rice ( oryza sativa ) is not only the most important staple food feeding a large part of the world population , but also an important model organism for biological studies of crops as well as other related plants ( 1,2 ) . for this reason , rice was chosen as the first crop for whole genome sequencing . the availability of genome sequences of the two most common cultivated rice subspecies , indica 93 - 11 and japonica nipponbare ( 3,4 ) , along with the resequencing of cultivated and wild rice accessions ( 5 ) , enables the in - depth characterization of rice genes ( 6 ) , exploration of agronomically important traits ( 7 ) and investigation of rice diversity and domestication ( 8) . however , building standardized rice reference genomes with comprehensive and accurate annotations remains a formidable challenge . , conducted manually by dedicated experts . to perform curation , expert curators often administer raw biological data , conduct a thorough literature search , extract essential information from multiple publications , curate the information using structured and controlled vocabularies and then submit the information to a knowledge database [ e.g. , the reference sequence database ( 11 ) at the national center for biotechnology information ] to make it public . however , with the exponentially exploding volume of rice knowledge and other relevant data , expert curation is becoming more laborious and time - consuming . keeping biological knowledge in expert - curated databases comprehensive , up - to - date and accurate is increasingly lagging behind knowledge creation , or worse , not being done at all in fields where insufficient funds can be allocated to curation ( 14 ) . simply put , although expert - curated databases have traditionally proven important for scientific research , they are struggling with the flood of knowledge . explosive growth in the volume of rice data requires a large number of people getting involved in knowledge curation , viz . community curation exploits the whole power of the scientific community for knowledge curation ( 1519 ) . a case in point that harnesses community intelligence in knowledge integration is wikipedia ( http://www.wikipedia.org ) . wikipedia is an online encyclopedia , allowing any user to create / edit any content . it features collaborative knowledge curation , up - to - date content , huge coverage and low cost for maintenance ( 20 ) . despite fears that the openness of editorial capacity could lead to incorporation of significant flawed content ( 21 ) , broad participation in wikipedia not only increases knowledge coverage and keeps knowledge up - to - date , but also improves knowledge accuracy (  with enough eyeballs , all bugs are shallow ; http://oreilly.com/web2/archive/what-is-web-20.html ) . owing to the extraordinary success of wikipedia , it has been advocated that biological databases go wiki ( 23 ) . as a consequence , more than a dozen biological wikis ( 2442 ) have been constructed to exploit the full potential of the scientific community for knowledge curation , such as ecoliwiki for the model bacteria escherichia coli ( 27 ) , gene wiki for human gene annotation ( 28 ) and pdbwiki for protein structures ( 31 ) . to date , however , there is no community - curated resource for rice . to establish a platform for community integration of rice data and to facilitate efficient management of community knowledge on rice , here we develop ricewiki ( http://ricewiki.big.ac.cn ) , a wiki - based , publicly editable and open - content platform for community curation of rice genes unlike extant relevant databases , ricewiki features harnessing community intelligence in curation of rice genes , quantifying users contributions in each curated gene and providing explicit authorship for each contributor in any given gene , with the aim to attract more participation from the scientific community in collaborative and collective curation of rice genes . ricewiki has been implemented using mediawiki ( http://www.mediawiki.org ; a free and open source wiki engine ; version 1.18.4 ) , mysql ( http://www.mysql.org ; a free and popular relational database management system ; version 5.1.58 ) and php ( http://www.php.net ; a widely used general - purpose scripting language ; version 5.2.17 ) on a red hat enterprise linux server . the wide adoption of community intelligence in knowledge curation is primarily attributable to free wiki software such as mediawiki that provides a collaborative framework for knowledge collection , management and dissemination ( that powers wikipedia ) . mediawiki allows any user to add , modify or delete any content ( with customized permission control for editing ) via a web browser without any extra add - ons and thus enables web content to be edited easily , swiftly and collaboratively by multiple different users . history ; every change made to a page can be stored ; the user responsible for every change can be identified and every history revision can be reviewed or recovered . built on mediawiki , ricewiki enables users to be involved in an ongoing process of creation and collaboration that constantly changes the contents . thus , ricewiki can significantly ease the process of knowledge collection , curation and sharing , befitting the exploding volume of biological data . in addition , mediawiki allows any user to develop customized functionalities by packaging a bunch of codes as mediawiki extensions . authorreward ( http://www.mediawiki.org/wiki/extension:authorreward ) in ricewiki , with the aim to attract more participation from the