The Rice Annotation Project Database (RAP-DB): 2008 update

Tsuyoshi Tanaka, Baltazar A. Antonio, Shoshi Kikuchi, Takashi Matsumoto, Yoshiaki Nagamura, Hisataka Numa, Hiroaki Sakai, Jianzhong Wu, Takeshi Itoh, Takuji Sasaki, Ryo Aono, Yasuyuki Fujii, Takuya Habara, Erimi Harada, Masako Kanno, Yoshihiro Kawahara, Hiroaki Kawashima, Hiromi Kubooka, Akihiro Matsuya, Hajime NakaokaNaomi Saichi, Ryoko Sanbonmatsu, Yoshiharu Sato, Yuji Shinso, Mami Suzuki, Junichi Takeda, Motohiko Tanino, Fusano Todokoro, Kaori Yamaguchi, Naoyuki Yamamoto, Chisato Yamasaki, Tadashi Imanishi, Toshihisa Okido, Masahito Tada, Kazuho Ikeo, Yoshio Tateno, Takashi Gojobori, Yao Cheng Lin, Fu Jin Wei, Yueie Hsing, Qiang Zhao, Bin Han, Melissa R. Kramer, Richard W. McCombie, David Lonsdale, Claire C. O’donovan, Eleanor J. Whitfield, Rolf Apweiler, Kanako O. Koyanagi, Jitendra P. Khurana, Saurabh Raghuvanshi, Nagendra K. Singh, Akhilesh K. Tyagi, Georg Haberer, Masaki Fujisawa, Satomi Hosokawa, Yukiyo Ito, Hiroshi Ikawa, Michie Shibata, Mayu Yamamoto, Richard M. Bruskiewich, Douglas R. Hoen, Thomas E. Bureau, Nobukazu Namiki, Hajime Ohyanagi, Yasumichi Sakai, Satoshi Nobushima, Katsumi Sakata, Roberto A. Barrero, Yutaka Sato, Alexandre Souvorov, Brian Smith-White, Tatiana Tatusova, Suyoung An, Gynheung An, Satoshi Oota, Galina Fuks, Joachim Messing, Karen R. Christie, Damien Lieberherr, Hyeran Kim, Andrea Zuccolo, Rod A Wing, Kan Nobuta, Pamela J. Green, Cheng Lu, Blake C. Meyers, Cristian Chaparro, Benoit Piegu, Olivier Panaud, Manuel Echeverria

Research output: Contribution to journalArticle

256 Citations (Scopus)

Abstract

The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://www.w3.org/1999/ http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume36
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 1 2008

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Databases
Genome
Genomics
Genes
Oryza
High-Throughput Nucleotide Sequencing
Access to Information
DNA Transposable Elements
Expressed Sequence Tags
Publications
Complementary DNA
Clone Cells
RNA
Technology

ASJC Scopus subject areas

  • Genetics

Cite this

Tanaka, T., Antonio, B. A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., ... Echeverria, M. (2008). The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Research, 36(SUPPL. 1). https://doi.org/10.1093/nar/gkm978

The Rice Annotation Project Database (RAP-DB) : 2008 update. / Tanaka, Tsuyoshi; Antonio, Baltazar A.; Kikuchi, Shoshi; Matsumoto, Takashi; Nagamura, Yoshiaki; Numa, Hisataka; Sakai, Hiroaki; Wu, Jianzhong; Itoh, Takeshi; Sasaki, Takuji; Aono, Ryo; Fujii, Yasuyuki; Habara, Takuya; Harada, Erimi; Kanno, Masako; Kawahara, Yoshihiro; Kawashima, Hiroaki; Kubooka, Hiromi; Matsuya, Akihiro; Nakaoka, Hajime; Saichi, Naomi; Sanbonmatsu, Ryoko; Sato, Yoshiharu; Shinso, Yuji; Suzuki, Mami; Takeda, Junichi; Tanino, Motohiko; Todokoro, Fusano; Yamaguchi, Kaori; Yamamoto, Naoyuki; Yamasaki, Chisato; Imanishi, Tadashi; Okido, Toshihisa; Tada, Masahito; Ikeo, Kazuho; Tateno, Yoshio; Gojobori, Takashi; Lin, Yao Cheng; Wei, Fu Jin; Hsing, Yueie; Zhao, Qiang; Han, Bin; Kramer, Melissa R.; McCombie, Richard W.; Lonsdale, David; O’donovan, Claire C.; Whitfield, Eleanor J.; Apweiler, Rolf; Koyanagi, Kanako O.; Khurana, Jitendra P.; Raghuvanshi, Saurabh; Singh, Nagendra K.; Tyagi, Akhilesh K.; Haberer, Georg; Fujisawa, Masaki; Hosokawa, Satomi; Ito, Yukiyo; Ikawa, Hiroshi; Shibata, Michie; Yamamoto, Mayu; Bruskiewich, Richard M.; Hoen, Douglas R.; Bureau, Thomas E.; Namiki, Nobukazu; Ohyanagi, Hajime; Sakai, Yasumichi; Nobushima, Satoshi; Sakata, Katsumi; Barrero, Roberto A.; Sato, Yutaka; Souvorov, Alexandre; Smith-White, Brian; Tatusova, Tatiana; An, Suyoung; An, Gynheung; Oota, Satoshi; Fuks, Galina; Messing, Joachim; Christie, Karen R.; Lieberherr, Damien; Kim, Hyeran; Zuccolo, Andrea; Wing, Rod A; Nobuta, Kan; Green, Pamela J.; Lu, Cheng; Meyers, Blake C.; Chaparro, Cristian; Piegu, Benoit; Panaud, Olivier; Echeverria, Manuel.

