1. Community annotation with EcoliWiki and GONUTS
Daniel Renfro, Brenley McIntosh, Deborah Siegele and Jim Hu
Texas A&M University (College Station, TX)
Abstract GONUTS & CACAO Participation Recruitment
Community participation in content generation and maintenance for biological
databases has long been viewed as a possible solution to the problems of cost Scoreboard - Tracks team annotations, challenges and points in real time. Recruited via Institution
and scalability that limit the classical model for biocuration. The success of
Wikipedia has inspired a proliferation of biological wikis. EcoliWiki and GONUTS GO consortium TAMU
are two wikis that are designed for distinct but overlapping purposes. EcoliWiki is UCL
modeled on typical model organism databases, with a central component being Miss State
gene-centric pages about genes, their products, expression and regulation, and Phage Meeting Mich State
evolution. GONUTS is a Gene Ontology browser and repository for term-specific Penn State
usage notes for GO. It also supports community annotation for proteins with Wisconsin-Parkside
UniProt accessions. EcoliWiki and GONUTS share common wiki infrastructure for N. Dakota State
automated creation of pages from templates, handling references, and capturing Central Florida
tabular data to enable structured data mining. Both use the directed acyclic graph
struture of mediawiki categories to capture relationships between pages. PortEco Steering Committee Swarthmore
Wisconsin
So far, the initial fear that wikis would introduce chaos into annotation has not ASM General Meeting Hofstra
been a problem. Instead, a common problem faced by wikis and other community ASM CUE N. Texas
annotation systems is that biologists have only weak incentives to participate in TAMU Seminar speakers Miami Ohio
content curation. To increase participation and couple annotation to common
career goals for academic biologists, we created the Community Assessment of Other Houston Baptist
Community Annotation with Ontologies (CACAO). In CACAO, biologist get
teaching credit for having teams of students participate in GO annotation. Team and Individual Contributions - A table on each team’s page tracks
Annotation is done as an intercollegiate competition on the GONUTS website, annotations from team members. A similar table shows each annotation contributed
and annotations, along with student-generated notes are submitted to GO and
UniProt after review by curators. CACAO leverages the expertise of students,
by the individual biocurator. Growth in CACAO Activity
faculty supervisors, and biocurators and could be a viable model for other kinds of
community efforts.
Adapting wikis for annotation
• Traditional models of community curation create barriers to user participation
• Contributions are invisible while gatekeepers evaluate them
• Partial information is discouraged
• Wikis provide immediate feedback and allow submission of smaller units of
information
• But wikis are traditionally too unstructured for efficient extraction of
structured data
• TableEdit is a mediawiki extension developed for EcoliWiki to address this
problem
Challenges and Rebuttals – Submitted challenges are displayed in a table that
allows for multiple challenges and rebuttals.
GONUTS & Electronic Jamborees
Annotation jamborees were first described
for the annotation of the Drosophila
genome
"Because the breadth of expertise necessary to annotate a
complete genome does not exist in any single individual or
organization, we hosted an "Annotation Jamboree" involving
more than 40 scientists from around the world, primarily from the
Drosophila research community. Each was responsible for
organizing and interpreting the gene set for a given protein family
or biological process. Over a 2-week period, jamboree
participants worked to define genes, to classify them according to
predicted function, and to begin synthesizing information from a
GO Annotations genome-wide perspective."
- Adams et al. (2000) The genome sequence of Drosophila
Gene Ontology (GO) is the de facto ontology for functional annotation. GO melanogaster. Science 287:2185-2195
annotations for Escherichia coli gene products can be added to EcoliWiki
(http://ecoliwiki.net) while annotations for any protein in UniProt can be added
to GONUTS (http://gonuts.tamu.edu) by any registered user. Having multiple investigators travel to a
single site is hard. GONUTS allows the
Reference Genome project of the GO
consortium to organize annotation
Assessment by Experienced Students jamborees via conference calls and over
- Graduate students or undergraduates who have completed at least 1 semester the internet.
of CACAO initially assess every annotation as acceptable, unacceptable, requiring
changes or requiring additional review by a professional biocurator. In addition, Other groups can use GONUTS in similar
these students judge challenges and refinements. ways.
Genes of interest for an annotation jamboree are tagged in GONUTS. These tags
allow a set of software tools to generate graphs and tables that compare the GO
annotations for each gene in the group.
