Getting Organized with Zotero

Zotero 4For those of us in the academic world, it can be difficult to keep track of and organize our resources and information. Books and papers are quickly consumed, and information once thought important can become lost in files (or piles)—forgotten. Often we find somewhat hidden chapters on various topics tucked inside books whose titles do not betray their contents. Remembering those great hidden chapters or what we’ve found valuable is not always easy. Keeping track of what we own is not always easy. So how can all of these resources be organized to minimize our overlooking these many gems we’ve found over the years? Enter Zotero.

From the Zotero homepage:

Zotero [zoh-TAIR-oh] is a free, easy-to-use tool to help you collect, organize, cite, and share your research sources. It lives right where you do your work—in the web browser itself.

Many reading this post are probably already using Zotero to manage citations in research papers. Zotero does this very well, and Zotero’s documentation includes a helpful collection of video tutorials. This post will not cover the same material.

Zotero can be used to organize references, resources, and even a personal library—more than simple citation management. Below is what I have found to be the best use of tags, folders, notes and other various features available within Zotero. This work can be time consuming (possibly weeks or months chipping away a bit at a time). But it isn’t difficult work. So one can often multitask while organizing (I suggest lectures on iTunesU or watching Phineas and Ferb). If you will only use Zotero to write papers for a few years while in school, this post is probably not for you. For those who will continue to research and study, organizing now will likely save you time down the road. My example is based on arranging a (primarily) theological library, but this model should prove easily adaptable to any discipline.


There are two primary means of organizing in Zotero—tags and folders. Grouping references is as simple as assigning a tag to an item based upon a personally created ‘keyword’, or dragging an item into a folder. Because an item can be in any number of folders at the same time (think iTunes’ ‘playlists’), tags and folders can seem like two routes to do the exact same thing. And in many ways, they function identically. The only slight advantages I have found in favor of folders is visual. (1) You can create a hierarchical folder system (folders, subfolders, sub-subfolders, etc.) that can be helpful if you like to browse through lists. (2) Folders seem more readily to lend themselves to longer, descriptive titles than tags. Tags won out for me.


Tags offer more benefits than folders. Zotero has great search features. With tags I simply type my tag title in the search bar to see results, without scrolling through a list of folders (my tags are short). For me, this is much faster. The search bar will not find folders. The advanced search allows you to combine tags in a search. If I wanted to see all my resources for Dispensational and Covenant theology together, I could. You cannot open two folders at once.

Tagging is faster than filing. I can type multiple tags faster than scrolling back and forth to drop an item in multiple folders (more drastic if there are dozens of folders). Type a tag, hit ‘return’, and the cursor is already in the box for the next tag.

Use tags to see broader relationships between resources. Select a tag and other tags you’ve given those items appear in black in the tag cloud. You may find that many items with a given tag also all have another particular tag. (This can be shown on a much more limited scale with folders by holding the ‘option’ key to see the other folders any single reference is in.)

Tags export, folders do not. This is more important than you might think. If you spend all this time working on a folder system and then someday need to leave Zotero or use an additional reference manager, your folders will not travel with you. So if you find yourself frequently writing in Mellel (for Hebrew), and decide to switch to a manager that works better with Mellel, your folders would disappear. Tags would stay. I would rather not risk doing the work twice. Tags also stay if you export references to a friend (beneficial only if you use the same tags).

Zotero automatically tag items

Uncheck ‘automatically tag items’

For tagging to be useful, you must adopt a consistent method. UNCHECK the box next to “automatically tag items with keywords and subject headings” under ‘preferences’. (If you use the Firefox extension and the Standalone, uncheck this in both.) This may be helpful in some disciplines, but it is not helpful for those in biblical studies. Information pulled from different databases will often produce different tags even for the same reference. Also, unless you know well the various keyword and subject headings for these databases, you’ll end up with hundreds of tags that hold no meaning for you. It is better to be consistent and create your own tags. Now delete all of those tags you didn’t create. (Right-click + delete. It’s tedious.)

