in mammals , a small fraction of the genome ( e.g. in human ) is transcribed into messenger rnas , whereas the most represents a transcribed 
dark matter that does not encode for proteins . among them , long non - coding rnas ( lncrnas ) are prevalently transcribed from mammalian genomes and are present in large amounts in mammalian cells ( 14 ) .
evidence has accumulated that lncrnas play significant roles in numerous fundamental biological processes such as transcription , translation , cell cycle , imprinting , splicing and protein localization ( 57 ) and are highly implicated in cancer progression ( 814 ) and development of many other human diseases such as mendelian disorders , cardiovascular diseases and neurological disorders ( 1417 ) .
advances in studies of non - coding rna and consequently the increasing number of lncrnas identified have resulted in the development of several lncrna - related databases . among them ,
gencode , which aims at annotating all functional elements in the human genome ( 4 ) , has made a comprehensive annotation of gene structure ( gene loci , transcript loci , exon number and splicing boundary ) of 23 898 human lncrna transcripts ( version 19 ) .
noncode ( 18 ) collects 95 135 lncrna transcripts in human obtained from published literatures and databases ( version 4.0 ) .
lncipedia ( 19 ) contains a total of 32 181 human lncrna transcripts and incorporates related statistics such as protein - coding potential , secondary structure information and microrna binding sites ( version 2.1 ) .
lncrnadb ( 20 ) focuses on collecting function annotations based on the published literatures and , to date , only about 200 lncrnas have been included in lncrnadb .
another database , rfam , centers on non - coding rna families and thus does not provide specialized information for an individual lncrna ( 21 ) .
it can be seen that although these existing databases offer valuable information on different aspects and different level of coverage of the lncrna universe , there is a lack of a dedicated database for human lncrnas that provides lncrna transcript details coupled with the capability to make data update and curation in a smooth and easy way .
specifically , existing databases are most dependent on expert curation and thus laborious to comprehensively update the fast growing number of newly discovered lncrnas .
wikipedia ( http://www.wikipedia.org ) , an online encyclopedia , is an extraordinarily successful example that relies on the community knowledge in information integration and allows people from all over the world to create / edit any content .
wikipedia features collaborative information integration , huge coverage , up - to - date content as well as low - maintenance cost .
many attempts have been made in application of wiki for biological data integration ( 2225 ) .
for example , rfam , dedicated to rna families , has adopted the wiki technology for community curation . according to its name
, lncipedia looks like a wiki resource , but in fact it is not fully open to the scientific community for data provision / edit . considering the exponentially accumulated volume of lncrnas , it is desirable to exploit the knowledge of the broad scientific community for collaborative integration and curation of lncrna information ( 2630 ) . here
this platform is wiki - based and open - content , publicly editable and aimed at community curation of human lncrnas . unlike existing relevant databases , lncrnawiki features comprehensive integration of information on human lncrnas , cataloging 105 255 non - redundant lncrna transcripts obtained from multiple different resources .
moreover , it harnesses collective knowledge for collecting , editing and annotating information on human lncrnas and rewards community - curated efforts by quantifying contributions of users and providing explicit authorship based on their quantified contributions , aiming to exploit the knowledge of broad scientific community in addressing collectively collaborative curation of human lncrnas .
therefore , lncrnawiki has the potential to serve as an up - to - date and comprehensive knowledgebase for human lncrnas .
lncrnawiki is built based on mediawiki version 1.19.1 ( http://www.mediawiki.org ) , which is an open source wiki engine , mysql version 5.1.58 ( http://www.mysql.org ) a popular and free relational database management system , and php version 5.2.17 ( http://www.php.net ) , which is a scripting language .
these were implemented on a red hat enterprise linux server . in order to make lncrnawiki more attractive for participants from the broader scientific community in tasks of collaborative curation of lncrnas
authorreward ( http://www.mediawiki.org/wiki/extension:authorreward ) , an extension to mediawiki that allows for obtaining customized functionalities ( 31 ) .
 authorreward quantifies participants contribution considering both edit quality and edit quantity , and provides explicit authorship based on these quantified contributions .
it has been successfully demonstrated in ricewiki ( 32 ) , where it has attracted more than 800 participants in collaborative curation of 600 genes .
we also integrated jbrowse ( version 1.11.4 ) ( 33,34 ) into lncrnawiki to facilitate visualization of the genomic context and transcript structure for each lncrna .
we integrated lncrna sequences and annotation information ( e.g. genomic location , transcript structure ) from three data sources : gencode ( version 19 ; 23 898 human lncrna transcripts ) , noncode ( version 4.0 ; 95 135 human lncrna transcripts ) and lncipedia ( version 2.1 ; 32 181 human lncrna transcripts ) .
n in each data source , and as a result , a total of eight lncrnas in lncipedia were removed .
second , we excluded lncrnas with ambiguous naming scheme ; in each data source , two or more lncrna transcripts having 100% sequence identity on the whole transcript length ( based on blastn results ) and occupying the same genomic location but having different ids are considered as questionable lncrnas . consequently , 14 , 20 and eight lncrnas were removed from gencode , noncode and lncipedia , respectively .
