Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Protein–Protein Interaction Data, Semantic-based Management

  • Pietro Hiram Guzzi
Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_969

Definition

Semantic-based management of protein interaction networks refers to all the approaches of analysis of protein–protein interaction data that uses knowledge encoded into biological ontologies. Semantic approaches for studying high-throughput data have been largely used to mine genomic data. The application of these computational approaches to the study of interaction network can broad the application scenario of them and simultaneously can help the understanding of processes and pathway related to a given interaction networks. From this consideration, the possibility to extract valuable knowledge by the application of semantic-based algorithm and databases arises.

Characteristics

The analysis of biological data coming from different experiments initially aimed at the identification of a single gene or protein that was related to the investigated biological scenario. For instance, the analysis of microarray data aimed at the identification of a single or a group of genes whose...

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References

  1. Cannataro M, Guzzi PH, Veltri P (2010) Protein-to-protein interactions: technologies, databases, and algorithms. ACM Comput Surv 43:11–136. doi:10.1145/1824795.1824796, doi: http://doi.acm.org/10.1145/1824795.1824796. URL http://doi.acm.org/10.1145/1824795.1824796
  2. Louis du Plessis, Nives kunca, and Christophe Dessimoz. The what, where, how and why of gene ontologya primer for bioinformaticians. Briefings in Bioinformatics, 2011. doi: 10.1093/bib/ bbr002. URL http://bib.oxfordjournals.org/content/early/2011/02/16/bib.bbr002. abstract
  3. Pesquita C, Faria D, Falcao AO, Lord P, Couto FM (2009a) Semantic similarity in biomedical ontologies. PLoS Comput Biol 5(7):e1000443. doi:10.1371/ journal.pcbi.1000443, ISSN 1553–7358, http://dx.doi.org/10.1371/journal.pcbi.1000443
  4. Pesquita C, Faria D, Falco AO, Lord P, Couto FM (2009b) Semantic similarity in biomedical ontologies. PLoS Comput Biol 5(7):e1000443, doi: 10.1371/journal.pcbi.1000443. URL http://dx.doi.org/10.1371y.2Fjournal.pcbi.1000443

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Department of Experimental Medicine and ClinicUniversity Magna Gratia of CatanzaroCatanzaroItaly