How to Choose a Reference Manager?
This article gives an overview of Mendeley, Zotero and JabRef, three most popular, free reference managers.
Table of Contents
- What are reference managers and why use them?
- Advanced reference managers
2.1. Mendeley
2.2. Zotero
2.3. JabRef - Conclusion
- Online Reference Managers
1. What are reference managers and why use them?
Hopefully if you are reading this, you already went through an exhausting process of manually entering citations and references in your document. For documents that include more than 10–15 references, this process can become impossible to handle manually. This is exactly why you should stop procrastinating and finally install that manager that your colleague mentioned 2 semesters ago.
Reference manager doesn’t only provide help with proper numbering of citations, it is also used for organizing your documents (in PDF format) in folders. This way you can easily find an article that you read a month or a year ago.
So, you can go from these unorganized and randomly named pile of documents:
To these nicely organized documents which supports searching a document by title, abstract, key words etc.:
2. Advanced reference managers
Here I will provide short comparison of 3 most popular, free reference managers:
- Mendeley,
- Zotero and
- JabRef.
2.1. Mendeley
Mendeley is free reference manager software which includes free version with possible upgrading to a version with more storage space for documents.
Given that Mendeley library can be accessed on all devices with prior registration, the data must be stored in the cloud, for which 2 GB of storage space is available in the free version of the application. So far, I am using only a free version and it is has been more than enough.
Mendeley can be downloaded and used as a desktop version on multiple devices or simply as an online version. Mendeley synchronizes all changes so that the library is available on all devices within your user account.
- Uploading bibliography
If you have a PDF file of a document you want to cite, it can be drag-and-dropped directly where Mendeley automatically generates the title, author’s name, number of pages, journal name, etc. Of course, this is not perfect every time. If some of the details weren’t recognized, that reference is stored in a special folder called “Needs Review” so you can review it or manually enter some data.
For better organization, different folders can be created. Another useful thing for teamwork is the ability to create a public group/folder so that references can be accessed by all contributors.
- Adding notes
What I find the most useful with Mendeley is the ability to open a PDF file inside of the Mendeley application and add notes or highlight certain parts. These notes can be visible from the homepage of desktop application which is useful if you are looking for certain document and cannot remember the name. Documents can also be searched by notes you left.
- Browser extension
Mendeley Web Importer is available for all major browsers and is used for directly storing references in a library without the need to open desktop or internet application.
You just need to find article you like on a browser and click the Mendeley Web Importer button. This reference is now synced in your chosen folder on your account.
- MS Word and LaTeX add-ins
Mendeley citation plugin for text editor (e.g. Microsoft® Word) is easy to install (explained here) and automatically synchronized with your Mendeley account library. The plugin enables quick and easy citation of references from your own library and generation of a bibliography of cited works at the end of the paper.
Here, most importantly, Mendeley citation plugin updates the correct order of citations if changes in document occur.
The citation style can easily be changed even when the document is finished. Changing any of the references within the Mendeley application will also update the references in Word.
As far as LaTeX is concerned, the bibliography can be easily exported in BIB format (in Mendeley application go to: Tools — Options —BibTeX — Enable BibTeX syncing and enter Path). BibTeX syncing enables all new changes in the reference to be automatically updated to saved BibTeX document. References are accessed in LaTeX by calling the citation key which is defined automatically for each reference within the Mendeley bibliography according to the first author’s last name and the year of publication. This can be also changed manually. It is also possible to export the entire library or individual groups.
2.2. Zotero
Zotero is also a free referencing manager software which comes as a desktop or online version. Its graphical interface is largely equivalent to Mendeley's.
It offers more possibilities in what is visible on home screen. Bibliography can be sorted by Title, Creator, Item type, Date, Year, Publisher, Publication, Date Modified and even Notes (improvement over Mendeley).
Zotero allows the use of the application without creating an user account, in which case the library is not synchronized to the Zotero account. The storage limit of 300 MB is activated only when the account is synchronized with the Zotero servers.
- Uploading bibliography
Zotero provides the same capability of uploading bibliography as Mendeley. By dragging and dropping a PDF document into the application, the document remains stored in PDF form and as a reference.
- Adding notes
Zotero provides all the previously described Mendeley capabilities including adding of the notes. Zotero also opens PDF in directly in its application. There you can highlight, mark or add notes to specific part of text. It even offers the possibility of selecting an area with a rectangle.
If you leave a general note on your reference, that note is visible from home screen in Zotero application which is an improvement with regard to Mendeley.
- Browser extension
Zotero also offers a plug-in for all popular Internet browsers, the Zotero Connector, but it provides a lower level of interactivity than Mendeley add-on. For example, by clicking on the Zotero add-on , the reference is automatically stored in the library without the user’s ability to check the details and make a final decision.
It is not possible to manually change the reference data created by the Zotero add-on in browser. The reference needs to be accessed in the Zotero application after saving if you’d like to make changes or double check everything.
In addition, Zotero does not find all the references that exist on that web page, but only one main, which is then stored in the library.
- MS Word and LaTeX add-ins
The Zotero add-in for Microsoft Word works in a very similar way and has the same capabilities as the mentioned Mendeley plug-in so I will not explain it further. Both Mendeley and Zotero use the Citation Style Language (CSL) which offers more than 10,000 citation and bibliography styles.
In Zotero it is also possible to export a library in BibTeX format, but it is necessary to install a plugin to enable constant synchronization of the existing Zotero library with the exported one.
