title: Functional annotation of the Arabidopsis genome using controlled vocabularies.
abstract: 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.
authors.affiliation: Carnegie Institution, Department of Plant Biology, Stanford, California 94305, USA.
authors.forename: Tanya Z
authors.initials: TZ
authors.lastname: Berardini
authors.forename: Suparna
authors.initials: S
authors.lastname: Mundodi
authors.forename: Leonore
authors.initials: L
authors.lastname: Reiser
authors.forename: Eva
authors.initials: E
authors.lastname: Huala
authors.forename: Margarita
authors.initials: M
authors.lastname: Garcia-Hernandez
authors.forename: Peifen
authors.initials: P
authors.lastname: Zhang
authors.forename: Lukas A
authors.initials: LA
authors.lastname: Mueller
authors.forename: Jungwoon
authors.initials: J
authors.lastname: Yoon
authors.forename: Aisling
authors.initials: A
authors.lastname: Doyle
authors.forename: Gabriel
authors.initials: G
authors.lastname: Lander
authors.forename: Nick
authors.initials: N
authors.lastname: Moseyko
authors.forename: Danny
authors.initials: D
authors.lastname: Yoo
authors.forename: Iris
authors.initials: I
authors.lastname: Xu
authors.forename: Brandon
authors.initials: B
authors.lastname: Zoeckler
authors.forename: Mary
authors.initials: M
authors.lastname: Montoya
authors.forename: Neil
authors.initials: N
authors.lastname: Miller
authors.forename: Dan
authors.initials: D
authors.lastname: Weems
authors.forename: Seung Y
authors.initials: SY
authors.lastname: Rhee
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D016208:Databases, Factual; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D018875:Vocabulary, Controlled