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Ingesting large & hybrid digital collections
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My institution has some experience with larger, heterogeneous collections, though our local practice is still evolving as we add larger and more complex collections to our holdings. I only have one link I can send your way as an example -- a collection of digital files relating to a redistricting project: http://www2.mnhs.org/library/findaids/gr00558.xml. This finding aid dates back to 2012 and is already a bit outdated for what we plan to do with new/incoming collections, but I think it gives you the general idea.
As you can see from that example, we (generally) rely heavily on original order, and use our descriptive tools (generally EAD finding aids) to try and aid researchers in finding what they're looking for. When there are dependencies between multiple digital objects, we keep them all together in a single .zip download rather than separate them out. The level of description varies in our collections; we previously described every file (as in the above example), but with newer and more homogeneous collections (such as large collections of digital photographs) we tend to describe them at the series level.
I hope that provides some help!