This is an additional step which needs to be taken when comparing to Mendeley. Nevertheless, the Better BibTeX plugin is easy to install and allows you to choose to keep the library updated, which is otherwise not available, as can be seen in Figure below (“Keep updated” check box). Click on File — Export Library to get the following dialog box:
Zotero automatically generates citation keys based on the author’s last name, first word in the title of the work, and the year of publication for example:
a book “Russell Roy (1967) Principles of Statistics, Technometrics, 9:4, 698” will have a citation key: Roy_Principles_1967.
Because of this, citation keys are long and can appear clumsy in LaTeX. There is actually a workaround which requires an user input in the Extra field in Zotero application:
If we export this library in BibTeX format, article citation key is successfully changed into “Something_shorter”:
2.3. JabRef
JabRef is free reference manager software available only as a desktop application. The graphical interface shown in picture is very similar to Mendeley and Zotero application with fewer features available.
You cannot make an account which means that the files are saved locally and cannot be accessed from multiple computers (unless you export and save a library of course).
- Uploading bibliography
It is easy to import references in BibTeX format. JabRefs main intention is to be used to generate a library in BIB format for use in LaTeX. Because of that, it does not offer its own citation styles. Also, PDF file cannot be viewed inside the JabRef application as it does not store them in the cloud but locally. Clicking on a reference takes you to your locally saved file on your computer.
JabRef also offers the ability to drag and drop a number of files and automatically generate reference data. Unlike in Mendeley, the user is not additionally informed to verify the entered data.
- Adding notes
In JabRef you can add only general notes about a reference, but they are not clearly visible on the home screen. Instead, they can be accessed only after selecting a particular reference in your library.
Because of the fact that PDF files cannot be opened inside of the application, notes are limited to simple comments.
- Browser extension
The JabRef extension for the Internet browser provides similar capabilities as the Mendeley extension and allows viewing and changing reference data before saving it to the library. By clicking on JabRef extension, JabRef application will be opened.
The separate dialog box of opened JabRef application is shown in figure. It is better than Zotero extension as it provides user with capability of checking reference data before storing it to the library. But Mendeley extension is more intuitive, interactive and faster as it does all that in the dialog box opened in browser.
- MS Word and LaTeX add-ins
JabRef is primarily intended for use with LaTeX and therefore offers limited capabilities when used in Microsoft Word.
I would definitely recommend using Mendeley or Zotero if you are writing in Word.
Regardless of that, it is possible to use it in Word (not the most elegant solution). First, it is necessary to export bibliography data in XML format and import it into Microsoft Word’s own referencing system. By doing this, synchronization is not enabled which means when changes are made in the bibliography in JabRef, the changes are not visible in Microsoft Word. Second option would be to install the Bibtex4Word plugin, which allows citing references that are stored in BibTeX format .
Back to LaTeX. In JabRef your library needs to be saved in BibTeX file format. Thus, making changes in JabRef and hitting ctrl+s automatically saves the modified data to your file which means that the changes will be visible in LaTeX.
Automatic generation of citation keys needs to be set in JabRef so that all tags are according to the your preferences. This can be done in Options — Preferences — Citation Key Generator. The default settings are to generate by author’s last name and year of publication.
3. Conclusion
- Storage space
Mendeley offers 2GB of cloud space in free version and Zotero only 300MB. JabRef doesn’t offer online storage space.
Mendeley: +1, Zotero: +1/2, JabRef: 0
- Graphical interface and notes
Mendeley and Zotero have a similar graphical interface with the same capabilities. They both offer the possibility to open a file within the application itself, where it is possible to leave notes in the file. JabRef, on the other hand, doesn’t save the PDF file, but only saves the link to the local storage location.
Mendeley: +1, Zotero: +1, JabRef: 0
- Browser extension
All three mentioned tools offer an Internet browser extensions, with the Zotero extension having the fewest options for use. Zotero automatically saves the reference after clicking on the extension button without giving the user a possibility to double check generated data.
Mendeley: +1, Zotero: +1/2, JabRef: +1
- MS Word add-in
Mendeley and Zotero offer a fairly similar add-in for Microsoft Word where you can add citations, a full bibliography, and sync and update with bibliography changes. JabRef is primarily intended for export in BibTeX format.
Mendeley: +1, Zotero: +1, JabRef: 0
- LaTeX compatibility
All three tools offer bibliography export in BibTeX format, making them suitable for use in LaTeX. However, Mendeley has the option of automatically synchronizing the BibTeX file with changes in the bibliography, while Zotero requires a plugins to be installed for this purpose (but it is very simple).
Mendeley: +1, Zotero: +1/2, JabRef: +1
Final score
Mendeley: 5 points
Zotero: 3.5 points
JabRef: 2 points
4. Online reference managers
If you are still not convinced and think it is simpler to just use online reference managers such as EasyBib.com or Cite This For Me, this final chapter will show some key problems. These tools don’t need to be downloaded and exist exclusively as an online version, but miss some key features that every good reference manager should have:
- References have to be manually entered — no drag and dropping pdf
- They support automatic entry of references only through their search engine (title or doi is needed)
- Export of references is not supported
- Integration with text editors (MS Word) is only partial (EasyBib) or non-existed (Cite This For Me) hence, they do not update citations inside the document if changes occur
- You have to manually copy a citation and paste it inside your text
- Lots of pop-up advertisements
