wide range of Sequencing and Analysis Projects in GOLD before depositing sequence data to the Integrated Microbial Genomes (IMG) system for analysis. GOLD conforms with and supports the rules set by the Genomic Standards Consortium (GSC) Minimum Information standards. The current version of GOLD (v.7) has seen the number of projects and associated metadata increase exponentially over the years. This paper provides an update on the current status of GOLD and highlights the new features added over the last two years.

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          Earth BioGenome Project: Sequencing life for the future of life

          Erich D. Jarvis, Gene Robinson, Warren E Johnson … (2018)
          Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.
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            IMG/M: integrated genome and metagenome comparative data analysis system

            I-Min Chen, Victor Markowitz, Ken Chu … (2016)
            The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review (ER) companion system (IMG/M ER: https://img.jgi.doe.gov/mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.
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              International Code of Nomenclature of Prokaryotes.

              Charles Parker, Brian J Tindall, George Garrity (2015)
              This volume contains the edition of the International Code of Nomenclature of Prokaryotes that was presented in draft form and available for comment at the Plenary Session of the Fourteenth International Congress of Bacteriology and Applied Microbiology (BAM), Montréal, 2014, together with updated lists of conserved and rejected bacterial names and of Opinions issued by the Judicial Commission. As in the past it brings together those changes accepted, published and documented by the ICSP and the Judicial Commission since the last revision was published. Several new appendices have been added to this edition. Appendix 11 addresses the appropriate application of the Candidatus concept, Appendix 12 contains the history of the van Niel Prize, and Appendix 13 contains the summaries of Congresses.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 08 January 2019
                Publication date (Electronic): 24 October 2018
                Publication date PMC-release: 24 October 2018
                Volume: 47
                Issue: Database issue , Database issue
                Pages: D649-D659
                Affiliations
                Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
                Author notes
                To whom correspondence should be addressed. Tel: +1 925 296 5768; Fax: +1 925 296 5850; Email: tbreddy@ 123456lbl.gov . Correspondence may also be addressed to Nikos C. Kyrpides. Tel: +1 925 296 5718; Fax: +1 925 296 5666; Email: nckyrpides@ 123456lbl.gov
                Article
                Publisher ID: gky977
                DOI: 10.1093/nar/gky977
                PMC ID: 6323969
                PubMed ID: 30357420
                SO-VID: 89d6c99e-475f-4d04-869a-47d2e3549b1c
                Copyright © Published by Oxford University Press on behalf of Nucleic Acids Research 2018.
                License:

                This work is written by (a) US Government employee(s) and is in the public domain in the US.

                History
                Date accepted : 08 October 2018
                Date revision received : 04 October 2018
                Date received : 14 September 2018
                Page count
                Pages: 11
                Funding
                Funded by: Department of Energy Joint Genome Institute
                Award ID: DE-AC02-05CH11231
                Categories
                Subject: Database Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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