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Manually curated database of rice proteins

Pratibha Gour, Priyanka Garg, Rashmi Jain, Shaji V. Joseph, Akhilesh K. Tyagi, Saurabh Raghuvanshi
2013 Nucleic Acids Research  
Digitization of the experimental data via manual curation: concept The manual curation workflow adopted in developing the database is designed to digitize the actual experimental data published in peer-reviewed  ...  The database also has protein-protein interaction data for 199 rice proteins as well as DNA-protein interaction data for 51 rice proteins. How to access the database?  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt1072 pmid:24214963 pmcid:PMC3964970 fatcat:wxsisvg6fneifl3vcuoa5simhi

LocSigDB: a database of protein localization signals

S. Negi, S. Pandey, S. M. Srinivasan, A. Mohammed, C. Guda
2015 Database: The Journal of Biological Databases and Curation  
Manually Curated Database of Rice Proteins A unique curated database of rice proteins based. protein expression levels (for rice and Arabidopsis only), con-Output data were further manually curated with  ...  A hand-curated structural database dedicated to protein-protein interactions with Provides comprehensive information of interacting proteins in rice, where the Its data comes from manually curated protein-protein  ...  Such database entitled 'Manually Curated Database of Rice Proteins'. Here, we present a census of 1,542 manually curated RBPs that we have C.  ... 
doi:10.1093/database/bav003 pmid:25725059 pmcid:PMC4343182 fatcat:grzf5xbakna3lkdgopm5saaxge

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics

Y. Ito
2004 Nucleic Acids Research  
As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes.  ...  The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome.  ...  This work was funded by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Rice Genome Simulator Project SY-1102).  ... 
doi:10.1093/nar/gki083 pmid:15608281 pmcid:PMC540037 fatcat:pg6csrotsnhvnl75lsysikgjuy

Plant Protein Annotation in the UniProt Knowledgebase

M. Schneider
2005 Plant Physiology  
ACKNOWLEDGMENTS We would like to thank Alan Bridge, Michael Tognolli, and Sylvain Poux for critical reading of the manuscript.  ...  Manual Annotation and Minimal Redundancy Currently, the UniProt project has over 100 staff members, with five plant biologists assigned full time to the curation of plant proteins and protein families.  ...  With our newly established rice project, we will also increase the coverage of the detailed annotation of proteins of monocot origin.  ... 
doi:10.1104/pp.104.058933 pmid:15888679 fatcat:khnmftwseraablpqrqqxansis4

The Institute for Genomic Research Osa1 Rice Genome Annotation Database

Q. Yuan
2005 Plant Physiology  
We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species.  ...  Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed.  ...  ACKNOWLEDGMENT The efforts of the TIGR Bioinformatics department in generating a suite of tools and resources for eukaryotic sequence and annotation are appreciated.  ... 
doi:10.1104/pp.104.059063 pmid:15888674 fatcat:sbvxbr3vhndapmr6giqloe5usy

DRTF: a database of rice transcription factors

G. Gao, Y. Zhong, A. Guo, Q. Zhu, W. Tang, W. Zheng, X. Gu, L. Wei, J. Luo
2006 Bioinformatics  
DRTF contains 2,025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2,384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation  ...  sequence alignment of the DNA binding domains for each TF family.  ...  Combining automated InterPro scans and BLAST searches with careful manual curation, we have identified TFs in both indica and japonica, and constructed a database of rice transcription factors named DRTF  ... 
doi:10.1093/bioinformatics/btl107 pmid:16551659 fatcat:iloohkhw35folnknkjhqrba3ju

MGOS: Development of a Community Annotation Database forMagnaporthe oryzae

Anupreet Kour, Kevin Greer, Barbara Valent, Marc J. Orbach, Carol Soderlund
2012 Molecular Plant-Microbe Interactions  
Over 900 genes have been manually curated based on various biological databases and the scientific literature.  ...  Magnaporthe oryzae causes rice blast disease, which is the most serious disease of cultivated rice worldwide.  ...  Kour performed most of the manual annotation and coordination of the manuscript. We thank A. Descour for her work on adding the PAVE interface to MGOS and for help with maintenance and R.  ... 
doi:10.1094/mpmi-07-11-0183 pmid:22074346 fatcat:kgincexhnvcnjhhwoyyqnkwkjy

Involving community in genes and pathway curation

Sushma Naithani, Parul Gupta, Justin Preece, Priyanka Garg, Valerie Fraser, Lillian K Padgitt-Cobb, Matthew Martin, Kelly Vining, Pankaj Jaiswal
2019 Database: The Journal of Biological Databases and Curation  
We summarize the strategy, workflow and outcomes of these exercises, and discuss the role of community biocuration in advancing databases and genomic resources.  ...  In two pathway curation jamborees, Plant Reactome curators tested strategies for introducing researchers to pathway curation tools, harnessing biologists' expertise in curating plant pathways and developing  ...  We thank volunteer community curator, Bijayalaxmi Mohanty, for compiling the list of 75 rice genes that are transcriptionally regulated in response to cold that we used in the curation workshop for writing  ... 
doi:10.1093/database/bay146 pmid:30649295 pmcid:PMC6334007 fatcat:k76ydfk3nnf5fjcsuub47tsnr4

