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Sue Rhee, Carnegie Institution

The Arabidopsis Information Resource (TAIR; www.arabidopsis.org) is a community database for Arabidopsis thaliana that provides access to curated data about the structure and function of this model plant genome. This workshop is designed for users who wish to more effectively utilize the curated data and curation software resources in use at TAIR. Specifically we will address curation of three major data types curated at TAIR:metabolic pathways, gene structure and gene functional annotation.

Part I. Metabolic Pathway

Using AraCyc as an example we will demonstrate how the Pathway Tools software developed at SRI International can be used in conjunction with a curated reference pathway database (MetaCyc) to develop an Pathway/Genome Database (PGDB) for sequenced genome. AraCyc was the first plant PGDB computationally predicted, and has since undergone extensive manual curation. This workshop introduces the contents of MetaCyc and AraCyc databases, and the major functions of the Pathway Tools software which supports creating, editing, Web-publishing, and comparative analyses of PGDBs.

Part II. Gene Structure Annotation

Following the final genome annotation release from TIGR (v5.0), TAIR has assumed responsibility for updating the Arabidopsis annotation using a combination of automated and manual processes. To this end, we have designed a new MySql curation database (Assignment DB) to store a variety of sequence objects and supporting evidence along with a Java API and adaptor that permits direct database access using the Apollo editing tool. We will outline the methods employed to produce both the previous (TIGR 5.0) and latest (TAIR) releases and demonstrate the tools available at TAIR for accessing structural annotation data. We will also describe our plans for improving the annotation pipeline and visualization software.

Part III. Gene Function Annotation

In addition to annotating gene structures, TAIR curators annotate gene function using terms developed by the Gene Ontology (GO) Consortium that describe the molecular function, biological process, and subcellular location of a gene product. We will use TAIR's GO annotations to demonstrate how controlled vocabularies allow for standardization of annotation and assist in comparative genomics. We will describe the process of GO annotation at TAIR and how the annotations can be used to classify large data sets or to facilitate annotation of other sequenced plant genomes. We will demonstrate how to access TAIR's GO annotations in bulk and to derive a global view of the status of functional annotation of the Arabidopsis genome.

This page last updated Wednesday, 12-Oct-2005 21:40:11 EDT