Affiliations: Network Service Solution Business Group, Content
Sharing Service Business Unit, NTT Software Corporation, 223-1 Yamashita-Cho,
Naka-ku, Yokohama, Kanagawa 231-8554, Japan | Genome Exploration Research Group, RIKEN Genomic
Sciences Center (GSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa
230-0045, Japan | Genome Science Laboratory, Discovery and Research
Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198,
Japan | 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
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.
