Neuroscientist users see and exchange the instance documents representing data and queries for data shown on the top layer, and groups develop resource- and domain-specific data models. These are represented in the grey layers, containing both highly specialized models (e.g., cortical and thalamic anatomy, as shown) as well as more general structures that others may make use of (layer beneath this, which may, for example, contain structures for describing general anatomic structures such as 'brain structure' or 'fiber connection'). These in turn are supported by more generic libraries of definition components shown in brown.

The next two layers in orange are plumbing and utility constructs that provide essentially an enhanced data type library over what XML schema offers. In particular, fixed constructs are declared for defining controlled vocabulary fields, units of measure, and structured numeric data containers. This collection of types is termed BrainMetaL, as in "meta-language".

Finally, the bottom two layers represent the technology standards BrainML is based on: XML, XLink, and XML Schema.