Best Citation Manager Zotero - Papers - Mendeley

Review of the Best Citation Managers and How to Choose One

This post is geared towards students, residents, physicians, or researchers who need to keep track of journal articles and references. There is so much information out there and, as healthcare professionals, we need to be constantly aware of the new evidence and old evidence that guides our practice. However, you may have found it difficult to consistently organize, annotate, locate, or prioritize these articles.

Why You Need a Citation Manager

Given your busy schedules, you want to have a way to easily import and reference these articles when needed. But if you are like most healthcare professionals, these articles end up swamping your desk and computer with no great way of organizing them. You are right, your time ought to be focused on high level tasks, and should not be spent on hours of organizing journal articles!

Whether you are a student just trying to find a way to better organize your journal articles or a seasoned researcher, you must have a system to organize your journal articles if you want to keep sane.

I was in this situation as well when I first started trying to do research as a 1st year medical student. I was bombarded with articles and ended up just having a bunch of random PDFs cluttering my desktop. Needless to say my first research project was a flop.

Over the past 15 years however, I’ve tried to optimize the way I organize my references and citations to improve the way I work to prevent future failed projects. That’s when I started to discover the power of citation managers. Implementing a citation managers as a busy academic physician was essential for me to successfully publish multiple journal articles and even a text book.

Even if you don’t do much research, you still need to keep up to date on your current field. I have found that anyone from students, residents, community physicians, academic physicians, and researchers can all benefit from using a citation manager. Many graduating medical students and residents have thanked me for teaching them how to use citations managers during their training and mentioned how much it helped them succeed in their future careers. I hope this posts can help you as succeed as well.

How a Citation Manager Saves You Time

  1. Easily organizes your articles
  2. Automatically names your articles based on MetaData
  3. Finds articles quickly
  4. Share articles with colleagues
  5. Collaborate with groups

How to Implement a Citation Manager in 2 Steps

So you may have heard of some citation managers, but never took the step to implementing one because it seemed too confusing. Well in order to to implement a citation manager you have to do just 2 things:

1) Choose the Right Citation Manager for You

2) Properly Organize Your Articles Using the Citation Manager

In this article we will focus on how to find the best citation manager for your particular situation. If you are interested in further learning how to organize your articles in an optimal way I created an online course with instructional videos on exactly how to do that as well, check it out below:

The Top 3 Best Citation Managers

It sounds like such a simple decision, but picking out a citation manager is extremely important. You could be using this program for years or even decades to come. Yes you can switch between programs, but they usually don’t translate over perfectly. In this post, I will go in detail, in my opinion, the top 3 citation managers: Mendeley, Zotero, and Papers. As a disclaimer, I used to use EndNote earlier in my career but have gravitated away from it since I believe these other 3 citation managers are more user-friendly, functional, and cheaper. At the end of the post, I will tell you which program I think is the best overall as well as best for specific scenarios. 

Review of Citation Managers Pros and Cons

In order to help you choose, I will go over the pros and cons of all 3 programs with respect to the following categories/features. It looks like a lot of features but they are just the essential ones that I think are most relevant for you.

  • Summary Table of All Features
  • Release Date
  • Free Trial
  • Pricing
  • Automatic Naming Based on Meta Data
  • Web Importer Ability
  • Microsoft Word Citation
  • Google Docs Citation
  • Web, Desktop, Tablet, and Smart Phone Access
  • Reading Articles on the Citation Manager
  • Annotation of PDFs
  • Sharing and Emailing Articles
  • Embedded Metrics, Citations, and Twitter mentions
  • Group Collaboration
  • Custom Tags
  • Overall Best Citation Manager
  • Overall Best Free Citation Manager
  • Summary Table of All Features
  • Next step: Organize your Journal Article

Summary Table of All Features:

Release Date

All 3 of these citation managers were released around the same time.

  • Mendeley was released in August 2008 and is owned by Elsevier
  • Zotero was released in October 2006
  • Papers was released in February 2007 and bought over by Readcube/Digital Sciences in 2016 (who too had a referencing tool since 2010). The two products were merged creating the latest version of Papers launched in 2018. 

Summary: All 3 citation managers have been around for over 10 years with reputable companies. So NO Clear Winner.

Pricing

All 3 plans have a free and paid versions. Keep in mind that every 1GB is about 700 articles. So depending on how many articles you have, this will definitely impact the pricing.

Mendeley: Free for 2 GB (700 articles) with no end date. Then $55/year for 5GB or $165/year for unlimited storage. Just keep in mind that, even though Mendeley offers the most amount of free cloud storage, it also has the most expensive paid plans. 

Zotero: Free for 0.3 GB (100 articles) with no end date. Then $20/year for 2 GB (1400 articles); $60/year for 6 GB (4200 articles); $120/year for unlimited storage.

Papers: Free 30 day trial with unlimited storage. Then $36/year for students or $60/year for non-students for unlimited storage. Papers has the most limited free plan but has the cheapest overall paid plan for unlimited storage. In addition, I was able to get a Zen Productivity exclusive 25% discount off the first year for you (for non-students)! To get access to this discount just sign up for the $10 online course on how to organize your journal articles. The money you save costs less than the course itself!

