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Title: Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

Abstract

The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects. These are integrated with over 312 metadata fields from which 58 are controlled vocabularies with 2067 terms. The web interface facilitates submission of a diverse range of Sequencing Projects (such as isolate genome, singlecell genome, metagenome, metatranscriptome) and complex Analysis Projects (such as genome from metagenome, or combined assembly from multiple Sequencing Projects). GOLD provides a seamless interface with the Integrated Microbial Genomes (IMG) system and supports and promotes the Genomic Standards Consortium (GSC) Minimum Information standards. Here, this paper describes the data updates and additional features added during the last two years.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [1]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Prokaryotic Super Program
  2. King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1482516
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 45; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING

Citation Formats

Mukherjee, Supratim, Stamatis, Dimitri, Bertsch, Jon, Ovchinnikova, Galina, Verezemska, Olena, Isbandi, Michelle, Thomas, Alex D., Ali, Rida, Sharma, Kaushal, Kyrpides, Nikos C., and Reddy, T.  B.  K.. Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. United States: N. p., 2016. Web. doi:10.1093/nar/gkw992.
Mukherjee, Supratim, Stamatis, Dimitri, Bertsch, Jon, Ovchinnikova, Galina, Verezemska, Olena, Isbandi, Michelle, Thomas, Alex D., Ali, Rida, Sharma, Kaushal, Kyrpides, Nikos C., & Reddy, T.  B.  K.. Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. United States. doi:10.1093/nar/gkw992.
Mukherjee, Supratim, Stamatis, Dimitri, Bertsch, Jon, Ovchinnikova, Galina, Verezemska, Olena, Isbandi, Michelle, Thomas, Alex D., Ali, Rida, Sharma, Kaushal, Kyrpides, Nikos C., and Reddy, T.  B.  K.. Thu . "Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements". United States. doi:10.1093/nar/gkw992. https://www.osti.gov/servlets/purl/1482516.
@article{osti_1482516,
title = {Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements},
author = {Mukherjee, Supratim and Stamatis, Dimitri and Bertsch, Jon and Ovchinnikova, Galina and Verezemska, Olena and Isbandi, Michelle and Thomas, Alex D. and Ali, Rida and Sharma, Kaushal and Kyrpides, Nikos C. and Reddy, T.  B.  K.},
abstractNote = {The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects. These are integrated with over 312 metadata fields from which 58 are controlled vocabularies with 2067 terms. The web interface facilitates submission of a diverse range of Sequencing Projects (such as isolate genome, singlecell genome, metagenome, metatranscriptome) and complex Analysis Projects (such as genome from metagenome, or combined assembly from multiple Sequencing Projects). GOLD provides a seamless interface with the Integrated Microbial Genomes (IMG) system and supports and promotes the Genomic Standards Consortium (GSC) Minimum Information standards. Here, this paper describes the data updates and additional features added during the last two years.},
doi = {10.1093/nar/gkw992},
journal = {Nucleic Acids Research},
number = D1,
volume = 45,
place = {United States},
year = {Thu Oct 27 00:00:00 EDT 2016},
month = {Thu Oct 27 00:00:00 EDT 2016}
}

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Works referenced in this record:

IMG/M 4 version of the integrated metagenome comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Chu, Ken
  • Nucleic Acids Research, Vol. 42, Issue D1, p. D568-D573
  • DOI: 10.1093/nar/gkt919