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

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.

Figure 1.

The four level project classification system implemented in v.5 to describe Studies, Biosamples, Sequencing Projects and Analysis Projects. Studies group one or more related Biosamples. Biosamples describe an individual sample of genetic material. Sequencing projects are the sequencing deliverables from the Biosamples. Analysis projects are the data processing methods applied to sequencing projects. (A) Biosamples may be merged prior to sequencing projects (e.g., 16S amplicon data combined prior to sequencing). (B) Sequencing Projects may be merged prior to analysis (e.g., multiple single-cell genomes combined for assembly).

Figure 2.

Study Biosamples, ecosystem categories and sequencing strategies. Each point is a GOLD study. The size of the point represents the number of ecosystem categories within a Study. The position on the y-axis denotes the number of Biosamples within a Study. The color of each point indicates the number of unique sequencing strategies used within a Study.

Figure 3.

Sequencing and analysis projects per Study over time. Color denotes the number of sequencing strategies used within a Study. The size of the point indicates the number of analysis projects within a Study.