The SfN Neuroscience Database Gateway (NDG; http://big.sfn.org/NDG/site) lists approximately 100 neuroinformatics resources, including nearly 80 specialized databases of experimental data maintained by individual laboratories and communities. Specialization promotes data quality and relevance, but renders integration difficult. Combining data from different databases or using results from a query in one to retrieve data from another involves manually interacting first with one interface, then the other, and combining downloaded results by hand. We have been developing the BrainML modeling language (see http://brainml.org) to help automate this process at the content level, and we present here the BrainML Exchange (BrainML-X) protocols for database interoperability at the functional level. BrainML allows the data models from multiple neuroinformatic resources to be expressed in a common format without danger of conflict or ambiguity, supporting semantic alignment. The BrainML-X protocols, consisting of XML ...