The research takes three fundamental Internet Academic Journals (IAJ), which are China National Knowledge Infrastructure (CNKI), Chongqing VIP Information Co., Ltd. (VIP) and Beijing Wanfang Data Co., Ltd. (WFD), as subjects to discuss digital publishing mechanism innovations for China’s science information communication system. After introducing main Internet environment, comparing journal characteristics, and explaining publishing & operation modes of the IAJs, the paper analyses important issues such as redundant contents, digitalization issues, illegal journals, standards construction, copyright and benefit distribution. By learning from research practices and open access, a new benefit distribution and copyright management mode based on the Third Party Agency (TPA) is proposed. Future IAJs operation modes are also discussed from the view of scientific research innovation and state of the art platform construction.
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