EndNote 1-2-3 Easy!: Reference Management for the Professional

By Abha Agrawal and Majid Rasouli

This book is intended for healthcare professionals, biomedical researchers, health policy experts, and graduate students who frequently write and publish scientific manuscripts in peer reviewed journals. This new edition updates earlier versions with an emphasis on the most currently available Clarivate Analytics software application EndNote X9, a widely used reference management software. 

For first-time users of EndNote X9, this book is a comprehensive and well-illustrated instruction manual for getting started, including detailed instructions on installation, creating reference libraries, and ultimately creating complete and accurate citation-based bibliographies necessary to achieve successful peer reviewed publications. There is also a full chapter devoted to careful guidance for the growing practice of citing references from online internet sources.  

For existing “power users” of current and earlier versions of EndNote, this book provides quick and easy access to a comprehensive compendium of nuanced and advanced features of this powerful software, with an emphasis on providing greater ease and control in coordinating and curating research materials and bibliographies with research collaborators and scientific writing teams.

The authors have also added new, state-of-the-art “how-to” guidance on a variety of methods of using EndNote, including PubMed, Google Scholar, Web of Science, Scopus and others.  Like many legacy software systems, Clarivate Analytics has also begun to offer an online “desktop” version of EndNote, a topic which is now also covered in Chapter 10 (EndNote Online) of this new edition. 

• Language: English
• Publisher: Springer
• Release date: Dec 18, 2019
• ISBN: 9783030248895

Book preview

© Springer Nature Switzerland AG 2019

A. Agrawal, M. RasouliEndNote 1-2-3 Easy!https://doi.org/10.1007/978-3-030-24889-5_1

1. Introduction to Reference, Bibliography, and Citation

Abha Agrawal¹   and Majid Rasouli²

(1)

A4 Clinics, Brooklyn, NY, USA

(2)

Biosystem Engineering Department, Bu-Ali Sina University, Hamedan, Iran

Abha Agrawal

Quick Summary

Reference: The address of the source of information in a manuscript.

Reference list / bibliography: A numbered or alphabetical list of references and other resources at the end of the manuscript (endnotes) or at the bottom of each page (footnotes).

In-text citation: Link to the reference in the body of manuscript.

Referencing styles: The author-date style (such as the Harvard style) and the footnote/endnote style (such as the Vancouver style).

Things You Will Learn in this Chapter

Basic concepts about some essential terms such as reference, reference list, bibliography, and citation and how they relate to the anatomy of a manuscript.

About referencing styles, including the Harvard style and the Vancouver style.

The benefits of using information technology instead of a pile of index cards for effective reference management.

Research and writing are integral parts of the professional work for researchers, academics, and biomedical professionals. Scientific manuscripts commonly include references to related information in literature. The inclusion of references in manuscripts substantiates arguments with evidence, as well as acknowledges the source of information being referred to. References may be cited from such a variety of sources as journals, books, conference proceedings, magazines, and newspapers, and the Internet. This chapter discusses the basic concepts related to the process of referencing as a foundation to the effective use of reference management software programs, such as EndNote.

Basic Concepts

Figure 1.1 outlines the concepts of reference, reference list, bibliography, and citation as they relate to the anatomy of a manuscript.

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Figure 1.1

Anatomy of a manuscript (showing two different referencing styles for illustration)

Reference

A reference is a short description or note that contains information about the source. Simply put, a reference is the address of the source. References enable the reader to access and verify the original source of information; by knowing the address of the source, a reader can look up the journal/book/web site, and so forth, in which the original material was published.

The following are some examples of references from commonly used sources:

Book Reference

Kohn Linda T., Corrigan Janet, Donaldson Molla S. To err is human: building a safer health system. National Academy Press, 2000.

Journal Article Reference

Jenny-Avital, E. R. Obesity and the risk of heart failure. N Engl J Med. 2002; 347(23); 1887–9.

Magazine Article Reference

Posner, M. I. (1993, October 29). Seeing the mind. Science, 262, 673–674.

Electronic Source Reference

Jonathan Amos. Scientists clone 30 human embryos. http://news.bbc.co.uk/2/hi/science/nature/3480921.stm. Accessed 12 February 2004.

Reference List and Bibliography

References may be included at the end of the manuscript as endnotes, or at the bottom of each page as footnotes. A reference list is a numbered or alphabetically sorted list of references that are cited in the text of the manuscript as endnotes or footnotes. Bibliography is a term typically used to indicate a comprehensive list of all the resources the author has consulted during the research. It may include resources in addition to those cited in the text. Note that the terms bibliography and reference list are often used interchangeably in common practice.

Citation

When references are included as endnotes/footnotes, how does the reader know which quote or text in the manuscript comes from which reference source? This is accomplished by attaching a link to the reference in the body of the manuscript in a short form, called a citation or in-text citation.

../images/114714_3_En_1_Chapter/114714_3_En_1_Figa_HTML.gif Technical Tip: Although we have described the puristic concept of the terms reference, citation, and bibliography, be aware that these terms are frequently used interchangeably.

