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References with Zotero

Streamlining reference management and collaboration with improved access to papers, books, electronic media, patents, and websites. 


As a scientist, chances are that you are using something like EndNote to manage references and create bibliographies. If you wonder how free alternatives compare and would like to facilitate collaboration within your lab, you might like to try Zotero - a powerful tool to collect, organize, cite, and share research sources. We have moved from Reference Manager to Zotero more than 5 years ago. Our shared reference-database is synchronized between scientists and download and integration of pdf documents and supplementary files is centralized. This approach reduced cost, improved document retrieval, reduced file-clutter (with everybody accessing the same properly named and linked documents), and facilitated coauthoring manuscripts and grants. We have extended the content of our database from papers and books to patents, media, and online content.
The setup includes a joint account at zotero.org to synchronize references between users and a local WebDAV server to host the associated files on site. Although standalone versions are available, most lab-members prefer to use the Firefox plugin. From PubMed or other websites everybody adds their required references to the database in browser and after synchronization, the secretary adds the properly named PDF documents. With the word processor plugin and the extensive style depository, adding the references to a text document is a breeze.
If you like how easy it is to add references to your scientific writing using proper software but have trouble coauthoring or sharing passages that include references from grants, publications, animal protocols, and reports, Zotero is for you.


The speed at which science generates new insights is continuing to increase. In the middle ages, science was mostly a one-man show. DaVinci was not part of a larger scientific community, so that he did not refer much to other people's work and most of his notes stand by themselves. Newton realized he was standing on the shoulders of giants and references have steadily increased along with scientific output. Luckily, we don't have to use typewriters to insert references and specialized software has greatly facilitated the process of adding and editing references.

The Problem: 

Adding references as a one-man-show creates redundancy with pdfs saved multiple times across computers and hard drives within a lab. It also eliminates the possibility for multiple authors to work on references at the same time. People that join a lab can have a hard time to adapt to a different software package. Sometimes they do not have access to commercial software on their personal computers or tablets and have a hard time co-authoring from remote.

The Solution: 

We were aiming for a solution with low cost of ownership that facilitates collaboration. For the software preferences were: open source, compatibility with existing infrastructure, large community, integrated file synchronization, note taking, full text search, and pdf standard compliance. After feature comparison of several free and commercial alternatives to Reference Manager (which we were using at the time), we went with Zotero. One indication how good of an alternative it was to commercial software was that Thomson Reuters (the company that makes EndNote) sued George Mason University, home of Zotero. The suit was later dismissed, but showed how threatening Zotero looked to the competition. We like Zotero for its ease of use, collaborative features (note and comments), search function, and ability to integrate various types of content (including websites, patents, movies or books).

Figure 1: Zotero is platform independent.


There are quite a few alternatives to Zotero. If you compare reference management software online, you might want to stay away from the Endnote, Mendeley, and Zotero websites for obvious bias. "limited citation styles", which has been resolved since years (endnote offers >6000 citation styles, zotero offers 7,793 styles as of May 2015. The "limited free storage", does not apply if you run your own WebDAV server (the 300 MB would cover a library of ~40.000 references). The free storage of Endnote (1GB) and Mendelay (2GB) would cover pdf and supplement for ~1000 or 2000 references, respectively. Our attachments on WebDAV are currently 7.5GB for 6000 references. For additional information please refer to a 2014 comparison of Mendeley, Zotero and Docear, or RefWorks, Endnote, Endnote online, Zotero, Mendeley, ColWiz, and Papers.
A recent alternative is the F1000 workspace. It has a few advantages over other tools, so please check it out to see if it meets your needs.


We have run a common Zotero-account for the lab that holds the reference library. Every scientist can add references from the browser with on click. The secretary downloads, renames, and adds PDFs and supplementary information as outlined in Table 1. References are added from this common library using the word processor plugin. At times where you don’t have access to the reference-library (e.g. working off your phone), or if you don't want to interrupt your flow, add a generic placeholder for references (we use "***REF" that can later be replaced).

Table 1: Zotero workflow 
Follow literature through custom pubmed searches (preferably via RSS from your favorite reader), mailing lists, and e-alerts.
Add references to the database preselecting the "to download" Zotero-folder.
For comments, add a new note to the reference starting with your initials.
Every Friday or on request: download the PDFs and supplement for references in the "to download" folder, name the files properly (last names of the first and last authors, journal, year, followed by up to four keywords in brackets) and add to each reference. If PDFs are not available to the public or through institutional subscription, add the reference to the "to order" Zotero-folder.
Check the "approved" Zotero-folder and order the respective PDFs through the library. Add to the reference upon arrival (after proper renaming).
Approve references in "to order" Zotero-folder by moving to the "to order" folder. Check "Duplicate Items" folder" and inconsistencies, add and edit comments and notes.


Our setup includes a joint account at zotero.org to synchronize references between users (~7000 references in a 50 MB database) and a local WebDAV server to host the associated files on site (currently 10,000 files in 6,000 folders at 7.5 GB). The 300 MB free online storage is generous, if you only need your library online and not the attachments. If you would like to get started with transferring your existing EndNote library to another citation manager, you can find easy to follow instructions online.
Additional information on setting up the syncing of your library is provided here.
We have used Zotero since 2009 without a glitch. Implementation is facilitated by the massive user base, the extensive online resources, and the timely release of patches and updates.

Figure 2: Zotero plugin in FireFox.


Gone are the days when you had to add references by hand or pay for software that does it for you. Try Zotero to manage your references and leverage the power of collaboration.

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