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Revision as of 09:12, 16 June 2014 by Lina Ma (talk | contribs) (Basic information)
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FAQ

Introduction

  • What is LncRNAWiki?
LncRNAWiki is a wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs), viz., a community-curated lncRNA knowledgebase. Unlike conventional biological databases based on expert curation, lncRNAWiki harnesses collective intelligence to collect, edit and annotate information about lncRNAs, quantifies users' contributions in each annotated lncRNA and provides explicit authorship to encourage more participation from the whole scientific community.

You can perform different types of contributions to make LncRNAWiki the online encyclopedia for lncRNA.

  • If you are a researcher, please share your knowledge and curate genes in your area of expertise.
  • If you are a teacher/investigator, community curation of lncRNA genes in LncRNAWiki can be incorporated as student assignments, where contribution can be quantified as a score.
  • If you are a student, you can work as a volunteer, e.g., data collection, content formatting.
  • If you are a journal publisher, please consider community curation as a compulsory post-publication when any lncRNA-related paper is accepted by the journal.
  • At the very least, please spread this news to any one who might be of interest.
You can perform different types of contributions to make LncRNAWiki the online encyclopedia for lncRNA.

LncRNAWiki Accounts

  • Is it allowed for any user to provide edits in lncRNAWiki?
LncRNAWiki allows any user to view and search but only registered users can add and edit content.
  • Why do I open my identity and become a registered user?
Open identity provided by registration not only improves content reliability, increases users’ collaborations and communications, but is also supportive to reward community-curated efforts by giving explicit authorship. It is of crucial significance for lncRNAWiki that would like to give credits to all contributors in reward for community-provided contents.
  • How do I acquire a LncRNAWiki account?
Please email the LncRNAWiki Team at lncwiki@big.ac.cn to tell us your preferred login name, real name, research interests, etc., and we will set up an account for you.
  • How do I update my account information or change password?
To update your account information, please log on first and then you may find a link named "My preferences" at the top right.
  • Why I can't log into lncRNAWiki?
    • Make sure that the Caps Lock key is not depressed. Passwords are case sensitive.
    • Make sure your browser is set to accept cookies.
    • Contact us at lncrnawiki@big.ac.cn.

Editing tips

Database content

Basic information

  • Genomic location: This information is obtained from GENCODE and LNCipedia annotation.
  • Same with: LncRNAs that have the same sequence and also the same genomic location in other databases. For lncRNAs that do not have genomic location, such as lncRNAs from NONCODE, same with means having the same sequence.
  • Classification: Classification based on genomic location and context
We obtained genome location information from Gencode and LNCipedia annotation and classified lncRNAs into the following nine groups.
    • Intergenic: lncRNAs are transcribed from intergenic regions.
    • Intronic: lncRNAs are transcribed entirely from introns of protein-coding genes.
    • Sense(contained): lncRNAs are transcribed from the sense strand of protein-coding genes and the entire sequence of lncRNAs are covered by protein-coding genes. Note, intronic lncRNAs are not included.
    • Sense(contain): lncRNAs are transcribed from the sense strand of protein-coding genes and cover the entire sequence of protein-coding genes.
    • Sense(overlap): lncRNAs are transcribed from the sense strand of protein-coding genes and part of their sequence are overlapped with part of the protein-coding genes.
    • Antisense(intronic): lncRNAs are transcribed from antisense strand of protein-coding genes and the entire sequences are covered by introns of protein-coding genes.
    • Antisense(contained): lncRNAs are transcribed from the antisense strand of protein-coding genes and the entire sequence of lncRNAs are covered by protein-coding genes. Note, antisense intronic lncRNAs are not included.
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Figure 1. Genomic location and context of lncRNAs. Protein-coding genes and their exons are represented by blue color, while lncRNAs and their exons are represented by red color.

Download

To facilitate people to perform genome-wide analysis of lncRNAs, we provide download of basic information of the non-redundant human lncRNAs (52,616 lncRNAs). Our present data is based on GENCODE V15, NONCODE V3.0, LNCipedia V2.1, and lncRNAdb (downloaded on Feb. 21st, 2013).