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Plant and Cell Physiology Advance Access published online on January 19, 2005
Plant and Cell Physiology, doi:10.1093/pcp/pci505
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Plant and Cell Physiology 2005 © The Japanese Society of Plant Physiologists (JSPP); all rights researved.
Received November 1, 2004
Accepted November 13, 2004

Mini Review

Biological Ontologies in Rice Databases - An Introduction of Activities in Gramene and Oryzabase

Yukiko Yamazaki 1* and Pankaj Jaiswal 2

1 Center for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
2 Department of Plant Breeding, Cornell University, Ithaca, NY-14853, USA

* To whom correspondence should be addressed.
Yukiko Yamazaki, E-mail: yyamazak{at}lab.nig.ac.jp


  Abstract

There have been accumulating an enormous amount of information and materials in the field of biology, such as nucleotide and amino acid sequences, gene and protein functions, mutants and their phenotypes, and literature references, produced by the rapid development in this field. Effective use of the information may strongly promote biological studies, and may lead to many important findings. It is, however, time-consuming and laborious for individual researchers to collect information from individual original sites and to rearrange it for their own purpose. A concept, ontology, has been introduced in biology to support and encourage researchers to share and reuse information among biological databases. Ontology has a glossary, named dynamic controlled vocabulary, in which relationships between terms are defined. Since each term is strictly defined and identified with an ID number, a set of data represented in biological ontology is easily accessible to automated information processing, even if the datasets are across several databases and/or different organisms. In this mini review, we introduce activities in Gramene and Oryzabase, which provide biological ontologies for Oryza sativa (rice).

Keywords: Gramene; ontology; Oryzabase; Oryza sativa (rice); database.
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