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

Reddy TB, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC - Nucleic Acids Res. (2014)

Bottom Line: The database currently hosts information for about 19,200 studies, 56,000 Biosamples, 56,000 sequencing projects and 39,400 analysis projects.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.

View Article: PubMed Central - PubMed

Affiliation: Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA tbreddy@lbl.gov.

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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.
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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.

Mentions: A study represents the highest-level organization. Studies include one or more Biosamples and their associated SPs and APs that have been grouped to investigate a related research topic of interest. For example, the HMP (16), GEBA (17,18) and KMG (21) studies represent typical cases where researchers set out to explore a specific topic by sequencing thousands of samples. Studies like GEBA-MDM (22) and FEBA (19) applied several different sequencing strategies (e.g. isolate genomes, single-cell genomes, metagenomes, transcriptomes, etc.) as part of a single study. Studies may be composed of one to hundreds of Biosamples from a wide range of ecological settings (Figure 2). Each Biosample may also yield several different SPs, each of which may yield multiple APs (Figure 3 and Table 1). Study IDs are referred to as ‘Gs’ IDs in the new system. A GOLD study is analogous to the NCBI's umbrella BioProject, and may contain one or more NCBI BioSamples.


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

Reddy TB, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC - Nucleic Acids Res. (2014)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4384021&req=5

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.
Mentions: A study represents the highest-level organization. Studies include one or more Biosamples and their associated SPs and APs that have been grouped to investigate a related research topic of interest. For example, the HMP (16), GEBA (17,18) and KMG (21) studies represent typical cases where researchers set out to explore a specific topic by sequencing thousands of samples. Studies like GEBA-MDM (22) and FEBA (19) applied several different sequencing strategies (e.g. isolate genomes, single-cell genomes, metagenomes, transcriptomes, etc.) as part of a single study. Studies may be composed of one to hundreds of Biosamples from a wide range of ecological settings (Figure 2). Each Biosample may also yield several different SPs, each of which may yield multiple APs (Figure 3 and Table 1). Study IDs are referred to as ‘Gs’ IDs in the new system. A GOLD study is analogous to the NCBI's umbrella BioProject, and may contain one or more NCBI BioSamples.

Bottom Line: The database currently hosts information for about 19,200 studies, 56,000 Biosamples, 56,000 sequencing projects and 39,400 analysis projects.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.

View Article: PubMed Central - PubMed

Affiliation: Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA tbreddy@lbl.gov.

Show MeSH