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ATPM 3.05
May 1997




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Review: EndNote Plus 2.0.1 and Endlink 2

by Belinda Wagner,


Product Information
Publisher: Niles & Associates
800 Jones St.
Berkeley, CA 94710
Phone: (510) 559-8592
Fax: (510) 559-8683
List Price: $299 (for bundle)
Substantial discounts for
educational institutions.

System 6.0.7 or higher
770K of free memory.
PowerPC Compatible (not native)

The Plug

Endnote is, in my opinion, the premier solution for organizing, storing, managing, searching, footnoting and formatting reference materials. If you have even an occasional need to keep track of where you found information and attribute facts and figures to their rightful source, Endnote is for you.

Endnote is both a reference database and a reference formatting application. For years it was a Mac-only application, but in 1995, it was expanded to Windows machines as well. As a scientist that regularly composes complex grants and manuscripts in Microsoft Word, I use this program extensively for every phase of planning and writing, from first Medline search to final draft.

The History

Our more clairvoyant ATPM readers may have seen this review coming as early as our 2.10 issue. In it, was a “Segments” piece where I mentioned Endnote. For those of you who have joined our readership since then, or who (like myself) are perpetually running low on spare “hard drive” storage capacity, I’ll recap:

”By April 3, 1990, the introduction alone had swelled to almost fifty pages containing nearly 400 references! ... About 9 PM I set Endnote to formatting and it percolated for about two hours before the references were appended, magically, to the end of my opus. One last spelling check and an edit session with the references and the thesis was DONE...”

Yes, it’s true. I’ve been an Endnote user since the inaugural version. More than seven years later, I’ve only needed to purchase a single upgrade. That’s how stable, versatile and compatible the software is.

When Endnote was first introduced in the late 1980's, its only competition on the Macintosh platform was a program called “REF52.” This monolithic piece of software required 10 Mbytes of hard drive space and over 1 Mbyte of RAM (remember, those were days when Macs came with 40 Mbyte hard drives and a maximum of 4 Mbytes of RAM). There was no way to use REF52 on the two core Macintosh SEs used by over 40 graduate students and postdoctoral scientists. The REF52 library files were far too large for the 800K floppies of the time and we needed precious hard drive space for more generally useful applications (Crystal Quest, Mines, Tetris... oops! I mean, Word, MacDraw, CricketGraph, Excel...).

Endnote revolutionized the way footnotes were incorporated into word-processed documents. It was lean, customizable and for the first time, a manuscript rejected by one journal could almost instantly be reformatted and resubmitted to another journal using the original document file, Endnote and the appropriate reference formatting “Style” filter. Documents and their corresponding reference libraries could be stored on a single 800K floppy, so Endnote could be installed and used on the core Macintoshes (without removing Crystal Quest, Tetris or Mines).

The Present

The Endnote Plus/Endlink combination of today is even more powerful, yet still uses less than 800 Kbytes of RAM. MS Word aficionados need only increase Word’s memory allocation by 800 Kbytes to add Endnote’s Add-In or Plug-In modules to its built-in menus (“Add-in” and “Plug-in” modules obviate the need to run Endnote as a separate application while composing documents in MS Word). Libraries themselves are very compact. Below is a snapshot of some of my libraries. Be aware that the references stored within these libraries include full abstracts and none have less than 30 entries, so each contains a large amount of information.

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”So,” you ask, “How does one use Endnote?” Well, first you need some references. For that you either have to go to the library, search any one of several commercial archives (my personal favorite is Medline), or consult your Funk and Wagnall’s. Second, you need a document in which you want to insert the references as footnotes.

Entering references into libraries is easy whether you’ve retrieved them from a database search or have a stack of Xeroxed articles. “References” don’t even need to be print sources. Endnote is completely user-configurable and versatile enough to use for organizing and referencing music, objets d’art, recipes, Web pages, videos, photos, etc. If you collect it, Endnote can help you organize it, retrieve it, and refer to it in whatever document format you choose.