lastly , since different databases may have different naming schemes and a given lncrna transcript may accordingly have different identifiers in different databases , we performed blastn across these three data sources .
lncrna transcripts having 100% sequence identity ( based on blastn results ) and occupying the same genomic location were regarded as the same lncrna .
finally , we obtained a total of 105 255 non - redundant lncrna transcripts ( figure 1 ) .
we also blasted these 105 255 lncrnas against lncrna sequences in lncrnadb ( 223 lncrnas in total as of july 21 , 2014 ) and found only 103 lncrnas have been functionally annotated ( supplementary table s1 ) , indicating that a large number of human lncrnas are poorly annotated and need a platform for community annotation of lncrnas .
data source of lncrnawiki . based on our previous study ( 7 ) and categories of derrien et  al .
( 35 ) , we classified the 105 255 non - redundant lncrna transcripts into seven groups according to their genomic location in respect to protein - coding genes , viz . ,
intergenic , intronic ( s ) , intronic ( as ) , overlapping ( s ) , overlapping ( as ) , sense and antisense ( figure 2 ) . the difference between our classification and derrien 's ( 35 ) is that we classified lncrnas that intersect protein - coding genes into sense or antisense by considering the whole transcript sequence instead of exonic region only .
classification of lncrnas based on their genomic location in respect of protein - coding genes .
intergenic : lncrnas are transcribed from intergenic regions ; intronic ( s ) : lncrnas are transcribed entirely from introns of protein - coding genes ; intronic ( as ) : lncrnas are transcribed from antisense strand of protein - coding genes and the entire sequences are covered by introns of protein - coding genes ; overlapping ( s ) : lncrnas that contain coding genes within an intron on the sense strand ; overlapping ( as ) : lncrnas that contain coding genes within an intron on the antisense strand ; sense : lncrnas are transcribed from the sense strand of protein - coding genes and the entire sequence of lncrnas are covered by protein - coding genes ( intronic lncrnas are not included ) , or the entire sequence of protein - coding genes are covered by lncrnas ( overlapping lncrnas are not included ) , or both lncrnas and protein - coding genes intersect each other partially ; antisense : lncrnas are transcribed from the antisense strand of protein - coding genes and the entire sequence of lncrnas are covered by protein - coding genes ( intronic lncrnas are not included ) , or the entire sequence of protein - coding genes are covered by lncrnas ( overlapping lncrnas are not included ) , or both lncrnas and protein - coding genes intersect each other partially .
meanwhile , transcripts are grouped together by classification categories , as well as by genes .
this information can be accessed at the homepage and at the bottom of the transcript page .
the content of every transcript in lncrnawiki is structured into two parts :  user - edit part and  basic information part .
the  user - edit part allows users to add or delete annotations . on the contrary ,
the  basic information portion is organized as a table and will be regularly updated by the lncrnawiki team based on the annotation information integrated from multiple different lncrna - associated sources .
the lncrna information in lncrnawiki was seeded from gencode , noncode and lncipedia , yielding a comprehensive integration of 105 255 non - redundant lncrna transcripts ( figure 1 ) .
this lncrna was collaboratively curated by four researchers , yielding 125 versions as of october11 , 2014 . ( a ) whole page , containing multiple different sections .
( b ) brief authorship information in reward for community curation and a one - sentence summary for the description of this lncrna .
it is a list of laboratories working on this lncrna 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 transcript i d , source , transcript structure , genome context , sequence information , etc .
authorreward extension that quantifies researchers contributions and provides explicit authorship according to their quantitative contributions .
the cutoff core for awarding authorship is configurable and set to 1 ( by default ) in lncrnawiki . 
basic information provides users with the basic details of lncrna such as genomic location , transcript structure and sequence .
 classification ,  length ,  genomic location ,  exon number ,  exons ,  genome context and  sequence.
source indicates the source database , as well as its version , from which this lncrna is obtained . 
same with provides ids of lncrnas that are considered to be the same entry in other lncrna sequence databases .
taking into account that the genomic context of lncrnas may offer insights into their function , the classification of lncrnas based on genomic location is of great biological significance in in - depth mining and analysis ( 7 ) .
we classified lncrnas into seven categories considering their genomic location in respect of protein - coding genes , i.e. sense , antisense , overlapping ( s ) , overlapping ( as ) , intergenic , intronic ( s ) and intronic ( as ) ( figure 2a ) .
according to the present data set , it is shown that the majority of human lncrnas belong to the categories of intergenic ( 59.2% ) and sense ( 24.4% ) ( figure 2b ) . the sub - section 
the  user - edit part includes three sections :  annotated information ,  labs working on this lncrna and  references ( figure 3 ) . 
