BioMANTA Ontology: The integration of protein-protein interaction data

Newman, Andrew, Hunter, Jane, Li, Yuan-Fang, Bouton, Chris and Davis, Melissa (2008). BioMANTA Ontology: The integration of protein-protein interaction data. In: M. Okada and B. Smith, InterOntology08. The Third Interdisciplinary Ontology Conference, Tokyo, Japan, (). 26-27 February, 2008.

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Author Newman, Andrew
Hunter, Jane
Li, Yuan-Fang
Bouton, Chris
Davis, Melissa
Title of paper BioMANTA Ontology: The integration of protein-protein interaction data
Conference name The Third Interdisciplinary Ontology Conference
Conference location Tokyo, Japan
Conference dates 26-27 February, 2008
Proceedings title InterOntology08
Place of Publication not found
Publisher not found
Publication Year 2008
Sub-type Fully published paper
Editor M. Okada
B. Smith
Total pages 5
Collection year 2009
Language eng
Abstract/Summary Protein-protein interaction (PPI) and biomolecular pathway data hold tremendous potential for drug discovery and development. However, relevant data sources are currently distributed across a wide range of disparate, large-scale, publicly- available databases, web sites and repositories and are described using a wide range of taxonomies and ontologies. Sophisticated integration, manipulation, processing and analysis of these data sets are required in order to reveal previously undiscovered interactions and pathways that will lead to the discovery of new drugs. The Semantic Web has been investigated as a solution to this problem by a number of projects that use RDF and OWL to integrate, represent and analyze protein interaction data. However, existing applications have suffered from certain limitations that hinder their usefulness. In this paper, we describe work being undertaken within the BioMANTA project that aims to identify and overcome the limitations associated with the application of Semantic Web technologies to protein interaction network analysis. In particular we describe the BioMANTA OWL ontology that has been designed to enable multiple data sources to be integrated within a single RDF triple store through a common PPI model. The primary aim of the BioMANTA ontology is to provide a practical means of facilitating the integration of semantically disparate data sets – it does not aim to provide a precise biological, chemical or physical model of how proteins interact. We also describe how this ontology was developed through the refinement, harmonization and extension of existing ontologies. Finally, we describe the mapping, integration and querying of a range of protein-protein interaction data sets, based on the ontology.
Subjects 280502 Data Storage Representations
270100 Biochemistry and Cell Biology
280000 Information, Computing and Communication Sciences
E1
080501 Distributed and Grid Systems
080505 Web Technologies (excl. Web Search)
890299 Computer Software and Services not elsewhere classified
970110 Expanding Knowledge in Technology
Keyword protein-protein interactions
semantic web
biomanta
RDF molecules
OWL
molecule ontology
Q-Index Code E1
Q-Index Status Confirmed Code
Additional Notes From Session VI: Contributed Short Papers.

 
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Created: Mon, 16 Jun 2008, 15:21:25 EST by Mr Christopher Davoren on behalf of School of Information Technol and Elec Engineering