Three Tips to Organize Thesis and Article Sources

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Whether for a dissertation, thesis, or class research paper, a literature review may expose you to hundreds of research papers that could contribute to your understanding of the field and possibly even be cited in a manuscript. So how do you keep track of these sources?

Here, I’ll describe three options for you to consider: keep an annotated bibliography, use spreadsheets, and use a citation management software.

Tip 1: Keep an Annotated Bibliography

An annotated bibliography is going to be a list of the sources that you’ve read along with important notes to explain the source’s importance and relevance to your research. While some people do this by hand, that can be laborious, particularly when you are searching for a source after the fact. My suggestion for the modern annotated bibliography is to use a searchable format such as Word, Rmarkdown, OneNote, EndNote, etc. These options allow you to easily re-reference a source and (re)identify sources that talk about particular concepts. To maximize your annotated bibliography, there are several key components to include in each entry (and here’s a worksheet):

  • Citation — In addition to the author(s) and year of publication, you should also make a note of the doi (so you can find it later using https://doi.org/[insert doi]), and the filename of the pdf. The filename is especially important since it allows you to find the pdf you already have, without opening 20 files one-by-one.

  • Methods — Are any of the methods used especially relevant to your work? This might be because you need the protocol, they are key to interpreting the data, and/or are insufficient (i.e., they provide an opportunity for you to improve the field).

  • Results — What are the key results and findings? What figure is central to their story?

  • Limitations — What are the limitations of the research? What could be done differently to improve the robustness of the research?

  • Your thoughts — What do you think about the paper? Use this as an opportunity to present your unfiltered thoughts, feelings, musings, and big ideas. That way you can find them later.

  • Follow up — Are there any references that you should read in the future?

Tip 2: Keep a Spreadsheet

Spreadsheets are another great option for keeping track of the sources you’ve identified in a searchable and easy to skim format. In this case, you would likely include more granular information about the source’s origins, citations, accessibility, etc. However, what you include may depend on how you plan to use the document.

For example, Dr. Raul Pacheco-Vega uses a “Conceptual Synthesis Excel Dump”. In addition to basic citation information, Dr. Pacheco-Vega includes columns to capture his thoughts on each references as well as cross references and potential quotations. It’s very much like a horizontally organized annotated bibliography.

For a more basic compilation of sources, Eastern Washington University has a sample chart that you can use to build your own and Kathleen Clarke describes a slightly more intricate method that links spreadsheet entries to easy file identification. More visual, or more easily overwhelmed, writers might consider adding a color-coordination system to their spreadsheets.

Tip 3: Use a Citation Management System

Citation management systems can be great tools for keeping track of relevant sources. I used to recommend Mendeley, however, it was put behind a paywall and underwent changes that make it more difficult to use and export your references if needed.

The open source (free) tool, Zotero is now one of the best options available for tracking and organizing sources. Not only does it have a browser extension to directly import references as you find them, it has an extensive reference and bibliography generation system. These can be easily formatted for text editors and used directly with Word, LibreOffice, and Google Docs. Zotero also features some handy organization and collaboration tools.

The more visual academics might want to consider Diigo. With both free and paid options, this program features tools to tag, archive, annotate, organize, and even share your online research (much like Zotero does). The most innovative tool, however, is one that enables you to sort your sources into a structured outline, potentially allowing you to more easily identify weak or understudied parts of your research.

Resources

Ada K. Hagan, Ph.D.
Ada K. Hagan, Ph.D.
Owner, Lead Consultant

I am a microbiologist with a passion for making science accessible. I hope to use my background in communications and higher education to help make scientific concepts more easily understood and make the academy more inclusive to future scientists from all backgrounds.