research-article

Using RDF for managing protein-protein interaction data

Authors:

Mario Cannataro,

Pietro H. Guzzi,

Pierangelo VeltriAuthors Info & Claims

BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology

Pages 664 - 670

https://doi.org/10.1145/1854776.1854909

Published: 02 August 2010 Publication History

Abstract

Biological function is mediated and controlled to a large extent by interactions among proteins. The study of interactions about proteins has lead to the accumulation of a large amount of data, also referred to as protein-protein interaction (PPI) data. Such data, stored in publicly available databases, are often queried by using simple key-based query interfaces with little semantic. Current PPI databases enable the retrieval of one or more proteins that interact with a target protein. Nevertheless, a lot of biological information available on different sources (e.g. Gene Ontology) is not currently used in such databases.

Semantic Web technologies offer more possibilities for the storage, querying and mining of such data. Thus, the annotation of existing protein interaction databases with biological information and the application of Semantic web techniques for the storage and analysis may result in more powerful querying interfaces and may enable the development of novel algorithms for PPI analysis. In a previous work we showed how to use such annotations to realize an annotated PPI database, here we present the mapping of such relational database in RDF enabling the use of Semantic web techniques.

The main contributions of this paper are: (a) the annotation of a protein interaction database, (b) the mapping of resulting annotated data into Resource Description Framework (RDF), and (c) a semantic based querying interface. In particular, a semantic-based query interface enables users to query these data by using biological concepts.

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Cited By

Makris CTheodoridis E(2015)Computational Methods for Modeling Biological Interaction NetworksPattern Recognition in Computational Molecular Biology10.1002/9781119078845.ch26(505-524)Online publication date: 18-Dec-2015
https://doi.org/10.1002/9781119078845.ch26
Rapti ATheodoridis ETsakalidis A(2013)Evaluation of Protein-Protein Interaction Management SystemsProceedings of the 2013 24th International Workshop on Database and Expert Systems Applications10.1109/DEXA.2013.39(100-104)Online publication date: 26-Aug-2013
https://dl.acm.org/doi/10.1109/DEXA.2013.39

Index Terms

Using RDF for managing protein-protein interaction data

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cover image ACM Conferences

BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology

August 2010

705 pages

ISBN:9781450304382

DOI:10.1145/1854776

General Chairs:
Aidong Zhang
SUNY at Buffalo
,
Mark Borodovsky
Georgia Tech
,
Program Chairs:
Gultekin Ozsoyoglu
Case Western Reserve University
,
Armin Mikler
University of North Texas

Copyright © 2010 ACM.

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Published: 02 August 2010

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BCB'10: ACM International Conference on Bioinformatics and Computational Biology

August 2 - 4, 2010

New York, Niagara Falls

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Cited By

Makris CTheodoridis E(2015)Computational Methods for Modeling Biological Interaction NetworksPattern Recognition in Computational Molecular Biology10.1002/9781119078845.ch26(505-524)Online publication date: 18-Dec-2015
https://doi.org/10.1002/9781119078845.ch26
Rapti ATheodoridis ETsakalidis A(2013)Evaluation of Protein-Protein Interaction Management SystemsProceedings of the 2013 24th International Workshop on Database and Expert Systems Applications10.1109/DEXA.2013.39(100-104)Online publication date: 26-Aug-2013
https://dl.acm.org/doi/10.1109/DEXA.2013.39

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