Reference Management in Manuscript Preparation: A Technical Guide for Zotero

Citation style

Citation styles dictate how sources are credited in academic and professional writing. The American Medical Association (AMA) citation style is widely used in medical, health, and scientific writing. It follows a numerical superscript system for in-text citations and a numbered reference list at the end. The American Psychological Association (APA) style, widely used in social sciences, follows an author-year format for in-text citations (e.g., Mondal et al., 2020) and includes a reference list with full source details, arranged commonly alphabetically. The Modern Language Association (MLA) style, common in humanities, particularly literature and language study, uses an author-page format for in-text citations (e.g., Mondal 75–80) and a page for full references.^[6] The Vancouver style, frequently used in medical and scientific research, employs a numerical citation system where sources are cited with superscript or bracketed numbers in the text (e.g.,^[1]), corresponding to a numbered reference list.^[7] There are various style deviations as some uses the citation before punctuation, some aft er, some superscripts numbers, some superscripts square bracketed numbers. The Chicago style offers two formats. The “notes and bibliography” system, preferred in history and humanities, uses super-scripted numbers for citation and reference in footnotes or endnotes on the same page. The “author-date” system, similar to APA, used in social sciences. In “author-date” style, page numbers are included in in-text citations when quoting directly or referencing a specific passage (Mondal 2025, 75) but omitted when citing the overall work or general ideas (Smith 2025).^[8] The citation styles are shown in Table 2.

Reference style

A complete reference includes several essential components to ensure proper attribution and retrieval. These components are shown in Table 3. These components can be used to formulate the reference according to the styles. While taking any citation from PubMed, it provides the option to get a reference in AMA, APA, MLA, and NLM format, as shown in Figure 1a. While accessing an article from PubMed, one can click on the “Cite” button that opens an option to copy or download the reference. Here, users have the option to change the preferred reference style. A similar citation export facility is provided by many other journals. For example, while reading an article from the Indian Journal of Nuclear Medicine,^[9] one can use the “cite” option to save the reference [Figure 1b].

Close

Figure 1:

A screenshot from (a) PubMed and (b) journal web page showing the option to get reference of a published article

Export to PPT

Figure 2 shows a reference style for a published journal article with more than 6 authors in Vancouver style.^[10,11] There are some variations of the Vancouver style, used by various journals. It typically lists up to six authors, with “et al.” used when there are more than six, although some journals allow “et al.” aft er three authors. Some journals may even ask for enlisting all authors. The publication year in four digits is used commonly. However, many journals ask for using date and month along with year, if available. Some journals ask to only use the volume number, and some ask to use the issue number in parenthesis. Majority of the journals use continuous pagination throughout a volume. For example, if a journal publishes four issues in a volume throughout the year, it uses page number continuously (like 1–30 in first issue, 31–45 in second issues and likewise). Hence, mentioning issue number does not hamper the effective identification of source pages. Page ranges are usually presented in a shortened format (e.g., 123-9 instead of 123–129), although some journals prefer the full range. Many of the journals use electronic article number instead of page numbers. For articles available online, a digital object identifier number is used at the end. Some of the journals may ask for the full website link of the article. In relation to case, some journals prefer title case (capitalize first letter of each major word) some prefer sentence case (capitalize first letter of first word of a sentence and proper noun). These deviations oft en depend on journal-specific guidelines or editorial preferences. Hence, authors must check the author guidelines provided by journals before formatting references.

Close

Figure 2:

An example of a reference in Vancouver style

Export to PPT

Manual management

Various methods can be used to save references and inserting in a manuscript. However, among the methods, using the comment feature of the word processing soft ware is an easy method. While writing a manuscript, authors can write any text in a specific location (e.g., [ref]) and insert a comment in MS Word where a reference is needed. Authors can copy the reference text from the source and paste it in the comment box [Figure 3]. For doing this, authors can select the text (e.g., [ref]), go to “review” and click on “new comment.” This will open a comment box where the reference text can be saved. This allows easy insertion, deletion, or modification. At the final stage when all addition and deletion is complete, all comments can be copied individually and compiled at the end of the document, and numbered accordingly. This method provides flexibility in managing references manually while avoiding errors caused by renumbering during revisions.

Close

Figure 3:

Screenshot of Microsoft Word 2021 where an author added comments aft er sentences where citations are required

Export to PPT

Management with tools

There are both free and paid soft ware programs for reference management. Free tools such as Zotero and Mendeley are widely used, offering robust features for reference management without any cost. Subscription-based tools such as EndNote and RefWorks provide advanced functionalities for professional researchers and institutions, oft en including additional support and integration options.^[14] Table 4 shows the most commonly used soft ware applications for reference management. Many word processors, such as Microsoft Word, also come with integrated citation managers that streamline the referencing process directly within the document.^[15] However, these are commonly not used by authors as it requires manual data entry for reference.

Reference management soft ware applications have the ability to import references from a variety of databases, which saves time and ensures accuracy in citation.^[16] These tools allow users to organize references into folders or libraries, facilitating easy access and management of a large number of sources. Another significant advantage is the automatic generation of citations and bibliographies in various citation styles, which simplifies the process of adhering to specific formatting requirements. In addition, many tools offer collaboration features and cloud synchronization, enabling multiple users to work on the same reference library and access it from different devices. In the next segment, the reference management in Zotero is described briefly.^[17]

Installation

For setting the Zotero, three steps to follow [Figure 4]. First, authors need to install the Zotero soft ware on computer [Figure 4a]. It is available for Windows, Mac, and Linux. Then, they need to install the browser connector [Figure 4b]. The connector is available for Chrome, Firefox, and Edge. The Connector for Safari is bundled with Zotero soft ware. Finally, the author should add the Zotero Word add-in. For that, aft er opening the Zotero soft ware, authors should click on “edit,” then “settings,” and then “cite.” Scrolling down will show a button for “install Microsoft Word Add-in.” If it is already installed, it will show reinstallation option as shown in Figure 4c. Here, authors will also get the option to add installation option for LibreOffice (a free soft ware similar to Microsoft Office) add-in. These three steps make the computer capable of using reference management by Zotero.

