At the moment I'm using Zotero to organize my paper collection and for my current work I'm very happy with it's possobilities to organize content (folders and tags).

However, working on bigger projects a hierarchical tag structure would come in handy where subtags can be assigned to lead-tags (or something similar). Is there any reference program that can do that?

  • Welcome to AC.SE. I am inclined to think that this is a "big list" question that will be filled with answers about the way people deal with this for every piece of reference management software. Can you edit the question to elaborate on what other software you have tried and why they fail.
    – StrongBad
    Commented Apr 24, 2013 at 8:00
  • I agree with @DanielE.Shub. I'm betting there is a way to do this in Zotero (by hook or by crook) and a focused question about it might find the person who knows how to do it. As it stands, it looks like a list generator and will probably be closed.
    – Ben Norris
    Commented Apr 24, 2013 at 11:34
  • @boo2060 Why do you need hierarchical tags? Isn't in enough to a) have folders with subfolders OR b) always use some tags, de facto making them hierarchical (e.g. put always physics for all topics with physics)? Commented Apr 24, 2013 at 15:28

4 Answers 4


JabRef is a reference manager using the BibTeX format. It uses the concept of groups, i.e. papers can be put into groups, and it allows to create a hierarchical group structure. Since one paper can be put into any number of groups, it is essentially hierarchical tagging.

With JabRef, one can even configure for individual groups whether a group will automatically include the content of any subgroups (analog to tagging), or will include the content of any supergroup (refining), or just include the papers assigned exactly to this group (as in a classical folder structure).

  • Zotero allows this as well.
    – Tomas
    Commented Mar 16, 2016 at 16:20

It seems that in the current version of standalone Zotero (4.0.28), you can nest folders in the left pane, and add a document or reference to several such folders.


Check out Citavi.

It supports keywords, categories, and groups. Categories can be organized hierarchically. Among many other features, Citavi also allows you to save quotations, comments, summaries, and your own ideas, and to organize and structure them before you start writing. Citavi is Windows-only at the moment, but a web version is being developped. The video "Citavi 5 in a nutshell" explains the main features: https://www.youtube.com/watch?v=X3vbWIcljDQ

(I work for Citavi)


This is a question which has often come up on the webz.

I am not really sure of your exact requirements but Mendeley has some of the functions or you could develop a workaround. See this and this. I have also heard good things about Sente but I have not used it.

These are solutions for Macs though. I am not sure about Windows and do not know if that is a constraint which you have. Personally, I use a hierarchical folder system in Mendeley and export to BibTeX and add tags - which, so far, seems to work well enough.

Are you seeking more, in general of optimizing your academic workflow? In case you haven't heard of it, I suggest visiting this blog. It updates sporadically but most of the good stuff is in there. I hope this helps.

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