BNFO 301 
Introduction to Bioinformatics
How to Create a Bibliography
Spring 2013 

Finding research articles

  1. Why create a bibliography?
  2. Building a bibliography
  3. Format of bibliography

Why create a bibliography?
Creating a bibliography is the first step in what will be a semester-long process of developing a research proposal. Creating a nearly exhaustive bibliography on a narrow subject will immediately vault you into a position of scientific expertise in your chosen field. It's ridiculously easy to become an expert, if you set limits, and everyone should experience the feeling of knowing more than almost anyone in the world on a topic. If you do this right, you should have that feeling.

Building a bibliography
Your goal is to find every article written since the beginning of time concerning your chosen topic. Obviously, if your chosen topic is "The Molecular Basis of Cancer" you will exceed the days of your life and the capacity on your hard drive finding all pertinent articles. It is essential that you define your topic narrowly, progressively restricting it as you learn more on the topic, enough so that you emerge with a respectable number of articles, perhaps a few dozen, but a number that exhausts what is available.

You will probably be the first person on earth to go through this excercise with your particular topic. You will therefore become the world's leading expert on what articles have been written in the area you have defined. Note that I'm not suggesting that you read all those articles. But absorbing the message of their titles will help you see what has been done in the area and what has not. That's a big step in itself.

Here are some strategies that might be helpful (and here's more help):

  • Start with something specific
    If you begin with a huge fuzzy idea (Parkinson's Disease,... ecology,... marmosets), you are likely to lose your way in the literature. Instead, try starting with a specific article -- perhaps one suggested by a review article given to you. Identify a topic within it and treat it as your focus.
     
  • Go backwards in time through references
    Identify references in your focus article that speak to the matter at hand. Don't be led astray by references that connect primarily through methodology.
     
  • Go forwards in time through citation analysis
    Use Web of Science (or similar) to lead you to articles that cite key references you have found.
     
  • Find and exploit a pertinent review article
    Let the reviewer do your work for you. The main use of a review article is to organize a field and point you to useful references.
     
  • Organize your references
    You're going to quickly run out of air unless you have a system to keep track of what you've found. There's software designed specifically for this purpose. Mendeley is an example of free software that works well, allowing you to organize references, search through their full text, and provide tags that put the articles in categories you devise. You can also store your own notes on the article. Even Excel is better than nothing.
     
  • Name your references
    Give them personalities. The time honored way to do this is by naming references, generally the first author followed by the year. You'll find that you can have whole conversations with your mentor where half of the content are references: "Beezer et al (2001) said that..." and "Carpluss et al (2005) did pretty much the same thing in a different organism...".
     
  • Gradually flesh out the articles
    Write notes to yourself (see Organize your references, above), as you find something interesting concerning an article. The notes can remind you what the article is about.

    Format of bibliography
    The details of the format of your submitted bibliography is unimportant. APA format, Chicago citation style,... Sheesh! Who cares? There are almost as many reference formats as there are journals. What's important is that you are helpful to your reader. You can be helpful by:

    • Being consistent. Use the same format -- whatever it may be -- throughout.
       
    • Being complete. Provide the authors names, the title of the article, and the citation, including journal name, volume and page numbers.
       
    • Taking the extra step. Include a URL if available, making it easy for the reader to look up the article if interested.