RiceWiki:FAQ

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Contents

Introduction

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What is RiceWiki?

RiceWiki, a project of IC4R (Information Commmons for Rice) as well as a component of ScienceWikis, is a wiki-based, publicly editable and open-content platform for community curation of genes and Omics Knowledge in rice, viz., a community-curated resource of rice knowledge. Unlike conventional biological databases based on expert curation, RiceWiki harnesses collective intelligence to collect, edit and annotate information about rice, quantifies users' contributions in each annotated gene and provides explicit authorship for each contributor to encourage more participation from the whole scientific community. Welcome to join us !

How do I contribute to RiceWiki?

You can perform different types of contributions to make RiceWiki the online encyclopedia for rice.

  • 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.

How do I cite RiceWiki?

The primary 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:

Accounts

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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.

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 RiceWiki adopt?

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

How is the content of each gene organized?

The content of every gene in RiceWiki is organized into multiple sections, namely, Annotated Information, Structured Information, 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 gene 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. A live example is here.

What is Structured Information in each gene page?

Structured Information is organized structurally in the form of a table, including gene symbol, gene description, sequence information, expression profile, external links to other related databases, and a set of images from GBrowse showing the genomic context of the gene and the gene structure. A live example is here.

How is the structured data in Structured Information kept up-to-date and is it possible to lost community edits?

To keep the structured data up-to-date, a semi-automatic pipeline has been developed, which is set to periodically update information from related databases (e.g., RefSeq, Ensembl, RAP-DB). If a new version is available for the structured 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 genes are merged or split, or the structure 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 gene?

Labs working on this gene is a list of laboratories throughout the world working on this gene, 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 genes.

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 Ricewiki?

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 Ricewiki?

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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