An agent- and ontology-based system for integrating public gene, protein, and disease databases. Academic Article uri icon

Overview

MeSH

  • Animals
  • Artificial Intelligence
  • Humans
  • Oligonucleotide Array Sequence Analysis
  • Systems Integration
  • User-Computer Interface

MeSH Major

  • Biomedical Research
  • Computational Biology
  • Database Management Systems
  • Databases, Genetic
  • Genetic Predisposition to Disease
  • Genomics
  • Information Storage and Retrieval

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.

publication date

  • February 2007

has subject area

  • Animals
  • Artificial Intelligence
  • Biomedical Research
  • Computational Biology
  • Database Management Systems
  • Databases, Genetic
  • Genetic Predisposition to Disease
  • Genomics
  • Humans
  • Information Storage and Retrieval
  • Oligonucleotide Array Sequence Analysis
  • Systems Integration
  • User-Computer Interface

Research

keywords

  • Journal Article

Identity

Language

  • eng

Digital Object Identifier (DOI)

  • 10.1016/j.jbi.2006.02.014

PubMed ID

  • 16621723

Additional Document Info

start page

  • 17

end page

  • 29

volume

  • 40

number

  • 1