In a statement Wednesday, Tiffany Shlain, founder of the awards, described Prince as a "musical genius" and "a visionary, who recognized early on that the Web would completely change how we experience music."
The 47-year-old pop superstar was the first major artist to release an entire album, 1997's "Crystal Ball," exclusively on the Web, according to the announcement, and "long before MySpace and iTunes, Prince used the Web as a new way to distribute music, premiere videos and build his relationship with his fans."
His Web site, www.npgmusicclub.com, has more than seven full-length CDs of music unavailable elsewhere, the AP reports.
The awards ceremony will take place June 12 at Cipriani Wall Street in Manhattan. Rob Corddry of Comedy Central's "The Daily Show With Jon Stewart" will host the show.
Prince will be honored along with winners in 69 categories, as well as five other special-achievement recipients, including Thomas Friedman, a columnist for The New York Times; Gorillaz, a cartoon-fronted rock group; and the founders of the popular social networking site MySpace.com.
The awards, in their 10th year, are given by the International Academy of Digital Arts and Sciences, a group of more than 500 experts on the Internet and other specialties.
Winners and special-achievement honorees are limited to five-word acceptance speeches. Lifetime achievement recipient and former presidential candidate Al Gore drew laughs and headlines last year with "Please don't recount this vote."
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