A framework for scientific data modeling and automated software development

• Published in: Bioinformatics Vol. 21; no. 8; pp. 1678 - 1684
• Main Authors: Fogh, Rasmus H., Boucher, Wayne, Vranken, Wim F., Pajon, Anne, Stevens, Tim J., Bhat, T. N., Westbrook, John, Ionides, John M. C., Laue, Ernest D.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15-04-2005; Oxford Publishing Limited (England)
• Subjects: Biological and medical sciences; Biopolymers - analysis; Biopolymers - chemistry; Biopolymers - classification; Biopolymers - metabolism; Computer Simulation; Database Management Systems; Documentation - methods; Documentation - standards; Fundamental and applied biological sciences. Psychology; General aspects; Guidelines as Topic; Information Storage and Retrieval - methods; Magnetic Resonance Spectroscopy - methods; Magnetic Resonance Spectroscopy - standards; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Biological; Models, Chemical; Reference Standards; Science - methods; Software; Unified Medical Language System; Automation; Software development; Data storage; Standard; Large scale; Method; Modeling; Standards
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti234

Motivation: The lack of standards for storage and exchange of data is a serious hindrance for the large-scale data deposition, data mining and program interoperability that is becoming increasingly important in bioinformatics. The problem lies not only in defining and maintaining the standards, but also in convincing scientists and application programmers with a wide variety of backgrounds and interests to adhere to them. Results: We present a UML-based programming framework for the modeling of data and the automated production of software to manipulate that data. Our approach allows one to make an abstract description of the structure of the data used in a particular scientific field and then use it to generate fully functional computer code for data access and input/output routines for data storage, together with accompanying documentation. This code can be generated simultaneously for different programming languages from a single model, together with, for example for format descriptions and I/O libraries XML and various relational databases. The framework is entirely general and could be applied in any subject area. We have used this approach to generate a data exchange standard for structural biology and analysis software for macromolecular NMR spectroscopy. Availability: The framework is available under the GPL license, the data exchange standard with generated subroutine libraries under the LGPL license. Both may be found at http://www.ccpn.ac.uk; http://sourceforge.net/projects/ccpn Contact: [e-mail]