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First published online June 1, 2004; 10.1104/pp.104.040071

Plant Physiology 135:745-755 (2004)
© 2004 American Society of Plant Biologists

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GENOME ANALYSIS

Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies1

Tanya Z. Berardini, Suparna Mundodi*, Leonore Reiser, Eva Huala, Margarita Garcia-Hernandez, Peifen Zhang, Lukas A. Mueller2, Jungwoon Yoon, Aisling Doyle, Gabriel Lander, Nick Moseyko, Danny Yoo, Iris Xu, Brandon Zoeckler, Mary Montoya, Neil Miller, Dan Weems and Seung Y. Rhee

Carnegie Institution, Department of Plant Biology, Stanford, California 94305 (T.Z.B., S.M., L.R., E.H., M.G.-H., P.Z., L.A.M., J.Y., A.D., G.L., N.M., D.Y., I.X., B.Z., S.Y.R.); and National Center for Genome Resources, Santa Fe, New Mexico 87505 (M.M., N.M., D.W.)

Controlled vocabularies are increasingly used by databases to describe genes and gene products because they facilitate identification of similar genes within an organism or among different organisms. One of The Arabidopsis Information Resource's goals is to associate all Arabidopsis genes with terms developed by the Gene Ontology Consortium that describe the molecular function, biological process, and subcellular location of a gene product. We have also developed terms describing Arabidopsis anatomy and developmental stages and use these to annotate published gene expression data. As of March 2004, we used computational and manual annotation methods to make 85,666 annotations representing 26,624 unique loci. We focus on associating genes to controlled vocabulary terms based on experimental data from the literature and use The Arabidopsis Information Resource-developed PubSearch software to facilitate this process. Each annotation is tagged with a combination of evidence codes, evidence descriptions, and references that provide a robust means to assess data quality. Annotation of all Arabidopsis genes will allow quantitative comparisons between sets of genes derived from sources such as microarray experiments. The Arabidopsis annotation data will also facilitate annotation of newly sequenced plant genomes by using sequence similarity to transfer annotations to homologous genes. In addition, complete and up-to-date annotations will make unknown genes easy to identify and target for experimentation. Here, we describe the process of Arabidopsis functional annotation using a variety of data sources and illustrate several ways in which this information can be accessed and used to infer knowledge about Arabidopsis and other plant species.

1 This work was supported by the National Science Foundation (grant no. DBI–9978564) and the National Institutes of Health (grant no. HG02273–03).

2 Present address: Cornell University, Emerson Room 251, Ithaca, NY 14850.

www.plantphysiol.org/cgi/doi/10.1104/pp.104.040071.

* Corresponding author; e-mail smundodi{at}acoma.stanford.edu; fax 650–325–6857.

Received January 30, 2004; returned for revision January 30, 2004; accepted February 25, 2004.


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