Heterogeneous Biomedical Database Integration using a Hybrid Strategy: A P53 Cancer Research Database

Abstract

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.)

Nk-schemas: A novel algorithm for creating the views' schémas to materialize in hybrid mediator

“…Generally they can be divided into two categories: virtual and hybrid. Among the hybrid 978-1-4673-9669-1/15/$31.00 ©2015 IEEE * systems, those who have treated the materialization are: Ariadne [10][11] [12], CRDB [15] , Fulvis [16] et PHIS [17].…”

Fulvis: New approach for selecting views to materialize in hybrid information integration

“…We've studied many hybrid integration systems and we founded that only two of them (CRDB and Ariadne) have treated the problem and have proposed solutions [13]. [14] is a research project at the University of California, Irvine (UCI) that started about 2004, for the integration of data sources of a dozen of research laboratories for cancer therapy. The integration was performed using the capabilities of a relational DBMS.…”

“…(Functional assays) and (Structured assays) data are integrated by importation to the CRDB using the data warehouse approach. The data warehouse part of the CRDB is composed of two data marts: one regarding the (mutant) and the other concerns the (Molecular) [15].…”

Clinical Data Reuse or Secondary Use: Current Status and Potential Future Progress

“…Instead, data reuse relies on vertical data integration which is typically reflected in data warehouse architectures, to be filled from source systems with copied data using an ETL (extraction-transformation-loading) process [105][106][107]. This approach is chosen because source data can thus be cleansed and filtered.…”