it is helpful for users who do not have training in wiki techniques or curation to contribute edits and share knowledge , which simplifies editing significantly and lowers technological requirements for participation in curation of a wider community .  annotated information links to several sub - sections including 
regulation ,  diseases and  evolution , providing convenience of directing users to other sub - section(s ) of interest . considering the importance and the necessity of lncrna nomenclature
transcriptomic nomeclature. as most of the lncrnas have not been functionally studied , we named lncrnas based on their biological features such as genomic location , alternative splicing and expression level by basically following the rules of hgnc ( 36 ) ( figure 3 )
. users can add new sub - sections if necessary , while those that are irrelevant can be deleted .
edit link available to each sub - section and , moreover , can be made by using application programming interface for automatic entry of information .
 labs working on this lncrna contains a worldwide list of laboratories that work on this lncrna , thus facilitating collaboration and interaction in curation of this lncrna .
 references provides publications related to the lncrna and they are automatically formatted using the 
community - curated efforts are quantified and rewarded by explicit authorship , aiming to encourage more participants from the wider scientific community in collective and collaborative curation of lncrnas . in any given lncrna page ,
curation efforts for all participated contributors are quantified as contribution score which evaluates both quality and quantity of edits , and consequently , authorship is awarded to any contributor from the scientific community whose contribution score is greater than a cutoff score ( by default , it is 1 ) ( figure 3 ) .
each page at the top displays the brief authorship information , including contributor name(s ) , lncrna i d , hyperlink to this lncrna and last update time .
this information includes a pie chart to depict contribution scores for all involved contributors , edit quality and quantity for each contributor are illustrated by a histogram , and contributor names are listed in a table with contribution score , edit count , edit quality , edit quantity , last edit time and edit details .
in addition , when a newly identified human lncrna is reported , any user can create a new page to add specific information for this lncrna , enabling lncrnawiki to become an up - to - date and comprehensive knowledgebase for human lncrnas .
for example , we added to lncrnawiki ( http://lncrna.big.ac.cn/index.php/lunar1 ) lunar1 , a recently discovered human lncrna , immediately after the relevant paper was published online .
lunar1 is notch - regulated and it enhances mrna expression of igf1r ( insulin - like growth factor receptor 1 ) aiming at maintenance of human t - cell acute lymphoblastic leukemia ( t - all ) ( 37 ) .
lncrnawiki is a wiki - based database dedicated for human lncrnas , comprehensively integrating information on human lncrnas from multiple different resources and exploiting the wide scientific community to collect , edit and annotate human lncrnas .
it allows not only existing lncrnas to be edited , updated and curated by different users but also newly identified lncrnas to be added by any user . as the number of lncrnas grows fast and is contrasted by the small number of expert curators focused on lncrna , lncrnawiki has the potential to serve as an up - to - date and comprehensive knowledgebase for human lncrnas .
it should be noted , however , that lncrnawiki does not aim to replace traditionally expert - curated databases , but represents their important complement .
lncrnawiki relies on community intelligence to curate a wide range of lncrna - related topics , which thus can significantly reduce efforts and time of expert curators . with explicit authorship as a reward for community curation
, lncrnawiki bears the promise to attract more people ( especially field experts ) to share their expertise and to provide edits on lncrnas of their interest .
in addition , it is of great significance for authors of recent publications to curate their newly reported lncrnas and to submit their functional descriptions to lncrnawiki , facilitating information dissemination and maximizing the scope of knowledge sharing .
together , based on community curation , lncrnawiki has a potential to grow into an lncrna encyclopedia by the community , of the community and for the community .
future directions for lncrnawiki include integrating more types of data in the section of  basic information ( e.g. expression level , tissue - specific expression , orthologs ) from different sources and improving links to existing relevant databases , such as the lncrna - associated disease database lncrnadisease ( 38 ) and lncrna expression database nred ( 39 ) . to facilitate the detection and annotation of lncrnas
, we will also integrate analysis tools into lncrnawiki for lncrna detection and classification and employ automatic text mining in aid of lncrna - related literature curation .
strategic priority research program of the chinese academy of sciences [ xdb13040500 to z.z . ] ; national natural science foundation of china [ 31200978 to l.m . ] ; base research fund of king abdullah university of science and technology [ to v.b.b . ] ; 
funding for open access charge : strategic priority research program of the chinese academy of sciences [ xdb13040000 ] .
 long non - coding rnas ( lncrnas ) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases . in this report 
 we present lncrnawiki ( http://lncrna.big.ac.cn ) , a wiki - based platform that is open - content and publicly editable and aimed at community - based curation and collection of information on human lncrnas . 
 current related databases are dependent primarily on curation by experts , making it laborious to annotate the exponentially accumulated information on lncrnas , which inevitably requires collective efforts in community - based curation of lncrnas . 
 unlike existing databases , lncrnawiki features comprehensive integration of information on human lncrnas obtained from multiple different resources and allows not only existing lncrnas to be edited , updated and curated by different users but also the addition of newly identified lncrnas by any user . 
 it harnesses community collective knowledge in collecting , editing and annotating human lncrnas and rewards community - curated efforts by providing explicit authorship based on quantified contributions . 
 lncrnawiki relies on the underling knowledge of scientific community for collective and collaborative curation of human lncrnas and thus has the potential to serve as an up - to - date and comprehensive knowledgebase for human lncrnas . 