A standard format/language of the internet is the eXtensible Markup Language (XML) developed by the World Wide Web Consortium (W3C). XML is meant to be a means for describing and validating complex documents. XML itself is very general, but there exists specializations within various domains. One of these domains is the Chemical Markup Language (CML) which has many structures associated with (organic) chemistry. Being a specialization of XML means that CML can use the extensive set of software for transmitting information over the internet that has been developed for XML. In addition, there are also software packages that have developed specifically for CML. CML has become a de facto standard for transmitting chemical information over the web.

JTHERGAS uses CML to store the structural information of molecules (CMLStructures) , radicals and substructure within the mySQL (a widely used public domain software for the manipulation of databases) which requires ASCII representations within the database tables.