Develop and apply your own tagging system to each reference. I have created a tagging outline to help me be consistent and map out potential relationships. You may download my tagging outline here. (This is a Word doc. Feel free to adapt it to your own needs.) I use abbreviations ending with periods for most tags in order to cut down on false-positive search results (the ‘all fields’ search also searches ‘notes,’ ‘abstracts,’ etc.). If you use abbreviations, use those that are easy to remember. Many people already use abbreviations when taking notes, and many disciplines have standard abbreviations. I often create a type of hierarchical structure within a tag. So one tag may be ‘STheo.Bib.Iner.’ (Systematic Theology/ Bibliology/ Inerrancy). See my ‘Tagging Outline’ for the structural relationship and more examples (this method will become more clear as your read on). I have done this for a number of reasons, which I will explain below. For now, let me say it is faster for me to type this than to create a single tag for each of these areas. ‘STheo.’ is a common portion of tag, but when I hit the ‘B’ the tag gives me the correct autofill. So I don’t have to type out every tag every time. I type part and let Zotero autofill the rest. I may still give references multiple tags. However, some of those tags are combination tags. You do not have to use these combination tags to achieve the same organization scheme I have. If you are more comfortable tagging a reference entirely with single tags (‘STheo.’, ‘Bib.’, and ‘Iner.’), then do that. I do add tags for specific chapters of the Bible as well, though I do not end them with a period (NT.Rom.9).

zotero search tag

Tag search

Why I have chosen to tag this way. It is faster than typing all individual tags. Also, the periods between the parts of the tag allow me to search without typing an entire tag. I need only type ‘Iner.’ to find a reference with the above tag. So with one tag I have placed an item into what would have been multiple folders. Thinking about a folder structure, a search for ‘STheo.’ (caps don’t matter, by the way) will give me every result in the broad category of ‘systematic theology’ including this particular work. (I don’t type the quotation marks in the search.) A search for ‘Bib.’ will give me every result in subcategory of ‘bibliology’ including this particular work. And a search for ‘Iner.’ would give me only the results for the smallest subcategory on ‘inerrancy’. This saves me from dropping the reference into three separate folders.

zotero search tags

Combination tag search

Make broad connection by using tags carefully. Usually shared abbreviations will be used on a small scale, but it is not a bad idea to create connections across categories if they may be beneficial. Searching part of a tag may combine results. So typing ‘Jesus.’ pulls both the NT Jesus resources as well as the works discussing Jesus in the OT (typing more of the tag would narrow the results). Searching partial produces yet a different kind of quick combined search. (Click the thumbnail image to see these illustrated.)

Two more notes about my tagging grammar. ‘Sp.’ is used for specialty type studies. And ‘Gen.’ appears in a number of different categories as an ‘other’ reference catcher. I do not put every reference under the ‘Gen.’ tag. I use ‘Gen.’ when I have subcategories, but I know I will have works that won’t fall into the subcategories I have created. The random works go into the ‘Gen.’ tags.  I do not create subcategories for everything. There will always be a small amount of skimming through titles under any organizational method. I think everything should fall into the ‘Gen.’ type categories unless a search for a given tag produces too many results to easily skim through, you have more than around 10 works on a particular subcategory, or it is a category that you frequently refer to (and so want quicker and cleaner results). Don’t feel bound by my method. The ‘Gen.’ type category works for me until it produces too many results. Then I add another subcategory tag to pull some of those results out of the ‘Gen.’ tags.

Do not create unnecessary tags. I do not usually create tags for things such as names. Names in this field tend to be unique. I don’t need to create a tag for John Calvin or Origen when I can simply type ‘Calvin’ or ‘Origen’ into the search field and find the results I need. The search pulls their names from titles, subtitles, abstracts and notes (more on notes later). Names are simple searches where subjects are more complex and require tags as a means of consistency. I can’t see someone writing a book about Calvin while calling him by a different name. The same holds for modern authors. I don’t need a tag for ‘J. I. Packer’ when I can type ‘Packer’ and get the results I want (yes, there may be a random work with ‘packer’ in the abstract that you have to ignore). Don’t reduplicate what you already have in a simple search. DO create tags if something can be spelled multiple ways (Muslim/Moslem, multiple spellings for Gadhafi, etc.).

I also tag everything I actually own and the format in which I own it (unless it is in print, which is the default ‘owned.’ tag).


