Scientists have a surfeit of options to
choose from in the competitive market of reference-management
software.
Adam Rocker
didn't expect the software that managed his digital reference
library to flag up better ways he could be doing his research. But
his electronic filing system of choice, ReadCube, periodically scans
his library and suggests related papers, rather as some
music-file-management programs highlight recommended tunes. And that
feature, he says, has brought up some unexpected gems.
As a graduate student, Rocker, who is
now studying medicine at the University of Ottawa, was researching
bacterial infections in zebrafish. ReadCube highlighted a paper that
described a way to entrap the fish using microfluidics -- a field
whose literature he would not normally read -- that was much easier
than his own method. Being alerted to the research was "really
rewarding”, Rocker says, although he was ultimately too invested in
his own project to adopt the alternative approach.
As Rocker discovered, today's
reference-management tools go above and beyond simple electronic
filing. Rather like a Swiss-army knife, each tool now appeals to
customers by offering an ever-evolving set of extra features.
This article focuses on eight tools --
colwiz,
EndNote,
F1000Workspace,
Mendeley,
Papers,
ReadCube,
RefME and
Zotero
-- all competing in the reference-management market (see
'Reference-management
software' or download this Excel spreadsheet for a
fuller
comparison of the software ). Some excel at streamlining the
process of browsing and building literature libraries, whereas others
focus on creating bibliographies, aiding collaboration through the
use of shared workspaces or recommending papers. (One, ReadCube, is
owned by Digital Science, a firm operated by the Holtzbrinck
Publishing Group, which also has a share in
Nature's
publisher.)
Each tool
exists to help researchers to tame the digital flotsam and jetsam of
scattered, downloaded PDFs. Most scientists can relate to that
problem: as they grab PDFs from journal websites -- where they are
often assigned impenetrable alphanumeric codes as filenames -- and
dump them into any convenient folder, chaos can quickly take hold,
with multiple copies of files spread across hard disks.
"In science, or at least in my
experience, we tend to end up with a folder in the desktop with 3,000
really weirdly named PDF files, which we can never find when we need
them,” says Raúl Delgado-Morales, a neuroscientist at the
Bellvitge Biomedical Research Institute in Barcelona, Spain.
Reference-management tools address that
confusion by indexing a hard disk. Typically, the process of dragging
and dropping a PDF into an application window triggers the software
to try to identify it using the DOI or title, and to retrieve
relevant metadata (such as title, keyword and author names) from
online servers.
Researchers
can also assign software to monitor specific folders into which they
drop their files. They can then find PDFs through a simple search for
author name, keyword or, in some cases, their own notes.
Delgado-Morales solved his problem, for example, by organizing his
literature library with Papers, a user-friendly application that
automatically renames files according to any scheme he chooses. Other
tools offer similar functions, except for RefME -- a website and
mobile app -- which stores only lists of references and not the PDFs
themselves.
Core functions
Most of the tools help researchers to
import literature from a variety of online sources. Many offer in-app
searching of external databases such as PubMed and Google Scholar, as
well as web-browser plugins that grab reference data (and sometimes,
associated PDFs) from journal websites and other pages.
Zotero -- a free, open-source software
project -- was founded ten years ago specifically to tackle the
problem of extracting information from a web browser, says project
director Sean Takats of George Mason University in Fairfax, Virginia.
"That's the key feature of Zotero, and remains one of its
strongest compared to other reference managers,” he says. RefME
offers the unusual option of adding references by scanning a barcode
with a smartphone camera.
One of the best-known features of
reference-management software is the ability to insert in-text
references in a research paper and to create bibliographies in any
format. EndNote, a widely used commercial package, has offered this
feature for decades, but now faces competition from many modern
tools.
Many tools interface with common
word-processing software (usually Microsoft Word, but sometimes
OpenOffice and related freeware suites as well) so that a user typing
up a research article need only select the papers that they want to
mention and click a button to have codes inserted into the document
to mark the in-text reference. Later, the user can create a
bibliography and in-text citations according to several thousand
journal styles, picking his or her choice from a pull-down list.
Most tools include built-in PDF readers
for reading and annotating articles -- typically allowing users to
search through comments and notes -- as well as cloud-based
capabilities for syncing those comments (and the PDFs themselves)
between, for example, an iPad and a desktop computer. But ReadCube
and colwiz try to offer richer PDF reading experiences. In ReadCube,
for instance, in-line citations and author names in PDFs are rendered
as active hyperlinks to provide direct access to cited articles and
publication lists. The same functionality is available when viewing
and annotating PDFs on the websites of partnering publishers
(including, for ReadCube, Nature and Wiley; and, for colwiz, Taylor &
Francis).
Many of these tools can identify
articles related to specific items in a library, or recommend
articles on the basis of the library's content overall.
F1000Workspace -- like ReadCube -- uses an algorithm to do this. It
also taps into recommendations made by a community of 10,000 or so
specialists. However, many other stand-alone software products also
recommend papers (see
Nature
513, 129-130; 2014).
Set to share
Many tools now allow researchers to set
up group libraries or share key papers with distant collaborators,
although this process is carefully managed to prevent violation of
publishers' copyright. Those in public groups using Mendeley, for
instance, can share only information about a paper -- the equivalent
of a library-catalogue entry. Only users in private groups can share
and modify PDFs (and groups must upgrade to a paid account to add
more than three individuals).
Brenton Wiernik, an
organizational-psychology PhD candidate at the University of
Minnesota in Minneapolis, uses a shared library in Zotero for
collaborative projects involving systematic reviews and meta-analyses
of the literature in his field. Such efforts might involve 15-20
people, he says: some downloading articles into a shared library;
others reading them; still more adding annotations and tags and
logging key data.
According to Wiernik, the process is
akin to using a shared Dropbox folder, with the added benefit that
Zotero tracks and maintains metadata, notes and annotations. For
instance, researchers can use a dedicated tag to indicate that they
are processing an article, thereby signalling to collaborators that
they should work on a different article to avoid duplicated effort.
F1000Workspace and colwiz both extend
sharing to include features for preparing manuscripts and managing
projects. With F1000Workspace, researchers can use a plugin to upload
Microsoft Word manuscripts to a secure location, thereby enabling
team members to comment on the shared copy -- although the text
cannot be edited in the browser, says João Peres, the company's
product-development manager. Peres plans to implement a 'one-click'
article-submission feature that sends papers directly from
F1000Workspace to journal editors, starting with the journal
F1000Research. And colwiz also permits users to share
documents to an online drive for team members to view and comment on.
Given the highly overlapping feature
sets of these tools, a user's choice often comes down to particular
individual priorities. Richard Karnesky, a materials scientist at the
Sandia National Laboratories in Livermore, California, supports
Zotero for its open-source ethos, for example.
Perhaps the best reason for using a
reference manager is the technology's ability to provide a form of
searchable memory. Imagine, says Boyd Steere, a senior research
scientist at pharmaceutical firm Eli Lilly in Indianapolis, Indiana,
a desk piled high with printed papers: Post-it notes hanging out,
writing in the margins, doodles, notations, arrows and more. Today's
PDF-filled, digital folders are in many ways no easier to navigate.
With a digital reference manager, however, buried knowledge is just a
keyword search away.
