CONTENTS

EDITORIAL

NEWS

REVIEWS

VIEWS & POSITIONS

EVENTS DIARY

Issue 4, March 1998

ISSN 1368-1591

Beta review: EndNote 3.0

EndNote 3.0 is a fully-integrated bibliographic program that will search MEDLINE (and other remote databases) via the Internet, store the references in a searchable database, automate the process of citation, and maintain a hypertext link back to the original online article in full-text. It looks good.

As a student before the advent of the World-Wide Web, at medical school I would conduct MEDLINE searches on CD-ROM in the library, download the results to floppy disk, and import them into EndNote 1.0 on a computer elsewhere - a time-consuming process. EndNote 1.0 would store and sort the references, automate the process of inserting citations according to a particular format (style) into an article, and create an ordered bibliography at the end of the paper.

I was curious to see how far the program had come when Niles Software, Inc. (formerly Niles & Associates) asked me to review a beta release of version 3.0. The new version promised to combine previous functionality with the ability to search and store citations directly from online databases such as MEDLINE, now freely available on the Web. It also promised to link references in the bibliography with the full-text original article (if available) online. This review focuses on the new online searching features.

Installation and configuration

The test machine was a 68K Macintosh LC630 with 12 MB of physical RAM and virtual memory enabled. EndNote 3.0b requires a 386DX/25 MHz PC running Windows (3.1, 95, or NT), or any Mac, with 8 MB of RAM. The software was supplied on 2 high-density floppy disks. The full installation on the Mac occupies around 6.7 MB of hard disk space, mostly due to the large number of pre-configured styles and filters etc. supplied with the package. I used a standard dial-up PPP connection to the Internet to test the new features (although the program is still highly usable without these).

Online searching

Each search requires you to specify a remote database (e.g. MEDLINE) and an information provider (e.g. NLM), details of which are stored in a Connection File. The documentation provides an easy-to-follow 'guided tour' to connecting with and searching Ovid's practice MEDLINE database (containing records from 1993 only).

Simply select a Connection File to open using the File/Connect... menu (note that you may need to initiate a dial-up Internet connection manually in advance). A number of pre-configured Connection Files are provided, including MEDLINE from the NLM (PubMed) and Ovid. Any database you wish to search, however, must be compliant with the Z39.50 protocol to allow online searching from within EndNote (although text files downloaded from non-compliant databases can still be imported into an EndNote Library manually).

After connection you are presented with two windows, one for configuring your search, and the other showing retrieved references (see Fig. 1). References in the retrieved references window can then be selected and copied to a new or existing Library file using a pull-down menu or drag-and-drop. Strangely, 'Shift-clicking' on non-adjacent references to refine your choice relies on the Command key, not the Shift key at all.

Searching a variety of remote databases using EndNote as a common front-end means the user need only become familiar with one search interface, which certainly has theoretical advantages. This interface is fairly basic and may, therefore, be limiting. The pre-configured NLM MEDLINE filter does provide a usable selection of search attributes: Any field, Author, Year, Title, Journal, Volume, Pages, Keywords, and Abstract. Although you can effectively combine sets of search results by merging separate Library files, what's missing is the ability to limit or expand the search with reference to MeSH terms or other criteria. I ordinarily make heavy use of these features.

The NLM's MEDLINE database is now available free on the Internet. Some services, such as Ovid, SilverPlatter, and the BMA service, are access-restricted. In the this case you will be prompted for the user details. Luckily, Connection Files can be edited to make EndNote 'remember' the necessary user ID and password. I attempted to create a new Connection File for the BMA service, based on the Ovid Demo, but the BMA host refused to play (the BMA Library thought it should). I therefore tried my search using the BMA's Ovid Web interface, downloading the results as a text file. Unfortunately, the import filters supplied for importing searches saved in Ovid format did not work well.

