Institut Curie Collection
- Access to: Map of communities of hidden protein connections in Wikipedia network
English Wikipedia, containing more than five millions articles, has approximately eleven thousands web pages devoted to proteins or genes most of which were generated by the Gene Wiki project. These pages contain 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 other topics curated by independent, not coordinated collective efforts. Therefore, Wikipedia contains a directed network of protein functional relations or physical interactions embedded into the global network of the encyclopedia terms, which defines hidden (indirect) functional proximity between proteins.
We applied the recently developed reduced Google Matrix (REGOMAX) algorithm in order to extract the network of hidden functional connections between proteins in Wikipedia. Using this approach, we discovered tight communities which clearly reflect areas of interest in molecular biology or medicine. These communities were labeled by the title of the Wikipedia page associated with the community by the connector links, having the strongest internal connectivity.
Here we provide the hidden protein connection community map in an interactive form. The size of the nodes reflect the number of proteins in the community. Square nodes signify those communities identified in the 2017 Wikipedia network which do not have a match in the 2013 Wikipedia network. The width of the line reflects the number of oriented links between the communities. The network can be queried for a protein name or a part of the Wikipedia page title. All community node annotations are hyperlinked to the corresponding Wikipedia pages. Therefore, the interactive map serves as a convenient portal to the set of Wikipedia pages related to proteins and associated pages.
Accompanying web-site:
http://www.quantware.ups-tlse.fr/QWLIB/wikiproteinnets/
References:
Arxiv preprint: A.Zinovyev, U.Czerwinska, L.Cantini, K.M.Frahm and D.L.Shepelyansky. Revealing biological functions from Wikipedia network using reduced Google matrix. 2019. arXiv:1904.xxxxx[cs.SI].
Lages J, Shepelyansky D, Zinovyev A. Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks. 2018. PLoS One 13(1):e0190812.