Direct submission system and literature annotation of rice genes in Oryzabase

Oryzabase ("http://www.shigen.nig.ac.jp/rice/oryzabase/":http://www.shigen.nig.ac.jp/rice/oryzabase/) is a comprehensive rice science database ^1^. It houses a variety of genetic resources, relevant literatures, gene dictionary, DNA sequences, and basic information such as developmental biology and anatomy. In order to keep the gene dictionary up-to-date, literature annotation has been conducted manually since 1995. However as the publication of journal articles increases year by year after genomic sequences were released, it became more difficult to update the dictionary timely and in high quality without sufficient annotators. To overcome this difficulty, we applied machine learning and text-mining to extract known and unknown genes from journals. The machine extraction followed by manual annotation achieved promising results and increased efficiency in manual annotation. Furthermore a direct submission system where rice researchers can deposit new genes according to the standardized nomenclature ^2^ became operational in 2008. Recent advances will be introduced.

[1] Kurata, N. and Y. Yamazaki., Oryzabase, An Integrated Biological and Genome 
 Information Database for Rice. _Plant Physiology_ (2006) 140, 12-17 
[2] Susan R. McCouch, Gene Nomenclature System for Rice, Rice (2008) 1:72-8