Close

Figure 4:

Steps of preparing computer for Zotero – (a) installation of Zotero, (b) browser connector, and (c) word-processor soft ware add-in

Export to PPT

Creating a collection

To start working on Zotero, authors need to create a collection under the library. For that, they need to open the Zotero, click on “file” and then “new collection” and name the collection. In the next step, authors need to select the reference style. For that, they should click on “edit,” then “settings,” then “cite.” On the cite page, there will be options to select from the style list already available in Zotero. For additional reference style, click on “get additional styles” and a search window will open which has a total of 10,556 styles [Figure 5]. Search the reference style and click on the searched item and the reference style will be added to Zotero. Authors need to keep the Zotero open while writing document. Now, authors can start writing the manuscript on word processor soft ware (e.g., Microsoft Word).

Close

Figure 5:

Zotero settings window showing style manager and option of getting additional styles

Export to PPT

Saving references

Commonly, authors writing on the biomedical research field search articles from PubMed or the journal website. While reading the articles, authors should check for the paper icon in the right upper corner of the browser. Clicking on the icon will save the reference to the collection in Zotero [Figure 6a]. Many a time, due to poor internet connectivity, the capturing of article data from the webpage takes some time and clicking on the icon before full data load will save only web page information [Figure 6b upper panel], and not the information of the article. Hence, authors should wait a while on the web page of the article before saving the reference. If Zotero connector is not available to capture data from any particular page, the Z icon is shown [Figure 6b lower panel].

Close

Figure 6:

Saving reference from web pages containing publications – (a) button to click for saving reference, (b) the buttons which capture only webpage data (upper panel) and no data to save (lower panel), and (c) addition button to add reference manually (left panel) and data entry field (right panel)

Export to PPT

If the article is not available on the internet, and still, it needs addition to the collection, authors should use the “new item” icon (paper with plus sign) and select the type of source [Figure 6c left panel]. Aft er selecting, check the data entry panel on the right side and write the details [Figure 6c right panel].

Cite when write

While writing the article in Microsoft Word, authors should place the cursor where a reference to add. Clicking on the Zotero tab on the Microsoft Ribbon will show the panel of options [Figure 7]. Clicking on the “add/edit citation” will show the last saved reference. Authors should click on the reference and then click on the arrow button on the right size or press “enter” button of keyboard. If authors need to add a different citation saved previously, clicking on the Z icon on the window will give the option for “classic view.” In the classic view window, the full list of saved references will be shown, and authors can select the desired one.

Close

Figure 7:

Zotero options on the Microsoft Word ribbon

Export to PPT

With Zotero, authors can add citation in any part of the text, not following top to bottom rule. Even if any citation is removed, the numbering will be auto arranged with a click of “refresh” button.

In some instances, while inserting a citation, a large chunk of text is added instead of the citation. This is an error from the soft ware. Usually, undoing it and reinserting the citation solves the issue.

Inserting bibliography Aft er completing the manuscript and citations, to insert the references in the manuscript, authors use the “add/edit bibliography” [Figure 7] button. It will add all the references. It is not necessary to add this aft er the completion of manuscript writing. It can be added even aft er inserting the first citation and when adding more citations, the reference list will keep adding the references.

If authors want a different style of referencing (from Vancouver to APA), they can click on the “document preferences” [Figure 7], select the new style and click “ok” button and the reference style will be changed instantly.

Multiple references

When a reference is saved multiple times, Zotero may save the reference multiple times and can generate two or more citation numbers in the text for the same reference. To check it, authors should open Zotero reference lists (clicking on the library title). Then, check the creator column (shows author names) or title column (shows title of the articles) for multiple entries for a same reference. Authors should select those reference (press and hold Ctrl and click) and right click on those selected references and select and click on “merge items.” On the right panel, on the top, there will be number of items to combine (e.g., merge 2 items). Clicking on the button will combine the references to a single one and the citation numbering will be automatically arranged. If it is not done, click on the refresh button [Figure 7].

Syncing

Many of the authors use different computer systems in home and office and use cloud storage for their research documents. When working on different systems, authors can sync all the saved data in Zotero. For working on different systems, all the soft ware and connectors should be installed on all systems. Authors can use the “sync” options and create an Zotero account and login to that account in Zotero of other systems. On the Zotero homepage, there is a sync button; clicking on the button will sync the data, if not done automatically. However, authors should remember that a free account has a free storage of 300 MB. Beyond that, for a 2 GB plan, they charge $20 annually or $120 for an unlimited storage. Authors can delete old collections to free up space and keep using it free.

Exporting

Many of the journals ask for bibliography details as a file. For those journals, it becomes essential to export the references in a specific format. For exporting, authors should right-click on the collection name and click on “export collection.” Selecting the desired format and clicking on “OK” button will export the file on the computer disk. This option of exporting is also helpful when the Zotero has less space and new data to store. Authors can export the collection files and delete it from Zotero. Later, these files can be loaded if required. For example, a collection can be exported as “Zotero RDF” format and later double-clicking on the file will load all the references in the collection to Zotero with the collection name.