Managing a bibliography sucks, and I never found a good, cheap solution for the torturous process. The university provided RefWorks for free to students, but I found that it did not integrate well with MS Word; I wasted so many hours dealing with frustrating compiling errors and bugs. I ended up engineering a solution using Bibdesk and BibdeskToWord.
First, download these programs:
Bibdesk: http://sourceforge.net/projects/bibdesk/files/BibDesk/BibDesk-1.5.10/BibDesk-1.5.10.dmg/download
BibdeskToWord: http://warp.byu.edu/BibDeskToWord/BibDeskToWord.dmg
And some template files: http://warp.byu.edu/BibDeskToWord/BDtW-Templates.zip
Also download this sample BibDesk database: https://dl.dropboxusercontent.com/u/16113137/Example%20References.bib
And this .doc file that contains formatting information: https://dl.dropboxusercontent.com/u/16113137/ExportTemplatePLoS.doc
Install Bibdesk and BibdeskToWord, then open up Bibdesk. Ask Bibdesk to open a file (command+o), and open up the .bib file. It’s my bibliography that we’re going to use as an example and you should see a big list of references.
Now create a new Word document. Start inserting references by clicking and dragging a reference from Bibdesk into the word document. It should show up as: \cite{reference key}.
Put a whole bunch of them in. Now open up BibdeskToWord. You’ll have to tell it which templates to use. For the “Template for \cite:” fields, choose one of the BDtW template files that you downloaded from BDtW-Templates.zip. Which one you choose depends on the citation style you want, but go with “BDtW-AuthorYearParenCite.txt” for now. For the “Template File”, choose the .txt file that I have attached. Then click “Create/Update Bibliography”.
It should replace the \cite{reference key} in the word document with the actual citation. It will also create a bibliography that is formatted for PLoS One. If it doesn’t show up, right click the line that says something like “\bibliography{stuff}” and click “toggle field”. One big caveat that really frustrated me until I figured it out was that if you use track changes in Word (I hate track changes so much… how can one simple feature introduce so many complications to a workflow?!), you cannot have a citation that is within a track change bubble. Otherwise, it’ll give you an error and won’t compile.
To import citations, you can copy and paste the references directly from Google Scholar. When you’re in gscholar, click the gear icon at the top right to change your settings. Under “Bibliography Manager”, choose to Show links to import citations into Bibtex. Click save. Now search for a paper and click the Import into BibTex link under any search link. Hit command+A and copy. Then you can paste directly into Bibdesk.
These tools got me through my PhD. I only wish there was an automagic tool that scans through a pdf collection to add entries into a Bibdesk database with 100% accuracy.
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