DDBJ Update in 2023: the MetaboBank for Metabolomics Data and Associated Metadata

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2023 Nov 16

PMID 37971299

Authors

Takeshi Ara

Yuichi Kodama

Toshiaki Tokimatsu

Asami Fukuda

Takehide Kosuge

Jun Mashima

Yasuhiro Tanizawa

Tomoya Tanjo

Osamu Ogasawara

Takatomo Fujisawa

Yasukazu Nakamura

Masanori Arita

Affiliations

Soon will be listed here.

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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References

Sansone S, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O . Toward interoperable bioscience data. Nat Genet. 2012; 44(2):121-6. PMC: 3428019. DOI: 10.1038/ng.1054. View

Kodama Y, Shumway M, Leinonen R . The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res. 2011; 40(Database issue):D54-6. PMC: 3245110. DOI: 10.1093/nar/gkr854. View

Kodama Y, Mashima J, Kosuge T, Katayama T, Fujisawa T, Kaminuma E . The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. Nucleic Acids Res. 2014; 43(Database issue):D18-22. PMC: 4383935. DOI: 10.1093/nar/gku1120. View

Sarkans U, Fullgrabe A, Ali A, Athar A, Behrangi E, Diaz N . From ArrayExpress to BioStudies. Nucleic Acids Res. 2020; 49(D1):D1502-D1506. PMC: 7778911. DOI: 10.1093/nar/gkaa1062. View

Sansone S, Fan T, Goodacre R, Griffin J, Hardy N, Kaddurah-Daouk R . The metabolomics standards initiative. Nat Biotechnol. 2007; 25(8):846-8. DOI: 10.1038/nbt0807-846b. View

Sayers E, Bolton E, Brister J, Canese K, Chan J, Comeau D . Database resources of the National Center for Biotechnology Information in 2023. Nucleic Acids Res. 2022; 51(D1):D29-D38. PMC: 9825438. DOI: 10.1093/nar/gkac1032. View

Dai C, Fullgrabe A, Pfeuffer J, Solovyeva E, Deng J, Moreno P . A proteomics sample metadata representation for multiomics integration and big data analysis. Nat Commun. 2021; 12(1):5854. PMC: 8494749. DOI: 10.1038/s41467-021-26111-3. View

Kodama Y, Mashima J, Kosuge T, Ogasawara O . DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data. Nucleic Acids Res. 2018; 47(D1):D69-D73. PMC: 6323915. DOI: 10.1093/nar/gky1002. View

Brunak S, Danchin A, Hattori M, Nakamura H, Shinozaki K, Matise T . Nucleotide sequence database policies. Science. 2002; 298(5597):1333. DOI: 10.1126/science.298.5597.1333b. View

10.

Tanizawa Y, Fujisawa T, Kodama Y, Kosuge T, Mashima J, Tanjo T . DNA Data Bank of Japan (DDBJ) update report 2022. Nucleic Acids Res. 2022; 51(D1):D101-D105. PMC: 9825463. DOI: 10.1093/nar/gkac1083. View

11.

Fiehn O . Metabolomics--the link between genotypes and phenotypes. Plant Mol Biol. 2002; 48(1-2):155-71. View

12.

Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J . mzML--a community standard for mass spectrometry data. Mol Cell Proteomics. 2010; 10(1):R110.000133. PMC: 3013463. DOI: 10.1074/mcp.R110.000133. View

13.

Freeberg M, Fromont L, DAltri T, Romero A, Ciges J, Jene A . The European Genome-phenome Archive in 2021. Nucleic Acids Res. 2021; 50(D1):D980-D987. PMC: 8728218. DOI: 10.1093/nar/gkab1059. View

14.

Arita M, Karsch-Mizrachi I, Cochrane G . The international nucleotide sequence database collaboration. Nucleic Acids Res. 2020; 49(D1):D121-D124. PMC: 7778961. DOI: 10.1093/nar/gkaa967. View

15.

Federhen S, Clark K, Barrett T, Parkinson H, Ostell J, Kodama Y . Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records. Stand Genomic Sci. 2014; 9(3):1275-7. PMC: 4149001. DOI: 10.4056/sigs.4851102. View

16.

Clough E, Barrett T . The Gene Expression Omnibus Database. Methods Mol Biol. 2016; 1418:93-110. PMC: 4944384. DOI: 10.1007/978-1-4939-3578-9_5. View

17.

Suetake H, Fukusato T, Igarashi T, Ohta T . Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows. Gigascience. 2023; 12. PMC: 9944229. DOI: 10.1093/gigascience/giad006. View

18.

Suetake H, Tanjo T, Ishii M, Kinoshita B, Fujino T, Hachiya T . Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics. F1000Res. 2024; 11:889. PMC: 11282396. DOI: 10.12688/f1000research.122924.2. View

19.

Burgin J, Ahamed A, Cummins C, Devraj R, Gueye K, Gupta D . The European Nucleotide Archive in 2022. Nucleic Acids Res. 2022; 51(D1):D121-D125. PMC: 9825583. DOI: 10.1093/nar/gkac1051. View

20.

Tanizawa Y, Fujisawa T, Nakamura Y . DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2017; 34(6):1037-1039. PMC: 5860143. DOI: 10.1093/bioinformatics/btx713. View