Ask HN: How do you take, manage and retrieve notes from pdfs and online sources

I usually used to maintain a org file, and sometimes used Notes app on Mac OS. For online sources I have used hypothes.is for a while. But overall my notes are scattered all the place. I could not find a good way to organise and retrieve the notes when needed. Especially quotes from pdf books and other online sources. I want to be better organised in this regard. Please share your workflows and strategies to take and retrieve notes.