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Reference Management

Martin Fenner, Kaja Scheliga and Sönke Bartling

If I have seen further it is by standing on the shoulders of

Giants.
— Isaac Newton

Abstract Citations of relevant works are an integral part of all scholarly papers.
Collecting, reading, and integrating these references into a manuscript is a time-
consuming process, and reference managers have facilitated this process for more
than 25 years. In the past 5 years, we have seen the arrival of a large number of
new tools with greatly expanded functionality. Most of the newer reference
managers focus on the collaborative aspects of collecting references and writing
manuscripts. A number of these newer tools are web-based in order to facilitate
this collaboration, and some of them are also available for mobile devices. Many
reference managers now have integrated PDF viewers (sometimes with annotation
tools) for scholarly papers. Reference managers increasingly have to handle other
forms of scholarly content, from presentation slides to blog posts and web links.
Open source software and open standards play a growing role in reference man-
agement. This chapter gives an overview of important trends in reference man-
agement and describes the most popular tools.

M. Fenner (&)
Public Library of Science, San Francisco, CA, USA
e-mail: mfenner@plos.org
K. Scheliga
Alexander von Humboldt Institute for Internet and Society, Berlin, Germany
S. Bartling
German Cancer Research Center, Heidelberg, Germany
e-mail: soenkebartling@gmx.de
S. Bartling
Institute for Clinical Radiology and Nuclear Medicine, Mannheim University Medical
Center, Heidelberg University, Mannheim, Germany

S. Bartling and S. Friesike (eds.), Opening Science, 125

DOI: 10.1007/978-3-319-00026-8_8,  The Author(s) 2014
126 M. Fenner et al.

Introduction

Reference management is perceived to be tedious and time consuming by many

researchers, especially when it is done manually. In the past, references used to be
written on index cards and stored in boxes. Now, reference management software
allows for the digitalization of a personal collection of relevant scholarly publi-
cations. The earliest programs to manage the basic task of storing references and
adding them to manuscripts have been around for over 25 years (including End-
note and BibTeX/LaTeX-based programs which are still popular today), but each
individual entry had to be typed by hand. In the last 15 years we have seen a
number of significant developments that have made reference management much
easier for the researcher:
1. Retrieval of reference information from online bibliographic databases
2. DOIs and other persistent identifiers for bibliographic information
3. Automated management of PDF files
4. Open Access for easier access to full-text content
5. Web-based reference management for easier collaboration and use across
multiple devices
In this chapter we describe what reference managers are and provide an
overview of some reference management products. We do not make recommen-
dations as to which reference manager may be the best as this is a personal choice
and depends on the workflow of the individual researcher.

What is a Reference Manager?

A reference manager supports researchers in performing three basic research steps:

searching, storing, and writing (Fenner 2010a). It helps researchers find relevant
literature, allows them to store papers and their bibliographic metadata in a
personal database for later retrieval, and allows researchers to insert citations and
references in a chosen citation style when writing a text. To support those steps, a
reference manager should have the following functionalities as identified by
Gilmour and Cobus-Kuo (2011):
1. Import citations from bibliographic databases and websites
2. Gather metadata from PDF files
3. Allow organization of citations within the reference manager database
4. Allow annotation of citations
5. Allow sharing of the reference manager database or portions thereof with
colleagues
6. Allow data interchange with other reference manager products through standard
metadata formats (e.g. RIS, BibTeX)
7. Produce formatted citations in a variety of styles
8. Work with word processing software to facilitate in-text citation
Reference Management 127

