BNFO 301 
Introduction to Bioinformatics
How to Create a Bibliography
Spring 2015 

Finding research articles

  1. Why create a bibliography?
  2. Building a bibliography
  3. What to submit

Why create a bibliography?
Creating a bibliography is one of the first steps in what will be a semester-long process of completing a computational research project. You've no doubt created bibliographies before, but this one will be different in an important respect. This one will be a nearly exhaustive bibliography on a narrow subject, one that will immediately vault you into a position of scientific expertise in your chosen field. You probably won't believe this, but 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.

But there are far more than psychological benefits. An exhaustive bibliography gives you an outline of what is known and therefore what is NOT known. This will prove invaluable as you search for an unanswered question that will serve as the basis of your research project.

Building a bibliography
You're goal is to find every article written since the beginning of time to last Friday concerning your chosen topic. Obviously, if your chosen topic is "Repeated Sequences in DNA" 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 exercise 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 actually read all those articles, at least not right now. 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:

  • Start with something specific
    If you begin with a huge fuzzy idea (Repeated sequences,... ecology,... marmosets), you are likely to lose your way in the literature. Instead, try starting with a specific article -- why not one suggested on your group's topic page?
     
  • 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
    Citation searchers through Web of Science or Google Scholar can lead you to articles written after your key article and connected in some possibly interesting way to it.
     
  • 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. You of course know how to find review articles, and the group's topic page probably has one that will be usefult to you.
     
  • 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.

    What to submit
    E-mail the following:

    1. A statement of your topic, sufficiently constrained so that you can find an exhaustive list of references
    2. The method(s) you used to obtain the list of references
    3. The list of references

    The details of the format of your submitted bibliography are 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 (and to yourself). 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.
       
    • Including a URL if available. This extra step makes it easy for the reader (possibly you) to look up the article if interested.