Is someone aware of software that can help me create certain goals and research (sub)questions (digitally) and connect these questions in an organized way with the secondary literature on my computer, as well with my own notes.

I have over 2000 pdf files on my computer. The problem is that I don't want to create a new folder (and copy of the file) every time I come up with a new question.

Ideally, but not necessary, the software should also keep track of edit history and I should be able to make notes on files. It would also be nice if I could access my research organizer from everywhere, though this is not a necessary requirement.

I have looked into some software to manage bibliographies, but the main goal of this kind of software is to export the bibliography, rather than organize my research-questions, computer files, and own notes.

I suppose I want to create some kind of database/tree with the following structure

WEEK 1 ("short title comes here")

-- more detailed description of research question; goal/workplan/etc.

-- literature to read this week (software links correct files on my pc)

------- book 1

------- book 2

------- article 1

------- etc.

-- output

------- version (monday)

------- version (friday)

The software, ideally, must have a "search function" which redirects me to the correct node of the tree (i.e. "WEEK 1" not "this-pdf-contains-the-string.pdf")


3 Answers 3


Try using Microsoft's One Note. It recently became free to use and is a very good application to store your content, no matter how lengthy it may be.

  • Could you perhaps elaborate a little more on why it is a good choice?
    – jakebeal
    Commented Jan 31, 2015 at 20:06

I'm not sure there exists an all-in-one solution as you would like, however Docear is pretty close to what you want and allows you to organize your thoughts/files and connecting them.

On the meta level, I use a bare-bones website from Google Sites (free), set to private, to record daily thoughts and progress (searchable).

Hope it helps


You can try Evernote. It's a simple application yet powerful. You can even sync your notes between devices.

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