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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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Genomes OnLine Database (GOLD) v.8: overview and updates.

Supratim Mukherjee¹, Dimitri Stamatis¹, Jon Bertsch¹

¹DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Nucleic Acids Research

|November 5, 2020

Summary

The Genomes OnLine Database (GOLD) is a comprehensive, updated resource for global genome projects. It offers extensive metadata and an interactive interface, facilitating data sharing and analysis for researchers worldwide.

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Area of Science:

Genomics
Bioinformatics
Data Management

Background:

The Genomes OnLine Database (GOLD) is a critical resource for tracking global genome sequencing and analysis projects.
Accurate and comprehensive metadata are essential for understanding and utilizing genomic data effectively.

Purpose of the Study:

To provide an overview of the current status, features, and recent updates of the Genomes OnLine Database (GOLD).
To highlight GOLD's role in organizing and disseminating genome-related metadata to the scientific community.

Main Methods:

Manual curation and daily updates of genome project information.
Organization of data into hierarchical levels: Studies, Organisms, Biosamples, Sequencing Projects, and Analysis Projects.
Development and maintenance of an interactive web interface for data browsing and searching.

Main Results:

The current GOLD version contains over 1.17 million entries across multiple organizational levels.
The database incorporates over 600 metadata fields, including 76 controlled vocabulary tables with 3873 terms.
GOLD facilitates data submission to the Integrated Microbial Genomes (IMG) system and imports data from public repositories like GenBank and SRA.

Conclusions:

GOLD serves as a vital, continuously updated repository for genome project metadata.
Its comprehensive features and interactive interface support global genomic research and data integration.
Ongoing improvements ensure GOLD remains a valuable reference for the scientific community.