LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs

Abstract

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.

Figure 1.

Data source of lncRNAWiki.

Figure 2.

Classification of lncRNAs based on their genomic location in respect of protein-coding genes. (A) lncRNA categories. 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. (B) Proportions of human lncRNAs in different categories.

Figure 3.

Screenshots of the lncRNAWiki page for the lncRNA transcript MALAT-1, available at http://lncrna.big.ac.cn/index.php/ENST00000534336.1. 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. (C) Annotated information. It is organized as free text and links to several sub-sections. (D) Labs working on 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 ‘Cite’ extension. (F) Basic Information. It is organized structurally in the form of a table, including transcript ID, source, transcript structure, genome context, sequence information, etc. (G) Authorship details generated by the ‘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.