How to Organize Literature and Notes in Zotero (How to do X in Linguistics 13)

Reading, summarizing, and citing literature is an essential part of every student and researcher’s life. While there are many books and workshops on academic writing, there is less information on how to efficiently organize literature. For this reason, I offer an overview of how to organize literature and notes in Zotero. Specifically, I illustrate some of my own workflows for organizing the literature for my dissertation. I also discuss general features of Zotero. The interested reader who wants to learn more will benefit from the related links.


There are currently 603 items in my main library in Zotero. In addition, I have seven group libraries that contain literature for joint projects or specific literature that is not directly relevant to my dissertation. I set up Zotero when writing my MA thesis, and have been using it daily since I started working on my dissertation. So over the years, I discovered some tricks and features in Zotero that I was not aware of at first, and I aim to summarize them here.

This is not a guide for a complete beginner who may not know about Zotero or how to install it. However, the related links may help fill in some gaps. In general, though, I assume you already have Zotero installed and just want some insights into possible workflows that might help you manage your literature.

Adding Items

There are several ways to add new items to Zotero. You can import items from a .bib file or copy a BibTeX entry to your clipboard and insert it. Another way is to use the magic wand icon and add the item via a numeric identifier like DOI, ISBN, PMID, etc. I usually search for articles/books through my Firefox browser and use the Zotero extension to include an item. The advantage is that you can directly tag the item or add it to a collection of your choice.

Note that the metadata that is automatically populated may need to be adjusted. For example, I usually delete information that is not immediately relevant, update the capitalization of the title, insert the publisher’s address (if it is a book or book section), and check to make sure the authors are correct. I also add tags so the article does not get lost in the depths of my library. The following graphic is a schematic representation of an item in my Zotero library.

Figure 1: Schematic illustration of an item in my Zotero library.


In my library, I use a three-part tagging system. First, I have organizational tags that help me structure what I want to do with an item. These tags are: new, skim, read, and add note. I color-coded these tags to make them easier to find (new=orange, skim=green, etc.). Second, I use project tags to decide for which project the article is relevant. For example, I have a tag body-object colexifications for my study on colexifications between body and object concepts (Tjuka 2023). The tag thesis includes all the literature that will be incorporated into my dissertation. Third, I use content tags to group literature by a common theme, language family, method, or theory. This is an open class that will evolve as I add more literature to my library and will need to be refined from time to time as there can occur some overlap. I use these tags mainly at the beginning of a project to find literature that might be useful for my research question.

A new tag I created based on a discussion in our CALC group is entry point. This tag is reserved for articles that provide overviews or in-depth discussions of a particular topic and can serve as a starting point for finding more literature. For example, in my current project, I do not use methods from neuroscience, but in the future, I may want to integrate them. When this is the case, I can select the tags entry point and neuroscience to help me find a good place to start.

More about tags and collections:

Relations Between Items

Zotero provides several options for linking articles and notes. For example, to link an article to an edited volume, I create an item for the book and then use the Create Book Section from Book option with a right-click on the item. The book’s tags and metadata are transferred to the book section and all you have to do is add the book section’s title, authors, and page numbers. On the Related tab, the book or book section is displayed and you can easily jump from one to the other. You can use the same principle for journal articles of the same special issue.

Unfortunately, Zotero does not have the option to automatically display the contributions and table of contents of an edited volume or special issue (this seems to be an option in Mendeley). You can also use links within notes, which is described below. One thing that Zotero is still missing is an option to define different types of relations such as cited by, co-author, etc.

More about the related option:

File Storage

I use two options to save my files in Zotero. Most of the items in my library have a link to a file stored on my laptop. The files are all in a folder called Bibliothek (‘library’ in English). A handy feature of Zotero is that it automatically renames the file based on the metadata. For example, all my files have the same naming structure: “Author’s last name – Year of publication – First 50 characters of title”, i.e., Andersen - 1978 - Lexical universals of body-part terminology.pdf.

Another option is saving a stored copy of the file. However, I would recommend using this feature wisely, because there is a storage limit in Zotero that can quickly be exceeded if all files are saved as copies. For example, I use this option at times to read articles on my iPad. Unfortunately, Zotero does not currently support linked files in the Zotero iPad app.

More about storage:


One feature I did not use at the beginning, but now use extensively, is adding notes to articles. I use notes to write summaries of articles or to extract different types of information from an article. When I copy a sentence from a linked PDF, Zotero automatically creates a citation with a source and a link to the page. Note that the page numbers are not always correct, but with the link, you can quickly verify the page number.

