1. An introduction On behalf of the ”CAZypedia Consortium” Harry Brumer, Ph.D. Professor The Michael Smith Laboratories, UBC and School of Biotechnology, Royal Institute of Technology (KTH) brumer@msl.ubc.ca www.cazypedia.org

2. :About  CAZypedia is an online, community-driven effort to assemble a comprehensive encyclopedia of the enzymes and binding proteins involved in the synthesis and degradation of complex carbohydrates. –An evolving encyclopedia of carbohydrate-active enzymes – ”CAZymes” –CAZypedia is inspired by, and closely connected with, the actively curated CAZy Database (www.cazy.org). www.cazypedia.org

3. :CAZymes – pictorial overview www.cazypedia.org 128 families22 families 16 families 94 families Current total: >>100000 sequences

4. :Extension of the CAZy DB www.cazy.org Bernard Henrissat Pedro Coutinho

5. :Extension of the CAZy DB www.cazy.org Bernard Henrissat Pedro Coutinho

6. :Inspiration & genesis  CAZypedia is dedicated to the late Prof. Bruce Stone (LaTrobe Univ., AUS) –whose enthusiasm to create a comprehensive encyclopedia of carbohydrate-active enzymes was essential to the genesis of this project. –Envisioned a printed series of volumes  But: Producing a (comprehensive) encyclopedia of CAZymes is a huge task! –An active global research community  incredibly dynamic knowledge base –e.g., 128 GH familes – and counting... –Continuous generation of family-level information  Sequences  Functional properties  Mechanisms  3-D structures ... July 2006 23 rd ICS, Whistler www.cazypedia.org

7. :Generation shift  Print = static, WWW = dynamic –Wiki wiki ! –CAZypedia runs on MediaWiki, the same software as Wikipedia –Allows continuous updating, editing, tweaking... www.cazypedia.org April 2007 CBM7, Braunschweig July 2006 23 rd ICS, Whistler 17 May 2007 GH1 page sketch online

8. :Content  CAZypedia is an extension of the CAZy database –CAZypedia is family-based –CAZypedia is meant to be a distillation of the key work in the field. –CAZypedia is initially focussed on highlighting structural and mechanistic "firsts" in each of the CAZy glycoside hydrolase (GH) families.  In particular, primary literature is 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. www.cazypedia.org

9. :CAZypedia (is not Wikipedia)  CAZypedia strives 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. –Publicly viewable, not publicly editable (cf. Citizendium). –All contributors to CAZypedia are selected experts in the field. –Contributors' real names and biographies are visible in CAZypedia. –Page content is produced by designated Authors, overseen and edited by Responsible Curators Responsible Curator Author(s) www.cazypedia.org

10. :Responsible Curator  Selected by the team of Senior Curators, based on their specialist expertise and ability to participate in the active maintainance of entry content.  Responsible for editorial management of a designated CAZypedia page. –All questions regarding page content should be directed to the Responsible Curator. –Responsible Curators are the primary points of contact for arbitrating potential conflicts regarding information contained on their respective CAZypedia page. –Responsible Curators may also invite new authors to contribute to their assigned CAZypedia page, at their discretion and the discretion of the Senior Curators. www.cazypedia.org

11. :Author  A CAZypedia Author is a person responsible for creating and maintaining content of an assigned page. –One or more Authors is (are) assigned by the Responsible Curator of that page based on particular expertise. –An Author works closely with the Responsible Curator to ensure a high quality of CAZypedia content.  In some cases, the page Author and Responsible Curator may be the same person. –Issues regarding factual correctness and other content-related issues should by directed to the Responsible Curator of the page for arbitration/correction. www.cazypedia.org

12. :Community driven  CAZypedia strives to be a dynamic & community-based –Those wishing to help author an existing page may contact the Responsible Curator. –Those wishing to suggest a new page (i.e, become a Responsible Curator), may contact a Senior Curator.  Al Boraston (U. Vic)  Harry Brumer (UBC/KTH)  Gideon Davies (York, UK)  Shinya Fushinobu (U. Tokyo)  Harry Gilbert (Newcastle, UK)  Bernard Henrissat (AFMB, Marseille, FR)  Stephen Withers (UBC) www.cazypedia.org

13. :Soft launch  GH1: Online since 17 May 2007  First families linked from CAZy DB family headers –”External Resources”  CAZypedia highlighed in October 2008 publication from the CAZy team: –”The CAZy database is available at www.cazy.org. Information about selected families is available through the website and at www.cazypedia.org.” www.cazypedia.org

14. :Development & current status  June 2009: –Gordon Research Conference on Carbohydrates  Decision to ”go-live” –Responsible Curators subsequently invited for 73 GH families  Today: –80 GH pages ”Curator Approved”  16 ”Under Construction”  ca. 30 ”Unassigned” –21 Lexicon pages ”Curator Approved”  6 ”Under Construction” –1 GT page (beta-test) ”Curator Approved” www.cazypedia.org

15. :Future challenges  Essentially surround the volunteer nature of the project –Maintaining “freshness” of existing content –Stimulating Curators and Authors to initiate and complete pages in a timely manner –Identifying and enlisting new CAZypedians for unassigned pages –Content enrichment –Code improvement for “abandoned” software extensions www.cazypedia.org

16. An introduction On behalf of the ”CAZypedia Consortium” Harry Brumer, Ph.D. Professor The Michael Smith Laboratories, UBC and School of Biotechnology, Royal Institute of Technology (KTH) brumer@msl.ubc.ca www.cazypedia.org

17. :Extension of the CAZy DB www.cazypedia.org

18. :Inspiration & genesis  CAZypedia is dedicated to the late Prof. Bruce Stone (LaTrobe Univ., AUS) –whose enthusiasm to create a comprehensive encyclopedia of carbohydrate-active enzymes was essential in the genesis of this project....GH1: Online since 17 May 2007 April 2007 CBM7, Braunschweig July 2006 23 rd ICS, Whistler www.cazypedia.org