Refining your topic in the light of what you've found and read is a main goal for this next week, since you're heading toward a meeting with your faculty supervisor in the week of Nov 3-7, for which you need to have
Accordingly, the next two weeks will require a good deal of searching and thinking. Your citations need to be in the appropriate form (Ecology or Journal of Bacteriology format), and you need to be reading and annotating as well as finding, and delivering the citations and annotations to your faculty supervisor.

It's important to move beyond the simple searching with which exploration of a topic begins --to find new vocabulary and other ways to narrow your searches, and to gradually elaborate an understanding and develop a focus. Your report to me (assignment #3) should reflect your progress with this elaboration.

If you're in Dr. Simurda's group:
you may find it useful to look at the annual indexes in the bound volumes ofMicrobiology
and at Microbiological Reviews (Upper Level, Science Library)
We'll consider the anatomy of the article to make clear what 'primary' and 'secondary' are and how to tell the difference. And what to do with each, how to mine bibliographies, how to make sense of abstracts, how to manage unfamiliar terminology.
The example of Bollinger et al. Inbreeding avoidance increases dispersal movements of the meadow vole (Ecology vol 74 pp 1153-1156, 1993) summarizes handily.
There's a sense in which the primary literature isn't written to be read: it establishes ownership and priority for ideas and findings, validates its authors' professional identities, serves as a permanent record of scientific progress. It's read by specialists --and by students who are preparing to become specialists. It's customarily written in a pretty rigid style (generally avoiding the first person, often favoring the passive voice, spending little energy on verbal niceties). Few people read primary literature for pleasure.

Secondary literature exists to improve access to the riches of primary literature: to interpret, summarize, adjudicate, review --but primarily for specialist or at least scientific audiences.

Specialized databases are the key to the research and review literatures. We have quite a few to choose amongst, to learn to use, to experiment with, so the first question is how to choose? Most are accessible via links on the Biology Department page.

It seems that it's useful to distinguish between topics that are

Other databases that could be of use to all of the above include NSF grants (and for some NIH grants) and the Conference Papers Index in CSA, and of course UnCover. A link to a list of publishers' search utilities exemplifies the wave of the future.

Review articles present a specific sort of finding problem.

A basic skill to master is using the descriptors, identifiers and other coded fields (when available) to focus searches.

With any of these databases, a basic question is do we have the journal? [answer the question with a Title search in Annie], and often the answer is negative. While in theory it is possible to get almost anything by InterLibrary Loan (usually not possible to get MA and PhD theses), for Bio182 you are supposed to restrict your efforts to what we have at W&L (exceptional circumstances do arise, of course).

Most of these specialized databases offer abstracts, from which it's possible to learn a lot (and which often are sufficient basis for deciding whether to pursue an article). You do have to be careful not to claim to have read an article because you've read its abstract, and it's just plain unfair (and intellectually dishonest) to adjust the text of abstracts to construct bibliographic annotations.

Another question for each database: what is its coverage? Thus, BasicBIOSIS is limited to 1994 to 1997, a fact you really need to consider in using it. AGRICOLA goes back to 1970. UnCover starts in the early 1990s, and so on.

To quantify the comparative power of various databases, here's a matrix of references summarizing for Dr. Simurda's group's bacteria.
Another approach to the literature is available to us for a short trial (ends 20 Nov): citation indexing, via ISI's Web of Science.
The focus here is in an article's bibliography --in the sources it cites. The Web of Science allows one to search by author or subject or by article title, and then to view the retrieved article and its abstract in terms of

Thus, one can trace an article's influence forward in time (one might think of doing such a thing with a "seed reference", mightn't one?). An even more daring (and exhausting) use of citation indexing is to look at clusters and networks of citation, following an idea or a subject over time and analyzing patterns to identify classic articles (those which many people cite) and review articles (those which cite many articles). Ingenuity and elbow grease along these lines can lead to remarkable empirical insights and discoveries in the history of science.