My approach to creating notes depends on the relevance of the study in question. If it is an important study for my own research, I include a note with a summary, annotations, good quotes, specific topics, further readings, and examples. Within these notes, I can use the citation function [+] to add a link to another article in my library. To distinguish the content of the article from my own thoughts, I format my running comments in a monospaced font.

Some articles are not that relevant, but I have gotten into the habit of adding a short note to all articles in my library so I know why they are there. I skim the not-so-relevant articles and write down the type of article, the theoretical framework (if applicable), and bullet points about the background, methods, and results of the study. It is even possible to tag each note or link it to other notes. In this way, Zotero can mimic some of the functions of a Zettelkasten and become your external brain.

More about notes:

Collections and Group Libraries

The default view is a library with all your items grouped into folders. I use folders, i.e. collections, mainly when I write conference abstracts or create a reading list for my classes. For projects, I do not use collections anymore because some of the literature I need is related to more than one project and it is easier to forget to add an item to a folder than to have a colorful tag next to the title indicating one of my projects (see above).

However, one option I find very useful in separating the wheat from the chaff is group libraries. They help me keep topics that are not directly related to my projects but are of broad interest to me outside of my main library. For example, I have a group library called “Phylolinguistics” with articles that interest me but are only marginally related to my projects. I also use group libraries for collaborative projects to share literature among colleagues while we work on an article.

More about collections:

More about group libraries:

Better BibTeX

There is a neat Zotero extension called Better BibTeX that can be used to structure bibliographic data. For example, you can specify that your citation key should look like this: auth.capitalize+year which results in the citation key Majid2010. I use Better BibTeX to structure the output of the .bib export and specify, for example, that certain fields such as abstract, keywords, and file are omitted.

In addition, there is the option to determine the quick copy format or to make titles case-sensitive. Note that Better BibTeX uses double curly braces to protect capital letters in the output (for an explanation, see: The output for the above citation key Majid2010 looks like this:

title = {Words for parts of the body},
booktitle = {Words and the mind: {{How}} words capture human experience},
author = {Majid, Asifa},
editor = {Malt, Barbara C. and Wolff, Phillip},
year = {2010},
pages = {58--71},
publisher = {{Oxford University Press}},
address = {{Oxford}}

You can easily select an item, press Ctrl+Shift+C, and the above output is saved to your clipboard.


As with all tools that make your life easier, it comes down to working with them. I have discovered a few other small tweaks in Zotero over the past three years that I now use unconsciously. In selecting the topics above, I have noticed how my reading, note-taking, and writing workflow has improved through consistent use of my Zotero library. It is certainly an evolving process, and I would encourage everyone to get started right away.

One of the challenges is staying consistent while improving your workflow and adding new items to your library. That is why, once a year, I clean up my library and check for inconsistencies. Of course, there is always something to fix, but using your library regularly makes it easier to stay on top of things.

Additional Links

Reference management systems:

Note-taking tools:

Knowledge base systems:


Tjuka, Annika. 2023. Cross-linguistic colexifications with body concepts: Metaphor, metonymy, analogy. Computer-Assisted Language Comparison in Practice. (February 6, 2023).

Cite this article as: Annika Tjuka, “How to Organize Literature and Notes in Zotero (How to do X in Linguistics 13),” in Computer-Assisted Language Comparison in Practice, 6.1: 23–28 [first published on 6/03/2023], URL:, DOI: 10.15475/calcip.2023.1.3.

Download the article as PDF: calcip-06-03.pdf

Grant Information: This project has received funding from the Max Planck Society as part of the CALC³ Research Project ( The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright information: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

OpenEdition suggests that you cite this post as follows:
Annika Tjuka (March 6, 2023). How to Organize Literature and Notes in Zotero (How to do X in Linguistics 13). Computer-Assisted Language Comparison in Practice. Retrieved July 22, 2024 from

This entry was posted in How to do X in Linguistics? and tagged , , on by .

About Annika Tjuka

My main goal is to answer questions about linguistic diversity with a focus on language variation in word meanings. I have a BA and MA degree in linguistics from the Humboldt University Berlin and am currently pursuing a doctorate at the University of Jena. I am a language scientist studying patterns and causes of words with multiple meanings. For my work, I use data from language documentation, large-scale databases, and computational methods. In my Master’s thesis, I conducted the first systematic study of body part extensions such as table leg and foot of the mountain. I examined the frequency of 95 expressions in 13 languages and the preferences for underlying analogy patterns based on similarity in shape, spatial orientation, and function. The first project of my doctoral research established the Database of Cross-Linguistic Norms, Ratings, and Relations for Words and Concepts (NoRaRe), which contains 98 datasets from linguistics and psychology across 40 languages including 65 word properties.

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