Native format of BKchem is based on XML and is called CDML (chemical drawing markup language). This format is, on contrary to CML (chemical markup language) which is designed to describe the chemistry from the semantic point of view, designed to describe the chemical drawing from the perspective of representation.
CDML is however just internal format of BKchem and does not have any broad acceptance. To use the graphical output of BKchem it was necessary to export the data into some standard graphical format, preferentially SVG. This approach has however disadvantage that it forces users to maintain two versions of each document, one with data for BKchem and one with their graphical representation. Fortunately it is possible to embed foreign data into SVG and because SVG is ideal format for vector graphics I have embedded CDML into it. This way we have format (available from version 0.1.1) that can be immediately viewed in SVG enabled programs and still has the data necessary for right interpretation by BKchem. To distinguish this new format from normal SVG I use the term CD-SVG.
This means that you can store the drawings you create in BKchem in two formats - CDML and CD-SVG. Both these formats are also available in their gzipped form (compression by gzip is almost standard way to make XML files smaller) which needs usually only 10-25% of the space needed by the unzipped form. Preferred file format is CD-SVG or if you need smaller file size its gzipped form. If you don't need the SVG representation you can also use the pure CDML. (Export to pure SVG is also available).