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

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          Abstract

          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.

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          IMG 4 version of the integrated microbial genomes comparative analysis system

          Victor Markowitz, I-Min Chen, Krishna Palaniappan … (2013)
          The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).
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            The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

            Konstantinos Liolios, I-Min Chen, Konstantinos Mavromatis … (2010)
            The Genomes On Line Database (GOLD) 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 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. 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 a (Meta)Genome Sequence (MIGS/MIMS) specification. 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/
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              The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

              Ioanna Pagani, Konstantinos Liolios, Jakob Jansson … (2011)
              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.
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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 (hwp): nar
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 28 January 2015
                Publication date (Electronic): 27 October 2014
                Publication date PMC-release: 27 October 2014
                Volume: 43
                Issue: Database issue , Database issue
                Pages: D1099-D1106
                Affiliations
                [1 ]Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
                [2 ]Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
                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: +1 925 927 2580; Fax: +1 925 296 5666; Email: nckyrpides@ 123456lbl.gov
                Article
                DOI: 10.1093/nar/gku950
                PMC ID: 4384021
                PubMed ID: 25348402
                SO-VID: 9288823d-8327-4a54-bb9b-cb5683ae1fd1
                Copyright © Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.
                History
                Date accepted : 29 September 2014
                Date received : 16 September 2014
                Page count
                Pages: 8
                Categories
                Subject: Database Issue
                Custom metadata
                cover-date 28 January 2015

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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