19th International CODATA Conference
Category: Poster, Multi-disciplinary Use

Polymorphism Markup Language (PML) for the interoperability of data on SNPs and other sequence variations

Dr. Hideaki Sugawara (hsugawar@genes.nig.ac.jp), Dr. Hiroshi Mizushima, Dr. Tokio Kano, Yasumasa Shigemoto, Yoichi Hashimoto, Isao Tomabechi, Naoki Sakagami, Masayuki Ikawa, Takashige Oroguchi, Toshiyuki Katagiri
DNA Data Bank of Japan, National Institute of Genetics, Japan


A SNP is a single nucleotide change in the genome sequences. SNPs often modify amino acids in a gene resulting in the diversity of individual responses to stimuli, e.g. drugs. They can even cause serious diseases.

Thus, many countries and international consortiums have been carrying out a large scale survey on SNPs data. In the meantime, databases are available on-line, e.g.

However, their data structure and access methods are heterogeneous. Therefore, Japan Biological Informatics Consortium (JBIC) has analyzed their systems and developed Polymorphism Markup Language (PML) based on XML. It is now possible to assemble and analyze SNPs data from distributed heterogeneous database in XML documents described by PML.

In 2003, JBIC organized the 1st International Biodata Interoperability Conference to have international discussions on SNPs data standardization. It is an outcome of the conference that JBIC together with European Bioinformatics Institute submitted PML to Life Science Research (LSR) of Object Management Group (OMG) in response to the request for proposal for the standardization of SNPs data. The proposal is supported by: University of Helsinki, Finland; Stanford University, USA; Yale University, USA; Karolinska Institute, Sweden; National Institute of Genetics, Japan; National Cancer Center, Japan; Japan Science and Technology Agency, Japan. JBIC will host in June 2004 the 2nd International Biodata Interoperability Conference to improve PML.