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. 2024 Jan 5;52(D1):D67-D71.
doi: 10.1093/nar/gkad1046.

DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata

Takeshi Ara  1 , Yuichi Kodama  1 , Toshiaki Tokimatsu  1 , Asami Fukuda  1 , Takehide Kosuge  1 , Jun Mashima  1 , Yasuhiro Tanizawa  1 , Tomoya Tanjo  1 , Osamu Ogasawara  1 , Takatomo Fujisawa  1 , Yasukazu Nakamura  1 , Masanori Arita  1
Affiliations

DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata

Takeshi Ara et al. Nucleic Acids Res. .

Abstract

The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) provides database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), DDBJ accepts and distributes nucleotide sequence data as well as their study and sample information along with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute (EBI). Besides INSDC databases, the DDBJ Center provides databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank) and human genetic and phenotypic data (JGA: Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics (NIG) supercomputer, which is also open for domestic life science researchers to analyze large-scale sequence data. This paper reports recent updates on the archival databases and the services of the DDBJ Center, highlighting the newly redesigned MetaboBank. MetaboBank uses BioProject and BioSample in its metadata description making it suitable for multi-omics large studies. Its collaboration with MetaboLights at EBI brings synergy in locating and reusing public data.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
The MetaboBank MAGE-TAB format consists of the IDF and SDRF metadata, raw, processed data files and MAF. IDF provides an overview of the study, protocols, publication and submitter information. SDRF provides sample characteristics and the relation between samples, platforms, raw and processed data files and MAF.
Figure 2.
Figure 2.
(A) The MetaboBank search page. Users can search MetaboBank and MetaboLights studies by free-text and refine the search result using facets. (B) The study details page shows the study content and the download links to the metadata and data files.
See this image and copyright information in PMC

References

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