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There are lots of different ways that people organize their sources when writing a research paper. Some use spreadsheets, some use research diaries, some use citation managers. The correct method is the one that works for you.
A research diary is basically a document where you detail the steps you took to find your sources. It often includes the different databases you used to search for information and the search terms you used, as well as a list of sources and their citations. It becomes really useful as a method of source organization when you add in summaries and other information about the sources (such as why you picked them to read in the first place).
Research diaries can be formatted like a journal, a list, or even a table.
Spreadsheets can be very useful for keeping track of sources, especially if you have more than a handful. Each row has a single source, and for each source you can include whatever information you might need.
Spreadsheets are often used by researchers to help them see different connections between sources, or shared themes across the literature. They are sometimes called a synthesis matrix. The Excel file linked below has two templates you can use or modify.
Citation managers are software you can install on your computer to help you organize your sources. They can be complicated to set up correctly, but once they are ready to use, they can store all of your research notes and PDFs, and they can drastically simplify the writing and citing process.
Zotero is a very popular open-source citation manager, but there are others out there as well.