ASSIGNMENT OF THE WEEK: #8
Searching the primary literature.
This assignment begins a several-week long exercise in finding, reading and understanding the primary cell biology literature. The primary literature reports the results of original research by scientists. Papers of this type usually contain an abstract, materials and methods, results, discussion, and literature cited sections, and are peer reviewed meaning they are reviewed anonymously by experts in the field prior to publication. The library holds subscriptions (paper and on-line) for many journals of this type. Review articles summarize many primary literature articles and are generally restricted to a specific topic. Reading review articles is a good way to learn about a topic, but they should not be cited as the source of a particular idea. Articles about the primary literature such as those found in newspapers, books, and journals like Scientific American are not considered the primary literature since they contain secondary accounts of the primary literature and are written for a general audience.
Publishers of journals containing the primary literature usually maintain websites where you can read the table of contents and often abstracts of papers, or perhaps download the full-length papers. JMU subscribes to many of these electronic journals so while you may think they are free, they actually cost hundreds to thousands of dollars per year.
This week you will use an Internet database to find 5
papers from the primary literature that are 1) relevant to this course,
2) available on-line,
interest to you, and 4) are not on a medical topic or involve human subjects.. Because the titles of journal papers may not
general terms, we recommend using your textbook to find
technical terms likely to occur in a title or abstract.
Search the database
using those technical terms. For this first assignment each of
simply make a list of five papers with full references (authors, year,
journal, volume, pages). All five papers should relate to one
topic of interest. Again, avoid clinical studies or papers on humans.
Before adding a reference to your list make sure the
journal is available on-line from JMU. If you can't tell this
from the database, use the
Carrier Library. Once you
are ready to print a paper you must obtain the PDF
file since it will
take less paper to print and will include all of the figures as they
appear in the printed journal. You may need to download a (free)
Acrobat Reader if you are not using a JMU computer. HTML files will not be acceptably. Please
don't print the HTML versions of articles - they use much more paper
and may not contain full-sized images.
Searching Using PubMed
There are now various databases on the web with which to search the primary literature on a particular topic. The library maintains a page with resources that Biologists often use called the Research Guide. One database that we use frequently is called PubMed. PubMed is a project developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), located at the National Institutes of Health (NIH). It was developed in conjunction with publishers as a search tool for accessing literature citations and linking to full-text journals at Web sites of participating publishers. In addition to providing abstracts, PubMed also maintains links to relevant DNA and protein sequences in the sequence databases.
Try the following practice search to learn how to use PubMed. Suppose you wanted to find a paper describing promoter elements in the rubisco gene from spinach. Rubisco is the carboxylase enzyme in photosynthesis.
Turn in one typewritten page containing:
10/1/08 Copyright (C)
Jonathan Monroe, firstname.lastname@example.org.
All rights reserved.