Building a Library

Libraries are built by manual input or by using Endnote’s companion application, Endlink, to directly import references from online searches or from any “text-only” file. Here, I’ll describe how I import the results of a typical Medline search into an Endnote library. First, references are exported from the online database via e-mail. Once received the e-mail message is saved as a text file:

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I’ve included “invisible” characters for a reason. They are key to understanding how Endlink “Filters” function and you need to know how your particular file “looks” to Endlink.First, notice that the line preceeding the first reference is blank. A blank line is a convenient delimiter between individual references. However, both online services and e-mail programs send and save text in different formats, so it’s important to check the structure of your file, just in case you have to “tweak” your online search preferences or one of the pre-packaged Endlink filters.

Pre-packaged Endlink filters are fairly complete. The only minor “tweak” I made was to add an extra space between the field delimiters (e.g., AU, TI, IN) and the hyphen. Notice there are two spaces sent by my online service, whereas Endlink’s filter specified only one).

Hard carriage returns are another concern. Endlink will interpret a hard return as the end of the field entry. I use ClarisWorks macros to quickly and easily remove hard carriage returns and extra spaces from fields containing more than one line of text (AB, TI, and IN are the most common).

Once the text file is ready for importing, open an existing library or create a new one and choose “Import...” from the “File” menu. A dialog window appears where you choose your text file from which to import, the Endlink filter with which to parse the field entries and whether you want to import all references, discard duplicates or put duplicate references into a separate file. When Endnote is finished importing, the summary window displays the recently imported references. This automatic selection of new references is quite handy for using “Term lists” to optimize your library for consistent usage.

Maintaining Consistency

When submitting any kind of manuscript that contains footnotes, consistency is a priority. A bibliography looks unprofessional if one reference cites a journal article as being published in the “Proceedings of the National Academy of Science, USA” and another reference abbreviates the same journal as “PNAS.” The task of managing footnotes and bibliographies within large manuscripts used to be almost a second career, it was so massive an undertaking. Use Endnote, and you’ll hardly need to think about it.

There are two levels to managing consistency within a database. First, how are references listed in the Endnote library? My online database uses the unabbreviated name of every journal, while I prefer to use simple acronyms when I enter references manually. Second, different publishers use different abbreviation conventions, so sometimes the same reference needs to appear in one bibliography as “Proc. Nat’l. Acad. of Sci.” and in another as “PNAS.”

However, Endnote has an easy-to-use feature to manage both situations — the “Terms list.” Each Endnote library is created with its own set of Terms lists that can be linked to any field (a single field can be linked to only one terms list, but a term list can be linked to multiple, related fields). Terms lists allow you to impose global consistency on output when there is inconsistency of input (a common situation when there is more than one user or source of reference input). Keywords used to search your library can be standardized, journal names can be associated with up to four sets of abbreviated styles, etc. Endnote recognizes and provides a convenient workaround to the inherent incompatibility between the way most of us assemble and use reference libraries versus the demands for perfection by editors and publishers of manuscripts.

Dynamic Management of Footnotes

So, you’ve got some references in a library and you’re writing your opus. Inserting reference “markers” is easy with Endnote. Merely switch to Endnote via the Application menu (MS Word users can choose the Endnote module from the “Tools” menu). Choose reference(s) from an open library’s summary window, “Copy” them from the Endnote menu, switch back to your text document and “Paste.” Endnote brackets the inserted reference with special characters.

While these special characters look a little funny onscreen, they serve a vital purpose. Endnote Plus allows completely dynamic footnote management. The special reference marker brackets are not “seen” by the word processing application as text characters. So, you can change any text’s color, font, etc. and not alter Endnote’s ability to recognize what is and is not a reference while formatting. This also means you can use () or [] or true in your text for comments or other non-citation text, even if the final formatted document uses these characters to indicate a footnote. Endnote knows which symbols surround references and which to ignore.

