Choosing and using bibliographic software

I’m sure most of you out there have a collection of articles gathered from many journals, and neatly (or not) filed away in your office. Reading and indexing information from the literature used to mean trips to the library with the photocopy card and sitting down with the highlighter to read them.

Starting in the late 90’s, many journals started posting abstracts and full text articles online. Pubmed also became a huge resource for searching the most recent literature for citations. All of these electronic references need to be stored somewhere, and paperless filing is becoming a much more viable option. Hard drives have almost limitless memory, and interfaces for saving references electronically have become much more user friendly. Now you need to decide how to choose bibliographic software, and how you will use it.

Endnote

The market leader in reference software is Endnote. It’s been around for many years, and is flexible and fairly easy to use. It is a proprietary program, though an educational discount through a college or university makes it much more affordable. UC Davis actually bought a campus-wide license last year. They tend to upgrade to a new version once every year or two, which means you have to spend another $100.00. It’s a disadvantage, though the upgrades have all been good. I actually played ultimate frisbee with a couple of the programmers for Endnote in Philadelphia, and they assured me the new code was a good thing. One caveat is that Thomson Corporation owns the top three reference manager programs; Endnote, Reference Manager and Procite. There are more options on the market now, so the prices may start to come down in the future.

How do you use it?

Endnote is a great program. I created one big library for my references so that I can search for anything. If you break it up into small libraries on different subjects, you might end up doing multiple searches. Endnote has good import filters since it’s the most popular program. If you are at a journal’s website and want to save a reference, most have a link that says “Download to reference software”. Regardless of which one you are using, just click and choose your program. The file should show up in your library; if not you just need to import it from where it was saved. Endnote allows browsing several databases from within the program as well. It’s a little less flexible, but the reference imports are easy and very fast.

Once you have your reference, you might want to organize your information by putting important points in the abstract in bold font, adding keywords to the keyword field, or adding your own notes or summary under the research notes field. All of these are searchable in the library, when you can’t remember what article you read it in. I use this method to organize my literature collection. Another fun feature is being able to save a PDF of the article, and placing a link in the reference file. If your notes aren’t enough, just click and read the original.

Reference manager software also makes life easier when writing articles. There is an interface with Microsoft Word that allows you to place chosen references from your library straight into the document. There are many output styles that conform to journal guidlines, including many from veterinary medicine. Just choose the right one to get an instant bibliography.

Web based reference software

For those who want a library that is accessible to multiple users or available online, there are many more options available now. I’ve tried CiteULike, which has a good interface and the ability to create user groups. VetRadiology is the group where I have been collecting the recent imaging literature. Other free options are Connotea from Nature publishing, and Zotero which is a Firefox extension. (Using Firefox as a browser is a subject for another post!) A popular proprietary web-based manager is RefWorks, which has a yearly fee.

More information

Depending on your needs, some of these will be better options for you than others. There is a great article on Wikipedia that compares the different reference manager software in terms of operating system, cost, options etc. If you are not using this type of software, you should! You’ll save time and be more productive after investing some time in learning more about it.