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Incremental Construction of Biological Networks by Relation Extraction from Literature

[ Vol. 10 , Issue. 2 ]


Dragana Miljkovic, Vid Podpečan, Tjaša Stare, Igor Mozetič, Kristina Gruden and Nada Lavrač   Pages 177 - 190 ( 14 )


This work focuses on automated incremental development of biological networks. The Bio3graph approach to information extraction from biological literature is extended with new features which allow for periodical updates of network structures using newly published scientific literature. The incremental approach is demonstrated on two use cases. First, a simple plant defence network with 37 components and 49 relations created manually by merging three existing structural models is extended in two incremental steps, yielding the final model with 183 relations. Second, a complex published network of defence response in Arabidopsis thaliana, containing 175 nodes and 524 relations, is incrementally updated with information extracted from recently published articles resulting in an enhanced network with 628 links. The results show that using the demonstrated incremental approach it is possible to automatically recognise new knowledge about the selected biological relations published in recent literature. The newly implemented Bio3graph extension offers an effective way of merging and visually representing the initial networks and the networks generated from texts thus enabling fast discovery of relations which can potentially enhance the existing models.


Biological literature, biological networks, information extraction, plant defence.


Jožef Stefan International Postgraduate School, Ljubljana, Slovenia.

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