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One of the difficulties of exchange of isomerism database is to resolve the problem of data transmission between databases with different structure. Extensible markup language (XML) is described by the format which is unrelated to platform, language and protocol. It can resolve format problem in data exchange. It provides the best data model and exchange standard for isomerism database. JMS has platform independence. It provides an optimal interface criterion for data transmission based on isomerism platform. The paper mainly expounded the format criterion of isomerism data converting.