基因组在线数据库（GOLD）v.5：一个基于四级（元）基因组计划分类的元数据管理系统。
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification.
作者信息
Reddy T B K, Thomas Alex D, Stamatis Dimitri, Bertsch Jon, Isbandi Michelle, Jansson Jakob, Mallajosyula Jyothi, Pagani Ioanna, Lobos Elizabeth A, Kyrpides Nikos C
机构信息
Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
出版信息
Nucleic Acids Res. 2015 Jan;43(Database issue):D1099-106. doi: 10.1093/nar/gku950. Epub 2014 Oct 27.
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.
相似文献
1
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification.基因组在线数据库（GOLD）v.5：一个基于四级（元）基因组计划分类的元数据管理系统。
Nucleic Acids Res. 2015 Jan;43(Database issue):D1099-106. doi: 10.1093/nar/gku950. Epub 2014 Oct 27.
2
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements.基因组在线数据库（GOLD）第6版：数据更新与功能增强
Nucleic Acids Res. 2017 Jan 4;45(D1):D446-D456. doi: 10.1093/nar/gkw992. Epub 2016 Oct 27.
3
Genomes OnLine database (GOLD) v.7: updates and new features.基因组在线数据库（GOLD）v.7：更新和新功能。
Nucleic Acids Res. 2019 Jan 8;47(D1):D649-D659. doi: 10.1093/nar/gky977.
4
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata.《基因组在线数据库》（GOLD）v.4：基因组和宏基因组项目及其相关元数据的现状。
Nucleic Acids Res. 2012 Jan;40(Database issue):D571-9. doi: 10.1093/nar/gkr1100. Epub 2011 Dec 1.
5
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.2007年的在线基因组数据库（GOLD）：基因组和宏基因组项目及其相关元数据的状况。
Nucleic Acids Res. 2008 Jan;36(Database issue):D475-9. doi: 10.1093/nar/gkm884. Epub 2007 Nov 2.
6
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.基因组在线数据库（GOLD）v.2：全球基因组计划监测工具
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D332-4. doi: 10.1093/nar/gkj145.
7
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.《基因组在线数据库（GOLD）》2009 年报告：基因组和宏基因组项目及其相关元数据的现状。
Nucleic Acids Res. 2010 Jan;38(Database issue):D346-54. doi: 10.1093/nar/gkp848. Epub 2009 Nov 13.
8
Genomes OnLine Database (GOLD) v.8: overview and updates.基因组在线数据库（GOLD）v.8：概述和更新。
Nucleic Acids Res. 2021 Jan 8;49(D1):D723-D733. doi: 10.1093/nar/gkaa983.
9
The MAR databases: development and implementation of databases specific for marine metagenomics.海洋宏基因组学专用数据库的开发与实施：MAR 数据库。
Nucleic Acids Res. 2018 Jan 4;46(D1):D692-D699. doi: 10.1093/nar/gkx1036.
10
BioSamples database: an updated sample metadata hub.BioSamples 数据库：更新的样本元数据中心。
Nucleic Acids Res. 2019 Jan 8;47(D1):D1172-D1178. doi: 10.1093/nar/gky1061.
引用本文的文献
1
Macronutrients-availing microbiomes: biodiversity, mechanisms, and biotechnological applications for agricultural sustainability.获取大量营养素的微生物群落：生物多样性、机制及对农业可持续性的生物技术应用
Folia Microbiol (Praha). 2025 Apr;70(2):293-319. doi: 10.1007/s12223-024-01220-w. Epub 2024 Nov 27.
2
Enhancing soil health and strawberry disease resistance: the impact of calcium cyanamide treatment on soil microbiota and physicochemical properties.提高土壤健康和草莓抗病性：氰胺钙处理对土壤微生物群和理化性质的影响
Front Microbiol. 2024 Mar 21;15:1366814. doi: 10.3389/fmicb.2024.1366814. eCollection 2024.
3
Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem.在西非萨赫勒地区的一个农业生态系统中，水稻发育阶段调节根际细菌和古菌的共生关系以及对长期无机施肥的敏感性。
Environ Microbiome. 2023 May 17;18(1):42. doi: 10.1186/s40793-023-00500-1.
4
Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity.印度喜马拉雅地热带（IHGB）中来自锡金温泉的宏基因组组装基因组（MAG）的基线数据，展示了其潜在的碳水化合物活性酶（CAZymes）和硫-氮代谢活性。
World J Microbiol Biotechnol. 2023 May 3;39(7):179. doi: 10.1007/s11274-023-03631-2.
