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
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