Josephy Lab Software Handbook

Reference Manager

www.refman.com

You'll wonder how you ever lived without it, once you watch this program build an automatic Bibliography for your term paper! RefMan handles all aspects of creating bibliographies for papers or theses. It is especially powerful when combined with PubMed.

RefMan allows you to create a personal database of literature references. You can enter them by hand, but it's much easier to download them from PubMed.

PubMed Downloads

Go to PubMed and select the paper of papers you want, e.g. by searching for papers by a particular author. Choose "Display PubMed format". Then download the resulting file as, e.g., SMITH.TXT. Now, go to RefMan and choose "Capture". Select Definition Name = NLM PubMed and input the name of your file. The references are imported automatically, with the authors' names, title, journal, page numbers, etc. - even the abstract, if available from PubMed - placed in the correct fields. One point of caution: PubMed will occasionally include annotations, such as "See Comments in vol. xyz") in the titles. You should delete these by hand to prevent them appearing in the titles. By following this procedure, you can quickly build a substantial personal database of hundreds of references, free of errors.

RefMan can be used on its own as a database. You can search for references by a given author, or search on keywords. This is useful while you are composing a paper, although it's pretty much as easy to browse PubMed itself.

The most important feature of RefMan is that it works within Word or WordPerfect as a reference builder. Once installed, it adds itself to the Tools menu in the word-processor program. You can then use RefMan to insert references as you write your paper, by choosing "Insert Citation". Type in the name of the author, and the corresponding references will appear in a window; click on the one you want, and RefMan inserts it in your paper automatically {DeBruin, Josephy, et al. 1998 ID: 1197}.

Building the bibliography

Once you have finished the draft of your paper, RefMan builds the references and bibliography completely automatically. Choose "Scan Document" and the program identifies all the references. Then choose "Generate Bibliography". Choose the Journal style you wish to use (there is a database of styles for hundreds of major journals, or you can custom-build your own). The program will then finish the job for you. The citations in the text will be replaced by the format required for the journal you have chosen, such as [1] or {Jones et al., 1997}. The Bibliography will be built in the correct style and added to the end of the paper (or at another position, if you wish). If you choose the numbered-reference style, RefMan automatically tracks repeated references to a particular paper, so that a subsequent reference is given the same number as the first reference (in the past, one had to do this within the word-processor, using the "Mark Reference" and "Mark Target" commands).

February 1, 2000

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