In: Nucleic Acids Research, Vol. 36, No. SUPPL. 1, 01.01.2008.

Research output: Contribution to journalArticle

Tanaka, T, Antonio, BA, Kikuchi, S, Matsumoto, T, Nagamura, Y, Numa, H, Sakai, H, Wu, J, Itoh, T, Sasaki, T, Aono, R, Fujii, Y, Habara, T, Harada, E, Kanno, M, Kawahara, Y, Kawashima, H, Kubooka, H, Matsuya, A, Nakaoka, H, Saichi, N, Sanbonmatsu, R, Sato, Y, Shinso, Y, Suzuki, M, Takeda, J, Tanino, M, Todokoro, F, Yamaguchi, K, Yamamoto, N, Yamasaki, C, Imanishi, T, Okido, T, Tada, M, Ikeo, K, Tateno, Y, Gojobori, T, Lin, YC, Wei, FJ, Hsing, Y, Zhao, Q, Han, B, Kramer, MR, McCombie, RW, Lonsdale, D, O’donovan, CC, Whitfield, EJ, Apweiler, R, Koyanagi, KO, Khurana, JP, Raghuvanshi, S, Singh, NK, Tyagi, AK, Haberer, G, Fujisawa, M, Hosokawa, S, Ito, Y, Ikawa, H, Shibata, M, Yamamoto, M, Bruskiewich, RM, Hoen, DR, Bureau, TE, Namiki, N, Ohyanagi, H, Sakai, Y, Nobushima, S, Sakata, K, Barrero, RA, Sato, Y, Souvorov, A, Smith-White, B, Tatusova, T, An, S, An, G, Oota, S, Fuks, G, Messing, J, Christie, KR, Lieberherr, D, Kim, H, Zuccolo, A, Wing, RA, Nobuta, K, Green, PJ, Lu, C, Meyers, BC, Chaparro, C, Piegu, B, Panaud, O & Echeverria, M 2008, 'The Rice Annotation Project Database (RAP-DB): 2008 update', Nucleic Acids Research, vol. 36, no. SUPPL. 1. https://doi.org/10.1093/nar/gkm978
Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H et al. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Research. 2008 Jan 1;36(SUPPL. 1). https://doi.org/10.1093/nar/gkm978
Tanaka, Tsuyoshi ; Antonio, Baltazar A. ; Kikuchi, Shoshi ; Matsumoto, Takashi ; Nagamura, Yoshiaki ; Numa, Hisataka ; Sakai, Hiroaki ; Wu, Jianzhong ; Itoh, Takeshi ; Sasaki, Takuji ; Aono, Ryo ; Fujii, Yasuyuki ; Habara, Takuya ; Harada, Erimi ; Kanno, Masako ; Kawahara, Yoshihiro ; Kawashima, Hiroaki ; Kubooka, Hiromi ; Matsuya, Akihiro ; Nakaoka, Hajime ; Saichi, Naomi ; Sanbonmatsu, Ryoko ; Sato, Yoshiharu ; Shinso, Yuji ; Suzuki, Mami ; Takeda, Junichi ; Tanino, Motohiko ; Todokoro, Fusano ; Yamaguchi, Kaori ; Yamamoto, Naoyuki ; Yamasaki, Chisato ; Imanishi, Tadashi ; Okido, Toshihisa ; Tada, Masahito ; Ikeo, Kazuho ; Tateno, Yoshio ; Gojobori, Takashi ; Lin, Yao Cheng ; Wei, Fu Jin ; Hsing, Yueie ; Zhao, Qiang ; Han, Bin ; Kramer, Melissa R. ; McCombie, Richard W. ; Lonsdale, David ; O’donovan, Claire C. ; Whitfield, Eleanor J. ; Apweiler, Rolf ; Koyanagi, Kanako O. ; Khurana, Jitendra P. ; Raghuvanshi, Saurabh ; Singh, Nagendra K. ; Tyagi, Akhilesh K. ; Haberer, Georg ; Fujisawa, Masaki ; Hosokawa, Satomi ; Ito, Yukiyo ; Ikawa, Hiroshi ; Shibata, Michie ; Yamamoto, Mayu ; Bruskiewich, Richard M. ; Hoen, Douglas R. ; Bureau, Thomas E. ; Namiki, Nobukazu ; Ohyanagi, Hajime ; Sakai, Yasumichi ; Nobushima, Satoshi ; Sakata, Katsumi ; Barrero, Roberto A. ; Sato, Yutaka ; Souvorov, Alexandre ; Smith-White, Brian ; Tatusova, Tatiana ; An, Suyoung ; An, Gynheung ; Oota, Satoshi ; Fuks, Galina ; Messing, Joachim ; Christie, Karen R. ; Lieberherr, Damien ; Kim, Hyeran ; Zuccolo, Andrea ; Wing, Rod A ; Nobuta, Kan ; Green, Pamela J. ; Lu, Cheng ; Meyers, Blake C. ; Chaparro, Cristian ; Piegu, Benoit ; Panaud, Olivier ; Echeverria, Manuel. / The Rice Annotation Project Database (RAP-DB) : 2008 update. In: Nucleic Acids Research. 2008 ; Vol. 36, No. SUPPL. 1.
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abstract = "The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://www.w3.org/1999/ http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.",
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T1 - The Rice Annotation Project Database (RAP-DB)

