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RIKEN Information R&D and Strategy Headquarters Life Science Data Sharing Unit

Unit Leader: Shuichi Onami (D.V.M., Ph.D.)

Research Summary

Shuichi Onami (D.V.M., Ph.D.)

To promote open science in the life sciences, the Unit conducts research and development to collect a wide variety of research data in the life sciences produced by RIKEN and facilitate secondary use. With all of RIKEN’s life science research centers’ participation, we will develop the foundation for open science in the life sciences and pioneer a new style of life sciences.

Main Research Fields

  • Informatics

Related Research Fields

  • Life / Health / Medical informatics
  • System genome science
  • Multimedia database
  • Biological Sciences
  • Biology
  • Medicine, Dentistry & Pharmacy
  • Agricultural Sciences

Keywords

  • Open science
  • Data integration
  • Life science data
  • Biological data science
  • Metadata

Selected Publications

  • 1. Abugessaisa, I., Ramilowski, JA., Lizio, M., Severin, J., Hasegawa, A., Harshbarger, J., Kondo, A., Noguchi, S., Yip, C., Ooi, J., Tagami, M., Hori, F., Agrawal, S., Hon, C., Cardon, M., Ikeda, S., Ono, H., Bono, H., Kato, M., Hashimoto. K., Bonetti. A., Kato, M., Kobayashi, N., Shin, J., de Hoon, M., Hayashizaki, Y., Carninci, P., Kawaji, H., and Kasukawa, T.:
    "FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs"
    Nucleic Acids Research 49, gkaa1054. (2020). doi: 10.1093/nar/gkaa1054:
  • 2. Tsugawa, H., Ikeda, K., Takahashi, M., Satoh, A., Mori, Y., Uchino, H., Okahashi, N., Yamada, Y., Tada, I., Bonini, P., Higashi, Y., Okazaki, Y., Zhou, Z., Zhu, Z., Koelmel, J., Cajka, T., Fiehn, O., Saito, K., Arita, M., and Arita, M.:
    "A lipidome atlas in MS-DIAL 4"
    Nature Biotechnology 38, 1159–1163 (2020). doi: 10.1038/s41587-020-0531-2
  • 3. Tanaka, N., and Masuya, H.:
    "An atlas of evidence-based phenotypic associations across the mouse phenome"
    Scientific Reports 10, 3957 (2020). doi: 10.1038/s41598-020-60891-w
  • 4. Morita, M., Shimokawa, K., Nishimura, M., Nakamura, S., Tsujimura, Y., Takemoto, S., Tawara, T., Yokota, H., Wemler, S., Miyamoto, D., Ikeno, H., Sato, A., Furuichi, T., Kobayashi, N., Okumura, Y., Yamaguchi, Y., and Okamura- Oho, Y.:
    "ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks"
    Nucleic Acids Research 47(D1), D859-D866 (2019). doi: 10.1093/nar/gky951
  • 5. Kobayashi, N., Kume, S., Lenz, K., and Masuya, H.:
    "RIKEN MetaDatabase: a database platform for health care and life sciences as a microcosm of linked open data cloud"
    International Journal on Semantic Web and Information Systems 14(1), 140-164 (2018). doi: 10.4018/IJSWIS.2018010106
  • 6. Shimogori, T., Abe, A., Go, Y., Hashikawa, T., Kishi, N., Kikuchi, S. S., Kita, Y., Niimi, K., Nishibe, H., Okuno, M., Saga, K., Sakurai, M., Sato, M., Serizawa, T., Suzuki, S., Takahashi, E., Tanaka, M., Tatsumoto, S., Toki, M., U, M., Wang, Y., Windak, K. J., Yamagishi, H., Yamashita, K., Yoda, T., Yoshida, A. C., Yoshida, C., Yoshimoto, T., and Okano, H.:
    "Digital gene atlas of neonate common marmoset brain"
    Neuroscience Research 128, 1-13 (2018). doi: 10.1016/j.neures.2017.10.009
  • 7. Tohsato, Y., Ho, K. H. L., Kyoda, K., and Onami, S.:
    "SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena"
    Bioinformatics 32(22), 3471-3479 (2016). doi: 10.1093/bioinformatics/btw417

Related Links

Lab Members

Principal investigator

Shuichi Onami
Unit Leader

Core members

Masanori Arita
Senior Scientist
Takeya Kasukawa
Senior Scientist
Norio Kobayashi
Senior Scientist
Tomomi Shimogori
Senior Scientist
Hiroshi Masuya
Senior Scientist
Hideo Yokota
Senior Scientist
Yuki Yamagata
Research Scientist
Musashi Imaizumi
Technical Staff I
Fangfang Wang
Technical Staff I

Contact Information

2-2-3 Minatojima-minamimachi, Chuo-ku,
Kobe, Hyogo
650-0047 Japan

Email: sonami [at] riken.jp

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