All things you need to know about reference manager tools: Mendeley, Zotero, and Endnote.

Three most popular reference manager tools

Why do you need a reference manager?

When you are writing a manuscript, you need to put in references afterward, which will be a hassle if you have to do it manually. But fortunately today some tools and software have been developed to organize and manage your references very easily.

Reference manager tools also track your articles and organize everything for you so you have all your literature in one place which is basically a very nice thing to have when you are working on a project, a bachelor thesis, master thesis, or even your Ph.D. thesis.

You can just use a reference manager, and then everything will be in one place, and everything is where you need to be. There are several different programs and tools that let you put in those references, and that you can use it as a citation tool with plugins in Word or blogs, Google Docs, etc. This post will review three of the most reputable citation manager tools, EndNote, Mendeley, and Zotero. Let’s start the comparative study from the Price.


The first argument is that there is a subscription fee for Endnote, while Zotero and Mendeley are free of charge. But it is a little bit more complicated than that. For example, many institutions have a license from Endnote. So it might be free for you as well, just like Mendeley and Zotero. If you’re buying EndNote for the first time, you have to pay € 276 as a One-time purchase of EndNote 20 Full License, and you get unlimited storage for all your PDFs and references. EndNote gives you a discount if you are a student, which makes it € 132 for a One-time purchase as well. 

Mendeley and Zotero are free from the beginning, but you may upgrade them by paying the subscription fee. Mandalay has free storage for 2 GB, and if you want more, you can purchase more storage which is a subscription, so you pay the money every year. Zotero has the same system, but the free version only has 300 MB as free storage for you. If you want to have the 2 GB storage, which Mendeley already offering for free, then you should pay $20 a year. Here is the individual price table regarding the Zotero storage subscription fee.

Therefore, note that Endnote has a One-time purchase while and Mendeley and Zotero have a subscription-based business model. So if you need a lot of storage, it might be best to go for Endnote rather than Zotero or Mendeley. Let’s go to the second point, which is Organization.


An important question that may arise here is that how these reference manager tools actually manage your references. The answer is that they basically do it all in the same way. It’s just a list of all your papers, and when you click on each one, you can see the metadata for that one. It means you can see the year, the authors, the journal title, volume, pages, issue, etc. You can also open the PDF of the full-text that is linked to that paper. You can change the metadata in all tools if it is necessary. Regarding the organization, every program also has a folder structure so that you can create many folders and layers for categorizing your articles according to your projects, thesis, research works, etc. The folders are visible on the left side of the tools page.

One thing that EndNote has and Mendeley and Zotero lag is customization for your columns, meaning that you can customize, create and remove columns in your program panel. All reference manager tools have tag options, so you can just click on the Tag button and add as many tags as you want, which helps for better reference organization. For example, you can tag your papers as general or technical ones. Let’s review the next point, which is Annotation.


If a PDF file is linked to your article in the reference manager tool, you can annotate and make notes on the file. You can highlight some parts of the text, underline it and also make some sticky notes. In Zotero, if you open a PDF, it goes to a third-party app. 


Of course, no one intends to enter every citation in a research work manually. We just want to use a reference manager tool to do it for us in the right style. There are many different styles for citations (almost 10,000 different citation styles) that you can use for your projects. Mendeley and Zotero work with the CSL (Citation Style Language), an open-source project that helps format citations and bibliographies. It has a repository of almost 10,000 citation styles, so the possibilities are endless when you’re using Mendeley and Zotero. Endnote has its own system for the citation and has almost 6,000 citation styles that seem to be enough for every project you need to do. You can also customize styles or add new citation styles that work for all three reference manager tools.

Every reference with the same citation style should look the same if you’re using Mendeley, zero, or EndNote. However, it does matter in practice, and there are differences between output you get from reference manager tools which is mostly due to the metadata that was put in. So, if you are not putting the right metadata in your reference manager, you will not be able to generate the right references in your project. Most of the time, the reference manager can get the metadata from the PDF. But make sure you check that because it’s not always correct or some information is missing. It’s very important to have the right metadata there for the accuracy of your references in your projects.


It is important to know that on what devices Mendeley, Zotero, and Endnote work. Here are the devices available for these three reference manager tools.


Plug-in for browser:

When you find a paper in your browser, and you want to add it to your reference manager, you should use the So-called web importers, which are plugins for your browser. The browser plug-ins let you add the references to the reference manager tool you are using. Both Mendeley and Zotero have web importer options, and EndNote also has a similar thing but lets you only connect to one specific library or website. So it’s not across all websites you are using, and it’s not a plugin for Chrome.

Plug-in for Words, LaTex, and Google Docs

All three reference managers work with Microsoft Word, but more and more people are using other text formatting programs these days. One of which is LaTex which has a very good function for formatting formulas while it’s not so great for references. So you have to export all

the references from your reference manager to BibTex, which is a sort of code for your metadata, and then you have to import those in your LaTex file again. Endnote, Mendeley and Zotero, all export the data to BibTex so you can use them if you are working with LaTex. Another text-formatted tool that’s getting more and more attention under academics is Google Docs. It’s very nice when you’re doing collaborations or when you’re working on a study project together. But unfortunately, Endnote and Mendeley do not support Google Docs. Zotero, however, has a plug-in that you can use for Google Docs, and that will let you put in the references in the same way as in word basically, which is very nice if you are using Google Docs for collaborating.

Regarding the price, both Mendeley and Zotero are proposed. But Mendeley has more storage for the free option in comparison with Zotero. Mendeley is advised due to its great integration with multiple devices. Just use Zotero, if you are interested in an open-source reference manager tool. If you need a customizer program, get EndNote which has the most functionalities and is best customizable for your needs. If you are working on research work as a collaborator, use Zotero since it has a Google Docs plugin so you can put all the references in your collaborative Google Docs documents. Now it seems you can use this post to find the reference manager that suits your needs.

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