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– ecoliwiki@gmail.com– 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