Abstract
English Wikipedia, containing more than five millions articles, has approximately eleven thousands webpages devoted to proteins or genes most of which were generated by the Gene Wiki project. These pagescontain information about interactions between proteins and their functional relationships. At the same time,they are interconnected with other Wikipedia pages describing biological functions, diseases, drugs and othertopics curated by independent, not coordinated collective efforts. Therefore, Wikipedia contains a directednetwork of protein functional relations or physical interactions embedded into the global network of theencyclopedia terms, which defines hidden (indirect) functional proximity between proteins. We applied therecently developed reduced Google Matrix (REGOMAX) algorithm in order to extract the network of hiddenfunctional connections between proteins in Wikipedia. In this network we discovered tight communitieswhich reflect areas of interest in molecular biology or medicine. Moreover, by comparing two snapshots ofWikipedia graph (from years 2013 and 2017), we studied the evolution of the network of direct and hiddenprotein connections. We concluded that the hidden connections are more dynamic compared to the directones and that the size of the hidden interaction communities grows with time. We recapitulate the results ofWikipedia protein community analysis and annotation in the form of an interactive online map, which canserve as a portal to the Gene Wiki project.