PAID Citation Manager

Mendeley
3/5
Zotero
3/5
Papers (Winner)
5/5

FREE Citation Manager

Mendeley (Winner)
5/5
Zotero
4/5
Papers
3/5

Automatic PDF Naming Based on Metadata

This is an extremely important feature of citation managers and in my opinion the best one. Forget all of those days of downloading a pdf and having to rename it. All you have to do is drag any research article pdf (no matter how it is named) into the citation manager and it will automatically rename the article based on the metadata it finds. This saves tons of time! See the Video Below:

Fortunately all 3 citation managers can do this. Sometimes it doesn’t find the correct data and you can edit the metadata yourself if you need to. Zotero does require an extra step by right clicking on the article and manually asking it to search for the metadata and input the name. 

Automatic PDF Naming

Mendeley (Tie)
5/5
Zotero
4/5
Papers (Tie)
5/5

Web Browser Importer Ability

This function allows you to get articles directly from the web either using sites such as PubMed or Google Scholar. This way you don’t even have to manually download the PDF in the first place. All you do is add a plugin to your browser which allows the citation manager to directly get the reference from your browser. In addition you can connect to your institution’s proxy login to directly download the PDF to the citation manager. 

All 3 citation managers have this function and support both PC and MAC. Mendely and Zotero support all major browsers including Firefox, Chrome, and Safari. Papers supports Firefox and Chrome but does not support Safari, so it gets one star off. 

All 3 citation managers have this function and support both PC and MAC. Mendely and Zotero support all major browsers including Firefox, Chrome, and Safari. Papers supports Firefox and Chrome but does not support Safari, so it gets one star off. 

Web Browser Importing

Mendeley (Tie)
5/5
Zotero (Tie)
5/5
Papers
4/5

Microsoft Word Citation Integration

Being able to cite in Microsoft Word is essential for any manuscripts you will be writing. All 3 citation managers are able to do this as well as provide the ability to choose between thousands of bibliography styles. They will also reorder your bibliography order number if you happen to change around your citations or switch paragraphs around. This saves a lot of time when you are doing revisions.

Microsoft Word Citation

Mendeley (Tie)
5/5
Zotero (Tie)
5/5
Papers (Tie)
5/5

Google Docs Citation Integration

As more users are going towards cloud-based team work, some people may be moving away from traditional Microsoft Word for manuscript preparation. Google Docs is a common way to share a manuscript among multiple people. If you use Google Docs extensively you will want to make sure you get a citation manager that can reference your citations in Google Docs. Zotero and Papers are both able to cite within Google Docs. Mendeley is unable to cite within Google Docs.

See below for example of the Papers citation manager integrated in Google Docs:

Google Docs Citation

Mendeley
0/5
Zotero (Tie)
5/5
Papers (Tie)
5/5

Web, Desktop, Tablet, and Smartphone Access

Being able to access your references when you need them is a big deal. All 3 citation managers have Web access as well as a corresponding desktop app. Papers is the only citation manager that has nearly identical web and desktop look, feel, functionality and design. 

Regarding tablet and smartphone devices, Mendeley and Papers both have their own apps. Zotero however, does not have its own native smartphone or tablet app. There are some 3rd party companies that make apps for Zotero but some have reported to not introduce any updates.

Web, Desktop, Table, and Smartphone Access

Mendeley
4/5
Zotero
3/5
Papers (Winner)
5/5

Reading Articles on the Citation Manager

If you are thinking about going completely digital than you will most likely be using your citation manager to read your articles as well. All the programs allow you to read the linked PDFs of the article. However there are definitely functions that you may be interested in when reading such as being able to see the article’s metrics, figures, related articles and referenced articles. How do these 3 programs stack up?

Mendeley has an embedded PDF reader function in its application that allows you to annotate (see section below) but it does not have any additional features beyond that.

Zotero is the most limited option since it does not open the PDF directly from Zotero but from a 3rd party application such as PDF expert. Unfortunately, it does not give you any additional features aside from reading it on the 3rd party app.

Papers has, hands down, the best reading functionality of any citation manager that I have ever encountered. It has tabs to see the the metrics of the article including Almetric score, citation numbers (with direct links to citations), figures, all references (with links to references), related articles (with links to related articles), and even a night or dark mode. It even downloads all of the supplemental files for you automatically to review. If you intend on primarily reading your articles on your citation manager, you should really consider Papers. 

Reading Functionality

Mendeley
3/5
Zotero
2/5
Papers (Winner)
5/5

Annotation of Articles

You may be thinking of using your citation manager as an annotation tool to place notes, highlight, or draw on it. This is especially convenient if you want to go completely paperless (highly recommend). All 3 citation managers give you ways to annotate. 

Zotero is the only one of the 3 that does not have an integrated annotation system. You will need to open the PDF from a third-party PDF reader like PDF expert and annotate there. It will save the annotated PDF after that. I think this is cumbersome and adds an additional step.

Mendeley and Papers both have an embedded annotation system that allows you to highlight and add notes directly to your articles. However, Papers also allows you to underline text, cross out text, and free draw on the article.

