An agent- and ontology-based system for integrating public gene, protein, and disease databases

Journal of Biomedical Informatics
R Alonso-CalvoD Pérez-Rey

Abstract

In this paper, we describe OntoFusion, a database integration system. This system has been designed to provide unified access to multiple, heterogeneous biological and medical data sources that are publicly available over Internet. Many of these databases do not offer a direct connection, and inquiries must be made via Web forms, returning results as HTML pages. A special module in the OntoFusion system is needed to integrate these public 'Web-based' databases. Domain ontologies are used to do this and provide database mapping and unification. We have used the system to integrate seven significant and widely used public biomedical databases: OMIM, PubMed, Enzyme, Prosite and Prosite documentation, PDB, SNP, and InterPro. A case study is detailed in depth, showing system performance. We analyze the system's architecture and methods and discuss its use as a tool for biomedical researchers.

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Citations

Jul 16, 2010·Journal of Biomedical Semantics·Allyson L ListerAnil Wipat
Aug 7, 2012·International Journal of Nanomedicine·Victor MaojoCasimir Kulikowski
Apr 26, 2008·Journal of the American Medical Informatics Association : JAMIA·E Patrick ShironoshitaMansur R Kabuka
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Feb 2, 2008·Journal of Biomedical Informatics
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Feb 2, 2010·Pediatric Research·Victor MaojoMartin Fritts
Nov 3, 2021·Archives of Gynecology and Obstetrics·Leyi NiCong Chen

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