Sorry for the delay in getting back to you. Life...
W.r.t. annotations made in Papers 3 not being seen in other apps: I've previously written a few scripts to export note+highlight annotations from Papers 3 to, say, Finder folders of individual files, the clipboard, DEVONthink, Bookends, or Evernote A script which would export all note+highlight annotations to Skim likely would be also possible.
Given that Papers3 doesn’t seem to be under development any longer, I will likely migrate to something else. This is really sad for me because Papers has the features I want in a reference manager. Nothing else out there seems to have
all the same features. As I use LaTeX, BibDesk would be a logical move, but it doesn’t auto-populate all the fields like Papers3, especially when dragging and dropping and PDF. Highlighting the text to specify each of the fields is just a pain...
Most of these things should be possible with Keypoints, and are (partially at least) already implemented: aggregating, scripting, searching, sorting, grouping by keyword/label/publication/file, automatically jump to PDF, etc.
Awesome 👏
Other things from your list are planned, like sharing of info with other apps or users. I'd also love if my app would be able to push notes to a static site generator so that you could easily publish your notes and share them publicly on the web (or within your research group's intranet).
Very nice! 👍
In general, one of the goals with Keypoints is that your notes should be reusable as much as possible, and that they can be exported or shared in various ways. This is still work that needs to be done, though.
Very good. Let me know if I can help in any way.
W.r.t. automation of some tasks, could you give some examples of tasks that you'd like to get automated?
Off the top of my head I was thinking of something like: Having a rule or agent type of thing that would automatically highlight predefined keywords in a pdf. Another nice feature would be to automatically group or link notes based on their content or some other specification, if that makes any sense.
The last item on your list is the only item where I'm not really sure if this can be supported in Keypoints. In Keypoints, a note is usually connected to a single PDF file (and publication).
To me, this is where Keypoints could be the best thing going! This is a shortcoming of everything out there (in my opinion)!
However, you can, of course, insert links to other files (or notes, publications, keywords, labels, etc) into a note
This would be moving toward what I am thinking about and would definitely be an improvement to most everything on the market.
In what situation would you want to link a note to multiple PDFs?
When reading, writing, or working on a manuscript or grant application, I would love to have a single source of information (i.e., a note) about a specific topic. For example, currently I have 15 notes, one for each study/pdf, where I comment that placebo analgesia reduced pain and was associated with brain regions XYZ. I would rather have a single note where the same comment is associated with all 15 PDFs. Does that make any sense? In some ways I guess my idea is somewhat similar to a smart group, but that still doesn’t fit the need I am trying to describe.
As always, thanks for the time and please let me know if I can help in any way.
Side note: If you had a 'donate' button somewhere, I'd happily contribute.
Cheers,
Jason