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DataDirect XQuery http://www.datadirect.com/products/xquery/
An embeddable software product based on the XQuery and XQJ standards that enables Java developers to access both relational and XML data sources using a single XQuery query.
http://www.csse.monash.edu.au/~bren/JSX/ http://www.csse.monash.edu.au/~bren/JSX/
Serializes Java objects to and from XML, with no class modifications needed - works automatically for all objects. It reverse engineers the Java standard for serialization, and uses it when needed. requires JDK1.2 or higher. [JSX1 is GPL; JSX2 is commercial]
http://www.exist-db.org/ http://www.exist-db.org/
A native XML database featuring index-based XPath query processing, extensions for keyword search and XUpdate support. [Open Source, LGPL]
Infonyte GmbH http://www.infonyte.com/en/index.html
The Infonyte product suite stores, queries, and processes native XML without bothering about limited main memory and processing capabilities. It is W3C DOM compliant and requires only a Java Virtual Machine. [Commercial]
JET Code Generator http://jmatrix.net/content/jetgen_home.jsp
Java database access code generator based on XML and XSLT. It includes a example complete with Ant build scripts.
X-Hive/DB http://www.x-hive.com/
XML Database in form of a Java-based persistent DOM implementation. [Commercial]
XML-DBMS http://www.rpbourret.com/xmldbms/index.htm
Java packages for transferring data between XML documents and relational databases. [Open Source, Public Domain]

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