What I do is an interaction between the following:
Article <-> Tags <-> Hypotheses <-> Synthesis <-> Prediction <-> Research
So I might read an article, then tag the article/figures with the relevant tags. If it's for a specific project, I keep a list of tags on a separate page. This ensure that I use the tags consistently, so that I can find all the relevant articles later.
I purposefully keep the tags general, like "psychiatric conditions" rather than "depression, mania, schizophrenia" etc. When I reach the hypotheses page, this means that I can form relatively general hypotheses, and then nest them into gradually more specific hypothesis that are specifically supported by the articles.
Then, I use those hypotheses to form new predictions. These predictions turn into new research questions, which I either explore via the literature or doing my own experiments.
An example of this might be: "Wood 2018" <-> #Procedural Memory #Habits <-> Habits are part of procedural memory [[H]] <-> Habits are part of procedural memory [[H]] & Procedural memory is stored in the basal ganglia [[H]] <-> Damage to the basal ganglia disrupts habits [[H]] <-> Seger 2011
This affords me a lot of flexibility in total processing time; I don't spend a lot of time forming hypotheses that aren't interesting/necessary for me, I can quickly tag a lot of sources, and I can quickly collate those sources on a specific topic when necessary.
You might say that the first half of the workflow is "induction", the second half "deduction and confirmation".
I would love it if you had any questions or comments, but just writing this up has been useful for me as well.
You can shoot me an email on "mr [dot] sh4rpeye" at gmail.
I'm currently contemplating how to use it as functionally as possible (categorise articles by subject? By hypothesis? Both?), so would love to chat about it if you'd like