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Integration of Biological Data with Semantic Networks

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In recent years, the broad utilization of high-throughput experimental techniques resulted in a vast amount of expression and interaction data, accompanied by information on metabolic, cell signaling and gene regulatory pathways accumulated in the literature and databases. Thus, one of the major goals of modern bioinformatics is to process and integrate heterogeneous biological data to provide an insight into the inner workings of a cell governed by complex interaction networks.

The paper reviews the current development of semantic network (SN) technologies and their applications to the integration of genomic and proteomic data. We also elaborate on our own work that applies a semantic network approach to modeling complex cell signaling pathways and simulating the cause-effect of molecular interactions in human macrophages.

The review is concluded with a discussion of the prospective use of semantic networks in bioinformatics practice as an efficient and general language for data integration, knowledge representation and inference.

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Keywords: Semantic networks; biological data integration; knowledge representation; ontology; protein interactions; semantic web

Document Type: Research Article

Affiliations: Division of Infectious Diseases, Department of Medicine, D 452 HP, VGH, 2733 Heather Street, Vancouver, B.C. Canada V5Z 3J5.

Publication date: August 1, 2006

More about this publication?
  • 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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