Dynamic footnoting keeps track of all references within a document,whether they are formatted or not. Unformatted citations appear within the body of the text in a special Endnote format that lists first author, publication year and a number which is Endnote’s internal pointer to the reference. Also, there is no bibliography in an unformatted document.

Formatted, in-text citations usually appear as superscripts, bracketed numbers [1], or author/year combinations (Sluzewska, et al., 1996). Bibliography entries are either appended as a summary list to the end of the document, or are printed at the bottom of the page where the in-text citation appears.

If you are writing a manuscript with strict page limitations, it’s easier to edit a formatted document. This is not a problem for Endnote. Your text can contain a mixture of formatted and unformatted in-text citations or you can add or delete any in-text citation(s). Endnote will keep track of them. Simply reformat the document and Endnote will update both the in-text citations and the bibliography. The power and versatility of dynamic foonoting is demonstrated in the series of screen shots below:

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As I mentioned at the beginning of this review, the Introduction chapter of my thesis contained approximately 400 citations. Keeping track of each and every one manually would have been, well, a nightmare. Seven years ago Endnote transformed that monumental management challenge into a stress-free non-issue and the current version continues to perform even more impressive magic today.

The Future

Niles & Associates has recently teamed up with The UnCover Company. The duo is offering an incredible service combination to authors who routinely monitor several publications for late-breaking publications in their field and use Endnote to manage their reference libraries. The “Reveal” service offered by the Uncover Company allows subscribers to receive customized e-mail monitoring of over 17,000 periodicals. For an annual fee of $25, subscribers can specify up to 25 key topics with which to scan the entire database for related articles. Also, subscribers can receive tables of contents listings from up to 50 journal titles. A special EndLink filter available from Niles and Associates will import these matches directly to Endnote libraries (although I don’t yet know if you still have to save the e-mail message as a text file, nor whether that file will require editing prior to importation).

I’m very excited about signing up for this feature. I currently pay our library more than UnCover’s annual fee just to receive Xeroxed tables of contents from only FIVE journals, so the table of contents monitoring alone is worth the switch to UnCover! The added bonus of keyword searches across the entire collection is just icing on the cake.

I believe I’ll be still be using Endnote when I write my memoirs...

The Specifics

EndNote Plus 2 is compatible with the following word processing formats:
Microsoft Word 3-6.0.1
WordPerfect 1-3.5
MacWrite Pro 1-1.5
MacWrite II
MacWrite 5.0
WriteNow 2-4
Nisus 3-3.4
FrameMaker 3.0-4.0 (MIF format)
Rich Text Format
Plain Text

EndNote Plus Add-in and Plug-In Module for Microsoft Word:

If you use Microsoft Word for the Macintosh, you’ll be able to take advantage of the integration of EndNote Plus and Microsoft Word 5 and 6. The EndNote Add-in for Word 6 and the Plug-In Module for Word 5 provide you with easy access to references as you write. The EndNote Add-in and Plug-In Module install EndNote Plus commands in Words Tools menu so that you can accomplish all of your bibliographic tasks from within Word. Both the Add-in and Plug-In Module are included in all packages of EndNote Plus for the Macintosh.

[apple graphic] Copyright © 1997 Belinda Wagner, Belinda J. Wagner, Ph.D. is a molecular biologist and a faculty member of Bowman Gray School of Medicine in North Carolina. She studies how cells respond to their environment during wound healing.

Reader Comments (1)

Jack Barr · August 31, 2006 - 15:29 EST #1
As with all ATPM articles, I found this one on Endnotes very informative. I do still have one question. Since virtually all biology journals reference in text and do not use footnotes, I have, in the past, hesitated using Endnotes. I am also a very long in the tooth field biologist and most of my former colleagues never advanced beyond file cards for filing/storing references. So, I wonder if Endnotes is the best software application out there for someone like me, or is there, perhaps, some other application more appropriate? Thank you for any comments. Keep up the excellent work; I rely on ATPM frequently.
Regards, Jack.

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