LncRNAWiki:FAQ

Introduction

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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.

How do I contribute to LncRNAWiki?

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.

• 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.

Accounts

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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 lncrnawiki@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.

Contribution Quantification

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What is edit quantity?

A wiki page can be collaboratively curated by multiple users and thus may have different edit versions. For each edit version, the edit quantity amounts to the edit distance in comparsion with its previous version, that is, the minimum number of edit operations required to transform one string into the other.

What is edit quality?

For each edit version, the edit quality corresponds to whether the edit persists in comparison with the last version, ranging from -1, when the edit is entirely reverted (short-lived), to 1, indicating that the edit is totally preserved in the last version (long-lived).

How is contribution quantified?

For each version that is contributed by a specific person, his/her contribution is quantified as its edit quality multiplied by its edit quantity.

What is the contribution score as displayed at the bottom of each wiki page?

Since one person may perform many discontinuous edits and accordingly contribute multiple versions for a wiki page, his/her contribution score for this page is the sum over all contributed versions.

Where can I find more information about how to quantify community-curated efforts?

Please see our published paper: AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification, Bioinformatics, 2013, 29(14):1837-1839.

Curation

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What is curation?

In life sciences, curation or biocuration involves the translation and integration of information relevant to biology into a database or resource that enables integration of the scientific literature as well as large data sets. Accurate and comprehensive representation of biological knowledge, as well as easy access to this data for working scientists and a basis for computational analysis, are primary goals of biocuration. See here for more information.

What is the difference between expert curation and community curation?

Traditionally, biological knowledge has been aggregated through expert curation, conducted manually by dedicated experts. However, with the burgeoning volume of biological data and contrastingly the small number of expert curators, expert curation becomes more and more laborious and time consuming, increasingly lagging behind knowledge creation. Accordingly, community curation—harnessing community intelligence for knowledge curation, bears great promise in dealing with the flood of biological knowledge.

What kind of curation does LncRNAWiki adopt?

LncRNAWiki features community-based curation, viz., exploiting the full potential of the scientific community for collaborative curation of lncRNA transcripts. In addition, LncRNAWiki invites field experts and authors of publications to get involved in curation.

How is the content of each transcript organized?

The content of every gene in LncRNAWiki is organized into multiple sections, namely, Annotated Information,Basic Information, Annotation (From Gencode),Annotation (From LNCipedia),Annotation (From lncRNAdb), Labs working on this gene, and References, as well as a one-sentence summary for gene description at the top of each page.

What is Annotated Information in each transcript page?

Annotated Information is organized as free text and of great helpfulness for users who share their knowledge and contribute edits without training in the curation or wiki techniques. It can also fall into several sub-sections, such as Function, Evolution, Expression, etc., making it convenient to direct users to the sub-section(s) of interest. Although these sub-sections are preset, new sub-section can be easily added and irrelevant sub-section(s) can be deleted.

What is Basic Information in each transcript page?

Basic information includes‘Transcript ID’,‘Genomic location’,‘Same with’,‘Classification’, ‘Sequence'. ‘Transcript ID’refers to the original lncRNA ID in each database. ‘Same with’ provides IDs of lncRNAs that are considered to be the same entry in other databases. There is no standard classification of lncRNA at present, and the classification of lncRNA based on genomic location is suggested to be of great biological significance. GENCODE project 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 further classified human lncRNAs into nine groups

What is Annotation in each transcript page?

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’. If users want to find information such as lncRNA secondary structure and miRNA binding, they can refer to ‘Annotation from LNCipedia’. If users want to find literature reported information such as expression, evolution, and biological functional, they can refer to ‘Annotation from lncRNAdb’.

How is the annotation data from other databases kept up-to-date and is it possible to lost community edits?

To keep the annotation data up-to-date, a semi-automatic pipeline has been developed, which is set to periodically update information from related databases (e.g., GENCODE, LNCipedia, lncRNAdb). If a new version is available for the annotation data, the pipeline will first detect community edits by comparing the current version to the new one, and then merge community edits into the gene page if available. In addition, MediaWiki provides each page with an associated page named “History” and every change made to a page is stored. Thus, community edits can also be easily identified and recovered.

If lncRNAs are merged or split, or the annotation is significantly updated, are the community edits still considered valid?

It depends. “With enough eyeballs, all bugs are shallow”. Whether these edits are valid or invalid, is determined by the whole scientific community. If these edits are reverted (short-lived), it means that these edits are considered invalid by the community and accordingly the edit qualities will be negative, which further lead to negative contribution score. If these edits are long-lived, it indicates that these edits are valid and widely accepted by the community, the edit qualities will be positive.

What is the purpose of Labs working on this lncRNA?

Labs working on this lncRNA is a list of laboratories throughout the world working on this lncRNA, facilitating communication and collaboration in curation. Currently, we are developing an extension, with the aim to automatically send an invitation to authors for curation of specific lncRNAs.

Editing Tips

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How do I format the text?

Please find information here.

How do I add links?

Please find information here.

How do I search in LncRNAwiki?

Please find information here.

How do I track changes?

Please find information here.

What is watchlist?

Please find information here.

How do I edit pages?

Please find information here.

How do I put images into LncRNAwiki?

Please find information here.

How do I create lists?

Please find information here.

How do I add tables?

Please find information here.

What are categories?

Please find information here.

How do I manage files?

Please find information here.

How do I redirect pages?

Please find information here.

How do I add references?

Please find information here.