1. EcoliWiki and GONUTS Wiki-based Systems for Community Annotation Jim Hu Dept. of Biochemistry and Biophysics Texas A&M University

2. Acknowledgements EcoliWiki/GONUTS Team –Dave Clements –Nathan Liles –Brenley McIntosh –Debby Siegele –Daniel Renfro –Anand Venkatraman –Adrienne Zweifel GO consortium Chris Elsik EcoliHub Team Leaders –Barry Wanner PI, Purdue –Walid Aref, co-PI, Purdue –Tyrell Conway, co-PI, Oklahoma –Mike Gribskov, co-PI, Purdue –Peter Karp, co-PI, SRI –Daisuke Kihara, co-PI, Purdue Funding NIH U24-GM077905 URLs:http:ecolihub.org http:ecoliwiki.net http:gowiki.tamu.edu

3. Overview Why wikis? –Some useful properties of wikis for community curation –modifying a familiar wiki system (MediaWiki) for genomics Live demos –Gene Ontology and the Gene Ontology Normal Usage Tracking System (GONUTS: http:gowiki.tamu.edu ) –EcoliWiki ( http:ecoliwiki.net )

4. "Wikifying" Genome Annotation The need for ongoing annotation and reannotation is accelerating Expertise is distributed across broad communities of scientists The need for ongoing annotation and reannotation is accelerating Expertise is distributed across broad communities of scientists

5. Some properties of MediaWiki Out of the box –Familiar UI from Wikipedia –Easy creation of new pages –Collaborative editing –Revision histories –Every page has an associated discussion page –Relatively simple markup, especially for internal and external links –Categories –Watchlists –Large open source developer community –Upload system for images and other file types –Extensions As modified by us and others –TableEdit –Page creation from templates –Reference management –Web services –Contributor credit on each pages –Embed videos –Embed chat sessions

6. For the live demos Anyone can view without logging in –http://gowiki.tamu.eduhttp://gowiki.tamu.edu –http://ecoliwiki.nethttp://ecoliwiki.net We require registration to edit due to spam issues –Vampire model –For PAG, login with Username: Demo Password:pag The Demo user can create accounts but cannot edit We'll keep this password working through the pag meeting For more info/discussion –ecoliwiki@gmail.comecoliwiki@gmail.com –GMOD –Facebook groups: EcoliHub WikiOmics

7. GONUTs (http://gowiki.tamu.edu) Started as a wiki- based usage guide Each ontology term is a MW Category –MW supports DAGs as Categories! Each term page has a notes area for user notes on usage term pages list examples of genes that were annotated to this term

8. MOD gene pages Gene pages from established Model Organism Databases provide examples of best practices

9. User-created gene pages Annotation pages based on UniProt IDs

10. Supporting Annotation Jamborees in Cyberspace RefGenome subgroup of GO Consortium –collaboration on annotation consistency –Electronic Jamborees via teleconference –Uses GONUTS to collect and compare

11. Supporting Annotation Jamborees in Cyberspace RefGenome subgroup of GO Consortium –collaboration on annotation consistency –Electronic Jamborees via teleconference –Uses GONUTS to collect and compare