Managing Full-Text Content

Reference management has traditionally been about managing information about scholarly content (authors, title, journal, and other metadata). With the switch to digital publication and the availability of content in PDF, as well as other formats, reference management increasingly dealt with managing this digital content: linking references to the full-text document on the computer, performing full-text search, making annotations in the PDF, managing the PDF files on the hard drive, etc. Papers was the first reference manager to focus on this aspect, but most reference managers now have functionality to manage PDF files.

Most scholarly journal articles are currently distributed via subscription journals. This makes it important to store a copy on the local hard drive for easier access, but it can also create problems when these PDF files are shared with collaborators (which most publishers do not allow, even within the same institution). Reference management software therefore has to make decisions as to what is technically possible and convenient for researchers vs. what is possible under copyright law (see chapter Intellectual Property and Computational Science).

Content published as Open Access does not have these limitations. This not only makes it much easier to share relevant full-text articles with collaborators, but it also means that we often do not need to store a copy of the full-text on the local hard drive, as the content is readily available.

Reference Management Tools

From the large number of available reference managers, we have chosen seven popular products that are described in more detail below. We have included a table that gives an overview of their basic features. A feature list is not the only criterion in picking a reference manager though; ease of use, stability, price, and available support in case of questions are equally important factors.


EndNote is a commercial reference management software package produced by Thomson Reuters. Endnote is one of the most popular reference managers and has been around for more than 20 years. It allows collecting references from online resources and PDFs. References from bibliographic databases can be imported into EndNote libraries. Full-text can be imported too. EndNote provides plugins for Microsoft Word and OpenOffice. References can be exported to BibTeX. While EndNote does not include any collaborative features, EndNote Web provides the functionality for collaboration with other users. Users can give group members read/write access to their references and import references from other people's libraries. Endnote also integrates with other bibliographic tools produced by Thomson Reuters, including Web of Science and ResearcherID.


Mendeley is a reference manager developed by a London based startup, but has been bought by Elsevier earlier this year. Its strength lies in its networking and collaborative features, and also in providing facilities for easily managing PDF files. It offers both a desktop and a web version with synchronized bibliographic information, allowing access from several computers and collaboration with other users. PDF files can be imported into Mendeley desktop and metadata such as authors, title, and journal are automatically extracted. It is possible to do a full-text search, highlight text in PDFs, and add sticky notes.

The web version recommends papers to users based on their profiles and the content in their libraries. Users can create both private and public groups and share papers and annotations. Mendeley is free to use, but costs a monthly fee if the number of documents in Mendeley web or the number of private groups exceeds a limit.


Zotero is a popular open source reference manager, originally developed as a plugin for the Firefox browser. The newer Zotero Standalone offers the same functionality but runs as a separate program and works with Firefox, Chrome and Safari. Zotero also includes a hosted version in order to synchronize references across devices and share them in private or public groups.

Zotero allows users to collect and to organize a variety of web sources such as citations, full-texts, web pages, images and audio files directly in the browser. Citations from Zotero can be integrated into Microsoft Word and OpenOffice.


RefWorks is a commercial web-based reference manager by ProQuest. The Write N Cite utility enables the integration of references into Microsoft Word where intext citations and reference lists can be formatted into various styles. RefWorks makes it easy to collaborate with others as all references are stored in the webbased version. The Write N Cite utility can also work offline, but RefWorks is not the right tool for researchers with intermittent or poor Internet connectivity.


Papers is a commercial reference management software, now part of Springer Science+Business media. Initially Papers was only available for Mac, but now there are also versions for iPad and PC. Its main strength is its excellent handling of PDF documents (including metadata extraction) and its polished user interface, whereas the collaborative features are less developed than in some of the other products. Papers uses the Citation Style Language and provides a word processor plugin.


JabRef is an open source bibliography reference manager popular with LaTeX users. It runs on Java and is thus compatible with Windows, Linux, and Mac. The native file format is BibTeX which is the standard LaTeX bibliography format. The strength of JabRef is that references can be formatted directly in LaTeX, thus

Fig. 2 Feature comparison of popular reference managers (see also Fenner 2010b)

providing access and control over a wide range of citation styles. JabRef provides direct search and downloads from PubMed and IEEEXplore. There are plugins for word processing programs and also other Java based plugins, which expand the general functionality.


CiteULike is a free online reference manager and social bookmarking tool. References are primarily entered via a bookmarklet that captures bibliographic content in web pages. New entries are public by default and are added to the common library, but entries can be also made private. Users can assign tags to entries which make it easier to organize and search through content. References can be exported in BibTeX and RIS formats. The social networking features are the strength of CiteULike. Users can create profiles, connect with other researchers, and create and join groups where they can collaborate on library content.

Other Reference Management Products

Many other reference managers are available, including Citavi which is popular in some disciplines and also helps with knowledge management, and ReadCube which has a very nice user interface and a good PDF viewer. An extensive list and comparison of available reference management software can be found on Wikipedia (Fig. 2).[1]


Reference management has become easier, cheaper, and more social in the past few years, and this trend will continue. We will see the integration of unique author identifiers (ORCID, etc.) into bibliographic databases and reference management tools (see case in chapter Unique Identifiers for Researchers), and this will facilitate the discovery of relevant literature and the automatic updating of publication lists. We will increasingly see citations of datasets and other non-text content (see chapter Open Research Data: From Vision to Practice). Digital identifiers for content and support for the open Citation Style Language will also increase, as will the availability of open bibliographic information. Three areas still need improvement. Firstly, the automatic importing of the references of a particular publication, and the integration of reference managers into authoring tools. Secondly, the word processor plugins for reference managers still do not work together, and some of the newer online authoring tools (Google Docs, etc.) need to be better integrated with reference managers. Finally, instead of having references in plain text, which makes it difficult to get to the full-text and reformat it into a different citation style, publishers, institutions, and funders should start to ask for reference lists in standard bibliographic formats using digital identifiers.

  • [1] Comparison of reference management software: reference_management_software
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