Explore and compare working with JabRef, Papers3, and Word 2008

Over the years I’ve built up a large reference list. The list has now more than 5000 entries, which reflects

  • I’m getting old: I remember when Pubmed became available to everyone over the Internet (1997) and Google Scholar appeared in (2004).
  • It’s important to my teaching style to be able to present students with access to the papers used in my lectures.
  • I like to teach my courses (biostatistics, genetics, etc.,) from a perspective of historical context.
  • My research interests have changed.

I initially managed the list with the first version of EndNote, continuing through EndNote2 through EndNote5, then a few years with the excellent and free to use Mendeley until I reached their 2GB limit on the free account. I would have continued to use Mendeley but for their choice of subscription pricing as opposed to my preference for a purchase of a onetime license. That said, I settled on JabRef and have used it for years.  As a reference database, JabRef is tops in my book, plus it’s Open Source and cross-platform software. It’s less convenient working with manuscripts when you want to cite and build a bibliography, but it certainly works. JabRef works better with LibreOffice documents than Microsoft Office documents (see this post), but it can work with Word if you use Word’s bibiliography functions and with a little run-around. Since I’ve recently become interested in Papers, thought I’d share my notes as I go.

In this posting I present brief instructions for adding citations and a bibliography to a Word 2008 document with combinations of JabRef and or Paper3.

JabRef (ver 3.8.2) & Papers3

Goal: Import selected reference list into Papers3 from JabRef

  1. From JabRef, select one or more references. File→ Save selected as… to BibTex *.bib database.
  2. Start Papers3
  3. File→ Import→ BibTex library

Note: Papers3 will import my entire JabRef database, but that’s unnecessary for the example.

Papers3 + Word 2008

Goal: cite as you type; append bibliography to manuscript

  1. Type away in Word 2008
  2. When ready to insert a citation(s), press the control key twice. This brings up a Papers3 Search window. Notably, Papers3 does not have to be running.
  3. Enter relevant search word(s) and papers will show up in the results window. Among the nice features of Papers3, you can view the article.
  4. Click on Insert Citation, and it returns back to Word 2008
And here’s what it would look like in the Word document:

Here’s a citation of a Phylogenetics book {Adams, 2008}. Here’s a citation of an article on women in statistics {Anderson, 1992}.

  1. Once you are finished adding in citations, generate the bibliography by invoking the Papers3 search again (ctrl+ctrl), then select “Format manuscript” (Appendix).
  2. Nice to know: This method works  with the free Word Online — since you would need a full install of  Word/Office in order to insert citations and generate a bibliography, use of Papers3 may be a nice alternative. The method also works with Google Docs; again, there are options to gain this type of function in Google Docs, but they are either limited or cost (e.g., free version of EasyBib Add-on has very limited function).

JabRef + Word 2008

  1. From JabRef, select multiple papers. Export selected entries and save file as Sources.xml to Documents → Microsoft User Data
  2. Start Word 2008
  3. Type away.
  4. When ready to insert citation, bring up Citations Toolbox (View→ Toolbox→ Citations)
  5. Click on the Settings icon (bottom right of popup menu); Select Citation Source Manager
  6. If all is well, you will see the sources listed in the Master List panel. Select the references required and copy them to the Current List panel. Hold down Command key to select multiple references.

And here’s what it would look like in the Word document:

Here’s a citation of a Phylogenetics book (Adams, 2008). Here’s a citation of an article on women in statistics (Anderson, 1992).

  1. Once you are finished adding in citations, generate the bibliography by placing the cursor in the document where you want the bibliography to appear (e.g., end of document), then select from the menu bar: Insert → Document Elements→ Bibliography (Appendix).

Conclusion

Much easier to use Papers3 and Word 2008 together, although the results are pretty much the same. Frankly, if this was all you are looking to do with Papers, then probably not worth the additional cost. (However, Papers can do a lot more; I particularly like how it helps you manage all kinds of documents on your computer).

Appendix

Output from Word 2008, Insert → Document Elements→ Bibliography

Bibliography

Adams, D. C. (2008). Phylogenetic meta-analysis. Evolution , 62, 567-572.

Anderson, M. (1992). The history of women and the history of statistics. Journal of Women’s History , 4.

Output from Papers3, “Format manuscript”

Adams, D. C. (2008). Phylogenetic meta-analysis. Evolution, 62, 567–572.

Anderson, M. (1992). The history of women and the history of statistics. Journal of Women’s History, 4(1).