GOLDB

GOLDB catalogs global genome and metagenome sequencing projects and associated metadata to support project tracking and metadata standardization.

Key Features:

• Scope of content: Contains over 1.17 million entries across Studies (45,770), Organisms (387,382), Biosamples (101,207), Sequencing Projects (355,364), and Analysis Projects (283,481).
• Metadata breadth: Annotates entries with more than 600 metadata fields.
• Controlled vocabularies: Implements 76 controlled vocabulary (CV) tables comprising 3,873 terms for standardized metadata annotation.
• Curation and updates: Maintains a curated dataset with daily updates.
• External data integration: Imports projects from public repositories including GenBank and the Sequence Read Archive (SRA).
• Metadata validation for submission: Requires users to provide project metadata prior to submission of sequence information to the Integrated Microbial Genomes (IMG) system.

Scientific Applications:

• Aggregate resource for genomics: Provides a consolidated catalog of genome and metagenome projects for comparative and large-scale analyses.
• Metadata standardization: Supports enforcement and harmonization of metadata using controlled vocabularies.
• Reference dataset: Serves as a curated reference dataset compiled from GenBank and SRA for genomics research.
• Submission workflow support: Facilitates preparation and validation of metadata prior to IMG-based sequence analysis.

Methodology:

Daily curation and updates; imports project records from GenBank and the Sequence Read Archive (SRA); enforces metadata entry prior to forwarding sequences to Integrated Microbial Genomes (IMG); organizes entries into Studies, Organisms, Biosamples, Sequencing Projects, and Analysis Projects and annotates metadata fields using 76 CV tables (3,873 terms).