A reference manager is a software package that allows scientific authors to

collect, organize, and use bibliographic references or citations. The terms citation
manager or bibliographic management software are used interchangeably. The
software package usually consists of a database that stores references and citations.
Once a citation is inserted into the database, it can be reused to create bibliog-
raphies which are typically found at the end of a scientific text.
Almost all reference managers allow direct importing from bibliographic dat-
abases through direct access from the reference manager and/or bookmarklets that
import content from the web browser. Alternatively, references can be imported
from other reference managers or from files in the BibTeX standard format with
the help of import tools.
The reference database can then be searched, indexed, and labeled. Most ref-
erence managers offer tools for organizing the references into folders and sub-
folders. Some reference managers allow the inclusion of full-text papers in PDF
format. References can be shared via the Internet and organized into workgroups
so that all members can use the same reference database.
Reference managers offer tools for exporting citations and references into word
processing programs by selecting relevant items from the database. The citation
style can be selected from a corresponding database which contains styles that aim
to cover the requirements of a large number of scholarly publishers. Some refer-
ence managers allow for styles to be edited and saved.
There is a wide variety of reference management software, and the strengths
and weaknesses of reference management software are perceived differently
depending on the workflows of individual scientists. The deciding factor for a
particular reference manager is often its popularity within a particular community,
as collaboratively writing a manuscript is facilitated if all authors use the same
reference manager (see chapter How This Book was Created Using Collaborative
Authoring and Cloud Tools). Reference managers have been commercially
available for a long time, but free solutions offer comparable functionalities and
are increasingly gaining importance.
Some reference managers allow sharing, collaborative editing, and synchroni-
zation of reference databases across a private workgroup and/or publicly via the
Internet. Public sharing of references is the focus of online-only social book-
marking tools such as CiteULike and Bibsonomy, but is also available with other
reference managers. This functionality makes it possible to share Open Access
papers online (see chapter Open Access: A State of the Art) and to generate usage
statistics as a novel means of measuring scientific impact (see chapter Altmetrics
and Other Novel Measures for Scientific Impact).

Getting References into the Reference Manager

All reference managers provide the functionality to manually enter bibliographic

data. However, it is more convenient if the references are automatically extracted
from an online bibliographic database such as Web of Science, Scopus, PubMed,
128 M. Fenner et al.

or Google Scholar. Most reference managers can also import references directly
from a webpage, usually using information embedded via CoinS. All reference
managers can import/export references in the BibTeX and/or RIS format; this is a
convenient way to share reference lists with colleagues.

Bibliographic Databases

Some of the largest bibliographic databases (Web of Science, Scopus, and others)
are only available via a subscription. In the last 10 years we have seen the
emergence of an increasing number of openly available bibliographic databases.
This trend started with PubMed in the late 1990s, includes Google Scholar, and,
more recently, Microsoft Academic Search and the CrossRef Metadata Search, and
now also includes bibliographic databases built by reference managers themselves
(e.g. Mendeley or CiteULike). The availability of these databases increases the
options for researchers to automatically import citation information, either via
direct integration into the reference manager, or via a bookmarklet that captures
the bibliographic content on the web page.

COinS: Hassle-Free Import of Bibliographic Data

ContextObjects in Spans (COinS) is a method that includes relevant bibliographic

metadata of a scientific publication into the HTML code of a web page. If
appropriate plugins are installed in a standard web browser, the bibliographic
information of a reference can be easily retrieved by a reference manager, thus
omitting tedious copy and paste processes. For example, if a reference is found in
PubMed, a little symbol appears in the browser address line if the Zotero plugin is
installed. At the click of a button, all important bibliographic information will be
transferred into the Zotero database. Many scientific databases, scientific social
networks, and journals support COinS (Fig. 1).

Digital Object Identifiers and Other Unique Identifiers

Most journal articles can now be uniquely identified by a digital object identifier
(DOI). DOIs for journal articles are issued by CrossRef, a non-profit organization
that has most scholarly publishers as its members. DOIs can also be used for other
content, e.g. conference proceedings or book chapters. DataCite is another non-
profit organization that can issue DOIs, focusing on DOIs for datasets. There are
also other unique identifiers for scholarly content, e.g. the PubMed ID, PubMed
Central ID, or the ArXiV ID. These identifiers make it much easier to handle
Reference Management 129

bibliographic information: reference managers can extract the DOI from imported
PDFs, obtain more citation information using the DOI, store the DOI internally to
help find duplicate records, etc. Authors only need to worry about the DOI (or
other unique identifier), all the other information they need (authors, title, journal,
link to the full-text) can be obtained from it.

Standardized Bibliographic Data Formats: BibTeX and RIS

BibTeX and RIS are the two most established file formats for storing bibliographic
data, and one or both of these formats are supported by all reference managers.
Exporting data in a standardized format is important because it allows users to
backup their reference lists independently of the reference management software,
to switch from one reference manager to another, or to use multiple reference
managers in parallel.
• BibTeX has existed since the mid 1980s and was designed to be used in
combination with the typesetting system LaTeX. The format is now widely
supported by reference managers that work with Microsoft Word and other
authoring tools, and by online bibliographic databases such as Google Scholar.
• Research Information Systems (RIS) is a standardized tag format originally
invented by Research Information Systems (now part of Thomson Reuters). The
format is widely supported and has been adapted over time, e.g. to include a
field for digital object identifiers (DOIs).
• Endnote XML and Citeproc JSON are newer formats which are not yet as
widely supported. BibTeX and RIS are plain text formats. XML and, more
recently, JSON have evolved into the standard data exchange formats of the
Web, and are easier to process automatically. They may therefore over time
become the predominant formats for exchanging bibliographic information.

