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My personal method of adding large numbers of books is to clean up the author so they are all in the same form (for instance all are as firstname lastname not lastname, firstname). I then check the language and make sure that the title is actually the title and not the author name.
Once I get to this point I start checking the books and doing conversions if necessary. I use a custom column to note the quality of the book and if additional work is needed on them. (technical papers in pdf format tend to need work to display well).
I would also recommend that you decide on what metadata tags you want to use. Most books have tags like you would see on a website... in otherwords, everthing but the kitchen sink. If you don't start at the beginning you could have Non Fiction, Non-fiction, Nonfiction, Nonfiction History, Nonfiction Civil War etc. This can become very cumbersome and not very helpful when looking for a particular genre. You can always add more tags as you refine your library but putting thought into it at the beginning will be less work in the long run.
For the next batch of publications to add, I would recommend a temporary library where you would do the initial cleanup of name and title prior to running a duplicate check using the duplicates plugin (library option). After removing duplicate or marking them by using a custom column that exists in both the main library and the temporary addition library.
I would also recommend frequently running the duplicate check plugin. If there are books with duplicate titles and authors that are different editions you can mark them as "to ignore" in the duplicate check plugin if you want to keep both versions. Don't hesitate to use the "Comments" or add a "Notes" column for information you need on the books.
Good luck and don't get discouraged if it seems like a lot of work. The most important data to have correct are the Name, Title and ISBN as others have said. Get the names formatted right and the title and if the tags imported are garbage, clear those. Also double check the language. I have found books with two words of french in them labeled as French by mistake lol.
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