Journal Article

Biological Ontologies in Rice Databases. An Introduction to the Activities in Gramene and Oryzabase

Yukiko Yamazaki and Pankaj Jaiswal

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 46, issue 1, pages 63-68
Published in print January 2005 | ISSN: 0032-0781
Published online January 2005 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pci505
Biological Ontologies in Rice Databases. An Introduction to the Activities in Gramene and Oryzabase

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  • Biochemistry
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An enormous amount of information and materials in the field of biology has been accumulating, 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 data sets 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: Keywords: Database — Gramene — Ontology — Oryzabase — Oryza sativa (rice).; Abbreviations: GO, gene ontology; GRO, growth stage ontology; PO, plant ontology; QTL, quantitative trait locus; TO, trait ontology.

Journal Article.  3844 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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