How to use Zotero: a step by step guide for students

Zotero is a reference manager. Its own website describes it as a free, easy to use tool to collect, organise, annotate, cite and share research. It is open source, made by an independent nonprofit, and runs on Windows, Mac and Linux, with apps for iOS and Android.

A reference manager does three jobs that most students do by hand.

• It remembers every source. Author, year, title, journal, volume, pages and DOI, saved once and correctly.
• It keeps your reading in one place. The PDF, your highlights and your notes sit with the reference.
• It writes your citations. In Word, LibreOffice or Google Docs, in the style you choose, and it builds the reference list for you.

The last job is where it saves the most time. Change the style and every citation and every reference changes with it. Cite a paper in the text and it appears in the list; remove the citation and the reference goes too. The two problems in Nikhil's file, the wrong style and the missing references, were exactly the two problems Zotero fixes.

Zotero comes in two pieces, and you need both. Download them from zotero.org, not from a third party site.

1. Install the Zotero desktop app.This is the library itself. It keeps your references, PDFs and notes on your computer.
2. Install the Zotero Connector.A small extension for Chrome, Firefox, Edge or Safari. It adds a button to the browser that saves the paper you are looking at.
3. Open Word once.The plugins for Word and LibreOffice come bundled with Zotero and install themselves when you first start it. A Zotero tab appears in Word. If it does not, restart Word, or reinstall the plugin from the Cite section of Zotero's settings.
4. Make a free account, if you want a backup.With an account, Zotero syncs your library to its servers and to your other computers. Syncing the references and notes is free and unlimited. Each user also gets 300 MB of free storage for attached files such as PDFs.

Rutuja made Nikhil sign in on the first day. "Laptops get stolen and hard disks die," she said. "Your references should not die with them."

Keep the desktop app open, then use whichever door suits the source.

Nikhil started with the identifiers. Most of his journal papers had DOIs on their first page, so he pasted twenty at a time and watched them fill in. The references he had typed by hand turned out to have four wrong years and one misspelt author. Zotero took those details from Crossref and the other lookup services, not from his memory.

Still, check what comes in. Details saved from some web pages can be incomplete, titles may arrive in capitals, and a thesis or government report usually needs fields filled by hand. A reference manager can only format what it is given.

Zotero's help pages say to think of collections like playlists in a music player. A song can be on many playlists without being copied, and a paper can be in many collections in the same way. Nikhil made one collection for each chapter of his dissertation, and a subcollection under the review chapter for each theme.

Be careful with deleting. Removing a paper from a collection only takes it out of that collection. Moving it to the trash removes it from your library, and the trash keeps it for 30 days by default.

Duplicates creep in when you save the same paper twice. Click Duplicate Items in the left pane, check the pair, and click the merge button on the right. Zotero's help pages say to always merge duplicates rather than delete one, because merging keeps the collections and tags of both.

Double click a PDF in Zotero and it opens in Zotero's own reader. Select text and pick a colour to highlight or underline it, or add a note in the margin.

The useful part comes next. Right click the paper and choose Add Note from Annotations. Zotero gathers your highlights and comments into one note, and each one keeps a link back to its page in the PDF, with a citation. When you write, you know exactly where a point came from.

• Use one colour for each kind of point: yellow for findings, blue for methods, red for limitations.
• Write your comment in your own words next to the highlight, not later.
• Copy the key points into your literature review matrix, one row per paper.

This is the part Nikhil needed most. In Word, the plugin adds a Zotero tab with five buttons: Add/Edit Citation, Add/Edit Bibliography, Document Preferences, Refresh and Unlink Citations.

1. Place the cursorwhere the citation should go in your sentence.
2. Click Add/Edit Citation.The first time, Zotero asks you to choose a citation style for the document. After that, a search box appears.
3. Type an author or a word from the title,pick the paper and press Enter. To add a page number, type it, for example "p.34", before you press Enter.
4. Click Add/Edit Bibliographywhere the reference list should start. It updates by itself as you add citations.

To change the style, click Document Preferences and choose another one. Every citation and every reference changes at once. Zotero comes with the common styles, and its Style Repository has more than 10,000 more, so your university or journal's style is probably there. Nikhil switched from APA to his department's style in under a minute. Which style to use, and how they differ, is explained in citation styles explained.

In Google Docs, the Zotero Connector adds a Zotero menu with the same options; there the preferences item is simply called Preferences. The first time, Google asks you to allow access to your documents.

Zotero formats references; it does not check that they are right. Before Nikhil submitted, Rutuja made him read the reference list once, slowly, against the style guide.

• every author name is spelt as on the paper
• titles are in the case your style wants
• no reference has a missing year, volume or page range
• web pages, theses and reports have every field filled in
• the reference list has no paper you did not cite
• you used the style your department or journal asked for

Then keep two files. Your working file keeps its live Zotero citations, so you can still edit them. For the final copy, save a duplicate and click Unlink Citations in that duplicate only. This turns the citations and reference list into plain text. Zotero's help pages say unlinking cannot be undone and should usually be done only in a final copy. In Google Docs, its advice is to use File, Make a copy, and unlink in the copy.

A reference manager also helps you stay honest. When every quote and paraphrase is cited as you write, nothing is left uncited at the end. Our guide on how to avoid plagiarism explains the habits behind that.

Nikhil's new reference list was ready in two evenings, not two weeks. Both missing references turned up the moment he cited them through Zotero. When Dr. Patil later asked for a numbered style for a paper from the same work, it took him one click.