One problem, which will no doubt make the medical librarians among you chuckle, is that there's nobody to hold your hand when you go it alone with an online search from home. For example, how do you know whether the British Journal of General Practice is 'BJGP', 'Br. J. Gen. Pract.', 'Br J Gen Pract', or 'British Journal of General Practice'? How do you limit the dates of your search ('1995-98', '1995-1998', '1995 to 1998', or '1995,1996,1997,1998')? The point is that you must have already learned how to use MEDLINE, since no help is available from within EndNote or in it's manual. In contrast, most services on the Web provide online guidance should you need to refer to such a forgettable detail (e.g. see PubMed's Journal Database Browser). In recognition of this problem, Niles Software will attempt to collate information on what search options are available for the various databases (see http://www.niles.com/home/z3950.htm).

Library functions

Retrieved references are permanently stored in an EndNote Library file. You can create as many Libraries as you want, making it easy to keep related references together. The same interface that is used to search remote databases is used to search your own local Library files.

Look ma, no hands!

Once you have created your Library you can get on with writing a paper in your word processor. At the appropriate point in your text, simply copy-and-paste a reference from the Library window and EndNote will insert a place-holder. Once all the citations are in place, EndNote will format your paper according to the bibliographic style you have selected. The program will, for example, add a list of all the references you have cited in numerical order at the end of your paper, numbering citations within the text to match. This is much easier than the manual method, although there are a few minor bugs (changing 'BMJ' to 'Bmj', for example). In addition, EndNote's formatting abilities are dependent on your having a supported word processing package (it wouldn't format documents created in my ageing version of ClarisWorks, although newer versions are supported).

Citation styles provided include many examples from medicine and the sciences, including the widely-supported Vancouver style. What it doesn't do well is cope with the citation of online sources, a subject I have covered in my book. The Vancouver style was updated to accommodate the citation of online sources in 1997 (see Online Updates). In my tests, even when the reference type was changed from 'Journal article' to 'Electronic source', EndNote was not interested in including the URL in any bibliography (users must customise a style do so). I think this is a short-coming.

Hypertext-savvy (almost)

If your paper is written in HTML, EndNote can format it to append a bibliography in HTML as well. There are no hyperlinks created between the citation within the text and the bibliography at the end if you use your choosen style (e.g. Vancouver). Another short-coming, although clever people can create a custom solution. Those of us with less patience must create hypertext links between in-text citations and the references in a document's bibliography using a modified Author-Date style called 'HTML Style'. This will also apply appropriate text styles, such as bold and italic, to the bibliography. If you didn't start out with an HTML document, you can still apply HTML style to it; EndNote will not convert the remainder of the document into HTML (you need to do this in a text editor, or use a program capable of HTML export).

EndNote will hyperlink downloaded citations to original full-text articles, if these are available on the WWW. You can add these URLs manually if the database you are using does not associate them automatically. The Edit/Launch URL... command will open your Web browser and initiate a connection to a reference selected in the Library window. It really does work! Although this may be of limited use at present (unless you are subscribed to a full-text service) the complete BMJ will soon be available on the Web (initially without cost), widening the appeal of this feature to UK doctors.

Conclusion

In conclusion, if the beta version is any indication - and if the relase version irons out the bugs - I will be able to recommend EndNote 3.0 to anyone engaged in significant scientific or medical writing, providing they have a compatible word processor. I see the new online search features as an added bonus, useful for basic 'smash and grab' MEDLINE searches. For advanced searches (e.g. combining multiple result sets), I would recommend using a Web interface such as Ovid in preference, and importing the results into EndNote manually (this might require some experiment, however). With a list price of $299 (excld. academic/student discounts) the package is probably beyond the reach of many students or occasional authors, but attractive to the serious academic who must 'publish or perish'.

Society for the Internet in Medicine

Comments to: simq@cybertas.demon.co.uk

Copyright © 1998 Society for the Internet in Medicine. All rights reserved.
Date: March 1, 1998
Document URL: http://www.cybertas.demon.co.uk/simq/issue4/reviews.html