You can start annotating even before you have all of your resources. Sometimes, carefully reading and annotating an article will give you information, like keywords or author names, that will help you find other suitable resources.
You already read the abstract when you were deciding whether to use the article.
Read the introduction - the author or authors should tell you the main idea of the article. (If it is not labeled, this is the first paragraph or two.)
Read the conclusion - the author or authors should summarize how the article provided evidence for their main idea. (If it is not labeled, this is the last paragraph or two.)
Now that you know what they were trying to say and how they think they said it, read the rest of the article.
Keep in mind your purpose for reading. You think this article might support a project you are working on, so think about your research question as you read the article. Think about what you already know about the subject.
Consider using two different colors and a pencil while you are reading the text. The main color highlighter can be for the above points. A secondary color can be for words or phrases you don't understand or want to look up. The pencil is for your own comments in the margins (this is called "marginalia.")
Annotated bibliographies almost always contain a summary of the resource, whether the bibliography is intended to be descriptive / informative or analytical / critical. Most academic articles include an abstract: this is NOT what you use for your summary. Your professor wants to see what YOU got from the article.
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