JMSSJ On-line, Vol. 51 (2003) No. 5, pp. 542-549
HUP-ML: Human Proteome Markup Language for Proteomics Database
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    Ken'ichi KAMIJO *a), Hironori MIZUGUCHI b), Akihisa KENMOCHI c), Masao SATO c), Yoko TAKAKI a), and Akira TSUGITA a)

    *a) Proteomics Research Center, Fundamental Research Laboratories, NEC Corporation (34 Miyukigaoka, Tsukuba 305-8501, Japan) b) Internet Systems Research Laboratories, NEC Corporation (8916-47 Takayama-cho, Ikoma, Nara 630-0101, Japan) c) Bioinformatics Business Promotion Department, NEC Corporation (7-1, Shiba 5-chome, Minato-ku, Tokyo 108-8001, Japan)
We have proposed an XML format, HUP-ML (Human Proteome Markup Language), for proteomics database to exchange proteome data among researchers and to accelerate their collaboration. HUP-ML data model is proteome-analysis-oriented so as to incorporate such information as sample source, details of sample preparation, 2-D gel electrophoresis images, spot identification, amino acid sequences, MS spectrum data, and so on. We have developed prototypes of HUP-ML Editor and web-based database system as a tool for creating HUP-ML documents and a platform for sharing HUP-ML documents, respectively.
Key words: Proteomics, Database, XML (Extensible Markup Language), Bioinformatics
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