Help:Contents

FAQ

Introduction

• What is RiceWiki?

RiceWiki:Summary

• How do I contribute to RiceWiki?
  • 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 rice genes in RiceWiki 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 rice-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 RiceWiki the online encyclopedia for rice.

• How do I cite RiceWiki?
  • The citation for RiceWiki is:
    • RiceWiki: a wiki-based database for community curation of rice genes, Nucleic Acids Research, 2014,42(D1),D1222-D1228.
  • Other related publications:
    • 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.

RiceWiki Accounts

• Is it allowed for any user to provide edits in RiceWiki?

RiceWiki 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 RiceWiki that would like to give credits to all contributors in reward for community-provided contents.

• How do I acquire a RiceWiki account?

Please email the RiceWiki Team at ricewiki@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 RiceWiki?
  • 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 ricewiki@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

1. 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.

• Antisense(contain): lncRNAs are transcribed from the antisense strand of protein-coding genes and cover the entire sequence of protein-coding genes.

• Antisense(overlap): lncRNAs are transcribed from the antisense strand of protein-coding genes and part of their sequence 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.