An Integrated Phenotype Database of Arabidopsis Mutant Traits Developed Using Controlled Vocabulary

Arabidopsis thaliana is one of the most frequently studied plant species; however, only 30% of its genes have been analyzed and recorded with experimental evidences in a curated database. Phenotype observation is one of the important techniques for determining gene function, and hence, many databases of Arabidopsis mutants have been created. However, the data on Arabidopsis phenotypes in these databases are not uniform and consolidated, and therefore, a comparative study of the different databases is difficult. Here we have consolidated the phenotype data from several databases such as RAPID, RiceFOX, ArabidopsisFOX, and TrapperDB by using the controlled vocabulary method. For unifying the data, we used plant ontology that helps describe the growth stages and anatomical organs of the plants. We also used phenotypic quality ontology to describe the quantitative and qualitative attributes. We then applied these data to an integrated database that is an Arabidopsis genome information resource named RARGE (http://rarge.psc.riken.jp/). The users have unrestricted access to the entire database to run an extensive search for the phenotypes of loss-of-function and gain-of-function mutants; thus, mining other data resources for information becomes unnecessary because of RARGE. Our database can easily help to search multiple gene loci responsible for a particular change in the same or opposing traits. Thus, the database facilitates the determination of mutated genes related to the change in a trait or phenotype. In addition, information on full-length cDNAs is also available on the RARGE database.