I write a lot of research papers. Most of my work is aggregating references and putting together a new document for a specific topic. Right now, I spend a lot of time copying a section of a PDF or scan and pasting that into a new document (usually Obsidian, though this isn't as important). Once pasted then I add an annotation to a bibliography at the end of the new document.
What I'm looking to do is open my PDFs in an application (or website) select what I want as an excerpt of some kind. Then, tag and add my own comments/notes. Then, I want to be able to organize those snippets into an order that I'd like them to be in. I'd also like to be able to export that whole (or part) of what I've done into another document that I then edit. That new document contains my bibliography and each segment is annotated with a citation. This should work for text and images. e.g. if I want to select an image in a document and insert that into the new document then I can.
I'd like to be able to send my snippets and annotations to Obsidian and/or TexStudio.
TLDR;
- select text or images (equations, etc) in a pdf (or word doc or website) as a snippet with citation
- organize the snippets in a logical order
- send snippets with bibliography to Obsidian and/or TexStudio.
- edit new document as needed.
Liquidtext and MarginNote 3 kind of do some of this, but not the way I was hoping. I know Citavi has some of this functionality (but will not work on non-Windows systems and the web interface isn't as usable as Citavi on the desktop is, IMO). I haven't found that Zotero does what I'm looking for, but maybe I've not found how to do this through tutorial videos.