How to Avoid a Citation Headache

One of the most useful tools for academic research and writing papers is a reference manager. As a disclaimer, if you have not manually generated a bibliography, learn the fundamental principles of references before using an assistant tool. This concept is similar to how students should learn arithmetic before using a calculator.

What is a reference manager and why should I use one?

A reference manager is a tool/software that stores citations, which allow the user to insert in-text citations along with automatically generated bibliographies. The main advantages are the user can organize their citations in one place, search through an organized library, and add a self-sorted bibliography. There are many reference managers including Mendeley, Zotero, EndNote, RefWorks, and Papers.

Reference managers speed up the time-consuming task of manually inserting citations and creating a bibliography. One common issue with manual citation is updating the numbering of in-text citations chronologically whenever adding new ones to the text. However, with automatic updating, for example, using Nature format, the superscript in-text citation will go up or down accordingly. In addition, the bibliography will format accordingly, and will automatically be re-organized to the correct alphabetical order or numbering.

Another issue is the diverse number of journal citation styles which can be a nightmare for any author to remember the exact requirements for each submission. A reference manager can download the journal’s preferred style, and it will update in text and bibliographic styles accordingly. However, authors still need to consult journal submission requirements for the formatting of other sections.

Some reference managers also serve a dual purpose as a tool for organizing papers for quick searching, filtering, or sharing. For example, one can create their folders and branch subsections to organize papers for different projects. It is helpful to begin every project by reading the background literature, and that is the best time to start using a reference manager and/ journal article organizing tool.

How do I import citations/journal articles?

There are two main ways I import articles: website or PDF.

Web import:

Different programs have different methods so I won’t discuss the details too in-depth but will outline the general principles. Each software usually has a browser bookmark or extension/add-on. The booklet is usually a Java booklet. Make sure you disable any Adblocker/tracking protection that targets your reference manager. If you are unsure, turn off the Adblocker/tracking protection software for the webpages you want to extract citation info. Add that to the browser. When you are on the PubMed page reading the abstract, you can press this bookmark/add-on and it will save the citation metadata (author, dates, title, abstract) into your reference manager. If you extract the metadata when you are on a webpage where you have access to the full-text, it can also extract the pdf of the paper/paper itself. Sometimes, bugs can arise and the paper may not be extracted, despite your access. Typically, extraction works best on PMC, ScienceDirect, and major journal websites.

PDF import
Most PDFs of papers have its saved metadata; typically, only older, scanned copies will lack metadata. PDF is the most reliable way of uploading the paper itself and the citation data together as one entry. Go to your reference manager and either add individual PDFs or mass import all the pdfs from one folder.

How do I write and cite on Microsoft Word?

As Microsoft Word is the most popular text processing software, all of the major reference managers can export your citations into your paper as needed. Consult each reference manager for specific instructions on how they export into Word. I will use Mendeley as an example: install the word plug-in (found either on setup or under tools), go to the ribbon tab in Word and find the references tab. Look for the Mendeley symbol and click “insert in-text citation”. At the end of the paper, select “insert bibliography” and the full reference list will be inserted.

The in-text citations and the reference list will update automatically as you add more citations. However, be careful not to change the text field metadata. They have embedded macros that allow for the automatic updating but changing those macros will break the citation software’s ability to change the text. The macros are the main reason why one can’t change the format from Word to Google Docs.

Which reference manager should I use?

This is a personal choice, as there isn’t one clear, distinct winner for each person; rather, your choice depends on your computer’s operating system, and what you are looking for. Check out this guide from the University of Toronto libraries, comparing the different major reference managers. One notable program missing is ReadCube (Nature Publishing Group) and Papers which are both notably well integrated with Mac. Personally, I prefer Mendeley as it is free and it is simple to organize papers, which makes it easier for me to navigate all my different projects.
Overall, I would highly recommend all university students become proficient in using reference managers for their papers. It will help you avoid headaches as you start juggling multiple projects and papers.

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