F Martín-Sánchez | PubMed Health

PubMed2006

Analysis and management of HIV peptide microarray experiments.

OBJECTIVES: To develop a tool for then easy and user-friendly management of peptide microarray experiments and for the use of the results of these experiments for the study the immune response against HIV virus infection in clinical samples. METHODS: Applying bioinformatics and statistics for the analysis of data coming from microarray experiments as well as implementing a MIAME (Minimum Information About a Microarray Experiment) compliant database for managing and annotating experiments, results and samples. RESULTS: We present a new tool for managing not only nucleic acid microarray experiments but also protein microarray experiments. From the analysis of experimental data, we can detect different profiles in the reactivity of the sera with different genotypes. CONCLUSIONS: We have developed a new tool for managing microarray data including clinical annotations for the samples as well as the capability of annotating other microarray formats different to those based on nucleic acids. The use of peptide microarrays and bioinformatics analysis opens a new scope for the characterization of the immune response, and analyzing and identifying the humoral response of viruses with different genotypes.

Computational Biology↗

PubMed2006

Designing new methodologies for integrating biomedical information in clinical trials.

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 ontologybased 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.

Clinical Trials as Topic↗