What is Metabolomics?
Metabolomics is a research field to investigate the entire small molecules within cells. By definition, it includes analysis of oligosaccharides, oligopeptides, lipids, and nucleic acids. The analysis target, all metabolites, is called metabolome. Some say the field is the 3rd omics that follows genomics for all genes and proteomics for all proteins. However, metabolomics is a larger concept, including (small) peptides and nucleic acids. To elucidate the metabolome, we need to fully exercise various extraction- and measurement technologies.
This site is created, edited, and maintained by Arita Laboratory, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo. Descriptions on this website are, if not otherwise specified, written by Masanori Arita.
How to Cite Us
If you are interested in our Wiki-based database (including persist and volatile functions), please read our paper in BioData Mining. If you are interested in the classification strategy of flavonoid or other metabolites, please wait for our paper in preparation.
About this database
- Arita M., Suwa K. "Search Extension Transforms Wiki into a Relational System: a case for flavonoid metabolite database", BioData Mining 1:7, 2008
About Flavonoid classification
- Tokimatsu T., Arita M. "Viewing Flavonoid Through Metabolic Maps." Saibou Kougaku (in Japanese), 25(12):1388-1393, 2006
- Arita M., Tokimatsu T. "Detection of Monosaccharide Types from Coordinates" Proceedings of the 18th International Conference on Genome Informatics (Genome Informatics Series Vol.19), Singapore, 3-14, 2007 [PMID 18546500]
We are the only people! Currently, this site is write protected.
- Masanori Arita Ph.D (principal investigator)
- Kazuhiro Suwa (programmer)
- Miwa Yoshimoto (data curator)
- Toshiaki Tokimatsu, Ph.D
- Yukiko Nakanishi
- Yukiko Fujiwara
- Tadashi Gambe
- Grant-in-Aid for Scientific Research on Priority Areas "Systems Genomics" from Ministry of Education, Culture, Sports, Science and Technology, Japan (文部科学省科研費補助金 特定領域研究ゲノム「システム生命情報」
- Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Japan （JST-BIRD)
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Japan (JSTさきがけ シミュレーション技術の革新と実用化基盤の構築)
This site is build on MediaWiki. Total number of data pages is 20711.
Source code of our site specific extensions
- Volatile namespace
- Persist namespace
- Form tag in HTML
- Wbr tag in HTML
- SQL-like search
- String functions
- Calling Lua program
- MOL-format file functions
- Graph drawing