A Whistle Stop Tour of Reference Management Software: How I Stopped Worrying and Learned to Love the .RIS

Paula Younger
Part-time NHS Librarian (Bank) / Part-time freelancer

While it might not have seemed so at the time, 1989 was a pretty pivotal year: not only did the Berlin Wall come down in November, that was also the year of the World Wide Web (although Tim Berners Lee didn’t invent the first browser until the following year). In the past thirty years, the World Wide Web (and the Internet underlying it) has changed our lives almost beyond recognition. When it comes to retrieving and organising information, keeping track of and collating citations can be time consuming and difficult. 

When I first encountered reference management software in 2003, in a package called Reference Manager, the learning curve seemed so steep I wasn’t sure I’d ever get the hang of it. It was not unlike an Access database, and the interface looked quite similar, but it didn’t behave quite like other databases I knew. Now, despite the occasional quirks, I see reference management packages as an invaluable part of my everyday toolkit – although they sometimes seem to change so frequently it’s a task in itself to keep up sometimes. If you’d like a short historical overview of how reference management software has developed, check out Tom Roper’s presentation.

Put simply, reference managers allow you to collate citations from a range of databases and other sources. Most databases and journals now have a built-in export feature so that when you then import the records to Endnote, for instance, the metadata ends up in the right place. Mostly. The range of sources include native interfaces for CINAHL, the Cochrane Library, MEDLINE, Embase, and various library catalogues from the British Library, Worldcat, and others, including major publisher sites and Google Scholar. References can then be swiftly organised, typically into collections, groups or libraries. Another useful feature is the deduplication option, and for a quick overview, most reference managers allow you to sort by author, title, year, or other fields, as well as search within the records.

Several packages also offer a “Cite While You Write” option. As you’re creating your document, you can insert references into a text document in Word or Libre Office, creating footnotes, endnotes, or a bibliography. This approach also automatically renumbers citations if text is moved around.  Records can also be exported as a bibliography for inclusion in a literature search or other document. When it comes to export or output styles, built-in styles usually include “standard” Harvard or Vancouver. There are various pre-formatted styles available for download on the respective websites which can be added to the desktop versions.

If you’re feeling especially techy (or know a friend or colleague who enjoys a challenge), it is also possible to edit output styles and create your own in Endnote, Zotero and others (although either of those would be a set of articles on their own).

Depending on which bibliographic database or source you’re searching, a batch of references can be exported from the source and then imported into the reference manager. Most major journal websites also offer a download feature for individual citations in various styles (often under “Cite” or “Cite this article”). The .RIS files format is recognised by most reference management software; other formats typically available include .enw for Endnote, and .bib for Bibtex.

Although a little laborious and involving a lot of cutting and pasting, it’s also possible to create new references from scratch, and edit imported references (which aren’t always perfect or quite in the format you need). You can also usually add attachments to a record such as PDFs (check licensing arrangements with providers if necessary, to make sure this is allowed). Other fields often include a space for you to add your own notes, and include links to the url and/or DOI. In some cases, you can search selected databases from within the software.

Pubmed works a little differently: if you’re downloading straight from the pubmed.gov site, your citations will be in a format known as .nbib. Although Endnote, RefWorks, and Zotero can cope with direct imports of files in this format, if you’re using Mendeley, you’ll need to do a little reformatting. There is also sometimes an option to import PDFs direct to reference management software, but it is sometimes necessary to copy and paste metadata into various fields, depending on the original file.

Three of the most common packages are Endnote (from Clarivate Analytics), Mendeley (Elsevier), and Zotero (open source). All packages offer either a downloadable desktop version, or a version that sits in the cloud, usually with less functionality. There have been others over the years, including the now discontinued Reference Manager and RefWorks (ProQuest), which does not have a free version. Relatively new kid on the block Qiqqa might also work for you, although it looks as if they’re going to be discontinuing support for the web-based side of things in the near future, and it won’t work on Macs without additional software. For Mac aficionados, ReadCube Papers might fit the bill, although this is also a paid package. Increasingly, plugins and apps are becoming available, and there are also reference generators such as Cite This For Me (formerly RefME) and ZoteroBib. (The latter is Zotero’s own citation generator.)

Endnote – This offering from Clarivate Analytics (who acquired Thomson Reuters) is updated very regularly; 2020 sees yet another release. Endnote Basic (previously known as Endnote Web) is the freely available version, accessible via your web browser, which allows you to store up to 50,000 citations with a limited amount of disk space for attachments. If you’d like to compare features, here is a useful page.
Mendeley – This is also available online (Mendeley Web) or as a downloadable desktop version. As with the other reference managers, once your citations are saved into your collections or folders, it’s possible to search for authors, titles, publications, or any other piece of text. The desktop version has noticeably higher functionality than the online edition.
Zotero – Open source program Zotero is produced by the Center for History and New Media at George Mason University. This package also allows import, organisations, and generation of citations; it’s also possible to integrate it into Microsoft Word and LibreOffice Writer, and Google Docs.  Its interface is drag-and-drop, and it can also be configured to detect journal articles and other items online that can be imported instantly.  
Most common packages

Reference managers can save you hours if not days, but they’re not perfect. You might find you need to amend some of the imported references, for instance, while the deduplication can sometimes need a little bit of tweaking until you get it just right.

Output styles can often need a little tweaking, often due to variations between sources, and the fact that citation styles can vary. While standard sources like Cite Them Right are excellent, citation styles can vary between institutions. Sometimes they vary between departments at the same institution, and sometimes even within the same department. So, for academic papers, or preparing an item for publication, it’s always a good idea to double-check and triple-check the required style before submission.  

Not every reference manager will suit every user, either, so if possible, it’s a good idea to try out at least a couple before you settle on the best solution for you and your users. Most companies also produce comprehensive online training sessions and resources, and it’s always worth checking out YouTube and the companies’ own websites.

Useful Links:

HLG Newsletter
Winter 2020

One thought on “A Whistle Stop Tour of Reference Management Software: How I Stopped Worrying and Learned to Love the .RIS

  1. I’ve recently been playing with SciWheel and have quite liked it – mainly due to easy citation capture via the browser extension and particularly because it has nice PDF and webpage highlighting + note adding; and then you can see a summary of these highlights / notes next to citation record which could be very useful for research. And just yesterday I gave Paperpile a quick try and at first blush looked very easy to use and functional. It does have a small monthly fee but you can try it free for 30 days via your Google account or similar


Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: