Gene Ontology Toolkit: A Comprehensive Software Package for Working with Gene Ontology

Jing Ding1, Jun Xu2, Andy W. Fulmer
1dingjing@iastate.edu, Iowa State University; 2xu.j.1@pg.com, The Procter and Gamble Company

Gene Ontology Toolkit (GOT) is a Java GUI for working with GO. Its design was focused on easing the difficulties while working with GO, namely (1) prohibitive large number of terms and relationships for memorizing; (2) incomplete coverage of the GO terms; (3) incomplete coverage of gene products; and (4) labor-intensive and time-consuming manual merging of GO development efforts from different sources. The three integrated components (editor, annotator and merger) enable biologists to visualize and extend GO, annotate gene products with GO terms, and merge the extensions and/or the annotations with new release of GO or othersí extensions. The configuration of a GOT system is distributed to ensure flexibility and extensibility, i.e. the GUI is independent of the underlying GO database. It is therefore possible for several users to work on the same GO database simultaneously, as well as a user to work on several GO databases. In order to control the quality of a GO database under a multiple-user environment, GOT implemented a flexible user-privilege control mechanism. By default, a user can view the database as a browser. His/her modifications wonít be saved to the database unless he/she is granted with editor privilege. However, a browser can save the modifications to a file and submit it to an editor, who will decide whether to incorporate all or part of the modifications to the database.