Brianna Buljung

This chapter will help you:

  • Evaluate your existing research workflow and use of citations
  • Describe the role of citations in research and their importance in the scholarly conversation
  • Explore citation managers and their role in organizing research


Once you have begun to find sources for a research project, it is important to consider how those sources should be stored and organized. Some projects, especially theses and dissertations, can include hundreds of citations that need to be saved. Effective citation management allows you to sort, store, annotate, and ultimately use the sources related to your research. Good citation habits are important for ensuring the sources are available when you need them.

Citation managers are tools that enable you to create a library or collection of sources developed over time and used across projects. Most managers help you format your bibliography or reference list in whatever citation style is necessary without you manually formatting the citations. This chapter is going to describe the role that citations and management tools can play in your research. It will use Zotero, an open source software, as an example. However, there are many different tools available with different features and associated costs. It will describe some of the questions you should consider prior to selecting a citation management software.

Before you continue reading this chapter, spend time reflecting on your existing research workflow. Any time you incorporate a new tool to your workflow, it can be helpful to reflect on how it will impact or change your existing habits. Considering the following questions can help you to determine how a citation management tool might meet your needs:

  • How do I use and manage citations in my research now?
  • What tools, if any, am I using?
  • Is this process working for me?
  • What frustrations do I have with citation and source management?

Why Citation Management Matters

Citation and attribution of the information used in papers and projects is an essential element of the research process. Citing the sources used gives credit to the original creators of the information you are using in your project. They deserve acknowledgement for their contributions to the scholarly record on the topic. It can be helpful to think of scholarly discourse on a topic as a conversation between you, your sources and your readers. Your work builds on the conversation established by your sources. Your readers can use your work to further the discussion by citing you. Your bibliography provides the foundation upon which you built your research and shares your sources with the scholarly community.

Adequate citing helps establish your credibility as an author. Your work will be judged based on the quality of the sources used; incomplete citations and/or low quality sources could harm your credibility. Also, citations help you to distinguish between the multiple perspectives in your writing. A citation marker, such as a footnote, endnote or in-text citation, is a cue to the reader that the piece of information is from a source, distinguishing it from your perspective or voice as the paper’s author in the rest of the text.

The specific elements included in a citation can differ from style to style depending on the norms of that discipline or journal. Regardless of the specific style, the purpose of the citation is to convey enough information for the reader to locate the source. There are several elements that are common across most styles and item types such as author’s name, item title, container (typically a book, journal or website) and a link for digital resources. Special sources, such as laws, standards, technical reports and interviews may need additional information about the source or an associated report or standard number. Knowing the basic elements of a good citation will help you to read and evaluate others’ work and to ensure that your work is properly cited. This skill is helpful, even if you use a citation manager.

The figure below depicts a journal article citation in two styles, American Psychological Association (APA) and Modern Language Association (MLA). Although the specific placement of each element differs, both contain the same essential features of: author, title, journal, volume and issue and a link. The figure is color-coded to show where each element appears in a typical citation. The volume and page number are a key indicator that you are viewing a journal article. A permalink or Digital Object Identifier (DOI) is also very helpful for the reader. Find the most persistent identifier possible, using a DOI whenever possible. This identifier ensures the item is consistently findable. Try to avoid the often long link in the browser’s address bar. This link is often not persistent and can result in an error when used again.

journal article citation formatting and example in ALA and MLA formats
Examples of MLA and APA formatting for journal articles

A good workflow with research is essential to being an ethical, organized and efficient researcher. You have to be able to support your statements with the sources you have used. To do this, you need a good workflow that helps you to find, organize, store and ultimately cite the sources. Later chapters will discuss other aspects of the workflow including data collection and management. Taking the time to learn a new platform or change your habits should ideally improve your workflow or address frustrations. You may find that the tool solves a problem and meets your needs. In contrast, you might find that the new tool takes more effort than you would like or that it does not meet your needs. In those instances, additional reflection on your workflow and trying another tool may be necessary.

Some researchers enjoy formatting individual citations or use few citations, making manual management feasible. However, most researchers will amass a large collection of potential sources throughout a project, often using them across multiple products. The process of organizing and using these sources can be very time consuming or overwhelming. You may want to consider adopting a citation manager if you are:

  • Working with a large number of citations
  • Using the same sources across multiple projects or products
  • Easily frustrated by the nuances of specific citation styles
  • Collaborating with others on a research project

How to Organize Your Sources

Citation managers help you to organize citations by storing the associated metadata in your own personal collection or library. Many platforms can also help to store and organize PDFs, notes, images, data sets, web pages and more. Most managers allow you to take notes and tag individual items with keywords. Those notes and tags are searchable, helping you to find a specific source in your collection. Some citation managers, including Mendeley, allow you to highlight and annotate PDFs on the platform, saving the metadata, PDF and annotations in the same location. The most important feature of citation management software is the integration with word processing systems like Microsoft Word and Google Docs. They will format bibliographies and in-text citations in hundreds of different styles directly in your document. Many platforms will also allow you to share your citations and notes with others to enable collaboration on projects.

Once you have decided to try using a citation management software, you need to determine which one will best meet your needs. Each software will have different features and limitations. Some are freely available and others might have associated costs depending on features such as document storage capacity. The first factor to consider is cost. Will a free tool meet your needs? Will you need to store many PDFs? Some tools, like EndNote offer free online software but charge for the desktop version. Some universities subscribe to a particular platform providing free access to the campus community.

Second, consider your workflow and your research needs. What type of references do you primarily use? Some platforms are better for textual sources and others are better for images and other media sources. What specific features will you need? You might need a manager that integrates well with LaTeX editors, or that allows you to annotate PDFs. Find the manager that has the features that best meet the needs of your specific project or workflow.

