CAZypedia:About

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Welcome to CAZypedia!

Contents

Overview

CAZypedia is an encyclopedic resource on carbohydrate-active enzymes. It is inspired by, and meant to be a logical extension of, the CAZy database, which "describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds." Two excellent introductions to the CAZy classification are available [1, 2].

The origins of CAZypedia date back to the summer of 2006 through the spring of 2007, when the initial idea to create an encyclopedia of CAZymes was proposed by Bruce Stone and subsequently developed through discussions among a group of experts in the field. A brief history of major milestones in the evolution of CAZypedia is available on the History page. The News page documents other continuous developments, including the completion of individual CAZypedia pages.

Video presentation

A short presentation of CAZypedia for a general audience by Senior Curator Harry Brumer is openly available via the cIRcle repository at the University of British Columbia (click on the video link view in browser or download the entire 325 Mb video in WMV format; the CAZypedia presentation is at running time 37:00-55:50). The corresponding presentation slides are also available via cIRcle, and can be read independently of the video.

Contributors

CAZypedia openly welcomes contributions of new articles and editorial corrections from persons actively engaged in glycoscience research. A group of Senior Curators is responsible for setting editorial policy and ensuring that a high standard of articles is met. Individual pages are managed by Responsible Curators who act as editors of Author contributions; please see the links for more detailed descriptions of these roles. A user account is required before one can contribute to CAZypedia - Please see the User accounts section below.

A full list of CAZypedia contributors, linked to their individual curricula vitae, is available here.

Content

Although meant to be truly dynamic, in the spirit of the constantly evolving Wikipedia, the first incarnation of CAZypedia is focused on cataloging the structural and mechanistic "firsts" in each of the CAZy glycoside hydrolase (GH) families. In particular, primary literature will be cited which gives the first identification of enzyme active site residues, catalytic mechanism, three dimensional structure, or other important work which defines catalysis in a GH family or subfamily.

CAZypedia is not meant to be a direct repetition of the CAZy Database, nor of the GenBank and UniProt protein sequence databases, but a distillation of the key work in the field.

Editorial policies

The editorial policies of CAZypedia are inspired by the best aspects of Wikipedia and, in particular, Citizendium. CAZypedia will strive to be a dynamic, community-based effort, while at the same time balancing a high level of curation and editorial input to produce quality content.

In this respect, CAZypedia directly incorporates many of Citizendium's Fundamental Policies. For the purposes of CAZypedia, we have adapted these policies as follows:

The CAZypedia project is launching with some fundamental policies. Those who support these commitments are invited to contribute; those who reject any of these policies are kindly asked to abstain from participating.

The nature of the project

  1. The ultimate goal of the CAZypedia community, a global group of collaborators, is to create the most reliable encyclopedia of carbohydrate-active enzymes possible.
  2. CAZypedia will be a wiki. Edits will not be required to be approved before appearing on the wiki.
  3. CAZypedia will be devoted to simplicity, both in presentation of content and in the organization of the community. Special roles will not be created without excellent reason, and bureaucracy will be kept to the absolute minimum necessary.

Fundamental policies concerning content

  1. The content of CAZypedia will always be openly available for non-commercial use, although all copyright is retained.
  2. It will be the project's aim to make the content of CAZypedia:
  • accurate
  • based on published, credible research (i.e., all statements should be supported by reference to peer-reviewed publications of the highest possible standard)
  • neutral in sense
  • legal and responsible

Fundamental policies concerning community governance

  1. All contributors to CAZypedia must do so using their own real names.
  2. CAZypedia will be open to contribution by anyone (an Author) who is able to make a positive difference and who is willing to work collaboratively under the policies and management of the project.
  3. CAZypedia will invite subject area experts to serve as Responsible Curators. Responsible Curators will be expected to work "shoulder-to-shoulder" with Authors in the wiki. Among the things that Responsible Curators will be empowered, singly or collectively, to do are (1) to make decisions about specific questions, or disputes, concerning particular articles in a Responsible Curator's area of expertise, and (2) to approve high-quality articles. Responsible Curators will not have the right, except perhaps in very unusual cases, to "lock" articles and thereby prevent the collaborative process from continuing.
  4. CAZypedia will have a set of senior Responsible Curators of mature judgment specially empowered to enforce rules, comprising the Board of Curators. The enforcement of project rules is to be carried out using common sense and leniency.
  5. There will be a separation of powers: Responsible Curators will not be able to decide project policy, although the Senior Curators will remain open to suggestions from all contributors.

Statement of rights

  1. Contributors in good standing have a right to build CAZypedia without constantly having to do battle with people who are constantly breaking project rules or trying to undermine the project. There will be a process for rapidly removing rule-breakers from the project. While most people will enjoy the privilege of contributing to CAZypedia if they are able to make a positive difference, there is a blanket right neither to contribute nor to participate in the project's governance.
  2. The general public has the right to expect the quickest possible removal of copyright-protected and libelous material. Processes and tools will be created that make it difficult for libel to appear on articles concerning living persons and their activities, and for such to be removed as quickly as it is found.

More guidelines for CAZypedia contributors

These pages contain more information on Wikipedia's guidelines, which are in most cases applicable to the operation of CAZypedia. These are strongly recommended reading before authoring or curating CAZypedia:

  • What Wikipedia is not (Read: "What CAZypedia is not").
  • Simplified Wikipedia ruleset. Use a neutral point-of-view, write verifiable text, include only peer-reviewed information (no original research), be civil and well-behaved, and don't infringe copyright.

User accounts

You must have a user account before you can contribute to CAZypedia.

  • If you are interested in contributing to CAZypedia, please contact the Responsible Curator for the page to which you would like to contribute. If you want to contribute a new page or act as a Responsible Curator, please contact a Senior Curator.
  • Users must use their full name as their username when creating an account on CAZypedia.
  • After creating an account, we also request that all users fill in some biographical information about themselves on their user page. Your user page can be accessed by clicking your username at the top of any CAZypedia page after you have logged in.
  • It is strongly recommended to read the help pages on writing pages and inserting references before starting to write/edit for CAZypedia.

If you would like to begin working on CAZypedia as an Author or Responsible Curator, the Primary Curator, Harry Brumer, must first create an account for you. You can contact Harry via this contact form or via his user page. Once you have an account, please see our Getting Started Guide.

Privacy policies

CAZypedia's privacy policies are detailed here.

References

  1. Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (A BJ Classics review, online only). DOI: 10.1042/BJ20080382 [DaviesSinnott2008]
  2. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 | PubMed ID:18838391 | HubMed [Cantarel2009]
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