A service-based framework for pharmacogenomics data integration

Abstract

Data are central to scientific research and practices. The advance of experiment methods and information retrieval technologies leads to explosive growth of scientific data and databases. However, due to the heterogeneous problems in data formats, structures and semantics, it is hard to integrate the diversified data that grow explosively and analyse them comprehensively. As more and more public databases are accessible through standard protocols like programmable interfaces and Web portals, Web-based data integration becomes a major trend to manage and synthesise data that are stored in distributed locations. Mashup, a Web 2.0 technique, presents a new way to compose content and software from multiple resources. The paper proposes a layered framework for integrating pharmacogenomics data in a service-oriented approach using the mashup technology. The framework separates the integration concerns from three perspectives including data, process and Web-based user interface. Each layer encapsulates the heterogeneous issues of one aspect. To facilitate the mapping and convergence of data, the ontology mechanism is introduced to provide consistent conceptual models across different databases and experiment platforms. To support user-interactive and iterative service orchestration, a context model is defined to capture information of users, tasks and services, which can be used for service selection and recommendation during a dynamic service composition process. A prototype system is implemented and cases studies are presented to illustrate the promising capabilities of the proposed approach.

Keywords:

• Web services
• data as a service
• mashup
• context-awareness
• ontology

Acknowledgement

The project is funded by Basic Research Foundation of School of Information Science and Technology of Tsinghua. The authors first thank their research partner, Dr Quick Que from TGen for all guidance and advises. They also thank Mr Jilong Liu from Xiamen University for his help and collaboration in this research. The authors thank all the people for their supports and encouragement during this research project.