Difference between revisions of "Main Page"

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*<span class=plainlinks>[[:Category:Genes|Genes]]</span>
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*<span class=plainlinks>[[Special:CuratedGenes|'''Genes''']]</span>
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*[[RiceWiki:GeneFamilies|Gene Families]]
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*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]
 
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*[[RiceWiki:Chromosomes|Chromosomes]]
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*[[Special:BLAST|'''BLAST''']]
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*[[RiceWiki:Databases|Databases]]
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*[[RiceWiki:Templates|'''Templates''']]
 
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*[[RiceWiki:Genome_Browser|Genome Browser]]
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*[# '''Genome Browser''']
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*[[RiceWiki:Templates|Templates]]
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*[http://ngdc.cncb.ac.cn/databasecommons/search?term=Oryza%20sativa '''Databases''']
 
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*More than [[Special:CuratedGenes|'''1000 manually curated genes''']] are validated as high quality in RiceWiki.
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*Gene Expression Profiles retrieved from the [https://ngdc.cncb.ac.cn/red '''''IC4R-RED'''''] are integrated in RiceWiki.
 +
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']
 +
*[# '''35,717 Scientific Articles'''] associated with rice are provided for curators.
 +
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].
 
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*Featured genes: [[Os01g0883800]], [[Os02g0170300]], [[Os03g0149100]], [[Os08g0162100]]
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'''      |*******Recently Curated Genes*******|'''<br>'''    [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]'''    <br>'''    [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>'''    [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>'''    [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''
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*Stress-related genes: [[RiceWiki:Stress|a list of stress-related genes]]
 
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*Genes to be curated: [[RiceWiki:TBC|a list of genes to be curated]]
 
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*Curated genes: More than [[Curated Genes|''' 500 Rice Genes''']] have been curated.
 
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*'''[[Omics Knowledge Portal for Rice]]''': Sharing and Integrating the precious omics knowledge for rice.
 
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*Contribution score: [[Special:AuthorReward |quantified contributions]] by [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']
 
 
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*Literature: [http://literature.ic4r.org 31527] rice-related publications associated with rice genes
 
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*Transcriptome: gene expression profiles at 22 developmental stages and tissue types based on RNA-Seq
 
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*Variations: SNPs and INDELs (under collection)
 
 
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<!--------------main part one---------------->
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<!-----------Rice Genome Overview------------>
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<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div>
 +
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;">
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* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br>
 +
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]
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</div>
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<!-----------------Rice---------------------->
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<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div>
 +
<div style="padding:0.5em 0.5em;font-size:100%;">
 +
*As an important food
 +
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br>
 +
*As a biological model
 +
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div>
 
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<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured research</div>
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<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div>
 
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div>
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<div style="padding:0.5em 0.5em;font-size:110%;">
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<div style="padding:0.5em 0.5em;font-size:100%;">
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* '''Jun 29th, 2016''': The Upcoming Conference Note: [http://pgc.hzau.edu.cn/ '''The 17th Conference of Plant Genomics in China will be held in Fuzhou China from August 19th to 22th''']
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* '''Sep 04th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf2017 The 2017 Big Data Forum for Life and Health Sciences] will be held in Beijing China from October 13th to 17th.
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* '''Jun 25th, 2016''': [[Omics Knowledge Portal for Rice| '''The Omics Knowledge Portal for Rice was launched at RiceWiki. Welcome to join us and have fun!''' ]]
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* '''Jun 07th, 2017''': The Upcoming Conference Note: [http://www.ibc2017.cn/ The XIX International Botanical Congress in 2017] will be held in Shenzhen China from July 10th to 13th.
−
* '''Jun 21th, 2016''': [http://www.big.ac.cn/xwzx/xshd/201606/t20160621_4624539.html '''Seminar Note: Dr.Haixu from Indiana University will give a lecture  on 《Computational methods for characterizing spontaneous mutations in bacterial genomes using whole genome shotgun sequencing》''']
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* '''May 20th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/dpd The Workshop on DNA Methylation and Precision Medicine] will be held in Beijing China from June 08th to 10th.
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* '''Apr 19th, 2016''': [http://bigd.big.ac.cn/news/5 Dr. Zhang Zhang presented a talk at the 9th International Biocuration Conference.]
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* '''Nov 05th, 2016''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf The 2016 Big Data Forum for Life and Health Sciences] will be held in Beijing China from December 05th to 08th.
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* '''Mar 11th, 2016''': [http://bigd.big.ac.cn/news/2 '''A delegation from EMBL-EBI visited BIG Data Center''']
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* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.
−
* '''Jan 31th, 2016''': [http://www.cbrc.kaust.edu.sa/cbrcweb/sp/bd2016.php The staffs of BIG Data Center  presented a keynote lecture at the KAUST Research Conference in Saudi Arabia.]
 
