Emerging standards for interoperable biological systems

Abstract

This paper informs the reader on standards emerging for systems in biology to aid in the development and use of software and technologies in biology research to automate scientific workflows, integrate disparate systems, utilize grid computing to speed analysis, and facilitate code reuse. Two major technology changes have swept the computing landscape and offer opportunity to leverage access to databases. One change is the ubiquitous Web. The other major change is the establishment of open source software and specifically the development of open standards for exchanging data such as XML (extensible markup language). Bioinformatics has embraced open source and the sharing of data and tools for data managements as vehicles for improving the human condition. Community adoption of open source solutions become part of defining standards. Community processes to develop standards for data management and integration are developing along several fronts in biology. These categories include: tools/middleware, grid computing, ontologies, analysis and models. When building systems for use by biologists, we must be informed about standards for interoperability in order to leverage existing systems and code reuse instead of recreating the wheel.