論文

2021年12月17日

Development of RIKEN Plant Metabolome MetaDatabase.

Plant & cell physiology
  • Atsushi Fukushima
  • ,
  • Mikiko Takahashi
  • ,
  • Hideki Nagasaki
  • ,
  • Yusuke Aono
  • ,
  • Makoto Kobayashi
  • ,
  • Miyako Kusano
  • ,
  • Kazuki Saito
  • ,
  • Norio Kobayashi
  • ,
  • Masanori Arita

記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1093/pcp/pcab173

The advancement of metabolomics in terms of techniques for measuring small molecules has enabled the rapid detection and quantification of numerous cellular metabolites. Metabolomic data provide new opportunities to gain a deeper understanding of plant metabolism that can improve the health of both plants and humans that consume them. Although major public repositories for general metabolomic data have been established, the community still has shortcomings related to data sharing, especially in terms of data reanalysis, reusability, and reproducibility. To address these issues, we developed the RIKEN Plant Metabolome MetaDatabase (RIKEN PMM, http://metabobank.riken.jp/pmm/db/plantMetabolomics), which stores mass spectrometry-based (e.g. GC-MS-based) metabolite profiling data of plants together with their detailed, structured experimental metadata, including sampling and experimental procedures. Our metadata are described as Linked Open Data (LOD) based on the Resource Description Framework (RDF) using standardized and controlled vocabularies, such as the Metabolomics Standards Initiative Ontology (MSIO), which are to be integrated with various life and biomedical science data using the World Wide Web. RIKEN PMM implements intuitive and interactive operations for plant metabolome data, including raw data (netCDF format), mass spectra (NIST MSP format), and metabolite annotations. The feature is suitable not only for biologists who are interested in metabolomic phenotypes, but also for researchers who would like to investigate life science in general through plant metabolomic approaches.

リンク情報
DOI
https://doi.org/10.1093/pcp/pcab173
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/34918130
ID情報
  • DOI : 10.1093/pcp/pcab173
  • PubMed ID : 34918130

エクスポート
BibTeX RIS