IntEnz export module

The IntEnz export module dumps enzyme data in different formats, namely: If used outside of a web application - like the IntEnz web services - it should be built with the apps maven profile.

IntEnzXML

The main product of this application is the dump of IntEnz data in IntEnzXML format. XML files are generated for every single active entry, and also for the entire IntEnz database.
The structure of the XML is defined in the provided schema files.
The export is usually done just before every IntEnz release, roughly every month. The XML schema is used for output validation. The files are then manually copied to make them accessible from ftp://ftp.ebi.ac.uk/pub/databases/intenz/xml.
Currently, the following flavours of XML are available:
  • XCHARS (for eXtended CHARacterS): data which includes XML markup in the IntEnz database is exported /as is/. Example: EC 1.1.1.100 has an accepted name '3-oxoacyl-acyl-carrier-protein reductase'. The corresponding XML will be: 
    <accepted_name view="INTENZ,IUBMB,SIB">
3-oxoacyl-<xchars:protein>acyl-carrier-protein</xchars:protein> reductase
</accepted_name>
    The xchars namespace is defined in the root element of the XML file. For more information on the XML markup used in IntEnz, please refer to the XChars subproject.
  • ASCII: the IntEnz fields with XML markup are translated into ASCII. Following the same example, the ASCII flavour of EC 1.1.1.100's accepted name will be: 
    <accepted_name view="INTENZ,IUBMB,SIB">
3-oxoacyl-[acyl-carrier-protein] reductase
</accepted_name>

Sitemap

With every IntEnz release, a new sitemap XML file (sitemap.xml) is generated to be used by Google sitemaps in order to make every IntEnz entry available to Google indexing. Other search engines accept this standard too.

BioPAX

IntEnz is also dumped as one BioPAX file.