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Could the Semantic Web work for computations of biological interest in the way it's intended to work for movie reviews and commercial transactions? It would be wonderful if it could, so it's worth looking to see if its infrastructure is adequate to the job. The technologies of the Semantic Web make several crucial assumptions. I examine those assumptions;(More)
As a model for Neuropsychiatric dysfunction in NeuroAIDS due to HIV-1 infection and drug abuse, we analyzed gene expression in human neurons treated with cocaine and HIV-1 proteins tat and envelope (env). One-way ANOVA showed statistically significant genes among the treatment groups (p < or = 0.0005). The identified genes were then subjected to a(More)
RNA and protein gene expression technologies are revolutionizing our view and understanding of human diseases and enable us to analyze the concurrent expression patterns of large numbers of genes. These new technologies allow simultaneous study of thousands of genes and their changes in regulation and modulation patterns in relation to disease state, time,(More)
MOTIVATION Reliable, automated communication of biological information requires methods to declare the information's semantics. In this paper I describe an approach to semantic declaration intended to permit independent, distributed databases, algorithms, and servers to exchange and process requests for information and computations without requiring(More)
Many biological questions require reasoning with structure and function. We have begun by developing representations for structures which can be extended in a symmetric manner to functions. Each structure is represented as an arrangement of functional groups in a layered grammar. Expressing the function of these groups will then be equivalent to forming the(More)
a candidate for the degree of Doctor of Philosophy and hereby certify that in their opinion it is worthy of acceptance. ACKNOWLEDGMENTS First of all, I would like to thank my co-advisors, Dr. Chi-Ren Shyu and Dr. Dong Xu for providing professional direction and guidance. Dr. Shyu has given me solid, academic research training. During my doctoral study, he(More)
Databases of intermediary metabolism, and indeed of biochemistry generally, ooer computational challenges and opportunities to reorganize biological knowledge to facilitate exploration. Here I consider a simple case, that of the classiication of enzymatic reactions, and show how the classiication could be automated and extended using deductive technology.
Problems in implementing DNA and other types of molecular computers stem from the inherent physical nature of molecules and their reactions. The current theory of computation makes assumptions that at best are very crude approximations of the physical chemistry. A theory which took into account the physical chemistry would likely be very diierent from what(More)