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Volume 4

Special Issue
Ontology
Workshop
Tokyo 2003



Full article

In Silico Biology 4, 0003 (2003); ©2003, Bioinformation Systems e.V.  



MaXML: mouse annotation XML

Takeya Kasukawa1,2, Hidemasa Bono2, Yoshihide Hayashizaki2,3, Yasushi Okazaki2 and Hideo Matsuda4*

1 Network Service Solution Business Group, Content Sharing Service Business Unit, NTT Software Corporation, 223-1 Yamashita-Cho, Naka-ku, Yokohama, Kanagawa 231-8554, Japan
2 Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
3 Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
4 Laboratory for Genome Information Engineering, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531 Japan

*  corresponding author
   email: matsuda@ist.osaka-u.ac.jp


Edited by E. Wingender; received August 15, 2003; revised December 18, 2003; accepted December 22, 2003; published December 26, 2003


Abstract

Although the sequencing of the human genome and several model organisms is almost complete, the number of genes in the human is still in debate. cDNA (complementary DNA) is generated from mRNA that is transcribed from the genome and can be regarded as a gene itself; therefore, decoding cDNA sequences is important in characterizing genes. Recently, biologists have been able to describe more knowledge about genes in order to characterize them, and this information is generally called 'annotation.' Furthermore, annotation is important in understanding the systems of organisms in various fields of research. We therefore constructed the MaXML (Mouse annotation XML) format with which mouse cDNA annotation data can be exchanged and shared between laboratories more efficiently. Defining strict data types for annotations is difficult, but we consider XML a feasible format for describing them. We have used the MaXML format to express mouse annotation data in FANTOM DB. We have also developed tools and systems utilizing these MaXML data, including a parser and a server to provide data on-the-fly.

Key words: functional annotation, transcriptome, computational annotation, mouse cDNA