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Bioinformatics Advance Access published online on November 25, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti152
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 23, 2004
Revised October 11, 2004
Accepted November 12, 2004

Applications note

The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures

Norihiro Kikuchi 1*, Akihiko Kameyama 2, Shuuichi Nakaya 3, Hiromi Ito 2, Takashi Sato 2, Toshihide Shikanai 4, Yoriko Takahashi 1, and Hisashi Narimatsu 2

1 Mitsui Knowledge Industry Co., Ltd., Nakano-ku, Tokyo, Japan
2 Glycogene Function Team, Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
3 Glycogene Function Team, Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan; Shimadzu Corporation, Nakagyo-ku, Kyoto, Japan
4 Mitsui Knowledge Industry Co., Ltd., Nakano-ku, Tokyo, Japan; Glycogene Function Team, Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan

* To whom correspondence should be addressed.
Norihiro Kikuchi, E-mail: kikuchi{at}hydra.mki.co.jp


  Abstract

Summary: Bioinformatics resources for glycomics are very poor as compared with them for genomics and proteomics. The complexity of carbohydrate sequences makes it difficult to define a common language to represent them, and the development of bioinformatics tools for glycomics has not progressed. In this study, we developed a carbohydrate sequence markup language (CabosML), an XML description of carbohydrate structures.

Availability: The language definition (XML Schema) and an experimental database of carbohydrate structures using an XML database management system are available at https://phoenix.hydra.mki.co.jp/CabosDemo.html.


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