The research of complex systems is widespread in scientific fields, which mainly investigates how relationships among individual parts generate the collective behaviors of a system. This paper aims to analyze the effects of complex system in scientific knowledge by using the co-word occurrence analysis to the corpus of papers published in PNAS in the years 1999–2012. Surprisingly, the percentage of the papers containing ‘complex’ and ‘system’ contributing to the total accounts for 47%. The major topics of complex system, such as complex network, emergence, complexity, uncertainty also show growth trends. Some topic words in the social, biological, and physical sciences are selected by domain experts and are mapped into networks respectively based on their co-occurrence frequency. Finding is that ‘complex’ and ‘system’ are the core nodes in each network, which shows the importance of complex system in every research field.
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