Encyclopedia of Database Systems

2018 Edition
| Editors: Ling Liu, M. Tamer Özsu

Biological Networks

  • Amarnath GuptaEmail author
Reference work entry
DOI: https://doi.org/10.1007/978-1-4614-8265-9_1308


Biological pathways; Molecular interaction graphs; Protein-protein interaction networks; Signal transduction networks; Transcriptional networks


A biological network is a graph-structured representation of binarized interactions among biological objects. Typically, the nodes in such a graph represent biological molecules, and the edges are labeled to represent different forms of interactions between molecules.

Example: A transcriptional network is a directed graph where a node represents either a protein (a transcription factor) or a region of the chromosome such that the edges can be constructed from the protein node to the chromosomal region. The edge in the graph represents that the protein can initiate the transcription (production of messenger RNA) process.

Key Points

A biological network is typically a node and edge attributed graph, where the edges can have different semantics depending on the kind of network. In some networks, the edges may be weighted,...

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Recommended Reading

  1. 1.
    Baitaluk M, Qian X, Godbole S, Raval A, Ray A, Gupta A. PathSys: integrating molecular interaction graphs for systems biology. BMC Bioinf. 2006;7(1):55.CrossRefGoogle Scholar
  2. 2.
    Eckman BA, Brown PG. Graph data management for molecular and cell biology. IBM J Res Dev. 2006;50(6):545–60.CrossRefGoogle Scholar
  3. 3.
    Leser U. A query language for biological networks. Bioinformatics. 2005;21(Suppl 2):ii33–9.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.San Diego Supercomputer CenterUniversity of California San DiegoLa JollaUSA

Section editors and affiliations

  • Amarnath Gupta
    • 1
  1. 1.San Diego Supercomputer CenterUniversity of California San DiegoLa JollaUSA