5
Genomic landscape of the emerging XDR Salmonella Typhi for mining druggable targets clpP, hisH, folP and gpmI and screening of novel TCM inhibitors, molecular docking and simulation analyses.XDR 伤寒沙门氏菌的基因组景观，用于挖掘可成药靶点 clpP、hisH、folP 和 gpmI，并筛选新型中药抑制剂，进行分子对接和模拟分析。
BMC Microbiol. 2023 Jan 21;23(1):25. doi: 10.1186/s12866-023-02756-6.
6
The Genome of the Acid Soil-Adapted Strain OR191 Encodes Determinants for Effective Symbiotic Interaction With Both an Inverted Repeat Lacking Clade and a Phaseoloid Legume Host.适应酸性土壤的菌株OR191的基因组编码了与缺乏反向重复序列的进化枝和菜豆科豆科宿主进行有效共生相互作用的决定因素。
Front Microbiol. 2022 Apr 13;13:735911. doi: 10.3389/fmicb.2022.735911. eCollection 2022.
7
Characterizing Enterotypes in Human Metagenomics: A Viral Perspective.从病毒角度对人类宏基因组学中的肠型进行表征
Front Microbiol. 2021 Sep 29;12:740990. doi: 10.3389/fmicb.2021.740990. eCollection 2021.
8
Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling.探寻CRISPR-Cas系统中的厚尾现象：数据分析与数学建模
PLoS Comput Biol. 2021 Mar 26;17(3):e1008841. doi: 10.1371/journal.pcbi.1008841. eCollection 2021 Mar.
9
De novo genome assembly of Bacillus altitudinis 19RS3 and Bacillus altitudinis T5S-T4, two plant growth-promoting bacteria isolated from Ilex paraguariensis St. Hil. (yerba mate).巴氏芽胞杆菌 19RS3 和巴氏芽胞杆菌 T5S-T4 的从头基因组组装，这两种植物促生菌均分离自巴拉圭冬青（冬青属）。
PLoS One. 2021 Mar 11;16(3):e0248274. doi: 10.1371/journal.pone.0248274. eCollection 2021.
10
Genome Sequence of sp. Strain HB-N217, Isolated from the Marine Sponge sp.从海洋海绵物种中分离出的物种菌株HB-N217的基因组序列
Microbiol Resour Announc. 2021 Feb 25;10(8):e01410-20. doi: 10.1128/MRA.01410-20.
本文引用的文献
1
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project.模式菌株基因组百科全书，第一阶段：千种微生物基因组（KMG-I）计划。
Stand Genomic Sci. 2013 Dec 17;9(3):1278-84. doi: 10.4056/sigs.5068949. eCollection 2014 Jun 15.
2
Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.细菌和古菌基因组百科全书：对大量模式菌株进行测序
PLoS Biol. 2014 Aug 5;12(8):e1001920. doi: 10.1371/journal.pbio.1001920. eCollection 2014 Aug.
3
IMG 4 version of the integrated microbial genomes comparative analysis system.IMG 4 版整合微生物基因组比较分析系统。
Nucleic Acids Res. 2014 Jan;42(Database issue):D560-7. doi: 10.1093/nar/gkt963. Epub 2013 Oct 27.
4
IMG/M 4 version of the integrated metagenome comparative analysis system.IMG/M 4 版整合宏基因组比较分析系统。
Nucleic Acids Res. 2014 Jan;42(Database issue):D568-73. doi: 10.1093/nar/gkt919. Epub 2013 Oct 16.
5
Insights into the phylogeny and coding potential of microbial dark matter.微生物暗物质的系统发育和编码潜力的研究进展
Nature. 2013 Jul 25;499(7459):431-7. doi: 10.1038/nature12352. Epub 2013 Jul 14.
6
GenBank.GenBank。
Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. doi: 10.1093/nar/gks1195. Epub 2012 Nov 27.
7
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project.IMG/M-HMP：人类微生物组计划的宏基因组比较分析系统。
PLoS One. 2012;7(7):e40151. doi: 10.1371/journal.pone.0040151. Epub 2012 Jul 5.
8
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata.《基因组在线数据库》（GOLD）v.4：基因组和宏基因组项目及其相关元数据的现状。
Nucleic Acids Res. 2012 Jan;40(Database issue):D571-9. doi: 10.1093/nar/gkr1100. Epub 2011 Dec 1.
9
The Genomic Standards Consortium.基因组标准联盟。
PLoS Biol. 2011 Jun;9(6):e1001088. doi: 10.1371/journal.pbio.1001088. Epub 2011 Jun 21.
10
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.标记基因序列（MIMARKS）和任何（x）序列（MIxS）规范的最小信息。
Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.
Zotero 插件