Manage your references
Managing a bibliography or reference section—ensuring that all references are cited, and vice versa—is a tiresome task, especially for a lengthy article or a book. But help is to hand, in the form of reference management software.
Choosing reference management software
There is a wide range of reference management software. The most commonly used are Mendeley and Zotero, both of which are free. Table 5 compares their functionality.
Table 5: Comparison of Mendeley and Zotero reference citation software.
| Facility | Mendeley | Zotero |
|---|---|---|
| Desktop platforms | Linux, Mac, Windows | Linux, Mac, Windows |
| Mobile platforms | Yes | Third party |
| Citation plugins | LibreOffice, Microsoft Word | Google Docs, LibreOffice, Microsoft Word |
| Number of citation styles | >9,000 | >9,000 |
| Number of item types (journal article, book, etc.) | 20 | 36 |
| Browser plugin | Chrome, Edge, Firefox, IE, Opera, Safari | Chrome, Firefox, Opera, Safari |
| Unpaywall integration | No | Yes |
| Retraction Watch integration | No | Yes |
| Online library | Yes | Yes |
| Online account mandatory | Yes | No |
| Cloud storage mandatory | Yes | No |
| Free cloud storage | 2 GB | 300 MB |
| Use own cloud storage (Dropbox, Nextcloud, etc.) | Yes | Yes |
| Group collaboration | Yes | Yes |
| Store offline version of web page | No | Yes |
| Developer | Elsevier | Roy Rosenzweig Centre for History and New Media |
| License | Proprietary | GNU Affero General Public License (v. 3) |
Figure 7: Collecting references from Google Scholar, using Zotero.
Mendeley and Zotero offer similar facilities. As they are freely available, you can try them both, and choose the one that best fulfils your requirements and/or suits your personal taste. Some organizations provide institutional level access to one or the other.
Collecting and organizing literature
Both Mendeley and Zotero include browser plugins that allow you to download the meta data for articles from sources such as Google Scholar and, if available, the associated PDFs. References can then be organized in folders/collections, and keywords/tags added. Zotero includes Unpaywall integration: if you save an item from a webpage where Zotero cannot find or access a PDF, it will search for an open access PDF using data from Unpaywall.
Cite whilst you write
Figure 8: Citing whilst you write, with Zotero.
Reference management software allows you to cite references whilst writing, and will format the citations and references in the selected format as you write. This obviates the need to manage the reference list manually.
Citation and reference styles are available for most journals. The same styles are available with Mendeley and Zotero, as they use the styles from the open source Citation Style Language project. If you change the style used for a document, the citations and references will be reformatted accordingly.
Reference manager as research tool
Figure 9: Adding a note to an article, with Zotero.
Some of the functionality of a reference manager facilitates use as an online research tool:
Saving web page items (a sort of deluxe bookmark system)
Storing web pages offline (in Zotero only)
Annotating PDFs (Mendeley has a built-in PDF viewer; Zotero uses the default PDF viewer of your system)
Adding notes to items
Reference manager for group collaboration
If you would like to collaborate with colleagues, you can create a group—either private or public—within the reference manager. Items copied into a group folder will appear in the group’s page online. This facility requires the creation of an online account (which is mandatory in Mendeley anyway, but not in Zotero).
Figure 10: Creating a one-off bibliography with ZoteroBib.
Creating a one-off bibliography
If you would like to format a one-off bibliography, use ZoteroBib. ZoteroBib works within a browser, allowing you to build a bibliography from any computer or device, and then copy it to the clipboard or share it as a link. There is no need to install software or create an account.
Curating your library
Over time you will build up a library of articles and other references in your reference manager. You will have built this library from a range of sources, including search engines such as Google Scholar, the web pages of individual journals, by adding PDFs of articles directly and then their metadata—either automatically or manually—and by other means.
A library is only as useful as its organization (imagine a traditional library without any shelf marks or collections). Maintaining the organization of your personal library is best done whilst you build it, rather than waiting until you have hundreds or even thousands of items that require reviewing. A reference collection in Mendeley or Zotero is of course searchable even without any additional curation, but a search can only be as good as the metadata of the items. A little extra care as you add items will add great value to your library.
Consistent metadata
To ensure consistent and accurate metadata for the items in your library, it is best to check items as they are imported. There are a few things to look out for:
Do the title, authors’ names and publication title have the correct capitalization?
Does text that should be in italics (e.g. Genus and species names) have html tags (e.g.
<i>Loxodonta africana</i>)? These will ensure that the text will appear in italics in a bibliography.Does the item include keywords? This will help with organization (see also Using collections and tags).
Should the item be included in one or more collections?
Using collections and tags
Figure 11: Collections within the main Zotero library.
Organizing your library in collections (this is the term used in Zotero; Mendeley refers to a collection as a folder) has one great advantage: it allows you to browse through the items on a particular subject (think of browsing books on a particular subject in a traditional library).
Unlike a traditional library, however, an item in reference management software can occur in more than one collection. For example, you may have a collection that contains the articles you have authored (this is useful when somebody asks you for a copy of one of your publications), and each of these articles may also occur in one or more other collections. It is not obligatory to use collections: you may have some items in your library that do not belong to any collection (i.e. they are unfiled).
Figure 12: Using tags as a filter in Zotero.
You can also attach tags to items in your library. Tags are simply keywords, and if you import an item that has keywords, or add them manually following import, they will be added to the tags field. Tags provide another level of organization to your library, as you can both filter your library, or a particular collection, by one or more tags. You can also search on the tag field.
Removing duplicates
Over time, as your library grows, you will inevitably find that you have some duplicate—or even triplicate—references. Mendeley and Zotero can identify these, and you can merge them. It is better to merge rather than to delete one of the duplicates, as merging preserves the collections and tags of all merged items.
Figure 13: Removing duplicates from a Zotero library.
Considerations of quality
You need to be aware that there are now many journals that have substandard or even nonexistent peer review systems, and thus the material they publish is of dubious value. Unfortunately many of these journals are indexed on databases of scholarly research such as Google Scholar. This problem is particularly acute amongst new, online-only open access journals, some of which are principally commercial ventures rather than scholarly endeavours.
You need to be aware of this matter when incorporating articles into your library. Inclusion of research of unverified quality will diminish the value of your library, and scholarly journals will not usually allow you to cite articles from such sources. If you are unsure whether a journal is legitimate, there are two tools you can use:
The Directory of Open Access Journals is a community-curated list of open access journals (i.e. a white list). The list aims to include all open access scientific and scholarly journals that use a quality control system.
Beall’s List of predatory journals and publishers is a black list. It provides updated links to journals and publishers on Beall’s List (originally created by Jeffrey Beall, librarian at the University of Colorado), and links to predatory journals and publishers that have appeared since Beall closed his original list. This updated version of the list is maintained anonymously as a result of the problems Jefffrey Beall encountered in maintaining the list.
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