BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services.
Katayama, T., Kawashima, S., Micklem, S., Kawano, S., Kim, J-D., Kocbek, S., Okamoto, S., Wang, Y., Wu, H., Yamaguchi, A., Yamamoto, Y., Antezana, E., Aoki-Kinoshita, K. F., Arakawa, K., Banno, M., Baran, J., Bolleman, J. T., Bonnal, R. J. P., Bono, H., Fernández-Breis, J. T., Buels, R., Campbell, M. P., Chiba, H., Cock, P. J. A., Cohen, K. B., Dumontier, M., Fujisawa, T., Fujiwara, T., Garcia, L., Gaudet, P., Hattori, E., Hoehndorf, R., Itaya, K., Ito, M., Jamieson, D., Jupp, S., Juty, N., Kalderimis, A., Kato, F., Kawaji, H., Kawashima, T., Kinjo, A. R., Komiyama, Y., Kotera, M., Kushida, T., Malone, J., Matsubara, M., Mizuno, S., Mizutani, S., Mori, H., Moriya, Y., Murakami, K., Nakazato, T., Nishide, H., Nishimura, Y., Ogishima, S., Ohta, T., Okuda, S., Ono, H., Perez-Riverol, Y., Shinmachi, D., Splendiani, A., Strozzi, F., Suzuki, S., Takehara, J., Thompson, M., Tokimatsu, T., Uchiyama, I., Verspoor, K., Wilkinson, M. D., Wimalaratne, S., Yamada, I., Yamamoto, N., Yarimizu, M., Kawamoto, S., Takagi, T. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research 8:1677 (2019).
The jPOST environment: an integrated proteomics data repository and database.
Moriya, Y., Kawano, S., Okuda, S., Watanabe, Y., Matsumoto, M., Takami, T., Kobayashi, D., Yamanouchi, Y., Araki, N., Yoshizawa, A. C., Tabata, T., Iwasaki, M., Sugiyama, N., Tanaka, S., Goto, S., Ishihama, Y. The jPOST environment: an integrated proteomics data repository and database. Nucleic Acids Res. 47(D1):D1218-D1224 (2019).
Semantic Web Technologies to Integrate Life Science Data through GlyTouCan.
Yamada, I, Shinmachi, D., Aoki, N., Watanabe, Y., Okuda S., Aoki-Kinoshita, K. Semantic Web Technologies to Integrate Life Science Data through GlyTouCan. ISMB2018, Chicago (2018/7/6).
jPOSTrepo: an international standard data repository for proteomes.
Okuda, S., Watanabe, Y., Moriya, Y., Kawano, S., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Yoshizawa, A. C., Tabata, T., Sugiyama, N., Goto, S., and Ishihama, Y. jPOSTrepo: an international standard data repository for proteomes. Nucleic Acids Res. 45:D1107-D1111 (2017).
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
Deutsch, E. W., Csordas, A., Sun, Z., Jarnuczak, A., Perez-Riverol, Y., Ternent, T., Campbell, D. S., Bernal-Llinares, M., Okuda, S., Kawano, S., Moritz, R. L., Carver, J. J., Wang, M., Ishihama, Y., Bandeira, N., Hermjakob, H., Vizcaíno, J. A. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. 45:D1100-1106 (2017).
GlycoEpitope: A Practical Guide to Using Glycomics Databases.
Shujiro Okuda, Hiromi Nakao and Toshisuke Kawasaki GlycoEpitope: A Practical Guide to Using Glycomics Databases. 227-245 (2016). (ISBN: 978-4-431-56452-2)
New Filtering Functionality in GlyTouCan, The Glycan Repository.
Aoki, N. P., Aoki-Kinoshita, K. F., Shinmachi, D., Yamada, I., Tsuchiya, S., Matsubara, M., Okuda, S., Fujita, N., Suzuki, Y., Fujita, A., Solovieva, E., Shikanai, T., Kawasaki, T., Narimatsu, H. New Filtering Functionality in GlyTouCan, The Glycan Repository. ACGG2016 (2016/10/13).
Integrating Life Science Database with Semantic Web Technologies.
Shinmachi, D., Aoki-Kinoshita, K. F., Aoki, N. P., Yamada, I., Tsuchiya, S., Matsubara, M., Okuda, S., Fujita, N., Suzuki, Y., Fujita, A., Solovieva, E., Shikanai, T., Kawasaki, T., Narimatsu, H. Integrating Life Science Database with Semantic Web Technologies. ACGG2016 (2016/10/13).
jPOST for Asia and Oceania: Re-analysis Protocol.
Yoshizawa, A. C., Tabata, T., Moriya, Y., Kawano, S., Okuda, S., Watanabe, Y., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Sugiyama, N., Goto, S., Ishihama, Y. jPOST for Asia and Oceania: Re-analysis Protocol. AOHUPO2016, Taiwan (2016/9).
jPOST for Asia and Oceania: Current Status in 2016.
Moriya, Y., Kawano, S., Okuda, S., Watanabe, Y., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Yoshizawa, A. C., Tabata, T., Sugiyama, N., Goto, S., Ishihama, Y. jPOST for Asia and Oceania: Current Status in 2016. AOHUPO2016, Taiwan (2016/9).