Reference management software
By Dr Irenee Daly Page | 1
Foreword by Anthony Haynes
This resource is designed as a practical guide. It forms part of a series of guides for early-career researchers in the School of Technology. It was commissioned by the Department of Chemical Engineering and Biotechnology. Each guide in the series may be downloaded from the Write Your Research website (please see below for the URL).
Contents Introduction Workflow Endnote Papers Mendeley Zotero Other RMS/bibliographic software options
Grateful acknowledgement is due to the reviewer, Krishnaa Mahbubani.
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Introduction
Page | 2 Reference Management Software (RMS) is the term used to describe software that helps the researcher do some or all of the following: Find, read, share and annotate electronic reading material. RMS integrate (some to a greater or lesser degree) with word-processing software (e.g. MS Word), which allows for the writer to embed references into the text as they write. They also allow for the generation the bibliographic citations (references) at the end of your essay, thesis and/or journal article. Some also allow for citations to be imported from academic databases such as web of science or web of knowledge.
This review focuses on four of the most popular RMS systems, Endnote, Papers, Mendeley and Zotero. Suggestions for other RMS are listed at the end of the document.
Workflow
RMS are fast becoming an invaluable part of the academics toolkit. There are no absolute better or worse options when deciding which one to use: it’s a case of finding what works best for you. With this in mind, when choosing a RMS it is important to also consider your current workflow and what sort of integrated ecosystem you wish to create. It may be, that more than one piece of software is needed to create the working environment that is best for you. Consider other software that you use, and how they
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will collectively integrate. This is especially important as academics are increasingly moving away from only using MS Word to write. Options other than to MS Word include: Scrivener, Mellel, Nisus Writer Pro, DEVONthink, Pages, Openoffice, LaTeX§§. Page | 3
Equally there are numerous options for annotating PDFs: they include Preview, Adobe, Skim, PDF-notes and PDFpen for iPad. Other considerations may be whether you work between multiple computers (e.g. home and the lab) or if you use a tablet as part of your workflow.
With most environments, there will be a specific RMS that works well – but that does not mean you have to stick to that RMS. Most RMS have simple systems to transfer metadata from one to the other which allows you to use one for collating, reading and organising PDFs and a second for citing and creating bibliographies within your writing environment.
Endnote and Endnote WEB
Essential facts: Available from Adeptscience; 30-day free trial; PC and Mac; not free but student discounts available and some institutions provide free student licences (though not Cambridge).
As a RMS, Endnote is one that many researchers will have heard of as it has been available the longest. Of the RMS reviewed here,
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Endnote does the least in terms of additional features, but it can still provide a vital link in the workflow. From its inception its primary purpose was to manage references and to provide a cite- while-you write interface (i.e. the embedding of references into Page | 4 your document) and a resultant list of references at the end of your document-both of which it does very well. This is especially true if you use MSWord., Different reference styles can be chosen from a drop down menu, and you can also set up your own citation style.
At each new release Endnote has tried to provide further features so as to match what competitors offer. For example, other RMS systems such as Zotero and Mendeley provide an online depository. Endnote replied with Endnote WEB, which allows you to install a bookmarklet to capture sources. Although it works across all browsers and can be useful if working across different computers, synching with Endnote proper is not always straightforward and you can accidently create differences between endnote libraries-which is not something to be encouraged. In addition, Endnote does not have an online users forum to answer questions, which is quickly becoming integral to troubleshooting software issues. It is worth noting that each new version of Endnote requires the user to buy a new license.
In Cambridge Endnote WEB is available for free via your Raven login, but access is lost once you leave the university. As Endnote is supported by the university, the University Computation Service offers comprehensive training for use with MSWord and LaTeX.
Papers/Papers2
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Essential facts: Available from Mekentosj; 30-day free trial;
PC and Mac; Page | 5 Not free but students can get a 40% discount if they provide proof of being a student.
Papers has been said to do for PDFs what ITunes did for MP3s, in that it indexes and organises PDF files. You can tag, search and filter your files and group them into labelled collections-just like a music playlist. Papers provides a very nice, user-friendly and intuitive interface that is very easy to navigate.