Finally, consider your collaborations and the needs of your research group. If you are working with others, it can be helpful for the entire group to use the same citation manager and word processor. Coordinating systems and workflows can help your group to work more efficiently and share sources. There are several different charts available online to help you compare different citation managers and their features. The chart below is an example comparing 4 popular platforms: EndNote Web, EndNote Desktop, Zotero and Mendeley. It can help you to consider the features that might be most useful to you and any potential research collaborators.

Feature Comparison of Popular Citation Managers (accurate as of 2022)
Feature EndNote Web EndNote Desktop Zotero Mendeley
Searching across external database Yes Yes No No
Importing citations from other databases Yes Yes Yes Yes
One click to find full text​ No Yes No No
Browser plugin to extract citation from web pages Yes, quality varies​ Yes, quality varies​ Yes, can save snapshots of web pages​ Yes, can save snapshots of web pages​
PDF Annotation and highlighting​ No Yes Yes Yes
Searching PDFs and annotations No Yes Yes Yes
Collaboration ​ Private groups Private groups Private and public groups Private and public groups

Once you have decided which manager to use, follow the instructions on their website to download and/or install any necessary components. Some tools have a web browser plug-in or connector that helps to import sources into your collection. Another feature that sometimes requires installation is a word processor plug-in that connects your citation library to tools like Word or Google Docs. For example, when installing Zotero you will download and install the desktop app, then you can install the connector for your favorite web browser. It is good practice to close all instances of Google Docs, all Word documents and extra browser tabs before installing your citation manager. This can help to ensure the plug-ins are installed correctly.

Once you have installed the software, you can begin using its many features. It is important to learn about the different ways that your citation manager adds items to your collection. Often, the web browser connector will allow you to import items individually or in batches. Some, like Zotero, allow you to search from within the software by ISBN or DOI. Most managers will also have a manual entry option. This option is especially important for unique, unpublished and specialty sources. You can select the type of item and then fill in the fields. Many platforms will also allow you to import a batch of sources using a bibtex file. This feature is helpful when you are switching to a new platform and migrating your library or when you are using a tool like R to generate a script that collects sources for you.

Inside your library, it is important to get into the habit of organizing your items. You can use folders (or collections) to sort items. Depending on your project and workflow, you might organize by type, subject, methodology, or project. Also, get into the habit of tagging items with keywords and using the notes feature to save your thoughts or specific quotes. As seen in the figure below, the library is arranged by topic, making it easy to distinguish different projects. Below the folders on the left side, there are also 2 groups (or shared collections) and searchable tags. It can be a good habit to regularly evaluate duplicates and delete the extra citation.

Zotero platform with folders, groups and items
Sample Zotero account

Once you’ve adopted a citation manager, consistent use is key to ensuring that it becomes a helpful part of your research workflow. When you are locating, reading or evaluating sources, have the manager open. You can add sources and notes while you are working with the item. The notes feature allows you to capture your thoughts, questions and pertinent quotes, then saves them for when you begin writing. Many researchers find it helpful to review every item when it is added to the manager. The accuracy of the imported citation is dependent on the metadata available online. The importer often accesses inaccurate or incomplete metadata. The practice of checking citations at import will help you ensure that the metadata is correct and accurate while the item is still in front of you. It makes the source import process a bit more laborious, but you will know your citations are accurate when you begin the writing process. Some researchers also find it helpful to quickly generate a bibliography of all the items in a specific folder or for a specific project. This practice allows you to review the citation for each potential item that might be used. Then you can correct misspellings or incomplete citations early in the research process.

Some researchers prefer to use a typesetting tool like LaTeX or the web platform Overleaf instead of Word, Google Docs or another word processor. Some citation managers, such as JabRef are specifically designed to work well with LaTeX. Other managers, such as Mendeley, EndNote and Zotero allow you to export a bibtex file to your computer that can be uploaded to Overleaf and “called on” by your LaTeX document. As seen in the figures below, the ASEEpaper.bib file contains the bibliography items that are called on by the main.txt file.

screenshot of Overleaf main.txt with arrows to .bib file and reference section in the source view
The bibliography section of the main text file
screenshot showing several citations within main.txt file
Citations in the text that call on the .bib file

Tips for Managing Citations

To effectively incorporate citation management into your research workflow, remember:

  • Any tool you choose to use needs to integrate with your existing habits. If the tool makes the process more difficult, or if you use it inconsistently, then it may not be suitable for your workflow.
  • Adoption of new tools and processes can take time, it might be helpful to adopt the citation manager for a small-scale project or a sample of your sources. You can practice using the features of the tool and establish a workflow that meets your needs before you apply it to larger projects.
  • If you are collaborating and/or in a research group, it can be helpful to use the same platforms across the team. This will help you to share citations, folders and documents more easily.
  • When you are using citation managers and their browser plugins, take the time to review each citation as you are bringing it into your collection. You can ensure the information is accurate and complete, minimizing the need for additional edits later.


Now that you have a more in depth understanding of how to organize and manage your sources, consider the following in relation to a project or topic of your choosing:

  1. What aspects of citing and managing sources do you find most difficult or frustrating?
  2. How can you modify or improve your research workflow to help mitigate those aspects and incorporate better citation management?
  3. Reflect on the citation managers discussed in this chapter:
    1. Choose one and practice importing items, adding notes and organizing folders
    2. Do you think this is a tool you will incorporate into your workflow?
    3. What features do you particularly like or dislike?


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Navigating the Research Lifecycle for the Modern Researcher Copyright © 2024 (2nd Edition) by Brianna Buljung is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, except where otherwise noted.

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