scientific community for collaborative curation of rice genes . a wiki page can be collaboratively curated by multiple users and thus may have different edit versions . for each version that is contributed by a specific person , authorreward quantifies his / her contribution by factoring edit quality as well as edit quantity ; the edit quantity amounts to the edit distance in comparison with its previous version ( i.e. the minimum number of edit operations required to transform one string into the other ) , and the edit quality corresponds to whether the edit persists in comparison with the last version , ranging from 1 , when the edit is entirely reverted ( short - lived ) , to 1 , indicating that the edit is totally preserved in the last version ( long - lived ) . because one person may perform many discontinuous edits for a wiki page , his / her contribution score in this page is the sum of quantified contributions over all contributed edits . authorreward provides ricewiki with an authorship metric ; it quantifies users contributions and yields explicit authorship for each wiki page according to their quantitative contributions ( described later in the text ) . thus ,  authorreward bears the potential to increase community participation in ricewiki and to achieve community curation of massive biological knowledge . all extensions as well as software installed in ricewiki can be found at http://ricewiki.big.ac.cn/index.php/special:version . in ricewiki , users can access any content , but only registered users can perform the edits . this restriction is due to a trade - off between simplicity for users to make contributions and reliability of the edits provided . open identity provided by registration not only improves content reliability and increases users collaborations and communications , but it is also supportive to reward community - curated efforts by giving explicit authorship . thus , although the requirement of registration poses an unpleasant obstacle to community curation , it is of crucial significance for bio - wikis that would like to give credit to all contributors in reward for community - provided content . additionally , it is beneficial to greatly avoid vandalism or spammed content in bio - wikis , albeit , of course , there are multiple solutions for vandalism detection ( 43 ) . ricewiki incorporates the two common cultivated rice subspecies ( o. sativa indica 9311 and o. sativa japonica nipponbare ) and covers > 66 000 rice genes . as implemented on mediawiki , ricewiki inherits its features : each content page is associated with a discussion page ( where users can discuss content or leave a comment ) , a history page ( where revision as well as its contributor can be recognized ) and category terms ( that increase the usability for information management ) . the central objects of ricewiki are rice genes and thus each gene corresponds to a specific wiki page . to provide easy access to gene - specific pages , they are built based on gene identifiers . although they can also be based on gene names , it is noted that only a small part of rice genes has been well studied . with the ongoing studies on the biological functions of rice genes , a gene name often comes and goes as our knowledge about that entity increases , which would bring uncertainty of designations and synonyms of rice genes . thus , gene identifiers are relatively stable to refer to specific genes , as they do not change with the accumulation of novel information . the gene information in ricewiki was initially seeded from ncbi refseq ( 11 ) , ensembl ( 44 ) , rap - db ( 12 ) and msu rice genome annotation project ( http://rice.plantbiology.msu.edu ) . the content of every gene in ricewiki is structured into multiple sections , namely ,  annotated information ,  structured information ,  labs working on this gene and  references , as well as a one - sentence summary for gene description at the top of each page ( figure 1 ) . annotated information is organized as free text and is helpful to users who share their knowledge and contribute edits without training in the curation or wiki techniques , significantly simplifying edits provision and lowering technological entrance barriers for wider community participation in curation . it can also fall into several sub - sections , such as  function , evolution and  expression , making it convenient to direct users to the sub - section(s ) of interest . although these sub - sections are preset , new sub - sections can be easily added and irrelevant sub - section(s ) can be deleted . such arrangement with multiple sub - sections enables not only automatic entry of information via application programming interface but also facilitates users to intuitively edit the information by clicking an edit link available to each sub - section . on the contrary ,  structured information is organized structurally in the form of a table , including gene symbol , gene description , sequence information , expression profile , external links to other related databases and a set of images from gbrowse ( 45 ) showing the genomic context of the gene and the gene structure . albeit the structure of this table is preset , it also allows users to provide updates and additions . labs working on this gene is a list of laboratories throughout the world working on this gene , facilitating communication and collaboration in curation of this gene . figure 1.screenshots of the ricewiki page for the rice semidwarf-1 ( sd1 ) gene , available at http://ricewiki.big.ac.cn/index.php/os01g0883800 . this gene was collaboratively curated