A Tool Suite for the Gene Ontology

Chris Mungall, BDGP
John Richter, BDGP
Bradley Marshall, BDGP
Suzanna Lewis, BDGP

The goal of the Gene Ontology Consortium (GO) is to produce a dynamic
and inter-related set of controlled vocabularies that can be applied to
eukaryotes and prokaryotes, even as knowledge of gene-product roles
in cells is accumulating and changing. Prior to this year, these
vocabulary terms were maintained by curators editing flat files in a
text editor and data integrity was managed using CVS. Clearly better
technologies were needed to automate storage, editing, and presentation
of the GO. In early 2001 the gene ontology curators successfully made
the transition to a new vocabulary editor specifically designed for
this task. In addition, a new html-based browser that directly
retrieves data from the database is making its debut. Still other
applications to exploit the GO are in development (e.g. image
annotation, computed annotation support, logical assertions).

These applications were constructed using a suite of software tools
developed at the Berkeley Drosophila Genome Project (BDGP) that are
generally effective for use on directed acyclic graphs of terms. This
suite includes a relational database implementation for multiple
platforms, a perl api for querying the database, java data models and a
java plug-in interface to the editor. More information is available at
this URL.

http://www.fruitfly.org/annot/go/