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Publishing Resources for STEM Authors: Reference Management Tools

A guide with resources to accompany the workshops on publishing for gradute students and post-doctoral researchers.

Introduction to Reference Management Tools

Reference Management Tools, also referred to as bibliographic database software or personal bibliographic software, enable researches to more easily collect and manipulate the results of their literature searches.

The Impoartance of Citation

Citation -Why It is So Important in Scholarly Publishing

  • Anyone writing a scholarly paper - from a three-page paper for a freshman writing class, to a 500-page doctoral dissertation - is expected to properly cite his or her sources.  That means, providing in clear and understandable fashion, the information that a reader of the paper would need to track down that source material.  for example, citing a printed journal article, one should provide the author(s) name(s), the article title, the journal title, volume, issue, date of publication and page numbers.
  • But why is this expected?
    1. Attribution - If you have used information from someone else, you are expected to give the original source credit.  Not to do so, even if the original source is in the public domain, is plagiarism, a serious ethical offense in the scholarly world.  You would be, in effect, taking credit for someone else's hard work.  Moreover, how often a person's work is cited is considered a valuable measure of its importance to its field of research.
    2. Verification - If you have used information which is not completely presented in your paper, the reader must be able to go back and check the original sources, both to see whether you have reported the information accurately and to check how the original source gathered the information.
    3. Searchability - While this may not be important for that three-page freshman paper, most scholarly authors want to maximize the likelihood that others working in their field will be able to discover their work.  With the existence of databases which index cited references (see below), a proper citation of a relevant source can mean that other scholars seeking to find papers which build on that previous research will find your paper.
  • An interesting point-of-view on the ethics of citations and their uses is Prof. Jan Reedijk's editorial in Angewandte Chemie International Edition, "Citations and Ethics",
  • Proper citation requires adherence to a consistent citation style.

Citation Styles

  • In order to ensure that all the necessary information to identify and locate cited references is provided by authors, publishers (and instructors in university courses, and departments receiving theses and dissertations!) will generally stipulate what citation style they wish their authors to follow. 
  • There are dozens of different citation styles, varying in popularity depending on the subject area involved. Most will require the same types of information, but may differ in detail, and may differ significantly in the order the information in which the information is arranged.
  • See the "Style Guides" section of the "Scientific Writing Guides" page in this LibGuide for a list of important citation styles in the sciences and engineering.

Overview of Personal Bibliographic Software

Personal Bibliographic Software (PBS)

What can Personal Bibliographic Software do for you?

Why not just assemble a file of copies of the references you find? Or keep a folder of PDFs on your computer, or a spreadsheet listing the references you've downloaded? A PBS tool, designed expressly to handle literature references for researchers has several advantages:

  • Collect - Most PBSs allow you to direct export an answer set from a database search into the PBS, or allows you to import a file which you have previously downloaded. You can also manually input references if need be.
  • Organize - Most PBSs allow you to group references in files or folders, by, for instance, topic or project, for easy retrieval.
  • Format - The major PBS packages have citation styles used by a host of journals built in, so you can, with a simple selection, reformat your downloaded references into the format desired by your prospective publisher.
  • Share - Some PBSs allow you to grant access to your folders to other users, either as read-only or as read/write. This can be very  convenient when you are working on a group project and want everyone in the group to use and contribute to the library research.
  • Report - A PBS will allow you to generate formatted bibliographies from your selected references. In some cases, they will integrate with your word processing software to allow you to automatically generate and manipulate footnotes in your papers.

Desktop PBS

  • The first PBS systems were based on standard database software for personal computers, with customization to accommodate bibliographic data fields, and output to bibliographies according to particular citation styles.
  • Modern desktop PBS software can be extremely powerful and sophisticated.  Among such packages are:
    • EndNote ( from Clarivate Analytics, publishers of Web of Science. EndNote is available for both Windows and Mac OS, and is tightly integrated with Web of Science, ResearcherID and EndNote online (see below.)
    • Papyrus ( was developed for the Macintosh, and became very popular among Mac PBS users, later adding a Windows version.  Papyrus is no longer being updated, but the last versions of each are available free of charge at the website.
    • Zotero ( is a free bibliographic software tool.  It was originally developed (and is still available) as a plug-in for the Firefox web browser.  It is now also available as standalone software for Windows, Mac or Linux, which can connect to Firefox, Safari or Chrome web browsers.  It is designed to pluck bibliographic information directly from the browser screen. Fore more information about using Zotero, see the Zotero Workshop guide by Annie Platoff at
    •  For a large, if not comprehensive list of PBS packages and sites, see the Wikipedia article on comparison of reference management software at

Web-based PBS

  • In recent years, a variety of personal bibliographic tools have become available which store the database files on central servers, accessed through the Web.
  • Traditional-style PBS sites include:
    • RefWorks (  RefWorks is produced by ProQuest, and, unsurprisingly, is well integrated with ProQuest databases.  It requires either an individual subscription, or access to an institutional subscription.  UCSB does not have a RefWorks subscription at this time.
    • Zotero ( is a non-profit service, free to use, with features to let you collect, organize, cite and share your references.  One of its most important and useful features is a plug-in that lets you collect references directly from your browser screen, whether from databases, full text journals online or webpages.
    • EndNote online (  Like the desktop EndNote, EndNote online is produced by Clarivate Analytics, and closely integrated with the desktop product, with the Web of Science platform and with ResearcherID.  EndNote online is available free to all users with registration. (UCSB has access as part of the UC Web of Science subscription to a somewhat enhanced version, including UC-e-Links embedded in document records.)  Purchasers of desktop EndNote also receive an EndNote online account.  EndNote online is described in much greater detail below.
    • Mendeley ( is a free tool now owned by Reed Elsevier, publisher of scholarly books, journals and databases including Scopus.  It requires the download of software (Windows, Mac and Linux compatible), and stores both bibliographic references and electronic documents on a central server.  In addition to the traditional PBS functions, Mendeley also acts as a scholarly social network, enabling the user to share references, annotations and collaborate with other Mendeley users.  Mendeley also now as an iPhone app for mobile users. It is now a subsidiary of Reed Elsevier, and cooperates tightly with their Scopus database and ScienceDirect full text collections..

The UCSB Library supports Zotero and EndNote online. See the Zotero and EndNote pages for more information. Feel free to contact the librarians listed for additional training or assistance.

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