A system and method for creating and using a medical imaging bioinformatics annotated (“MIBA”) master file is disclosed. Creating the MIBA master file includes receiving image data, performing a first registration on the image data for obtaining in-slice registered data, and performing a second registration for registering the in-slice registered data to a three-dimensional (3D) model for obtaining source data. Creating also includes extracting voxel data from the source data and storing the voxel data in a MIBA database, receiving selection of a volume of interest, and extracting a portion of the voxel data corresponding to the volume of interest. The MIBA master file is created from the portion of the voxel data, which is stored in the MIBA database. The MIBA system receives a query, extracts data from the MIBA master file in response to the query, and presents the extracted data on an output interface.