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Direct submission system and literature annotation of rice genes in Oryzabase

Yukiko Yamazaki¹, Rie Tsuchiya¹, Takao Asanuma², Yo Shidahara² & Shingo Sakaniwa¹

Correspondence: (Login to view email address)

1. National Institute of Genetics
2. NalaPro Technologies

PPT (2.4 MB) PDF (940.4 KB)

Document Type:

Poster

Date:

Received 24 April 2009 04:20 UTC; Posted 24 April 2009

Subjects:

Genetics & Genomics, Bioinformatics, Plant Biology

Tags:

• rice genes
• Oryzabase
• literature annotation
• text mining
• semantic mining

Abstract:

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) 1:72-84

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Yamazaki, Yukiko, Tsuchiya, Rie, Asanuma, Takao, Shidahara, Yo, and Sakaniwa, Shingo. Direct submission system and literature annotation of rice genes in Oryzabase. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3164.1> (2009)

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