LncRNAWiki:FAQ

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Contents

Introduction

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What is lncRNAWiki?

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

How is lncRNAWiki organized?

The central entities of lncRNAWiki are human lncRNA transcripts. Thus, each transcript has a corresponding wiki page. Meanwhile, transcripts are grouped together by classification categories, as well as by genes. This information can be accessed at the homepage and at the bottom of the transcript page. Transcript-specific pages are generated based on transcript identifiers. The content of every transcript in lncRNAWiki is structured into two parts: ‘user-edit’ part and ‘Basic Information’ part. The ‘user-edit’ part allows users to add or delete annotations.

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 download the data?

Click here to download the data.

How do I search lncRNA in lncRNAWiki?

In the homepage, you can enter the ID of a lncRNA and press "GO", which will direct you to the transcript page. If you want to search by name or other keywords, "GO" and "Search" options can be used. If you want to search by sequence, "blast" option can be used.

How lncRNAWiki guarantee the quality of the users' submissions under a framework of wiki?

We have to highlight that there is no absolute guarantee of quality that can be given for every entry of any large-scale manually curated database. In this sense, our lncRNAWiki is in the same position as any other community-based curation system. However, we have implemented measures aimed at keeping the quality at high level and these are similar to those implemented in other community-based curation systems. First, lncRNAWiki is an open-identity database; users can view all content, but only registered users can perform edits. Open identity links a submission to the verified name of the submitter. Researchers will be careful of what they submit because everybody can access whole wiki content including the names of the submitters for any specific entry. In this way, entries (and their submitters) are open to criticism and entries can be changed. Second, when a user is going to add an lncRNA, the submitted lncRNA must be reported by at least one published paper and the annotation information has to cite the corresponding papers in the proper manner in the “References” section. Third, lncRNAWiki provides a framework where any member of the scientific community can be engaged in the process of collective and collaborative curation of human lncRNAs. Thus, we plan to invite field experts and authors of lncRNA publications to get involved in curation. This is facilitated through the section “Labs working on this lncRNA” for each lncRNA with the purpose to further improve the edit quality.

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 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 lncwiki@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 lncRNAs. In addition, lncRNAWiki invites field experts and authors of lncRNA publications to get involved in curation.

Simply speaking, lncRNAWiki adopts a combined way based on both expert curation and community curation.

How is the content of each transcript organized?

The content of every transcript in lncRNAWiki is organized into multiple sections, namely, Annotated Information,Basic Information, Labs working on this gene, and References, as well as a one-sentence summary for gene description at the top of each page. The user-edit part (Annotated Information, Labs working on this gene, References, and the one-sentence summary for gene description at the top of each page) allows users of LncRNAWiki to add or delete annotations. On the contrary, Basic Information is organized structurally in the form of a table.

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, 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 includs 10 sub-sections, ‘Transcript ID’, ‘Source’, ‘Same with’, ‘Classification’, ‘Length’, ‘Genomic location’, ‘Exon number’, ‘Exons’, ‘Genome context’, and ‘Sequence’. ‘Transcript ID’ refers to the original lncRNA ID in each database. ‘Source’ indicates which database and version this lncRNA is from. ‘Same with’ provides IDs of lncRNAs that are considered to be the same entry in other databases. We classified lncRNAs into seven groups based on their genomic location in respect to protein-coding genes, Intergenic, Intronic (S), Intronic (AS), Overlapping (S), Overlapping (AS), Sense, and Antisense. Most of the lncRNAs belong to only one category, a small number (1,020) belong to more than one category. Sub-sections of‘Length’, ‘Genomic location’, ‘Exon number’and ‘Exons’show the length, genomic location, exon number and genomic location of exons. The sub-section ‘Genome context’ will facilitate users to view the transcript structure and genomic context. ‘Sequence’is the lncRNA transcript sequence.

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, NONCODE). 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.

How can I add a new lncRNA?

If a lncRNA is newly reported in a published paper but is found not to be included by the present lncRNAWiki dataset after search (search by ID or name, and search by sequence), users can create a new page for this lncRNA. To guarantee the quality of the users' submissions, the submitted lncRNA must be reported by at least one published paper and the annotation information has to cite the corresponding papers in the proper manner in the “References” section. LncRNAWiki does not accept new lncRNAs that lack of support from published paper(s).

How can I edit or update the annotations of lncRNAs that have been included by lncRNAdb?

There are 104 lncRNAs that have been annotated by lncRNAdb in our present dataset. We established a new web page (well-known lncRNAs) to facilitate the easy access to these lncRNAs. To facilitate annotation or curation of these lncRNAs, we put lncRNAdb annotations in the transcript page and users can do their edits based on these annotations.

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.

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