SP has a documented process for constructing AIPs from SIPs. Please see the Workflow Charts for an overview of the process.
For most journal deposits into the repository, the Content Data Object format is unchanged from the SIP to the AIP. The content object's format would only be transformed if its current format was in danger of obsolescence.
The Provider-provided descriptive and structural metadata are normalized to a version of the NLM Journal Archiving and Interchange Tag set. The normalization actions and metadata are included in the preservation metadata generated by SP and stored separately from the content object.
The details of transformation and normalization are specific to each Provider, though the process is the same.
Digital Preservation Policy Librarian