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Biological information with XML (II):

  1. Data Integration and Exchange

  2. Data Storage

  3. Data Query (XML-Query)

Data Integration and Exchange

Data Storage

The biological data can be written in XML and stored in its native form (text format), which requires the database systems to manage these resouces effieciently. A database supporting XML is not realized. In this case how to query the stored biological data based on XML and the schema diffinition play an important role.

Data Query (XML-Query)

In order to use the biological information in a database, we need to exectue queries on it. Several query languages have been proposed to query XML documents, such as XQL, XML-QL and GQL. Although these languages offer similar capability in terms of data extraction, XML-QL is considered to be most expressive because XML-QL queries can constract new XML data from the results of queries. Since this data can be used as input to further queries, results can be refined through successive application of queries.

Here I'd like to introduce briefly the XQuery Language, which is still under developing by W3C, and is designed to be broadly applicable accross all types of XML data sources. XQuery is a functional language in which a query is represented as an expression. It supports several kinds of expression, and therefore its queries may take several different forms. The various forms of XQuery expressions can be nested with full generality, so the notion of a "subquery" is natural to XQuery. The input and output of a query are instances of a data model called the XML Query Data Model.

	FOR $ge IN (document("genome_set.xml")//genome)
	WHERE $ge/date = "2001Juni14"
	AND $ge/whose = "Example Genome Project"

For more information about XQuery.

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