2010 Student Research Conference:
23rd Annual Student Research Conference

Design and Development of a Second Generation Gene Annotation System
Kelsy M. Parker*, Molly Gibson, and Michael D. Miller
Dr. Jon Beck and Dr. Diane Janick-Buckner, Faculty Mentors

The maize shoot apical meristem (SAM) project's community gene annotation efforts require an efficient system for storing and exchanging annotation data between this and other similar projects. The key goals are to automate and enable our teams' annotation tasks and to enable seamless data linking and transfer between this and other annotation databases. To fulfill these needs, we developed a system that builds on lessons learned from a previous ad-hoc system. To facilitate compatibility with other annotation efforts, we designed the database schema to be highly compatible with the de-facto standard schema for biological information, Chado (http://gmod.org/wiki/Chado), incorporating similar terminology, modularity, and normal forms. We implemented the system with Ruby on Rails, which allows for explicit data modularization and an agile development process. Ongoing work centers around monitoring the biologists' workflows to find further opportunities for implementing controlled vocabularies, each instance of which reduces error and facilitates more structured data.

Keywords: database, community gene annotation, maize, schema

Topic(s):Computer Science
Mathematical Biology

Presentation Type: Poster

Session: 7-2
Location: SUB-GEO
Time: 4:15

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