Common Referencing Styles

There are two main styles of formatting in-text citations and references in a document: the author-date style and the footnote/endnote style (also known as the numbered style). In addition, there are a variety of other styles recommended by various journals and professional associations such as the Modern Language Association (MLA), the American Psychological Association (APA), and the American Medical Association (AMA).

Harvard style is an example of the author-date style. In this style, the in-text citation consists of the name of the author(s) and the year of publication, and an alphabetically sorted list of references is included at the end of the manuscript. The following is an example of the Harvard style. Note that in the reference list the two articles are listed in alphabetical order. The Berland article is listed first in the reference list though it is cited second in the text of the manuscript.

Harvard Style: Example

The World Wide Web is a unique, rapidly expanding medium of communication (Eng et al., 1998). Among the 52 million American adults with Internet access, 55% use the Web to get health information (Berland et al., 2001).

Reference List:

Berland GK, Elliott MN, Morales LS, Algazy JI, Kravitz RL, Broder MS, & et al. 2001. Health information on the internet: accessibility, quality, and readability in English and Spanish. JAMA, 285, 2612–21.

Eng TR, Maxfield A, Patrick K, Deering MJ, Ratzan SC, & Gustafson DH. 1998. Access to health information and support: a public highway or a private road? JAMA, 280, 1371–75.

Vancouver style is an example of the footnote/endnote style. In this style, the in-text citation consists of a reference number, and a numbered reference list, in order of appearance in the text, is included at the end of the manuscript. The following is an example of the Vancouver style. Note that in the reference list the two articles are listed in numerical order. The Eng article precedes the Berland article because it is referenced first in the manuscript.

Vancouver Style: Example

The World Wide Web is a unique, rapidly expanding medium of communication (1). Among the 52 million American adults with Internet access, 55% use the web to get health information (2).

Reference List:

Eng TR, Maxfield A, Patrick K, Deering MJ, Ratzan SC, Gustafson DH. Access to health information and support: a public highway or a private road? JAMA. 1998;280:1371-75.

Berland GK, Elliott MN, Morales LS, Algazy JI, Kravitz RL, Broder MS, et al. Health information on the internet: accessibility, quality, and readability in English and Spanish. JAMA. 2001;285:2612-21.

Table 1.1 provides a list of common referencing styles used in various disciplines and resources to learn more about them.

Table 1.1

Common referencing styles

Using Information Technology for Effective Reference Management

Managing references and creating appropriately formatted bibliographies are time-consuming, error-prone, and cumbersome processes when performed manually using the traditional method of storing references in a pile of index cards. Some inherent problems with the manual method include the following:

Scientific writing is an iterative process; references are frequently added, edited, or deleted while writing a manuscript. This requires changing in-text citations in the body of the manuscript and ensuring that the citations in the text correspond to the appropriate references in the bibliography.

Creating an appropriately formatted bibliography in compliance with the styling standards set by a publication requires considerable time and effort. For example, what would be an appropriate abbreviation for the journal name New England Journal of Medicine—NEJM or N Eng J Med? Should you use et al. for more than three author names, or more than four, or never? How should you describe author names in a given bibliographic style required by a specific publication—should it be Jones, SK, or Smith K. Jones? These questions often baffle authors while writing manuscripts.

If a manuscript needs to be resubmitted to another publication with a different style of bibliography, the process will require manually reformatting all the references into the new style, again a time-consuming task.

Fortunately, new sophisticated technology applications, called reference management software programs, are now available to facilitate the challenging process of reference management by allowing users to create personal digital libraries. Chapter 2 discusses various reference management software programs and their functions in detail. Subsequent chapters in the book provide step-by-step instructions on using EndNote® (version X9), one of the most commonly used reference management programs.

© Springer Nature Switzerland AG 2019

A. Agrawal, M. RasouliEndNote 1-2-3 Easy!https://doi.org/10.1007/978-3-030-24889-5_2

2. Reference Management Software Programs

Abha Agrawal¹   and Majid Rasouli²

(1)

A4 Clinics, Brooklyn, NY, USA

(2)

Biosystem Engineering Department, Bu-Ali Sina University, Hamedan, Iran

Abha Agrawal

Quick Summary

Reference management programs: Organize references in digital libraries to use with manuscript writing and other functions.

Functions: Store and manage references; automatically create, format, and update bibliographies; search and retrieve references and PDFs from Internet databases; read, review, annotate, and search PDFs; share libraries and groups of references; find the best-fit journal for your papers; access research from your desktop, online, or your iPad.

Comparison: EndNote is one of the most popular reference management software and is an excellent tool for the individual researcher. EndNote is the best option for major research projects, because it offers the most options for customization and formatting. Reference Manager is useful for large workgroups and networks. Zotero is a suitable choice for students, as it is free, runs as both a Web service and an off-line service on your personal device, and provides simple download of records. Mendeley is advisable for managing PDFs including automatic extraction of metadata from PDFs. It downloads records from several databases, backs up and synchronizes across multiple computers, and allows a private online account. EndNote Online provides limited features but has the benefits of low cost and access to your libraries anywhere on the Web.