T2 - 2008 update

AU - Tanaka, Tsuyoshi

AU - Antonio, Baltazar A.

AU - Kikuchi, Shoshi

AU - Matsumoto, Takashi

AU - Nagamura, Yoshiaki

AU - Numa, Hisataka

AU - Sakai, Hiroaki

AU - Wu, Jianzhong

AU - Itoh, Takeshi

AU - Sasaki, Takuji

AU - Aono, Ryo

AU - Fujii, Yasuyuki

AU - Habara, Takuya

AU - Harada, Erimi

AU - Kanno, Masako

AU - Kawahara, Yoshihiro

AU - Kawashima, Hiroaki

AU - Kubooka, Hiromi

AU - Matsuya, Akihiro

AU - Nakaoka, Hajime

AU - Saichi, Naomi

AU - Sanbonmatsu, Ryoko

AU - Sato, Yoshiharu

AU - Shinso, Yuji

AU - Suzuki, Mami

AU - Takeda, Junichi

AU - Tanino, Motohiko

AU - Todokoro, Fusano

AU - Yamaguchi, Kaori

AU - Yamamoto, Naoyuki

AU - Yamasaki, Chisato

AU - Imanishi, Tadashi

AU - Okido, Toshihisa

AU - Tada, Masahito

AU - Ikeo, Kazuho

AU - Tateno, Yoshio

AU - Gojobori, Takashi

AU - Lin, Yao Cheng

AU - Wei, Fu Jin

AU - Hsing, Yueie

AU - Zhao, Qiang

AU - Han, Bin

AU - Kramer, Melissa R.

AU - McCombie, Richard W.

AU - Lonsdale, David

AU - O’donovan, Claire C.

AU - Whitfield, Eleanor J.

AU - Apweiler, Rolf

AU - Koyanagi, Kanako O.

AU - Khurana, Jitendra P.

AU - Raghuvanshi, Saurabh

AU - Singh, Nagendra K.

AU - Tyagi, Akhilesh K.

AU - Haberer, Georg

AU - Fujisawa, Masaki

AU - Hosokawa, Satomi

AU - Ito, Yukiyo

AU - Ikawa, Hiroshi

AU - Shibata, Michie

AU - Yamamoto, Mayu

AU - Bruskiewich, Richard M.

AU - Hoen, Douglas R.

AU - Bureau, Thomas E.

AU - Namiki, Nobukazu

AU - Ohyanagi, Hajime

AU - Sakai, Yasumichi

AU - Nobushima, Satoshi

AU - Sakata, Katsumi

AU - Barrero, Roberto A.

AU - Sato, Yutaka

AU - Souvorov, Alexandre

AU - Smith-White, Brian

AU - Tatusova, Tatiana

AU - An, Suyoung

AU - An, Gynheung

AU - Oota, Satoshi

AU - Fuks, Galina

AU - Messing, Joachim

AU - Christie, Karen R.

AU - Lieberherr, Damien

AU - Kim, Hyeran

AU - Zuccolo, Andrea

AU - Wing, Rod A

AU - Nobuta, Kan

AU - Green, Pamela J.

AU - Lu, Cheng

AU - Meyers, Blake C.

AU - Chaparro, Cristian

AU - Piegu, Benoit

AU - Panaud, Olivier

AU - Echeverria, Manuel

PY - 2008/1/1

Y1 - 2008/1/1

N2 - The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://www.w3.org/1999/ http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

AB - The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://www.w3.org/1999/ http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

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