Annotation Capabilities

Mendeley
4/5
Zotero
2/5
Papers (Winner)
5/5

Sharing Articles on Social Media, Email, and Groups

If you are big into Twitter, LinkedIn, Facebook, or email for connecting with other colleagues, researchers, and the academic community you will need a citation manager that allows you to easily share articles directly from the program itself.

The only way to share articles, from what I could find, on Mendeley is to create a group on the program and then invite people. There is no direct email function or social media sharing function for Mendeley. The disadvantage of this is that it requires the other users to also have Mendeley. However the group function does create a forum type of experience if you can get enough users to come on it. 

Regarding Zotero, it also does not have any direct way to email a citation or share on social media. It also requires you to form a group and invite people to join, similar to Mendeley.

Papers is the only program that allows you to email citations and share citations on social media directly from the app. As you can see below with one click of the button on the right side, you can share on your social media profiles (Facebook, Twitter, LinedIn) or by email. 

Screen Shot 2020-03-12 at 22.30.11.png

Sharing on Social Media, Emails, and Groups

Mendeley
3/5
Zotero
2/5
Papers (Winner)
5/5

Embedded Metrics, Citations, and Twitter mentions

Evaluating the quality and impact of an article is extremely important when reading through it. Being able to see how many citations with direct links to the citations can be extremely helpful, especially if you are doing a literature review. The only citation manager that currently integrates real-time metrics into their program is Papers.

Relative Citation Ration (RCR)

Papers allows you to see the number as well as the links to ALL citations an article has. It also tells you the Relative Citation Ratio (RCR) a measure developed by the National Institutes of Health (NIH) to objectively assess the citation impact of articles relative to the average NIH-funded paper and the relative subject area of the article. A value of “1” indicates performing as expected, a value greater than 1 means the article has revived more citations for than other articles in the similar subject area. 

Altmetric Link and Twitter Mentions

In this expanding age of global reach and internet access, looking at the non-traditional impact of articles, outside of just citations, is also becoming more important. Having access to see the impact on the articles on which parts of the world or social media is becoming more important. The Papers app also links users to the Altmetric site for the specific article. This will give you information on worldwide geographical viewers as well as twitter mentions and direct links to the tweet and ability to reply to the twitter author. If you are big on Twitter this is an essential feature. 

Citations and Twitter Metrics

Mendeley
0/5
Zotero
0/5
Papers (Winner)
5/5

Custom Tags, Labels, Flags, and Folders

All 3 programs allow you to create custom Folders and Tags. This is very helpful in organizing your articles. If you want further customization such as flagging articles, color labeling, or giving 1-5 stars for article quality, Papers gives you those additional features whereas the other two programs do not. If you want to learn how to organize your articles using these features check out the online course. 

Custom Tags, Labels, Flags, and Folders

Mendeley
3/5
Zotero
2/5
Papers (Winner)
5/5

Overall BEST Citation Manager:

 If you are not just looking for a citation manager but a complete program that allows you to organize, annotate, share, and integrate metrics then, in my opinion, the Papers citation manager is the best program hands down. After doing research for over 10 years, this is the current citation manager I used and it has helped save me countless hours.

Overall it is the easiest and most user-friendly program out there. The reading functionality is the best allowing you to see figures, direct links to all article references, and the ability to annotate. I absolutely recommend Papers as a long term solution to any serious medical students, residents, researchers, or anyone doing any academic work. It will give you a significant advantage compared to your counterparts. Papers has definitely considered the point of view of how research is done in the modern era and is growing with the times. I don’t see this with the other two programs as much. 

The cost is minimal ($5 dollars a month) compared to all of the time you save and features it has. In addition, it is the cheapest paid program overall with the added benefit of unlimited cloud storage. To make it even cheaper, I got an exclusive 25% discount from Papers for Zen Productivity readers which you can access by clicking HERE or by entering the discount code PHYSICIANZEN (all caps) at checkout. I was only able to get a limited number of discounts, so first come first serve!

If you want to go further I also created a step-by-step online course on exactly how to organize your articles using the Papers App which you can access HERE. This course will go over all of the features in the Papers App and how to use them. 

Overall Best Free Citation Manager

If you have less than 700 articles you need to keep track of, just need basic features, or can’t come up with $3/month, then the best program for you is going to be Mendeley. It has enough features to get you through but misses out on social media sharing options, metrics, and reading function is okay. Keep in mind that once you pass the 2 GB mark (700 articles) you will need to switch to the paid version ($55-$165/year) which will cost you as much or more than Papers. 

Zotero is a very popular free citation manager, but I can’t wholeheartedly recommend it at this time. It only gives you 0.3 GB (150 articles) of free storage, annotation and reading function are very rudimentary, and it does not have a native smartphone app. Once you get past 0.3 GB (just 100 articles) you will need a paid subscription ($20-$120/year). 

Next step: How to Implement a Citation Manager and Organize your Journal Articles

I hope you found this article useful in helping you to decide what citation manger to pick. If you are ready to tackle organizing your journal articles and want a step by step process of how to do this you can check out the course I created to help you do this for just $15 for Physicians and $5 for Non-Physicians and includes CME credit!

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