View source for CAZypedia:About

<big>''Welcome to CAZypedia!''</big>

== Overview ==
''CAZypedia'' <cite>CAZypediaConsortium2017</cite> is an encyclopedic resource on carbohydrate-active enzymes.  It is inspired by, and meant to be a logical extension of, the [http://www.cazy.org/ 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 <cite>DaviesSinnott2008 Cantarel2009</cite>. An article describing the genesis and development of ''CAZypedia'' has been published in ''Glycobiology'' <cite>CAZypediaConsortium2017</cite>.

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 [[CAZypedia:History|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 [[Board of Curators|Senior Curator]] [[User:Harry Brumer|Harry Brumer]] is [http://hdl.handle.net/2429/39734 openly available via the cIRcle repository at the University of British Columbia] (click on the video link [https://circle.ubc.ca/flashstreamview/bitstream/handle/2429/39734/Brumer_H_CAZypedia_OAW2011.wmv?sequence=3 ''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 [https://circle.ubc.ca/bitstream/handle/2429/39734/Brumer_H_CAZypedia_OAW2011.pptx?sequence=1 presentation slides] are also available [http://hdl.handle.net/2429/39734 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 [[Board of Curators|Senior Curators]] is responsible for setting editorial policy and ensuring that a high standard of articles is met.  Individual pages are managed by [[Responsible Curator]]s 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|User accounts]] section below.

''A full list of ''CAZypedia'' contributors, linked to their individual ''curricula vitae'', is available [[:Category:Contributors|here]].''

== Content ==
Although meant to be truly dynamic, in the spirit of the constantly evolving [http://en.wikipedia.org/ 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 [http://www.cazy.org 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 [http://en.wikipedia.org/ ''Wikipedia''] and, in particular, [http://www.citizendium.org/ ''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 [http://en.citizendium.org/wiki/CZ:Fundamentals ''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 ===

# The ultimate goal of the ''CAZypedia'' community, a global group of collaborators, is to create the most reliable encyclopedia of carbohydrate-active enzymes possible.
# ''CAZypedia'' will be a wiki. Edits will not be required to be approved before appearing on the wiki.
# ''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 ===

# The content of ''CAZypedia'' will always be openly available for non-commercial use, although [[CAZypedia:Copyrights|all copyright is retained]].
# It will be the project's aim to make the content of ''CAZypedia'':

<blockquote>
* 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
</blockquote>

=== Fundamental policies concerning community governance ===

# All contributors to ''CAZypedia'' must do so using their own real names.
# ''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.
# ''CAZypedia'' will invite subject area experts to serve as [[Responsible Curator]]s.  [[Responsible Curator]]s will be expected to work "shoulder-to-shoulder" with [[Author]]s in the wiki.  Among the things that [[Responsible Curator]]s 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 Curator]]s ''will not'' have the right, except perhaps in very unusual cases, to "lock" articles and thereby prevent the collaborative process from continuing.  
# ''CAZypedia'' will have a set of senior [[Responsible Curator]]s 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.
# There will be a separation of powers: [[Responsible Curator]]s will not be able to decide project policy, although the [[Board of Curators|Senior Curators]] will remain open to suggestions from all contributors.

=== Statement of rights ===
# 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.
# 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'':
*[http://en.wikipedia.org/wiki/Wikipedia:What_Wikipedia_is_not What Wikipedia is not] (Read: "What ''CAZypedia'' is not").
*[http://en.wikipedia.org/wiki/Wikipedia:Simplified_Ruleset 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.
* See also this article: <cite>Logan2010</cite>.

== 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 [[Board of Curators|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 [[Help:Editing|writing pages]] and [[Help:References|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 [[Board of Curators|Primary Curator]], [[User:Harry Brumer|Harry Brumer]], must first create an account for you.  You can contact Harry via <email>brumer@msl.ubc.ca</email>.  Once you have an account, please see our [[Help:Getting Started Guide|Getting Started Guide]].'''

== Privacy policies ==
''CAZypedia's'' privacy policies are detailed [[CAZypedia:Privacy_policy|here]].

== References ==
<biblio>
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [https://doi.org/10.1042/BIO03004026 Download PDF version].
#Cantarel2009 pmid=18838391
#Logan2010 pmid=20941386
#CAZypediaConsortium2017 pmid=29040563
</biblio>