This article talks about the NYT e-book bestsellers lists and mentions
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The lists will be compiled from weekly data from publishers, chain bookstores, independent booksellers and online retailers, among other sources.
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RoyaltyShare, a San Diego-based company that tracks data and aggregates sales information for publishers, will work with The Times, provide data and offer an additional source of independent corroboration.
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The ebook fiction lists usually has at least a few self-publishers, so it's not all publisher info.