Help:Contents

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.

• How do I cite lncRNAWiki?
  • The citation for lncRNAWiki is:
    • Unavailable
  • Other related publications:
    • RiceWiki: a wiki-based database for community curation of rice genes, Nucleic Acids Research, 2014,42(D1),D1222-D1228.
    • On the classification of long non-coding RNAs, RNA Biology, 2013, 10(6),925-933.
    • AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification, Bioinformatics, 2013, 29(14):1837-1839.
    • Community intelligence in knowledge curation: an application to managing scientific nomenclature, PLoS ONE, 2013, 8(2):e56961.

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

• Formatting: http://www.mediawiki.org/wiki/Help:Formatting
• Images: http://www.mediawiki.org/wiki/Help:Images
• Links: http://www.mediawiki.org/wiki/Help:Links
• Tables: http://www.mediawiki.org/wiki/Help:Tables
• Lists: http://www.mediawiki.org/wiki/Help:Lists

Database content

Annotated Information

• Transcriptomic Nomeclature

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 four groups (intergenic, intronic, sense and antisense) based on their genomic location in respect to protein-coding genes. As it is more complicated for the condition of sense and antisense, we also listed different kinds of sense and antisense lncRNAs, which can be viewed through different categories.
  • 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 sequences of protein-coding genes.
  • Sense(overlap): lncRNAs are transcribed from the sense strand of protein-coding genes and part of their sequences 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.
  • Antisense(contain): lncRNAs are transcribed from the antisense strand of protein-coding genes and cover the entire sequences of protein-coding genes.
  • Antisense(overlap): lncRNAs are transcribed from the antisense strand of protein-coding genes and part of their sequences are overlapped with part of the protein-coding genes.

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.

Annotation (From GENCODE)

The annotation section now includes at most three sub-sections, namely, ‘Annotation from GENCODE’, ‘Annotation from LNCipedia’, and ‘Annotation from LncRNAdb’. We extracted genomic location information from GENCODE and LNCipedia and put this information in section ‘Basic Information’. Therefore, genomic location information is removed from the corresponding annotation sections. Also, sequence information is transferred to the section of ‘Basic Information’. For users who want to find detailed information of lncRNA exons, they can refer to ‘Annotation from GENCODE’.

Annotation (From LNCipedia)

If users want to find information such as lncRNA secondary structure and miRNA binding, they can refer to ‘Annotation from LNCipedia’.

Annotation (From LncRNAdb)

If users want to find literature reported information such as expression, evolution, and biological functional, they can refer to ‘Annotation from lncRNAdb’