Summary
Objectives:
To propose a modification to current methodologies for clinical trials, improving
data collection and cost-efficiency. To describe a system to integrate distributed
and heterogeneous medical and genetic databases for improving information access,
retrieval and analysis of biomedical information.
Methods:
Data for clinical trials can be collected from remote, distributed and heterogeneous
data sources.
In this distributed scenario, we propose an ontology-based approach, with two basic
operations: mapping and unification. Mapping outputs the semantic model of a virtual
repository with the information model of a specific database. Unification provides
a single schema for two or more previously available virtual repositories. In both
processes, domain ontologies can improve other traditional approaches.
Results:
Private clinical databases and public genomic and disease databases (e.g., OMIM,
Prosite and others) were integrated. We successfully tested the system using thirteen
databases containing clinical and biological information and biomedical vocabularies.
Conclusions:
We present a domain-independent approach to biomedical database integration, used
in this paper as a reference for the design of future models of clinico-genomic trials
where information will be integrated, retrieved and analyzed. Such an approach to
biomedical data integration has been one of the goals of the IST INFOBIOMED Network
of Excellence in Biomedical Informatics, funded by the European Commission, and the
new ACGT (Advanced Clinico-Genomic Trials on Cancer) project, where the authors will
apply these methods to research experiments.
Keywords
Database integration - clinical trials - ontologies - biomedical informatics - genomic
medicine