Things You Will Learn in This Chapter

What a reference management software program is.

The functions of reference management software programs.

About various reference management software programs and some criteria for choosing the right one.

About comparing EndNote®, Reference Manager®, EndNote Online®, Mendeley, and Zotero.

About other reference management software programs, including freeware/shareware programs, and their features.

What Is a Reference Management Software Program?

These are software programs that simplify the process of reference management by allowing the user to collect, store, and organize references; insert citations at the appropriate place in the body of the manuscript; and generate a list of references in an appropriately formatted bibliographic style. These programs work by creating a personal digital library (or database) of references. The references in a digital library can be easily searched, sorted, shared, and inserted in a manuscript to create accurate bibliographies.

Reference management programs were first introduced in the 1980s and have been used primarily to organize references, search databases for articles on a topic, and generate bibliographies. Over the years, users’ needs have changed, technology has advanced, and many new features have been added such as options for social networking and portable document format (PDF) file management.

A variety of reference management programs are available these days; the popular ones include EndNote, RefWorks, Zotero, and Mendeley. Each of these offers unique features that may be especially valuable to certain users. For example, of the above four products, EndNote is the only tool that has a direct export option for PubMed and offers a journal matching feature, known as Manuscript Matcher, to help users find the right journal for their manuscripts.¹

Lorenzetti and Ghali (2013) found that of the total 78 researchers who responded to their survey, 79.5% had used a reference management tool to prepare their manuscript. Of these, 98% respondents had used EndNote, Reference Manager, or RefWorks.²

EndNote is particularly popular as it is sold in most university bookstores in North America, as well as through independent distributors worldwide. As an illustrative sample, 12 of the top 25 universities in the United States (see footnote 1) and 4 of the top 15 Canadian universities (see footnote 2) provide EndNote site licenses to their users as a standard part of their services, and 8 of these universities’ library web sites offer EndNote for purchase. This widespread access at major academic institutions and adoption by sophisticated users lend tacit approval to the effectiveness of the EndNote software as a reference management tool.³

Functions of Reference Management Software Programs

Storing and Managing References

By storing references in a digital library, these programs provide you functionality inconceivable in the analog world of paper index cards—for example, they can search the library by multiple criteria such as author, title, journal, year, or keywords. Digital libraries can be stored in a computer, eliminating the need for shelf space for index cards. They can also be backed up easily to avoid losing reference data.

Some examples of the types of references that can be stored in a digital library include:

Articles from journals, magazines, and newspapers

Books and book sections

Grants, theses, and reports

Figures

Charts, tables, and equations

A reference needs to be entered into a library only once, either by manually typing it in the library (Chapter 5) or by automatically downloading it from an Internet database (Chapter 7). Then it can be used as many times as needed to create bibliographies.

Creating Bibliographies

You can easily insert in-text citations into the body of the manuscript and automatically create an appropriately formatted bibliography using a reference management software program. The useful functions of these programs for creating bibliographies include the following:

References are frequently added, edited, or deleted during the iterative process of writing. These programs greatly facilitate the process of automatically changing citation numbers in the body of the manuscript and ensuring that in-text citations correspond to the bibliography.

The bibliography can be automatically formatted according to a specific style, such as the Vancouver style or APA 6th style, or a style conforming to the requirements of the publisher.

These programs eliminate the guesswork out of accurately formatting bibliography and give you correct answers to questions such as "should the New England Journal of Medicine be cited as NEJM or N Eng J Med? and should et al. be used for more than three author names, or more than four, or never?"

If you need to submit your paper to another publication for reconsideration, these programs will save you trouble by easily modifying the in-text citations and reference list according to the style specifications of the new publication.

Chapter 8 describes using EndNote to create bibliographies.

Searching and Retrieving References from Online Databases

You can easily search various online databases such as Scopus®, Web of Science®, PubMed®, Ovid®, the Library of Congress, Google Scholar, and various university catalogs using these programs (Chapter 7). This minimizes the effort of going to the web sites of these Internet databases and learning their search mechanisms and syntax. Reference management programs also allow you to automatically retrieve selected references in your digital library without the need for manually entering references by typing. Automatic entry of references provides the following benefits:

Typing errors, such as in authors’ names or titles, are eliminated.

Correct abbreviations of journal names are entered in the library.

In addition to the essential reference information—such as title, author(s) names, journal, date of publication, and DOI—extra pieces of information about a given reference, such as the abstract and URL, are downloaded into the library.

Sharing References

You can easily share selected groups of references, manage team access, and track participants’ activity and changes.

Working with an iPad

EndNote enables you to easily view, edit, organize, and share research material on an iPad. By syncing your research library across iPad, online and desktop platforms, you increase the power of EndNote by gaining seamless access to reference library from multiple devices and platforms. You can download the EndNote for iPad App v2.4 via the Apple app store. Of note, there is no Android version of the EndNote available as of this