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Exploring community annotation of a mature model organism database
Todd W. Harris1, Lincoln D. Stein1, and the WormBase Consortium 2,3,4.
2007. Genome Informatics Meeting, Cold Spring Harbor Laboratory, NY
1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
2 Department of Genetics, Washington University at St. Louis, St. Louis MO
3 Wellcome Trust Sanger Genome Institute, Hinxton UK
4 Howard Hughes Medical Institute, Caltech, Pasadena, CA
Model Organism Databases (MODs) often employ teams of curators to cull observations from the primary literature. This process results in exceptional genomic annotation, particularly of fine-grained experimental observations not easily extracted and processed programmatically. However, intense curation is impractical for small research programs and is unlikely to be applied to the rapidly increasing number of available whole genome sequences.

To complement in-house curation, we have been exploring approaches that enable users to add and edit their own annotations to those already present at WormBase -- the MOD of C. elegans and related nematodes.

For example, individual Gene Report pages provide links to a MediaWiki-powered wiki site, where users can submit their own annotations and edit those left by others.

In addition, we are developing a new meta-data tagging system (a "Folksonomy"). Using a simple interactive web form, users can add short descriptive tags to independent objects in the database. Tags can be private or shared with the public. Private tags essentially act as quick bookmarks. Public tags are displayed on individual report pages as tag , where the font size of a given tag is related to how often it has been applied to the object. Objects can be searched according to the tags they carry, and tag intersections between objects can be used to elucidate previously unknown relationships.

Using these and other strategies, WormBase hopes to leverage the expertise of our users, thereby increasing the breadth, depth, and rate of functional annotation.


Todd W. Harris, PhD (harris@cshl.org)
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