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<!-----------Rice Genome Overview------------>
 
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<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Rice Genome Overview</div>
 
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<div style=" margin: auto;">[[File:RiceG.jpg]]</div>
 
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== ==
 
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<div style="padding:0.2em 0.5em;">
 
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====[[:Category:Japonica Genes | ''Oryza sativa Japonica'' Group]]====
 
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'''Chromosome'''
 
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[[:category:Japonica Chromosome 1|'''1''']].
 
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[[:category:Japonica Chromosome 2|'''2''']].
 
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[[:category:Japonica Chromosome 3|'''3''']].
 
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[[:category:Japonica Chromosome 4|'''4''']].
 
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[[:category:Japonica Chromosome 5|'''5''']].
 
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[[:category:Japonica Chromosome 6|'''6''']].
 
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[[:category:Japonica Chromosome 7|'''7''']].
 
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[[:category:Japonica Chromosome 8|'''8''']].
 
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[[:category:Japonica Chromosome 9|'''9''']].
 
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[[:category:Japonica Chromosome 10|'''10''']].
 
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[[:category:Japonica Chromosome 11|'''11''']].
 
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[[:category:Japonica Chromosome 12|'''12''']].
 
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[[:category:Japonica_Mitochondrion|'''Mt''']].
 
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[[:category:Japonica_Plastid|'''Pd''']]
 
  
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====[[:Category:Indica Genes | ''Oryza sativa Indica'' Group]]====
 
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'''Chromosome'''
 
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[[:category:Indica Chromosome 1|'''1''']].
 
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[[:category:Indica Chromosome 2|'''2''']].
 
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[[:category:Indica Chromosome 3|'''3''']].
 
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[[:category:Indica Chromosome 4|'''4''']].
 
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[[:category:Indica Chromosome 5|'''5''']].
 
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[[:category:Indica Chromosome 6|'''6''']].
 
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[[:category:Indica Chromosome 7|'''7''']].
 
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[[:category:Indica Chromosome 8|'''8''']].
 
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[[:category:Indica Chromosome 9|'''9''']].
 
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[[:category:Indica Chromosome 10|'''10''']].
 
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[[:category:Indica Chromosome 11|'''11''']].
 
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[[:category:Indica Chromosome 12|'''12''']]
 
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<!-----------------Rice---------------------->
 
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<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Rice Story</div>
 
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<div style="padding:0.5em 0.5em;font-size:110%;">
 
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[[File:Damifan.jpg|right|120px|margin: 5px|]]
 
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*As an important food
 
−
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br>
 
−
*As a biological model
 
−
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div>
 
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----
 
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<div style="padding:0.5em 0.5em;font-size:110%;">
 
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[[File:IC4R_Omics_Pic_Jian.png|right|bottom|frameless|274px|text-top|link=Omics_Knowledge_Portal_for_Rice|]]
 
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*Omics is a discipline of science and engineering for large-scale analysis of the functions and interactions of biological information, including [[Genome Sequencing Studies in Rice|'''Genomics''']], [[Epigenomic Studies in Rice|'''Epigenomics''']], [[MRNA-Seq_Related_Studies_in_Rice|'''Transcriptomics''']], [[Proteomic Studies in Rice|'''Proteomics''']], [[Metabolomics|'''Metabolomics''']], Lipidomics, Interactomics and [[Phenomics|'''Phenomics''']].
 
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* In order to make a comprehensive integration of published omics knowledge for rice, in 2016, we establish [[Omics Knowledge Portal for Rice|'''Omics Knowledge Portal for Rice (OKP4R)''']] in RiceWiki. [[Omics Knowledge Portal for Rice|'''(More...)''']]
 
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<div style="background:#f4f4f4; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">The Lastest Published Research on Rice Genes </div>
 
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<div style="padding:0.5em 0.5em;">
 
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* [http://www.ncbi.nlm.nih.gov/pubmed/?term=27200061 '''Chai, Chenglin, and Prasanta K. Subudhi. "Comprehensive Analysis and Expression Profiling of the OsLAX and OsABCB Auxin Transporter Gene Families in Rice (Oryza sativa) under Phytohormone Stimuli and Abiotic Stresses." Frontiers in plant science 7 (2016).''']
 
−
* Triplett, Lindsay R., et al. "A resistance locus in the American heirloom rice variety Carolina Gold Select is triggered by TAL effectors with diverse predicted targets and is effective against African strains of Xanthomonas oryzae pv. oryzicola." The Plant Journal (2016).
 
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* Che, Jing, et al. "An Al‐inducible expansin gene, OsEXPA10 is involved in root cell elongation of rice." The Plant Journal (2016).
 
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* Araus, Viviana, et al. "Members of BTB gene family regulate negatively nitrate uptake and nitrogen use efficiency in Arabidopsis thaliana and Oryza sativa." Plant physiology (2016): pp-01731.
 
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* Srikanth, B., et al. "Enhanced expression of OsSPL14 gene and its association with yield components in rice (Oryza sativa) under low nitrogen conditions." Gene 576.1 (2016): 441-450.
 
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* Liu, Erbao, et al. "Identification of a Candidate Gene for Panicle Length in Rice (Oryza sativa L.) Via Association and Linkage Analysis." Frontiers in plant science 7 (2016).
 
