@sanadsaad. Here is my workflow:
- All pdfs are captured, renamed, and organized in Paperpile. Paperpile is a powerful reference manager, simple to use, and can be used in both desktop and iPad.
- All pdfs are stored in Google Drive (this is how Paperpile works). You can also index them in DT to have the best of the two worlds.
- I read, add comments and highlighted the pdfs using Paperpile on iPad. Everything you do will be synced, and you will have all your work available on many platforms, including DT.
- Then, I export all comments and highlights to a markdown document (yes, you can do that in Paperpile) and index the markdown document in DT.
- I process the markdown document by writing permanent notes using the Zettelkasten approach (there is a book on how to do that in DT, including how to make links, etc.). When the markdown document is processed, I delete it.
- I use markdown for my permanent notes, keep them in a Dropbox file, and index them in DT. You can always import them to DT if you want.
- When writing a paper, I search all the relevant notes in DT, export them to Scrivener, create an outline, and then write the article.
- When I fell the first draft is good enough, I export it to MS Word (because journals ask an MS document), add the references using the Paperpile plugin, and complete my task.
Some additional thoughts:
- You do not need Scrivener to write your paper. You can do everything in DT.
- You can use Bookends instead of Paperpile, but after testing both apps a lot, I found Paperpile easier to learn, maintain, etc. Besides, reading pdfs on the iPad with the Paperpile app is an excellent experience.
- By following this workflow, you will increase your productivity. Do not waste too much time overthinking how to organize your permanent notes. Just set a time everyday to process your pdfs, write your permanent notes, and link your notes in meaningful networks. You will build a knowledge system that will help with your dissertation.
- DT has everything you need to be successful. Good luck!