You can upload PDFs already stored on your computer, and Papers will extract the metadata, i.e. recognise the journal name, the author’s name and the particulars of the journal. This is made available on a pane on the right hand side of the interface and notes on the article can also be added. Once all the PDFs are matched, the metadata can be exported to bibliographic software such as Endnote.
Search depositories e.g. JSTOR, PubMed, Scopus (and many others-mostly science depositories) are built-in to Papers which give simple one-click access to article abstracts. If your university library subscribes to the journal in question, you can set up papers so as to get direct access to the full article. Since the most recent release (Papers2), PDFs can now be read and annotated from within Papers. You can work remotely via an iphone/ipad app that allows synching with a primary computer.
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Papers2 resulted in the addition of two important features (Livfe- pronounced life and Magic Manuscripts), which makes this software almost a complete RMS package. Mendeley, which is Papers’ closest competitor, has always had a social networking Page | 6 aspect, and Livfe is Papers response. Livfe allows you to create collections of papers and then share them with colleagues, who also use Papers. This makes collaboration easier, as you can share the important references, (the actual PDF cannot be shared due to copyright but all the metadata is made available), with the collaborators regardless of where they are.
Previously Papers’ main limitation was that it was not able to generate a bibliography in your document. This has changed with the introduction of ‘magic manuscripts’, which allows you to find references, cite them in your document, and format bibliographies. Manuscripts runs from your menubar, and is activated by a keyboard shortcut that activates a small search window that floats over your word processing document.
Mendeley
Essential facts:
available from Mendeley; PC and Mac; free software.
Mendeley is an RMS that is comprised of two components: a desktop application that is a PDF and reference management application; and a web program, which is an online social network for researchers. Unlike Papers or Endnote, which require software
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to be downloaded to a personal computer, Mendeley requires the user to store metadata on its cloud server. Once registered, Mendeley users get 1GB of free web storage (more storage can be bought and there are different potential monthly plans), which Page | 7 means means the actual PDF’s can be stored either in the cloud or on a personal computer. Users can also create private groups and add up to 10 people in each.
Mendeley is probably closest to Papers in terms of the range of functions it offers. It allows you to organise, tag, search and filter your documents. Like Papers, metadata is extracted from the PDF’s and they can be read and annotated from inside the programme. Mendeley creates bibliographies at the end of documents - check compatibility with your word processor of choice. Again similarly to Papers, depositories can be searched. Based on the content of your own library, suggested authors and journals are made available.
Mendeley can also be set to watch folders, scanning them on start up to see if there are any new files that need to be added. References can be imported and exported to other software packages (endnote, Zotero, BibTex to name but a few) workflow. Because Mendeley is web-based working between different computer is more straightforward than it is with Papers, and there are also an iphone/ipad apps. Mendeley’s extra strength has always been its social networking side. You can search for friends and colleagues (who also use this RMS) and share papers. You can also be told about trending articles in your fields.
Zotero
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Essential facts: available from Zotero; PC and Mac;
Free software. Page | 8
Zotero is an RMS that started off as an extension of the Firefox web browser. It automatically senses content and allows you to add to your personal library via a single-tick. Many websites (most notably library catalogues) show a Zotero icon next to a reference, which when clicked on saves the full reference to your library. Zotero can also save a copy of the website or the full PDF. The advantage of Zotero is that it can also saves images, audio and video files. Zotero can also do in text citations and bibliographies via a plug-in for MS Word, which allows you to drag and drop straight into your paper. Zotero can also be synched between machines, and you can add notes and tags and create collections of papers for different projects. Zotero also allows groups to be set- up – this allows sets of documents to be shared with members very easily.
More recently Zotero launched a stand-alone product, that means it is no longer reliant on the use of Firefox-other browser such as Chrome or Safari can now be used. Zotero also has an online forum where help is quickly available from the Zotero user community.
Other RMS/bibliographic software options
Readcube, Sente, Bookends, citeulike refworks, jabRef, Qiqqa, BibTex, refbase, jumper2.0. If you wish to find out about any of
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these, just enter each into a search engine. You will find multiple reviews that discuss the relative merits of each. Taking time to determine which of these will work bet for you and your workflow will pay dividends in your research career. Page | 9
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