CELO: A System for Efficiently Building Informatics Solutions to Manage Biomedical Research Data

Traditional data management methods are unable to sufficiently support growing trends in biomedical research such as collection of larger data sets, use of diverse data types, and sharing of data among multiple laboratories. Although many technologies are readily available to help laboratories build data management solutions, many laboratories are not taking advantage of them. This may be due to hardware and software costs, the need for an informaticist to build customized solutions, and long development times. Several systems already exist which attempt to address the informatics needs of biomedical researchers. A review of these systems has revealed the benefits and drawbacks of various system design approaches, and has helped us to identify a set of core requirements for a system that will successfully serve the biomedical research community. In consideration of these requirements, we developed the Customizable Electronic Laboratory Online (CELO) system to help laboratories efficiently build cost-effective informatics solutions. CELO automatically creates a generic database and web interface for laboratories that submit a simple web registration form. Researchers can then build their own customized data management systems using web-based features such as configurable user permissions, customizable user interfaces, support for multimedia files, and templates for defining research data representations. An evaluation of the CELO system has demonstrated its ability to efficiently create customized solutions for research laboratories with basic data management needs. The evaluation has also highlighted areas in which CELO can be improved and has elucidated potential research problems that may be of interest to the biomedical informatics field

XGI: A Graphical Interface for XQuery Creation and XML Schema Visualization

XML (Extensible Markup Language) is used in many contexts of modern information technology to facilitate sharing of information between heterogeneous data sources and inter-platform applications. The prevalence of XML implementation in data storage and exchange necessitates a method to adequately query XML data. The World Wide Web Consortium (W3C) is proposing XQuery as the standard querying language for semistructured XML data. XQuery is designed for experienced database programmers, since its syntax and capabilities are analogous to the SQL relational query language. Therefore, the inherent complexity of formulating XQuery statements makes it an intimidating task for anyone, except an expert in the XQuery language, to construct queries. The development of XQuery Graphical Interface (XGI), a visual interface for creating XQuery in a graphical format, is motivated by the need to simplify the query formation for unskilled users and speed up the query construction for expert users. The implementation of XGI is mainly inspired by three existing systems: Query and Reporting Semistructured Data (QURSED), XQuery By Example (XQBE), and XBrain. A review of these systems and many other systems has helped us understand the benefits and drawbacks of various system design approaches, and has assisted us in identifying a set of features for XGI that will successfully reduce the complexity of creating queries in the XQuery language. XGI provides a web interface for users to explore their own XML source data schema, search for specific schema elements, and visually create queries in the XQuery language for the targeted XML data source. A validation of the XGI system has verified its ability to efficiently and accurately create queries for various XML data sources. From the validation, we have recognized some strengths and weaknesses of the XGI system compared to other systems. We also recommend several areas in which XGI can be improved