by nine researchers , yielding 89 versions as of 1 august 2013 . ( b ) brief authorship information in reward for community curation and a one - sentence summary for description of this gene . it is a list of laboratories working on this gene derived from references and provided by the community . ( e ) references , which are automatically generated and formatted with the help of the it is organized structurally in the form of a table , including gene symbol , gene description , sequence information , gene structure , etc . authorreward extension that quantifies researchers contributions and provides explicit authorship according to their quantitative contributions . the cutoff score for awarding authorship is configurable and set to 1 ( by default ) in ricewiki . screenshots of the ricewiki page for the rice semidwarf-1 ( sd1 ) gene , available at http://ricewiki.big.ac.cn/index.php/os01g0883800 . this gene was collaboratively curated by nine researchers , yielding 89 versions as of 1 august 2013 . ( b ) brief authorship information in reward for community curation and a one - sentence summary for description of this gene . it is a list of laboratories working on this gene derived from references and provided by the community . ( e ) references , which are automatically generated and formatted with the help of the it is organized structurally in the form of a table , including gene symbol , gene description , sequence information , gene structure , etc . authorreward extension that quantifies researchers contributions and provides explicit authorship according to their quantitative contributions . the cutoff score for awarding authorship is configurable and set to 1 ( by default ) in ricewiki . the major focus of ricewiki is to exploit the full potential of the scientific community in collaborative curation of rice genes . it should be noted , however , that one crucial essential to making knowledge aggregation successful in ricewiki and also in other bio - wikis is sufficient participation ( 19 ) , which requires a large number of people from the scientific community to curate biological knowledge collectively and collaboratively . unfortunately , the current status is that , despite the presence of well - constructed bio - wikis , most researchers seldom make direct contributions . the reason is well known : most people in areas covered by bio - wikis are in academic research fields , and the currency of academic research careers is authorship , and bio - wikis do not offer attributable authorship . it is an especially severe issue for young researchers , who are most open to new technologies such as wikis , but for whom one s publication record is the significant determinant to his / her academic professional success ( 41 ) . it is inevitably time - consuming and poorly motivating for researchers to spend time performing curation without career - advancing credit ( 46 ) as opposed to writing their next paper although , arguably , contributing to a common and open resource such as a bio - wiki may have much broader scientific impacts . there is no mechanism to reward people who perform knowledge curation in bio - wikis . it has been recognized that the major limitation deterring researchers from active participation in bio - wikis is the lack of explicit authorship and thus no credit for their contributions ( 17,19,41 ) . it should be also noted , however , that not all people care about authorship , e.g. , long - term wikipedia editors . despite this , authorship might be essential to academic - based researchers . to attract more participation from the scientific community for ricewiki and to make it a vivid platform for community curation of rice genes authorreward ( 47 ) , an extension to mediawiki , which provides a standard practice to reward community - provided contents in bio - wikis by quantifying researchers contributions and providing explicit authorship according to their quantitative contributions . for each gene - centric page in ricewiki , community curation is quantified as a contribution score for each contributor in which both edit quantity and quality are taken into account ( figure 1 ) . accordingly , authorship in ricewiki is awarded only to a contributor whose contribution score is > 1 ( by default ; this cut - off score is configurable ) . at the top of each page , we provide the authorship information , displaying contributor name(s ) , gene i d , hyperlink to this gene and last update time , which is aimed to encourage community participation and to show clearly how to cite community - curated efforts . additionally , at the bottom of each page , we present the detailed information , including a pie chart to visualize quantified contributions of multiple contributors who were involved in curating this gene , a histogram to depict the edit quantity and quality for each contributor and a table summarizing contributor name , contribution score , edit count , edit quantity , edit quality , last edit time and edit details . as one person may perform curations for multiple different pages , we define the total contribution of this person to ricewiki as the sum of multiple contribution scores in all participated pages . with explicit authorship as a reward for community curation , ricewiki has the potential to attract more people to share their expertise and to provide edits on genes of their interest . wikiomics in action ( 48 ) . considering the ever - growing volume of rice data and related literature and contrastingly the relatively small number of expert curators working on rice , it should be noted