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Incremental Construction of Biological Networks by Relation Extraction from Literature

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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.
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Keywords: Biological literature; biological networks; information extraction; plant defence

Document Type: Research Article

Publication date: April 1, 2015

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  • Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a wide range of the integration of biology with computer and information science.

    The journal focuses on reviews on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.

    Current Bioinformatics is an essential journal for all academic and industrial researchers who want expert knowledge on all major advances in bioinformatics.
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