Citation Styles and Citation Style Language

Citations can be formatted in many different ways: what information to include

(authors, title, journal, year, issue, pages), how to order and format this infor-
mation, and how to reference these citations in the main text (e.g. by number or
author/year). These so-called citation styles are important for printed documents,
but are not really relevant for digital content (where citations are exchanged in
BibTeX and other data formats). Unfortunately, most manuscript submission
systems do not accept references in digital format, and authors are forced to format
their references in the style requested by the publisher and include them as plain
text at the end of the manuscript (and, in turn, publishers then spend time and
money to get these references back into a bibliographic data format).
What publishers are really interested in are unique identifiers, such as the DOI, for
all references. This allows them to double-check the reference information against
130 M. Fenner et al.

Fig. 1 Showing COinS in action. At the click of a button, a reference is included into the
reference manager software (Zotero) from information that is contained in the COinS information
in the displayed web page: No need to manually copy references

bibliographic databases (using tools such as eXtyles), and to format the citations into
their preferred style. Citation information in free-text format can contain errors, and
these errors are propagated if citations are entered manually (see Specht 2010).
Citation styles are needed not only to correctly identify all references (for which
bibliographic formats and digital identifiers are better suited), but also to help the
researcher while reading the text. Citations are an important part of all scholarly
documents, and citation styles should facilitate that process. Even though a number
of common styles exist (e.g. APA, MLA, Chicago, Vancouver), there is no stan-
dard style for citations in scholarly documents, and with the differences in citation
practices between disciplines, it is not likely to ever happen. Some disciplines use
simple reference lists at the end of the document, whereas other disciplines use
footnotes at the bottom of pages and/or make heavy use of annotations.
Until it becomes standard practice to submit references in a bibliographic file
format together with manuscripts (some publishers do this already), authors must
resultingly deal with a large number of citation styles. This also often means
changing the citation style when a paper has to be resubmitted to another journal.
This is a time consuming endeavor, thus automating the process of adjusting to the
various citation styles is an important feature of all reference managers.
Most reference managers support a large number of citation styles: EndNote1
supports over 5,000 bibliographic styles, and Mendeley, Zotero, and Papers all
support 2,750 citation styles. Some reference managers include a style editor, in

1
EndNote Output Styles: http://endnote.com/downloads/styles
Reference Management 131

Examples of citation styles

DOI
http://dx.doi.org/10.1126/science.1197258
shortDOI
http://doi.org/dc3dhn
APA
Wolfe-Simon, F., Blum, J. S., Kulp, T. R., Gordon, G. W., Hoeft, S. E., Pett-Ridge, J., &
Oremland, R. S. (2011). A Bacterium That Can Grow by Using Arsenic Instead of
Phosphorus. Science, 332(6034), 1163-1166. doi:10.1126/science.1197258
Vancouver
Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, et al. A Bacterium That
Can Grow by Using Arsenic Instead of Phosphorus. Science [Internet]. American Association
for the Advancement of Science; 2011 Jun 2;332(6034):11636. Available from: http://
dx.doi.org/10.1126/science.1197258
Nature
Wolfe-Simon, F. et al. A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.
Science 332, 1163-1166 (2011)
BibTeX
@article{_Webb_Weber_Davies_et_al__2011, title = {A Bacterium That Can Grow by Using
Arsenic Instead of Phosphorus}, volume = {332}, url = {http://dx.doi.org/10.1126/
science.1197258}, DOI = {10.1126/science.1197258}, number = {6034}, journal = {Sci-
ence}, publisher = {American Association for the Advancement of Science}, author =
{Wolfe-Simon, F. and Blum, J. S. and Kulp, T. R. and Gordon, G. W. and Hoeft, S. E. and
Pett-Ridge, J. and Stolz, J. F. and Webb, S. M. and Weber, P. K. and Davies, P. C. W. and
et al.}, year = {2011}, month = {Jun}, pages = {1163-1166}}
RIS
TY—JOUR
T2—Science
AU—Wolfe-Simon, F.
AU—Blum, J. S.
AU—Kulp, T. R.
AU—Gordon, G. W.
AU—Hoeft, S. E.
AU—Pett-Ridge, J.
AU—Stolz, J. F.
AU—Webb, S. M.
AU—Weber, P. K.
AU—Davies, P. C. W.
AU—Anbar, A. D.
AU—Oremland, R. S.
SN—0036-8075
TI—A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
SP—1163
EP—1166
VL—332
PB—American Association for the Advancement of Science
(continued)
132 M. Fenner et al.