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

T. Itoh, T. Tanaka, R. A. Barrero, C. Yamasaki, Y. Fujii, P. B. Hilton, B. A. Antonio, H. Aono, R. Apweiler, R. Bruskiewich, T. Bureau, F. Burr (+83 others)
2007 Genome Research  
We thank all the participants of the First Rice Annotation Project Meeting (RAP1). We also thank the Computer Center for Agriculture, Forestry and Fisheries Research for assisting RAP1.  ...  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.  ...  The functions of these 28,540 proteins, which were inferred by BLASTX similarity searches against databases of proteins, were checked by manual curation.  ... 
doi:10.1101/gr.5509507 pmid:17210932 pmcid:PMC1781349 fatcat:ifpovjyd6nbzvba43hr2r4ugci

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

Hiroaki Sakai, Sung Shin Lee, Tsuyoshi Tanaka, Hisataka Numa, Jungsok Kim, Yoshihiro Kawahara, Hironobu Wakimoto, Ching-chia Yang, Masao Iwamoto, Takashi Abe, Yuko Yamada, Akira Muto (+5 others)
2013 Plant and Cell Physiology  
To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based  ...  The Rice Annotation Project Database (RAP-DB, http:// rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv  ...  We also thank Yukiko Yamazaki of the National Institute of Genetics for the valuable discussion on the literature-based manual curation.  ... 
doi:10.1093/pcp/pcs183 pmid:23299411 pmcid:PMC3583025 fatcat:d4on6zndmndplpue4t4r667aay

Comparison of rice and Arabidopsis annotation

Heiko Schoof, Wojciech M Karlowski
2003 Current opinion in plant biology  
This may be due to manual curation or the integration of extrinsic data such as EST and protein alignments.  ...  It is possible to predict the function of rice genes on the basis of homology searches against different protein (nr, Swiss-Prot; see Table 2 ) and protein-domain databases (Pfam, Prosite).  ... 
doi:10.1016/s1369-5266(03)00003-7 pmid:12667865 fatcat:zx3lyuhw4rf6hapov5qujpj5bm

Current Status of Rice Annotation Database (RAD)

Yuichi Ito, Isamu Ohta, Yoshiyuki Mukai, Baltazar A. Antonio, Michie Shibata, Mayu Yamamoto, Yukiyo Ito, Katsumi Sakata, Nobukazu Namiki, Takashi Matsumoto, Takuji Sasaki
2003 Genome Informatics Series  
Acknowledgments This research is funded by the MAFF grant SY-1102 and is part of the Rice Genome Simulator Project.  ...  Figure 1 : 1 Results of manual annotation using rice full-length cDNA. Figure 2 : 2 Current status of data incorporation.  ...  Annotation of finished PAC/BAC clones in other chromosomes have also been manually curated. These data have been incorporated in RAD at clone, contig and chromosome-levels.  ... 
doi:10.11234/gi1990.14.661 fatcat:2nfcwrl4jzadhjqdzqbcy4vaoe

Infrastructures of systems biology that facilitate functional genomic study in rice

Woo-Jong Hong, Yu-Jin Kim, Anil Kumar Nalini Chandran, Ki-Hong Jung
2019 Rice  
We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions  ...  Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems  ...  The Manually Curated Database of Rice Proteins (MCDRP) is an effort to digitize protein-related experiments. The concept of digitization addresses the demerits of text-based curation.  ... 
doi:10.1186/s12284-019-0276-z pmid:30874968 pmcid:PMC6419666 fatcat:zfqydgycnrahxjftpyg6cxd2v4

A High-Throughput Annotation System of Rice Genome Sequence at RGP

Atsuko Idonuma, Nobukazu Namiki, Takashi Matsumoto, Satoshi Nobushima, Shigehiro Honda, Takuji Sasaki
2002 Genome Informatics Series  
The system automatically performs BLAST searches against rice EST and nonredundant protein database; prediction of coding regions using FGENESH GENSCAN, RiceHMM, MZEF, SplicePredictor; and structural analysis  ...  The functions of the identified coding sequences are inferred from non-redundant protein database search with BLAST.  ... 
doi:10.11234/gi1990.13.541 fatcat:o7qpcfifbnbxfksv2bi6qxoore

Gramene: a bird's eye view of cereal genomes

P. Jaiswal
2006 Nucleic Acids Research  
Rice, maize, sorghum, wheat,  ...  Conflict of interest statement. None declared.  ...  We are thankful to numerous collaborators and contributors for help in curation and for sharing their datasets and tools.  ... 
doi:10.1093/nar/gkj154 pmid:16381966 pmcid:PMC1347516 fatcat:xbeiio34tvdmhdy55aisqjm6re
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