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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.

• 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

• The nomenclature of locus-specific transcripts

Example: hsa-N07QT0022001-SABC-LHPXX02 indicates the first non-coding transcript on the q-arm of chromosome 7 positioned on the 22th bin toward telomere, which resides in ABC gene locus in a sense direction, is a long transcript and highly expressed, and has an alternative promoter.

A locus-specific nomenclature is proposed as accession number for transcripts. It contains four consecutive segments joined by hyphens.

1. Segment 1 contains a three-letter code for species name. The standard naming convention is adapted: the first letter of genus name + the first two letter of the species name. For instance, Homo sapiens and Mus musculus are abbreviated as hsa and mmu, respectively.
2. Segment 2 contains 12 positions that display genomic information. The first three positions define the nature of a transcript and its residing chromosome. Capital letter N and C are dedicated to non-coding and coding transcripts, respectively. Chromosome numbers are indicated with two positions and 0 can be added to take the vacant position when the chromosome number is less than two digits (such as 01 and 07) or when X and Y are encountered (0X and 0Y are used). Transcription direction is, defined by the fourth and fifth positions, indicated with Q for the q-arms, P for the p-arms (when the transcript is on the centromere or telomere as well as subtelomeric and centromeric regions, the position is labeled as 0 rather than the definite Q or P), T for toward telomere, and C for toward centromere. The next seven digits are devoted to position the transcript; the first four define the bin number where the gene locus resides and the rest three define the number of transcripts within the bin based on first-come-first-name rule. The bins of a given chromosome are named from centromere to telomere in a nominal size of 100 Kb.
3. Segment 3 has four positions that define a gene locus. At the first position, S is used to indicate a non-coding transcript overlaps with a protein-coding gene on the same strand or in the same direction. A is used to indicate a non-coding transcript overlapping with the protein-coding gene on the antisense strand or in the opposite direction. For a protein-coding locus, the gene name is directly adapted. For a non-coding transcript, either the name of a nearby gene or a named non-coding RNA locus is abbreviated. When non-coding RNA has both S and A relationships with different protein-coding genes, S relationship is considered with priority.
4. The last segment is used to define the characteristics of all transcripts in a locus. Seven positions are included: (1) transcript size is defined as large (L, >500 bp), mediate (M, from 100 bp to 500 bp), and small (S, from 20 bp to 100 bp). (2) Expression level is defined in three categories that include highly (H, RPKM or similar units>100), moderate (M, from 10 to 100), and low (L, <10). (3) Alternative promoter (P), alternative exon (E), alternative poly (A) (A) are also indicated for all transcripts in the locus. When one or two of the three alternative forms are absent, X can be filled in to take the position(s). (4) Two digits are dedicated to accommodate the number of transcriptional variants.

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 annotation, 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’