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The chief guidance regarding finding annotated books in the collections is this 2009 blog posting
Finding Annotated Books [link]
Other resources pertinent to Princeton University Library's holdings include:
1. See the Collections File under the heading ANNOTATED BOOKS.
2. Gabriel Harvey's annotated books have been digitized [link] and in the Taylor Library are a number of importantly annotated books such as Defoe's copy of Bacon'sAdvancement of Learning and Lady Bradshaigh's copy of Clarissa.
3. Search the Weber catalogue of the Vergil collection for books with annotations, available online and as: Weber, Shirley, compiler. The Vergil collection in the Princeton University Library. A check-list and descriptive catalogue. (Princeton, N.J.: Princeton University Library, 1956) [(ExB) Z8932 .xP7]
4. See Sarah Reichart's 1987-88 study covering provenance and annotations in some of the Library's Italian incunables. A copy of this study is in the Collections File under "Incunabula."
5. The Library does have several famous annotated books and these are noted in articles in the Princeton University Library Chronicle, such as Ann M. Blair, "Lectures on Ovid'Metamorphoses: The Class Notes of a 16th-Century Paris Schoolboy" (L,2 [Winter 1989], p. 117-144 [ full text] and Anthony Grafton, "Gabriel Harvey's Marginalia: New Light on the Cultural History of Elizabethan England" (LII,1 [Autumn 1990], p. 21-24 [ full text]. Also see the work of Anthony Grafton and Lisa Jardine on annotated texts here in their From Humanism to the Humanities (London: Duckworth, 1986). [(F) LA106 .G73 1986b].
For general information on annotated books, try consulting one or all of the following:
1. Index of English Literary Manuscripts; see the end of the entries for each author. At the end are details about books annotated by each author. [(ExB) Z6611.L7 I5]
2. Robin Alston. Books with Manuscript (London: British Library, 1994). This lists books in the British Library with annotations in manuscript. [(ExB) Z1033.A84 B74 1994]
3. Roger Stoddard. Marks in Books: illustrated and explained, an illustrated catalog of an exhibition at the Houghton Library in 1985. (Cambridge, Mass.: Houghton Library, Harvard University, 1985. ) [(F) Oversize Z235 .S86 1985q]
4. Ellen Well's article "Marginalia" in vol. 48 of the Encyclopedia of Library and Information Science.