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 Nakaoka; Naomi 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

doi:10.1093/nar/gkm978

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

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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/.

Original language	English (US)
Pages (from-to)	D1028-D1033
Journal	Nucleic acids research
Volume	36
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkm978
State	Published - Jan 1 2008

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkm978

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Tanaka, T., Antonio, B. A., 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., ... Echeverria, M. (2008). The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic acids research, 36(SUPPL. 1), D1028-D1033. https://doi.org/10.1093/nar/gkm978

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, pp. D1028-D1033. https://doi.org/10.1093/nar/gkm978

@article{794a7bd73d364bbf838cc51c36baf4ca,

title = "The Rice Annotation Project Database (RAP-DB): 2008 update",

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/.",

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

note = "Funding Information: The authors thank Pankaj Jaiswal, Chengzhi Liang and Sharon Wei for the information about the positions of OMAP BAC ends, and Kumiko Suzuki and Chieko Kobayashi for their technical assistance. This work was supported by a grant from the Special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology of Japan, by a grant for the NIAS Genebank Project, and by a grant for the Project ANR OsmiR NT05-3 42996. Funding to pay the Open Access publication charges for this article was provided by National Institute of Agrobiological Sciences.",

year = "2008",

month = jan,

day = "1",

doi = "10.1093/nar/gkm978",

language = "English (US)",

volume = "36",

pages = "D1028--D1033",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "SUPPL. 1",

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TY - JOUR

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

N1 - Funding Information: The authors thank Pankaj Jaiswal, Chengzhi Liang and Sharon Wei for the information about the positions of OMAP BAC ends, and Kumiko Suzuki and Chieko Kobayashi for their technical assistance. This work was supported by a grant from the Special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology of Japan, by a grant for the NIAS Genebank Project, and by a grant for the Project ANR OsmiR NT05-3 42996. Funding to pay the Open Access publication charges for this article was provided by National Institute of Agrobiological Sciences.

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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U2 - 10.1093/nar/gkm978

DO - 10.1093/nar/gkm978

M3 - Article

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AN - SCOPUS:38549136871

SN - 0305-1048

VL - 36

SP - D1028-D1033

JO - Nucleic acids research

JF - Nucleic acids research

IS - SUPPL. 1

ER -

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

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