(continued)
DO—10.1126/science.1197258
PY—2011
UR—http://dx.doi.org/10.1126/science.1197258
ER—
Citeproc JSON
{‘‘volume’’:’’332’’,’’issue’’:’’6034’’,’’DOI’’:’’10.1126/science.1197258’’,’’URL’’:’’http://
dx.doi.org/10.1126/science.1197258’’,’’title’’: ‘‘A Bacterium That Can Grow by Using
Arsenic Instead of Phosphorus’’,’’container-title’’:’’Science’’,’’publisher’’:’’American Asso-
ciation for the Advancement of Science’’,’’issued’’:{‘‘date-
parts’’:[[2011,6,2]]},’’author’’:[{‘‘family’’:’’Wolfe-Simon’’,’’given’’:’’F.’’},{‘‘fam-
ily’’:’’Blum’’,’’given’’:’’J. S.’’},{‘‘family’’:’’Kulp’’,’’given’’:’’T. R.’’},{‘‘family’’:’’Gor-
don’’,’’given’’:’’G. W.’’},{‘‘family’’:’’Hoeft’’,’’given’’:’’S. E.’’},{‘‘family’’:’’Pett-
Ridge’’,’’given’’:’’J.’’},{‘‘family’’:’’Stolz’’,’’given’’:’’J. F.’’},{‘‘family’’:’’Webb’’,’’given’’:’’S.
M.’’},{‘‘family’’:’’Weber’’,’’given’’:’’P. K.’’},{‘‘family’’:’’Davies’’,’’given’’:’’P.
C. W.’’},{‘‘family’’:’’Anbar’’,’’given’’:’’A. D.’’},{‘‘family’’:’’Oremland’’,’’given’’:’’R.
S.’’}],’’editor’’:[],’’page’’:’’1163-1166’’,’’type’’:’’article-journal’’}

case a particular style is not yet supported. Citation styles used to be in proprietary
format and owned by the publisher of the reference manager, but the Citation Style
Language2 (CSL) has evolved as an open XML-based language to describe the
formatting of citations and bibliographies. Originally written for Zotero, CSL is
now also used by Mendeley, Papers, and many other tools and services. In 2012, a
web-based editor3 to create and edit CSL styles was launched, facilitating the
creation of additional styles.

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 jour-
nals. 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 institu-
tion). Reference management software therefore has to make decisions as to what

2
Citation Style Language: http://citationstyles.org/
3
Find and edit citation styles: http://editor.citationstyles.org/about/.
Reference Management 133

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

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

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
134 M. Fenner et al.

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

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

RefWorks is a commercial web-based reference manager by ProQuest. The Write

N Cite utility enables the integration of references into Microsoft Word where in-
text 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 web-
based 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

Papers is a commercial reference management software, now part of Springer Sci-

ence+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

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
Reference Management 135

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

CiteULike is a free online reference manager and social bookmarking tool. Ref-
erences 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.
136 M. Fenner et al.

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 Wiki-
pedia (Fig. 2).4

Outlook

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 man-
agement 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.

Open Access This chapter is distributed under the terms of the Creative Commons Attribution
Noncommercial License, which permits any noncommercial use, distribution, and reproduction in
any medium, provided the original author(s) and source are credited.

References

Fenner, M. (2010a). Reference management meets Web 2.0. Cellular Therapy and Transplan-
tation, 2(6), 1–13.
Fenner, M. (2010b). Reference manager overview. Gobbledygook. Available at http://
blogs.plos.org/mfenner/reference-manager-overview/.

4
Comparison of reference management software: http://en.wikipedia.org/wiki/Comparison_of_
reference_management_software
 Reference Management 137

Gilmour, R. & Cobus-Kuo, L. (2011). Reference management software: A comparative analysis

of four products. In Issues in Science and Technology Librarianship. Available at http://
www.istl.org/11-summer/refereed2.html.
Specht, C. G. (2010). Opinion: Mutations of citations. Available at http://www.the-scientist.com/
?articles.view/articleNo/29252/title/Opinion–Mutations-of-citations/.

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