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A database system for the analysis of biochemical pathways.

Abstract (Expand)

To provide support for the analysis of biochemical pathways a database system based on a model that represents the characteristics of the domain is needed. This domain has proven to be difficult to … model by using conventional data modelling techniques. We are building an ontology for biochemical pathways, which acts as the basis for the generation of a database on the same domain, allowing the definition of complex queries and complex data representation. The ontology is used as a modelling and analysis tool which allows the expression of complex semantics based on a first-order logic representation language. The induction capabilities of the system can help the scientist in formulating and testing research hypotheses that are difficult to express with the standard relational database mechanisms. An ontology representing the shared formalisation of the knowledge in a scientific domain can also be used as data integration tool clarifying the mapping of concepts to the developers of different databases. In this paper we describe the general structure of our system, concentrating on the ontology-based database as the key component of the system.

Authors: I. Rojas, L. Bernardi, E. Ratsch, R. Kania, U. Wittig, J. Saric

Date Published: 18th Jun 2002

Publication Type: Journal

Specific and Non-specific Effects of Potassium Cations on Substrate-protein Interactions in Cytocromes P450cam and P450lin

Abstract

Not specified

Authors: Eric Deprez, Edward Gill, Volkhard Helms, Rebecca C Wade, Gaston Hui Bon Hoa

Date Published: 2002

Publication Type: Journal

Comparative Binding Energy (COMBINE) Analysis of OppA−Peptide Complexes to Relate Structure to Binding Thermodynamics

Abstract

Not specified

Authors: Ting Wang, Rebecca C. Wade

Date Published: 2002

Publication Type: Journal

Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a new functional role for a buried arginine

Abstract

Not specified

Authors: P. J. Winn, S. K. Ludemann, R. Gauges, V. Lounnas, R. C. Wade

Date Published: 2002

Publication Type: Journal

Biomolecular diffusional association

Abstract

Not specified

Authors: Razif R. Gabdoulline, Rebecca C. Wade

Date Published: 2002

Publication Type: Journal

Elusive recognition determinants for ubiquitination

Abstract

Not specified

Authors: Amit Banerjee, Rebecca C. Wade

Date Published: 2002

Publication Type: Journal

Biologically relevant properties of copper-containing proteins analysed by means of semi-quantitative and quantitative theoretical descriptors

Abstract

Not specified

Authors: Francesca De Rienzo, Razif R. Gabdoulline, Rebecca C. Wade, M. Cristina Menziani

Date Published: 2002

Publication Type: InCollection

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