Abstract
Biomedical questions are usually complex and regard several different life science aspects. Numerous valuable and he- terogeneous data are increasingly available to answer such questions. Yet, they are dispersedly stored and difficult to be queried comprehensively. We created a Genomic and Proteomic Data Warehouse (GPDW) that integrates data provided by some of the main bioinformatics databases. It adopts a modular integrated data schema and several metadata to describe the integrated data, their sources and their location in the GPDW. Here, we present the Web application that we developed to enable any user to easily compose queries, although complex, on all data integrated in the GPDW. It is publicly available at http://www.bioinformatics.dei.polimi.it/GPKB/. Through a visual interface, the user is only required to select the types of data to be included in the query and the conditions on their values to be retrieved. Then, the Web application leverages the metadata and modular schema of the GPDW to automatically compose an efficient SQL query, run it on the GPDW and show the extracted requested data, enriched with links to external data sources. Performed tests demonstrated efficiency and usability of the developed Web application, and showed its and GPDW relevance in supporting answering biomedical questions, also difficult.
Highlights
A great amount of valuable and heterogeneous biomedical molecular data and information is increasingly produced thanks to the modern high-throughput technologies
To enable any user to compose queries, complex, on all data integrated in the Genomic and Proteomic Data Warehouse (GPDW), we developed a Web application in Java programming language using Servlets and Java Server Pages (JSP) technology
Through a visual interface (Figure 3), the user is only required to select, out of the features integrated in the GPDW, the ones and their attributes to be included in the query, together with the conditions on the data values to be retrieved
Summary
A great amount of valuable and heterogeneous biomedical molecular data and information is increasingly produced thanks to the modern high-throughput technologies It is stored in publicly accessible molecular biology databases that are continuously increasing in number and coverage of the included biomolecular entities, as well as of their described structural and functional biomedical features and associated phenotypes [1]. We describe and discuss the original Web application that we developed to access and search such valuable integrated biomolecular knowledge It leverages the GPDW metadata-based modular data schema to enable any user to visually perform queries, complex, whose extracted data can support answering difficult biomedical questions
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