The diagram above comes from the presentation we are looking at today. The transaction in the middle is the ITI 41: Provide and Register Document Set. This is the transaction that is used between a document source (the two boxes on the left), and the document recipient (the big box on the right).
Now, inside this box, the esMD project has created an index of the metadata. Then they put the documents in their enterprise content management system.
We usually call metadata indexing systems "registries". And an enterprise content management system can also be thought of as a repository. Interestingly enough, there is an IHE Profile that has transactions which index metadata in a registry and store the documents in a repository. It's called XDS.