There are two types of folders (collections) in Zotero, both of which are still very useful. I use folders to keep certain references very quick at hand (so no subfolders), to keep things in front of me that are importants (so I see them often), to hold references that would be difficult to tag, and to hold references that would change in status too often to them make worth tagging. (You can see my folders by clicking the thumbnail image in the ‘Notes’ section below.)

The basic collection is a static collection. Items are manually added to and removed from these collections. Click the folder icon and create a ‘new collection’. Here I have folders like ‘Urgent Reads’ and ‘To Buy’. These are things I want to be visually reminded of often. One might also create a collection for a current paper or project. After finishing, I would create a tag and delete that collection (ex: ‘NT.Mt.21.Paper’). A folder that always stays here is one I have labeled ‘Processing’. Here I keep references I have yet to check, tag, etc. If you are just starting this tagging process, select all of the references in ‘My Library’, drag them into this folder, and then delete them from this collection as you work through them (just hit the ‘delete’ key when the item is selected). This is a good way to keep track of items that still need work. It would be difficult to tag these and a hassle to delete the tag from each one. If there is a folder you want to remain at the top of the list, place a symbol before it (ex: !Processing).

The second type of collection is a saved search (like a Smartfolder on Mac). These appear as a slightly different type of folder, but it is best to think of them as saved searches. I have two of these collections at the moment. One I have titled ‘!Recently Added’. Here I have used the advanced search (click the magnifying glass) to create a search for ‘date added / is in the last / 2/ days’. I have found this VERY useful when adding several resources for papers (say, from a database) when I don’t have time to tag them right then. This keeps these new references from getting lost among the others. The folder keeps them at hand until I can get to them. If I don’t think I’ll get to them in the next 2 days, I select them and drag them into the ‘Processing’ folder. This works well for importing a large number of references as well (from another reference manager, Logos, etc.). This folder allows you to catch all the new references and push them into the ‘Processing’ folder. Then you can take as long as you want to work on them. The other saved search I have is ‘attachment file type / is / PDF’. I don’t use this as often, but for some reason I like to have all of my PDFs at hand. I have moved PDFs around frequently in the past, and I like having them collected for me to grab and drag somewhere. It’s a personal oddity.


Tagging Notes in Zotero

Example of a titled note with contents and in-note tags

The ‘notes’ field is an important and versatile field. I will often create a ‘note’ for notes that I take while reading a book or an article. This is an easy way to keep them accessible. Also, I often create a note for the table of contents of a book. This can be especially useful if the book is detailed and covers many related areas, if the book is an edited work with many authors (and you don’t feel like creating a reference ‘section of book’ for each one), or if the book has someone hidden chapters. Here I copy the contents from someplace like WorldCat or the library catalog and paste it into a note. (In Zotero, click the green arrow icon, and ‘library lookup’ to make this faster.) Then I tag THE NOTE (bottom of the note window) for categories only obvious by looking at the table of contents. I tag the note because searching will show both parent and child items, but the item with the actual tag will be in black font while the other will be in grey. If I have to look at the note to understand why a tag applies to that work, I want the search to make it obvious I should look at the note (by the black font). Also, if it is a longer note, I will usually type out the name of the tag next to the chapter it relates to and then highlight it to make it easy to find (you still have to actually tag the note though. This can also be done with notes that you have taken on that particular work.

Give your notes titles. The first line of the note is what appears in the main Zotero window. Avoid the guesswork of figuring out what a note is about by titling it. Type ‘Contents:’ into the first line of the note and hit return before pasting in the table of contents. Type ‘Reading Notes’ or ‘Summary’ or some other such title into your other notes.

Add names (of people) to notes if necessary. Often those names that do not appear in titles appear in chapter titles (think of ‘reader’ type works that give a sampling of various writers through history). If the person is still not named, just type the name as the title of a note (or list them if there are many). I would rather do this for a small handful of works than actually have to tag all of them.

Also, as you read through a book and find interesting ideas that might intersect with other categories, make a note and tag it with the other category (hard to do this well with the folder system!).


Use the ‘Related’ tab! Here you should link sources like book reviews to the actual book. Also, relate book sections back to the actual reference for the full book (hold ‘Shift’ to select and relate multiple references at once). If authors are writing in response to one another, relate those works. You may also want to relate opposing views. The related link can be very helpful. With it you can remember a portion of a book (that you have tagged) without having to remember the book. I can often remember content before I can remember the source.