that community curation is an important complement to expert curation , and community - based bio - wikis , like ricewiki , are not aimed for replacement of traditionally expert - driven databases . ricewiki harnesses community intelligence in curating a wide range of rice - related topics and thus can save considerable time and efforts of expert curators . to encourage collaborative curations of rice genes in ricewiki , expert curators can conduct quality control for community - contributed information and provide a variety of training ( e.g. , webinars , online tutorials and open discussion ) for the community on how to perform curation in an accurate and standard manner . meanwhile , journals can be also involved in curation by building a mechanism to regard community curation as a compulsory post - publication process and by providing obligations or incentives to authors submitting relevant information to ricewiki . such a mechanism has already been put into practice in the journal plant physiology , partnering with the arabidopsis information resource to increase the curation of arabidopsis . wider adoption of this practice would be enormously beneficial to curatorial efficiency , accuracy and reliability ( as testified by the admirable annotations for arabidopsis ) . therefore , the community as well as expert curators , authors , and journals should collaborate together to make ricewiki more influential and to achieve community curation of massive rice knowledge . future directions for ricewiki include establishment of close collaborations with laboratories in the world working on rice . rice knowledge and related data developed by many laboratories and researchers should be added to ricewiki and shared with the whole scientific community . we will also promote , as best as we can partnership with journals to require community curation as a compulsory post - publication . in addition , we encourage investigators / teachers to incorporate community curation of rice genes in ricewiki as student assignments . for example , n students collaborate to curate n rice genes , where n  3 , and contribution score for each student should be > 1 . ricewiki will continue to integrate more types of data ( e.g. , mutants , repetitive elements , expression and phenotyping ) from different resources and improve the connections with existing relevant databases . we have collected 40 000 rice - related publications from pubmed ( http://www.ncbi.nlm.nih.gov/pubmed/ ) , including title , author(s ) , affiliation(s ) , abstract and hyperlinks to the full text ( if available ) , and currently are attempting to dig out the . therefore , ricewiki will also integrate tools particularly for literature mining ( 49,50 ) and incorporate literature - based curated annotation , to realize automatic information retrieval and improve the credibility of community - provided contents . in response to an update of literature collection , ricewiki will build a mechanism to send an invitation to authors with recent publications for curation of specific genes ( 51 ) . in sum it exploits the whole power of the scientific community in collaborative curation of rice genes by rewarding community - provided content through contribution quantification and explicit authorship . such a collaborative community - contributed and contribution - rewarded resource would make it possible to build a rice encyclopedia by and for the scientific community ( 52 ) that harnesses collective intelligence for collaborative knowledge curation , covers all aspects of biological knowledge and keeps evolving with novel knowledge . 100-talent program of chinese academy of sciences [ y1slxb1365 to z.z . ] ; the national basic research and development program [ 973 program ; 2010cb126604 to j.x . ] ; national programs for high technology research and development [ 863 program ; 2012aa020409 to z.z . and j.x . ] , the ministry of science and technology of the people s republic of china . funding for open access charge : national programs for high technology research and development [ 863 program ; 2012aa020409 ] , the ministry of science and technology of the people s republic of china .
rice is the most important staple food for a large part of the world s human population and also a key model organism for biological studies of crops as well as other related plants . 
 here we present ricewiki ( http://ricewiki.big.ac.cn ) , a wiki - based , publicly editable and open - content platform for community curation of rice genes . 
 most existing related biological databases are based on expert curation ; with the exponentially exploding volume of rice knowledge and other relevant data , however , expert curation becomes increasingly laborious and time - consuming to keep knowledge up - to - date , accurate and comprehensive , struggling with the flood of data and requiring a large number of people getting involved in rice knowledge curation . unlike extant relevant databases , ricewiki features harnessing collective intelligence in community curation of rice genes , quantifying users ' contributions in each curated gene and providing explicit authorship for each contributor in any given gene , with the aim to exploit the full potential of the scientific community for rice knowledge curation . 
 based on community curation , ricewiki bears the potential to make it possible to build a rice encyclopedia by and for the scientific community that harnesses community intelligence for collaborative knowledge curation , covers all aspects of biological knowledge and keeps evolving with novel knowledge .