 
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Joining RiceWiki</div>
 
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<div style="padding:0.5em 1em;">
 
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* RiceWiki allows any user to view and search but only registered users can add and edit content.
 
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* To become a registered user, please email the RiceWiki Team at [mailto:ricewiki@big.ac.cn ricewiki@big.ac.cn] to tell us your preferred login name, real name, research interests, etc., and we will set up an account for you.
 
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* Please also spread this news to any one who might be of interest. [[File:Ppt_ico.gif | link=File:CommunityCuration-RiceWiki.pptx]]</div>
 
  
 
<!-------------Lab Information-------------->
 
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div>
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">About Us</div>
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'''Primary publication:'''<br>
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* Our group works in the field of [http://cbb.big.ac.cn Computational Biology and Bioinformatics] (CBB), currently with a particular focus on building biological knowledge wikis in aid of community curation of massive biological knowledge.
+
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]
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* '''Since January 1st, 2016, our lab has been merged as a founding group into BIG Data Center  in Beijing Institute of Genomics (http://bigd.big.ac.cn).'''
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'''Related publications:'''
 +
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]
 +
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]
 +
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]
 
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<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">2016 RiceWiki Community Curation Awards !</div>
 
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*[http://biocuration.org/dissemination/who-are-we/ '''Biocuration'''] involves the translation and integration of information relevant to biology into a database or resource that enables integration of the scientific literature as well as large data sets (from [http://biocuration.org/ '''International Society for Biocuration''']). In order to boost the development of Biocuration for Rice Genetic Knowledge, we offer bonuses for outstanding Biocurators in RiceWiki Community.The Qualifications for Election are as follows:
 
−
* The Curators who participate in RiceWiki Curation (from 01-01-2016 to 31-12-2016),if his/her gets a [http://ricewiki.big.ac.cn/index.php/Special:AuthorReward '''Contribution Score'''] (≥ 200) can receive a certificate from Big Data Center, plus a beautiful gift, such as [http://item.jd.com/10391529360.html '''Mi Band'''].
 
−
* The Curator who pass the above Election and get the Highest Score can an Smart Watch, such as [http://item.jd.com/1548534.html '''Apple Watch''']. 
 
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* All the awarding information will be shown in [http://wiki.ic4r.org/index.php/Main_Page '''RiceWiki'''] Website before March 31th, 2017.
 
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<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications Related With RiceWiki</div>
 
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* [http://www.ncbi.nlm.nih.gov/pubmed/26519466 Information Commons for Rice (IC4R)] (2016) ''Nucleic Acids Research'', 44(D1):D1172-D1180.
 
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* [http://www.ncbi.nlm.nih.gov/pubmed/24136999 RiceWiki: a wiki-based database for community curation of rice genes] (2014) ''Nucleic Acids Research'', 42(D1),D1222-D1228.
 
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* [http://www.ncbi.nlm.nih.gov/pubmed/23732274 AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification] (2013) ''Bioinformatics'', 29(14):1837-1839.
 
 
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Latest revision as of 02:37, 25 November 2025


Welcome to RiceWiki
86,216 rice genes inside
Contribute your efforts, further our knowledge.
Introduction
RiceWiki, a project of IC4R (Information Commmons for Rice) as well as a component of ScienceWikis, is a wiki-based, publicly editable and open-content platform for community curation of genes and Omics Knowledge in rice, viz., a community-curated resource of rice knowledge. Unlike conventional biological databases based on expert curation, RiceWiki harnesses collective intelligence to collect, edit and annotate information about rice, quantifies users' contributions in each annotated gene and provides explicit authorship for each contributor to encourage more participation from the whole scientific community. Welcome to join us !
Nothing great is ever accomplished in isolation. – Yo-Yo Ma
      |*******Recently Curated Genes*******|
     Os06g0683400, Os03g0125100, Os01g0192000     
     Os01g0848400, Os06g0107700, Os10g0563600 
     Os01g0919400, Os03g0180800, Os12g0583700
     Os09g0306400, Os10g0553300, Os09g0286400
Omics Knowledge Portal for Rice (OKP4R)
  • OKP4R: a multidisciplinary portal to share omics knowledge for rice. (More...)
Figure 1. Omics Knowledge Portal for Rice
Rice Story
  • As an important food
Rice is the seed of the monocot plants Oryza sativa (Asian rice) or Oryza glaberrima (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 (Full article...).
  • As a biological model
Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, indica and japonica, were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.
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Publications

Primary publication:

  • RiceWiki: a wiki-based database for community curation of rice genes. Nucleic Acids Research (2014), 42(Database issue):D1222-1228. PMID=24136999

Related publications:

  • Information Commons for Rice (IC4R). Nucleic Acids Research (2016), 44(D1):D1172-1180. PMID=26519466
  • Bringing biocuration to China. Genomics Proteomics Bioinformatics (2014), 12(4):153-155.PMID=25042682
  • AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification. Bioinformatics (2013), 29(14):1837-1839.PMID=23732274]
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