Do not forget about the ‘abstract’ field. I intentionally fill this field if have added a reference recommended by a professor or a friend, even if I have to go to publisher’s page and copy and paste it in (and I typically make a note). The abstract will help give me an idea of the book’s content (since I have likely not read it) when I see it in a search a couple months or years later. I may even add a note. I don’t want to be left wondering why the book is in my search results.


I fill this field with the Library of Congress call # for (at least) every book I personally own. Some databases can fill this field automatically (like Southern’s catalog). Organizing your physical library by Library of Congress is not difficult when using Zotero. You’ll likely find that about 90% of your books are grouped in what you would consider logical groups anyway (all the works on Matthew are together, etc.). Even without physically labelling the books, searching the title in Zotero, then clicking the ‘x’ to clear the search, will keep your title highlighted and show you the books around it (if you have them sorted by call number in Zotero at the time). Many books stand out on a given shelf, and seeing one of those titles in Zotero can point you right to the book for which you’re looking. Also, I suspect that many in our field who have under 1500 or so actual print volumes can already walk to a specific volume in the dark. We spend too much time staring at our books. So it won’t take long to remember locations for the odd (to us) 10% that don’t seem to fit logically. Having this number for other books can also make it easier if you need to run back to the library to take another look at a book you don’t own. (Students, again, use the ‘library lookup’ feature to make sure it is on the shelf before you run to the library.)


zotero fields

Uses for additional fields

Want to give items a ‘star rating’? Use a field like the ‘library catalog’ field (not the call # field) and put *s for stars. Then just make sure that field is displayed in the center column. This could be used for other things as well. I use ‘library catalog’ field to note that I have written a review for a resource (with and ‘r’) and the ‘language’ field to note the items I have mentioned on the blog (with a beta).

Showing the ‘type’ field in the center column can help you find what you’re looking for even faster. Let’s say you know the item you’re looking up is a journal article, search, and sort your items by type. It requires less scanning to find what you need.

My method is not for everyone, and it will likely recieve slight modification over time. Even if someone decides to follow what I have suggested, I would recommend readers look over Andy Nasseli’s reformation 21 post here. He adopts an extensive folder structure which some will prefer to this tagging method. It is well worth viewing. I’m simply tired of the folder system.

Moving from a folder system to a tag system is not terribly difficult. Create a tag. Open a folder. Select all the references and drag them onto the tag.

Zotfile is a free (though worth the suggested donation) addon that can automatically rename PDFs as you attach them (from the parent metadata or your own preference settings). This has made my life easier when trying to consistently name those PDFs downloaded from databases (by default they have obscure numbers for titles). This addon can also send PDFs to your iPad for reading and markup, and then retrieve them from your iPad, putting your highlighted text into notes (I don’t own an iPad, but I’m sure that is nice).

Remember, you can only prepare now for what you think may be helpful in the future. Every organizational method will have to be tweaked from time to time. If you search for something in Zotero and you don’t quickly get the results you want, make a few adjustments. Perhaps you need another, narrower tag. Find out what went wrong and fix it.

You can always rename tags later. So you can start with abbreviations and expand them later.

DO NOT move your Zotero folder to Dropbox as a backup! This can be disastrous. Google it; check the Zotero forums.
If you use both the Standalone and Firefox extensions, it is best not to have them both open at the same time. Google it; check the Zotero forums.

I welcome (kind) feedback. What are your suggestions? How are you organizing in Zotero? What questions do you have for me?

*Special thanks to Ivan Mesa for previewing a portion of this post and pushing me to set my method in print.

UPDATE 4/19/13 – I’ve added another (much) shorter post with a few notes about Zotero 4 here.



  1. Excellent!

  2. This is great! Thanks.

    When I talked to you earlier today I didn’t realize you had posted it back in March 🙂


  1. […] Vasut recently laid out his method for using Zotero. There are a lot of great tips there, and a few I will definitely be working into my work […]

  2. […] an earlier post, I discussed in depth how I organize and use Zotero. Here I will merely highlight and comment upon […]

  3. […] desk. I can easily determine if I already own a book by either looking at the shelves or checking Zotero. Other times though, I will see several new titles added to the ‘bargain’ wall at the […]

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