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Zotero, Endnote, Refworks, etc
Bibliographic management tools enable you to store library sources in your own personal database and then incorporate the citations seamlessly into your research paper in whatever format your writing seminar requires. Within these tools you can take also notes on the books and articles you find and search those notes by keyword.
Oxford Bibliographies is a great source/model for annotated bibliographies (many subjects are represented).
Getting Started with Zotero (video)