EcoliWiki and GONUTS
Wiki-based Systems for Community AnnotationJim Hu
Dept. of Biochemistry and Biophysics
Texas A&M University
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
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)
"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
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
For the live demos
• Anyone can view without logging in– http://gowiki.tamu.edu– http://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– [email protected]– GMOD– Facebook groups:
• EcoliHub• WikiOmics
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
MOD gene pages• Gene pages from
established Model Organism Databases provide examples of best practices
User-created gene pages
• Annotation pages based on UniProt IDs
Supporting Annotation Jamborees in Cyberspace
• RefGenome subgroup of GO Consortium– collaboration on
annotation consistency
– Electronic Jamborees via teleconference
– Uses GONUTS to collect and compare
Supporting Annotation Jamborees in Cyberspace
• RefGenome subgroup of GO Consortium– collaboration on
annotation consistency
– Electronic Jamborees via teleconference
– Uses GONUTS to collect and compare