As a graduate student in the life sciences, I read and markup a lot of academic papers related to my field. One of the practices that I’ve found helpful for retention is storage of highlights I make from papers I read as plain text, usually paired with the relevant citation and, depending on where I choose to store the text, a copy of the marked-up PDF. This workflow is also quite helpful when it comes time for grant or paper writing.
Despite a great deal of tweaking over the years, alas, I’m still not completely satisfied with this process. In the current incarnation, I import PDFs into PDF Expert on my iPad Pro for reading, highlighting, and annotation using the Apple Pencil. From there, I use one of the sharing features in PDFE to email a summary of the highlights to myself, which is then funneled into Ulysses for storage (currently in the process of switching this latter stage over to KeepIt, which is obviously more suited for archival purposes).
While this works in general, pieces of it often fail in the particular. The text of the extracted highlights especially is often plagued by broken formatting (errant spaces, carriage returns, etc.) that has proven difficult to resolve in an automated fashion, even using tools like Clean Text. It is also much more difficult than I would prefer to quickly generate a citation to append to these highlights for later reference.
I would appreciate any advice from people who have arrived at a satisfying system for this sort of work, particularly as it’s done on iPad.