Principles of Bioinformatics as Applied to Hydrogen-Producing Microorganisms

Access to computer technology is so widespread that few biologists do not make use of automated systems for managing laboratory data. The growth of the Internet and the development of software tools that facilitate management and dissemination of data in a networked environment have resulted in the proliferation of biological data resources that are now available to researchers throughout the world. The biohydrogen community is no exception, in that data relevant to hydrogen-producing microorganisms are available through numerous resources, many of which may be accessed via the World Wide Web. From genomics and sequence databases to culture collections and specialized data, the hydrogen producers are well-represented. The challenge is to develop a platform on which these data can be merged into a working tool that will meet the various requirements of a broad range of potential users. Environmental conditions, media/nutrient requirements, biochemical characteristics, metabolic pathways, genomics, and industrial process modeling are all aspects of a knowledge base that will be required to track the growing body of information about these organisms and the distinguishing characteristics that may result in the production of energy sources to improve the environment. Development of a working data management tool to serve the biohydrogen community will require adherence to accepted technical and semantic standards. The interdependence of information in disparate databases must be recognized and support for integrated queries involving multiple databases must be maintained. The disparity in data resources relevant to hydrogen producers may be more acute than for other microorganisms because several distinct taxa are represented and will be studied from a functional, rather than a taxonomic, viewpoint. This requires an interdisciplinary approach to data management problems and will require cooperation from a social and technical standpoint. A data model for the biohydrogen community, based on existing software used by culture collections that includes links to networked data resources, is presented. Such a system will serve not only individual laboratories but, importantly, the global biohydrogen community.