GXML: A Novel Method for Exchanging and Querying Complete Genomes by Representing them as Structured Documents

• Item type: Trans(1)
• 公開日: 1999-08-15
• タイトル: GXML: A Novel Method for Exchanging and Querying Complete Genomes by Representing them as Structured Documents
• タイトル / 言語: en
• タイトル: GXML: A Novel Method for Exchanging and Querying Complete Genomes by Representing them as Structured Documents
• 言語: eng
• キーワード / 主題Scheme: Other
• キーワード / 主題: 研究論文
• 資源タイプ / 資源タイプ識別子: http://purl.org/coar/resource_type/c_6501
• 資源タイプ: journal article
• 著者所属: CREST JST (Japan Science and Technology)
• 著者所属: Graduate School of Engineering Science Osaka University
• 著者所属: Graduate School of Engineering Science Osaka University
• 著者所属(英): en
• 著者所属(英): CREST, JST (Japan Science and Technology)
• 著者所属(英): en
• 著者所属(英): Graduate School of Engineering Science, Osaka University
• 著者所属(英): en
• 著者所属(英): Graduate School of Engineering Science, Osaka University
• 著者名: AARONJ.STOKES; HIDEO, MATSUDA; AKIHIRO, HASHIMOTO
• 著者名(英): Aaron, J.Stokes; Hideo, Matsuda; Akihiro, Hashimoto
• 論文抄録 / 内容記述タイプ: Other
• 論文抄録 / 内容記述: Complete DNA sequences (complete genomes) for an increasing number of organisms are becoming available each year for use in biological research. However genome project groups incorporate their own formats (or schemas) for representing the genome data accumulated by the projects. Such heterogeneity of their schemas prevents researchers from exchanging and comparing their data across genomes. In this paper we present a new method for exchanging and querying information on complete genomes. Since genomes and the genetic information encoded on them have a hierarchical structure they can be represented as a kind of structured document. We propose a document language called GXML for representing complete genomes. The document language based on XML can be used to exchange many kinds of genomic data and offers a high degree of extensibility. We also define a query language called GQL to operate on the genome documents. Using this language one can easily associate henes among different genomes and perform other biological analyses. We developed a prototype system based on the language. Using the system we executed several test queries. The results were consistent with those published in biological literature. The processor and memory requirements of the prototype system were accptable.
• 論文抄録(英) / 内容記述タイプ: Other
• 論文抄録(英) / 内容記述: Complete DNA sequences (complete genomes) for an increasing number of organisms are becoming available each year for use in biological research. However, genome project groups incorporate their own formats (or schemas) for representing the genome data accumulated by the projects. Such heterogeneity of their schemas prevents researchers from exchanging and comparing their data across genomes. In this paper, we present a new method for exchanging and querying information on complete genomes. Since genomes and the genetic information encoded on them have a hierarchical structure, they can be represented as a kind of structured document. We propose a document language called GXML for representing complete genomes. The document language, based on XML, can be used to exchange many kinds of genomic data, and offers a high degree of extensibility. We also define a query language called GQL to operate on the genome documents. Using this language, one can easily associate henes among different genomes and perform other biological analyses. We developed a prototype system based on the language. Using the system, we executed several test queries. The results were consistent with those published in biological literature. The processor and memory requirements of the prototype system were accptable.
• 書誌レコードID / 収録物識別子タイプ: NCID
• 書誌レコードID / 収録物識別子: AA11464847
• 書誌情報: 情報処理学会論文誌データベース（TOD）; 巻 40, 号 SIG06(TOD3), p. 66-78, 発行日 1999-08-15
• ISSN / 収録物識別子タイプ: ISSN
• ISSN / 収録物識別子: 1882-7799
• 出版者 / 言語: ja
• 出版者: 情報処理学会